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Sample records for rationally designed scaffold-based

  1. Rational drug design.

    Science.gov (United States)

    Mandal, Soma; Moudgil, Mee'nal; Mandal, Sanat K

    2009-12-25

    In this article, current knowledge of drug design is reviewed and an approach of rational drug design is presented. The process of drug development is challenging, expensive, and time consuming, although this process has been accelerated due to the development of computational tools and methodologies. The current target based drug design approach is incomplete because most of the drugs developed by structure guided approaches have been shown to have serious toxic side effects. Otherwise these drugs would have been an ideal choice for the treatment of diseases. Hence, rational drug design would require a multidisciplinary approach. In this regard, incorporation of gene expression technology and bioinformatics tools would be indispensable in the structure based drug design. Global gene expression data and analysis of such data using bioinformatics tools will have numerous benefits such as efficiency, cost effectiveness, time saving, and will provide strategies for combination therapy in addition to overcoming toxic side effects. As a result of incorporation of gene expression data, partial benefit of the structure based drug design is slowly emerging and rapidly changing the approach of the drug development process. To achieve the full benefit of developing a successful drug, multidisciplinary approaches (approaches such as computational chemistry and gene expression analysis, as discussed in this article) would be necessary. In the future, there is adequate room for the development of more sophisticated methodologies.

  2. Rational drug design applied to myeloperoxidase inhibition.

    Science.gov (United States)

    Van Antwerpen, P; Zouaoui Boudjeltia, K

    2015-06-01

    Rational drug design is a general approach using protein-structure technique in which the discovery of a ligand can be driven either by chance, screening, or rational theory. Myeloperoxidase (MPO) was rapidly identified as a therapeutical target because of its involvement in chronic inflammatory syndromes. In this context, the research of MPO inhibitors was intensified and development of new chemical entities was rationally driven by the research of ligands that enter into the MPO catalytic pocket. Actually, as soon as crystallography data of MPO have become available and its structure was virtually designed, the rational drug design has been applied to this peroxidase. Pharmaceutical industries and academic laboratories apply rational drug design on MPO by either optimizing known inhibitors or searching new molecules by high-throughput virtual screening. By these ways, they were able to find efficient MPO inhibitors and understand their interactions with the enzyme. During this quest of MPO inhibition, it appears that Glu268 is a crucial residue in order to optimize ligand-target interaction. This amino acid should be carefully considered by medicinal chemist when they design inhibitors interfering with MPO activity.

  3. Rational design of protein kinase inhibitors

    Directory of Open Access Journals (Sweden)

    Yarmoluk S. M.

    2013-07-01

    Full Text Available Modern methodological approaches to rational design of low molecular weight compounds with specific activity in relation to predetermined biomolecular targets are considered by example of development of high effective protein kinase inhibitors. The application of new computational methods that allow to significantly improve the quality of computational experiments (in, particular, accuracy of low molecular weight compounds activity prediction without increase of computational and time costs are highlighted. The effectiveness of strategy of rational design is demonstrated by examples of several own investigations devoted to development of new inhibitors that are high effective and selective towards protein kinases CK2, FGFR1 and ASK1.

  4. Rational design of improved pharmabiotics.

    LENUS (Irish Health Repository)

    Sleator, Roy D

    2009-01-01

    Herein we review the most recent advances in probiotic research and applications with particular emphasis on the novel concept of patho-biotechnology: the application of pathogen-derived (ex vivo and in vivo) stress survival strategies for the design of more technologically robust and effective probiotic cultures with improved biotechnological and clinical applications.

  5. Rational Design of Improved Pharmabiotics

    Directory of Open Access Journals (Sweden)

    Roy D. Sleator

    2009-01-01

    Full Text Available Herein we review the most recent advances in probiotic research and applications with particular emphasis on the novel concept of patho-biotechnology: the application of pathogen-derived (ex vivo and in vivo stress survival strategies for the design of more technologically robust and effective probiotic cultures with improved biotechnological and clinical applications.

  6. RATIONAL STEEL CORRUGATED PROFILE DESIGN

    Directory of Open Access Journals (Sweden)

    V. V. Kachurenko

    2015-08-01

    Full Text Available Purpose. The work sets forth the search results of new, more efficient design solutions for metal silos, namely, the analysis of existing types of profiles cross-section in a steel wall of such silo and development of less material-intensive section of corrugated profile.Methodology. To achieve the set goal there were researched the existing types of capacitive structure profiles and their strain-stress state under the load. The analysis was performed on the results of computational experiments. The prototype object was mathematical computer models. The calculations were made using the finite-element method. For computational experiment there was used the design-computing system Structure CAD for Windows. Findings. In this work there were obtained the data allowing to assess work of the profiles and to find more effective type of cross-section in terms of its material consumption. In the process of joint study of the authors a new type of profile for capacitive structures was developed; it has higher utilization efficiency and the attachment point of individual steel sheets with this type of profile. Both solutions are easy to install, reliable in operation and can be manufactured in the conditions of modern industrial production using standard equipment, materials and components. Originality. A new type of corrugated profile cross-section for steel silo walls was proposed; it has higher load carrying capacity and rigidity and allows reducing the metal thickness without changing the structure carrying capacity that results in material consumption reduction of the whole structure.For this and similar types of profiles there was designed and proposed the attachment point of individual corrugated sheets screwed with extending flange, which enables the unit connection in case of small size corrugations, where the distance is not sufficient to accommodate the bolt cap between the individual corrugations. Practical value.Application of the proposed

  7. Towards a formal logic of design rationalization

    DEFF Research Database (Denmark)

    Galle, Per

    1997-01-01

    Certain extensions to standard predicate logic are proposed and used as a framework for critical logical study of patterns of inference in design reasoning. It is shown that within this framework a modal logic of design rationalization (suggested by an empirical study reported earlier) can...... be formally defined in terms of quantification over a universe of discourse of ‘relevant points of view’. Five basic principles of the extended predicate logic are listed, on the basis of which the validity of ten modal patterns of inference encountered in design rationalization is tested. The basic idea...... of reducing modality to quantification is traced back to the philosophy of von Wright, and the approach is compared to that of related work on logic in design....

  8. Rational design of nanomaterials for water treatment

    Science.gov (United States)

    Li, Renyuan; Zhang, Lianbin; Wang, Peng

    2015-10-01

    The ever-increasing human demand for safe and clean water is gradually pushing conventional water treatment technologies to their limits. It is now a popular perception that the solutions to the existing and future water challenges will hinge upon further developments in nanomaterial sciences. The concept of rational design emphasizes on `design-for-purpose' and it necessitates a scientifically clear problem definition to initiate the nanomaterial design. The field of rational design of nanomaterials for water treatment has experienced a significant growth in the past decade and is poised to make its contribution in creating advanced next-generation water treatment technologies in the years to come. Within the water treatment context, this review offers a comprehensive and in-depth overview of the latest progress in rational design, synthesis and applications of nanomaterials in adsorption, chemical oxidation and reduction reactions, membrane-based separation, oil-water separation, and synergistic multifunctional all-in-one nanomaterials/nanodevices. Special attention is paid to the chemical concepts related to nanomaterial design throughout the review.

  9. Rational design of nanomaterials for water treatment

    KAUST Repository

    Li, Renyuan

    2015-08-26

    The ever-increasing human demand for safe and clean water is gradually pushing conventional water treatment technologies to their limits and it is now a popular perception that the solutions to the existing and future water challenges will highly hinge upon the further development of nanomaterial sciences. The concept of rational design emphasizes ‘design-for-purpose’ and it necessitates a scientifically clear problem definition to initiate the nanomaterial design. The field of rational design of nanomaterials for water treatment has experienced a significant growth in the past decade and is poised to make its contribution in creating advanced next-generation water treatment technologies in the years to come. Within the water treatment context, this review offers a comprehensive and in-depth overview of the latest progress of the rational design, synthesis and applications of nanomaterials in adsorption, chemical oxidation and reduction reactions, membrane-based separation, oil/water separation, and synergistic multifunctional all-in-one nanomaterials/nanodevices. Special attention is paid on chemical concepts of the nanomaterial designs throughout the review.

  10. Vaccines: from empirical development to rational design.

    Directory of Open Access Journals (Sweden)

    Christine Rueckert

    Full Text Available Infectious diseases are responsible for an overwhelming number of deaths worldwide and their clinical management is often hampered by the emergence of multi-drug-resistant strains. Therefore, prevention through vaccination currently represents the best course of action to combat them. However, immune escape and evasion by pathogens often render vaccine development difficult. Furthermore, most currently available vaccines were empirically designed. In this review, we discuss why rational design of vaccines is not only desirable but also necessary. We introduce recent developments towards specifically tailored antigens, adjuvants, and delivery systems, and discuss the methodological gaps and lack of knowledge still hampering true rational vaccine design. Finally, we address the potential and limitations of different strategies and technologies for advancing vaccine development.

  11. The rational design of photocatalytic semiconductor nanoparticles

    OpenAIRE

    2014-01-01

    This thesis reports the successful rational design of three highly active photocatalytic semiconductor nanocrystal (SNC) systems by exploiting morphology effects and the electronic properties of type II semiconductor heterojunctions. Novel architectures of colloidal SNCs are produced with the aim of suppressing exciton recombination and improving charge extraction for the successful initiation of desirable redox chemistry. Rod-shaped niobium pentoxide Nb2O5 nanocrystals (NCs) are shown to...

  12. Geology and Design: Formal and Rational Connections

    Science.gov (United States)

    Eriksson, S. C.; Brewer, J.

    2016-12-01

    Geological forms and the manmade environment have always been inextricably linked. From the time that Upper Paleolithic man created drawings in the Lascaux Caves in the southwest of France, geology has provided a critical and dramatic spoil for human creativity. This inspiration has manifested itself in many different ways, and the history of architecture is rife with examples of geologically derived buildings. During the early 20th Century, German Expressionist art and architecture was heavily influenced by the natural and often translucent quality of minerals. Architects like Bruno Taut drew and built crystalline forms that would go on to inspire the more restrained Bauhaus movement. Even within the context of Contemporary architecture, geology has been a fertile source for inspiration. Architectural practices across the globe leverage the rationality and grounding found in geology to inform a process that is otherwise dominated by computer-driven parametric design. The connection between advanced design technology and the beautifully realized geo natural forms insures that geology will be a relevant source of architectural inspiration well into the 21st century. The sometimes hidden relationship of geology to the various sub-disciplines of Design such as Architecture, Interiors, Landscape Architecture, and Historic Preservation is explored in relation to curriculum and the practice of design. Topics such as materials, form, history, the cultural and physical landscape, natural hazards, and global design enrich and inform curriculum across the college. Commonly, these help define place-based education.

  13. Rational Design of Biobetters with Enhanced Stability.

    Science.gov (United States)

    Courtois, Fabienne; Schneider, Curtiss P; Agrawal, Neeraj J; Trout, Bernhardt L

    2015-08-01

    Biotherapeutics are the fastest growing class of pharmaceutical with a rapidly evolving market facing the rise of biosimilar and biobetter products. In contrast to a biosimilar, which is derived from the same gene sequence as the innovator product, a biobetter has enhanced properties, such as enhanced efficacy or reduced immunogenicity. Little work has been carried out so far to increase the intrinsic stability of biotherapeutics via sequence changes, even though, aggregation, the primary degradation pathway of proteins, leads to issues ranging from manufacturing failure to immunological response and to loss of therapeutic activity. Using our spatial aggregation propensity tool as a first step to a rational design approach to identify aggregation-prone regions, biobetters of rituximab have been produced with enhanced stability by introducing site-specific mutations. Significant stabilization against aggregation was achieved for rituximab with no decrease in its binding affinity to the antigen.

  14. Towards the Rational Design of Nanoparticle Catalysts

    Science.gov (United States)

    Dash, Priyabrat

    This research is focused on development of routes towards the rational design of nanoparticle catalysts. Primarily, it is focused on two main projects; (1) the use of imidazolium-based ionic liquids (ILs) as greener media for the design of quasi-homogeneous nanoparticle catalysts and (2) the rational design of heterogeneous-supported nanoparticle catalysts from structured nanoparticle precursors. Each project has different studies associated with the main objective of the design of nanoparticle catalysts. In the first project, imidazolium-based ionic liquids have been used for the synthesis of nanoparticle catalysts. In particular, studies on recyclability, reuse, mode-of-stability, and long-term stability of these ionic-liquid supported nanoparticle catalysts have been done; all of which are important factors in determining the overall "greenness" of such synthetic routes. Three papers have been published/submitted for this project. In the first publication, highly stable polymer-stabilized Au, Pd and bimetallic Au-Pd nanoparticle catalysts have been synthesized in imidazolium-based 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM]PF6) ionic liquid (Journal of Molecular Catalysis A: Chemical, 2008, 286, 114). The resulting nanoparticles were found to be effective and selective quasi-homogeneous catalysts towards a wide-range of hydrogenation reactions and the catalyst solution was reused for further catalytic reactions with minimal loss in activity. The synthesis of very pure and clean ILs has allowed a platform to study the effects of impurities in the imidazolium ILs on nanoparticle stability. In a later study, a new mode of stabilization was postulated where the presence of low amounts of 1-methylimidazole has substantial effects on the resulting stability of Au and Pd-Au nanoparticles in these ILs (Chemical Communications, 2009, 812). In further continuation of this study, a comparative study involving four stabilization protocols for nanoparticle

  15. The effect of interface microstructure on interfacial shear strength for osteochondral scaffolds based on biomimetic design and 3D printing.

    Science.gov (United States)

    Zhang, Weijie; Lian, Qin; Li, Dichen; Wang, Kunzheng; Hao, Dingjun; Bian, Weiguo; Jin, Zhongmin

    2015-01-01

    Interface integration between chondral phase and osseous phase is crucial in engineered osteochondral scaffolds. However, the integration was poorly understood and commonly failed to meet the need of osteochondral scaffolds. In this paper, a biphasic polyethylene glycol (PEG)/β-tricalcium phosphate (β-TCP) scaffold with enhanced interfacial integration was developed. The chondral phase was a PEG hydrogel. The osseous phase was a β-TCP ceramic scaffold. The PEG hydrogel was directly cured on the ceramic interface layer by layer to fabricate osteochondral scaffolds by 3D printing technology. Meanwhile, a series of interface structure were designed with different interface pore area percentages (0/10/20/30/40/50/60%), and interfacial shear test was applied for interface structure optimization (n=6 samples/group). The interfacial shear strength of 30% pore area group was nearly three folds improved compared with that of 0% pore area percentage group, and more than fifty folds improved compared with that of traditional integration (5.91±0.59 kPa). In conclusion, the biomimetic PEG/β-TCP scaffolds with interface structure enhanced integration show promising potential application for osteochondral tissue engineering. Copyright © 2014 Elsevier B.V. All rights reserved.

  16. Design of perfect reconstruction rational sampling filter banks

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The design of rational sampling filter banks based on a recombination structure can be formulated as a problem with two objective functions to be optimized. A new hybrid optimization method for designing perfectreconstruction rational sampling filter banks is presented, which can be used to solve a class of problems with two objective functions. This method is of good convergence and mezzo calculation cost. Satisfactory results free of aliasing in analysis and synthesis filters can be obtained by the proposed method.

  17. Inverse Quantum Chemistry: Concepts and Strategies for Rational Compound Design

    CERN Document Server

    Weymuth, Thomas

    2014-01-01

    The rational design of molecules and materials is becoming more and more important. With the advent of powerful computer systems and sophisticated algorithms, quantum chemistry plays an important role in rational design. While traditional quantum chemical approaches predict the properties of a predefined molecular structure, the goal of inverse quantum chemistry is to find a structure featuring one or more desired properties. Herein, we review inverse quantum chemical approaches proposed so far and discuss their advantages as well as their weaknesses.

  18. The relationship between rational drug design and drug side effects.

    Science.gov (United States)

    Wang, Juan; Li, Zhi-xin; Qiu, Cheng-xiang; Wang, Dong; Cui, Qing-hua

    2012-05-01

    Previous analysis of systems pharmacology has revealed a tendency of rational drug design in the pharmaceutical industry. The targets of new drugs tend to be close with the corresponding disease genes in the biological networks. However, it remains unclear whether the rational drug design introduces disadvantages, i.e. side effects. Therefore, it is important to dissect the relationship between rational drug design and drug side effects. Based on a recently released drug side effect database, SIDER, here we analyzed the relationship between drug side effects and the rational drug design. We revealed that the incidence drug side effect is significantly associated with the network distance of drug targets and diseases genes. Drugs with the distances of three or four have the smallest incidence of side effects, whereas drugs with the distances of more than four or smaller than three show significantly greater incidence of side effects. Furthermore, protein drugs and small molecule drugs show significant differences. Drugs hitting membrane targets and drugs hitting cytoplasm targets also show differences. Failure drugs because of severe side effects show smaller network distances than approved drugs. These results suggest that researchers should be prudent on rationalizing the drug design. Too small distances between drug targets and diseases genes may not always be advantageous for rational design for drug discovery.

  19. Rational design of all organic polymer dielectrics

    Science.gov (United States)

    Sharma, Vinit; Wang, Chenchen; Lorenzini, Robert G.; Ma, Rui; Zhu, Qiang; Sinkovits, Daniel W.; Pilania, Ghanshyam; Oganov, Artem R.; Kumar, Sanat; Sotzing, Gregory A.; Boggs, Steven A.; Ramprasad, Rampi

    2014-09-01

    To date, trial and error strategies guided by intuition have dominated the identification of materials suitable for a specific application. We are entering a data-rich, modelling-driven era where such Edisonian approaches are gradually being replaced by rational strategies, which couple predictions from advanced computational screening with targeted experimental synthesis and validation. Here, consistent with this emerging paradigm, we propose a strategy of hierarchical modelling with successive downselection stages to accelerate the identification of polymer dielectrics that have the potential to surpass ‘standard’ materials for a given application. Successful synthesis and testing of some of the most promising identified polymers and the measured attractive dielectric properties (which are in quantitative agreement with predictions) strongly supports the proposed approach to material selection.

  20. Rational drug design paradigms: the odyssey for designing better drugs.

    Science.gov (United States)

    Kellici, Tahsin; Ntountaniotis, Dimitrios; Vrontaki, Eleni; Liapakis, George; Moutevelis-Minakakis, Panagiota; Kokotos, George; Hadjikakou, Sotiris; Tzakos, Andreas G; Afantitis, Antreas; Melagraki, Georgia; Bryant, Sharon; Langer, Thierry; Di Marzo, Vincenzo; Mavromoustakos, Thomas

    2015-01-01

    Due to the time and effort requirements for the development of a new drug, and the high attrition rates associated with this developmental process, there is an intense effort by academic and industrial researchers to find novel ways for more effective drug development schemes. The first step in the discovery process of a new drug is the identification of the lead compound. The modern research tendency is to avoid the synthesis of new molecules based on chemical intuition, which is time and cost consuming, and instead to apply in silico rational drug design. This approach reduces the consumables and human personnel involved in the initial steps of the drug design. In this review real examples from our research activity aiming to discover new leads will be given for various dire warnings diseases. There is no recipe to follow for discovering new leads. The strategy to be followed depends on the knowledge of the studied system and the experience of the researchers. The described examples constitute successful and unsuccessful efforts and reflect the reality which medicinal chemists have to face in drug design and development. The drug stability is also discussed in both organic molecules and metallotherapeutics. This is an important issue in drug discovery as drug metabolism in the body can lead to various toxic and undesired molecules.

  1. Evaluation of urban river landscape design rationality based on AHP

    Directory of Open Access Journals (Sweden)

    Qiao Lifang

    2008-12-01

    Full Text Available Abstract: An evaluation model for the rationality of the landscape design of urban rivers was established with the analytic hierarchy process (AHP method so as to provide a foundation for updating the landscape design of urban rivers. The evaluation system was divided into four layers, including the target layer, the comprehensive layer, the element layer, and the index layer. Each layer was made of different indices. The evaluation standards for each index were also given in this paper. This evaluation model was proved tenable through its application to the landscape design rationality evaluation of the Weihe River in Xinxiang City of Henan Province. The results show that the water quality, space, activity, facility, community, width of vegetation, sense of beauty and water content are among the most influential factors and should be considered the main basis for evaluating the rationality of the landscape design of urban rivers.

  2. Designing institutions for climate change: Why rational design involves technology

    Energy Technology Data Exchange (ETDEWEB)

    Coninck, H. de [Energy Research Centre of the Netherlands, Petten (Netherlands)

    2008-09-30

    This paper aims to explore how to augment the institutional solutions offered by current political theory for addressing the unprecedented problem of climate change. Although steering directly at emission reductions in an international treaty has benefits in terms of cost-effectiveness, the paper arrives at the conclusion that considerations around technological development should be drawn into the treaty equation in order to generate sufficient reciprocity to have a politically feasible international regime. It then argues that the benefits of technology agreements for climate change mitigation may be larger than commonly assumed, as they - if properly designed - could lead to real emission reductions and provide more flexibility to reach agreement in post-2012 negotiations than proposals modelled exclusively on the Kyoto Protocol or other types of absolute emission targets. Based on rational design of international institutions for environmental governance, and attempting to take into account considerations of technological dynamics and the 'sociotechnical system', contours of a possible environmentally effective and politically feasible international climate change agreements are sketched.

  3. Design rationalization and the logic of design: a case study

    DEFF Research Database (Denmark)

    Galle, Per

    1996-01-01

    various ‘sources of credibility’ of premises, items of general background knowledge, and several (abductive and deductive) patterns of inference which suggest a possible ‘logic of design’. Rationalization of decisions is defined, and many decisions are found not to be fully rationalized, despite...

  4. Computational approaches for rational design of proteins with novel functionalities

    Directory of Open Access Journals (Sweden)

    Manish Kumar Tiwari

    2012-09-01

    Full Text Available Proteins are the most multifaceted macromolecules in living systems and have various important functions, including structural, catalytic, sensory, and regulatory functions. Rational design of enzymes is a great challenge to our understanding of protein structure and physical chemistry and has numerous potential applications. Protein design algorithms have been applied to design or engineer proteins that fold, fold faster, catalyze, catalyze faster, signal, and adopt preferred conformational states. The field of de novo protein design, although only a few decades old, is beginning to produce exciting results. Developments in this field are already having a significant impact on biotechnology and chemical biology. The application of powerful computational methods for functional protein designing has recently succeeded at engineering target activities. Here, we review recently reported de novo functional proteins that were developed using various protein design approaches, including rational design, computational optimization, and selection from combinatorial libraries, highlighting recent advances and successes.

  5. Computational approaches for rational design of proteins with novel functionalities.

    Science.gov (United States)

    Tiwari, Manish Kumar; Singh, Ranjitha; Singh, Raushan Kumar; Kim, In-Won; Lee, Jung-Kul

    2012-01-01

    Proteins are the most multifaceted macromolecules in living systems and have various important functions, including structural, catalytic, sensory, and regulatory functions. Rational design of enzymes is a great challenge to our understanding of protein structure and physical chemistry and has numerous potential applications. Protein design algorithms have been applied to design or engineer proteins that fold, fold faster, catalyze, catalyze faster, signal, and adopt preferred conformational states. The field of de novo protein design, although only a few decades old, is beginning to produce exciting results. Developments in this field are already having a significant impact on biotechnology and chemical biology. The application of powerful computational methods for functional protein designing has recently succeeded at engineering target activities. Here, we review recently reported de novo functional proteins that were developed using various protein design approaches, including rational design, computational optimization, and selection from combinatorial libraries, highlighting recent advances and successes.

  6. Rational design of reconfigurable prismatic architected materials

    Science.gov (United States)

    Overvelde, Johannes T. B.; Weaver, James C.; Hoberman, Chuck; Bertoldi, Katia

    2017-01-01

    Advances in fabrication technologies are enabling the production of architected materials with unprecedented properties. Most such materials are characterized by a fixed geometry, but in the design of some materials it is possible to incorporate internal mechanisms capable of reconfiguring their spatial architecture, and in this way to enable tunable functionality. Inspired by the structural diversity and foldability of the prismatic geometries that can be constructed using the snapology origami technique, here we introduce a robust design strategy based on space-filling tessellations of polyhedra to create three-dimensional reconfigurable materials comprising a periodic assembly of rigid plates and elastic hinges. Guided by numerical analysis and physical prototypes, we systematically explore the mobility of the designed structures and identify a wide range of qualitatively different deformations and internal rearrangements. Given that the underlying principles are scale-independent, our strategy can be applied to the design of the next generation of reconfigurable structures and materials, ranging from metre-scale transformable architectures to nanometre-scale tunable photonic systems.

  7. Rational design of reconfigurable prismatic architected materials.

    Science.gov (United States)

    Overvelde, Johannes T B; Weaver, James C; Hoberman, Chuck; Bertoldi, Katia

    2017-01-18

    Advances in fabrication technologies are enabling the production of architected materials with unprecedented properties. Most such materials are characterized by a fixed geometry, but in the design of some materials it is possible to incorporate internal mechanisms capable of reconfiguring their spatial architecture, and in this way to enable tunable functionality. Inspired by the structural diversity and foldability of the prismatic geometries that can be constructed using the snapology origami technique, here we introduce a robust design strategy based on space-filling tessellations of polyhedra to create three-dimensional reconfigurable materials comprising a periodic assembly of rigid plates and elastic hinges. Guided by numerical analysis and physical prototypes, we systematically explore the mobility of the designed structures and identify a wide range of qualitatively different deformations and internal rearrangements. Given that the underlying principles are scale-independent, our strategy can be applied to the design of the next generation of reconfigurable structures and materials, ranging from metre-scale transformable architectures to nanometre-scale tunable photonic systems.

  8. Rational design of efficient modular cells.

    Science.gov (United States)

    Trinh, Cong T; Liu, Yan; Conner, David J

    2015-11-01

    The modular cell design principle is formulated to devise modular (chassis) cells. These cells can be assembled with exchangeable production modules in a plug-and-play fashion to build microbial cell factories for efficient combinatorial biosynthesis of novel molecules, requiring minimal iterative strain optimization steps. A modular cell is designed to be auxotrophic, containing core metabolic pathways that are necessary but insufficient to support cell growth and maintenance. To be functional, it must tightly couple with an exchangeable production module containing auxiliary metabolic pathways that not only complement cell growth but also enhance production of targeted molecules. We developed a MODCELL (modular cell) framework based on metabolic pathway analysis to implement the modular cell design principle. MODCELL identifies genetic modifications and requirements to construct modular cell candidates and their associated exchangeable production modules. By defining the degree of similarity and coupling metrics, MODCELL can evaluate which exchangeable production module(s) can be tightly coupled with a modular cell candidate. We first demonstrated how MODCELL works in a step-by-step manner for example metabolic networks, and then applied it to design modular Escherichia coli cells for efficient combinatorial biosynthesis of five alcohols (ethanol, propanol, isopropanol, butanol and isobutanol) and five butyrate esters (ethyl butyrate, propyl butyrate, isopropyl butyrate, butyl butyrate and isobutyl butyrate) from pentose sugars (arabinose and xylose) and hexose sugars (glucose, mannose, and galactose) under anaerobic conditions. We identified three modular cells, MODCELL1, MODCELL2 and MODCELL3, that can couple well with Group 1 of modules (ethanol, isobutanol, butanol, ethyl butyrate, isobutyl butyrate, butyl butyrate), Group 2 (isopropanol, isopropyl butyrate), and Group 3 (propanol, isopropanol), respectively. We validated the design of MODCELL1 for anaerobic

  9. [Scaffold-based Bone Tissue Engineering].

    Science.gov (United States)

    Holzapfel, B M; Rudert, M; Hutmacher, D W

    2017-08-01

    Tissue engineering provides the possibility of regenerating damaged or lost osseous structures without the need for permanent implants. Within this context, biodegradable and bioresorbable scaffolds can provide structural and biomechanical stability until the body's own tissue can take over their function. Additive biomanufacturing makes it possible to design the scaffold's architectural characteristics to specifically guide tissue formation and regeneration. Its nano-, micro-, and macro-architectural properties can be tailored to ensure vascularization, oxygenation, nutrient supply, waste exchange, and eventually ossification not only in its periphery but also in its center, which is not in direct contact with osteogenic elements of the surrounding healthy tissue. In this article we provide an overview about our conceptual design and process of the clinical translation of scaffold-based bone tissue engineering applications.

  10. Rational design of precursors for oxide ceramics

    Energy Technology Data Exchange (ETDEWEB)

    Apblett, A.W.; Georgieva, G. [Tulane Univ., New Orleans, LA (United States)

    1993-12-31

    The use of molecular species as precursors for inorganic materials has received considerable attention in recent years. As a result, metal-organic precursors are becoming increasingly sophisticated as particular decomposition mechanisms and specific stoichiometry are integrated into their design. The authors have pursued both of these design aspects for the development of low-temperature precursors for mono- and bi-metallic oxide materials. Thus, a great variety of metal complexes with 2- and 3-oximinocarboxylic acids, acyloin oximes, 2,4-diols, and diacetone alcohol have been prepared and their thermal behavior investigated. The results of this investigation and their application to the preparation of a variety of metal, oxide ceramics, will be discussed. Particular attention will be paid to precursors for alumina, titania, zirconia, perovskite-phase ferroelectric materials, and ferrites.

  11. Rational Design of Metal Ion Sequestering Agents

    Energy Technology Data Exchange (ETDEWEB)

    Raymond, Kenneth N.; Xu, Jide; Gramer, Christine

    1999-06-01

    This project addresses the fundamental issues and requirements for developing hazardous metal ion separation technologies applicable to the treatment and disposal of radioactive waste. Our research encompasses the following areas: the design and synthesis of metal ion specific sequestering ligands, structural and thermodynamic investigations of these ligand and the complexes formed with targeted metal ions, and the development and incorporation of these ligands into applied separation technologies as highly effective materials for hazardous metal ion decontamination.

  12. Rational Design of Zinc Phosphide Heterojunction Photovoltaics

    Science.gov (United States)

    Bosco, Jeffrey Paul

    The prospect of terawatt-scale electricity generation using a photovoltaic (PV) device places strict requirements on the active semiconductor optoelectronic properties and elemental abundance. After reviewing the constraints placed on an ``earth-abundant'' solar absorber, we find zinc phosphide (α-Zn 3P2) to be an ideal candidate. In addition to its near-optimal direct band gap of 1.5 eV, high visible-light absorption coefficient (>10. 4cm-1), and long minority-carrier diffusion length (>5 μm), Zn3P 2 is composed of abundant Zn and P elements and has excellent physical properties for scalable thin-film deposition. However, to date, a Zn 3P2 device of sufficient efficiency for commercial applications has not been demonstrated. Record efficiencies of 6.0% for multicrystalline and 4.3% for thin-film cells have been reported, respectively. Performance has been limited by the intrinsic p-type conductivity of Zn3P 2 which restricts us to Schottky and heterojunction device designs. Due to our poor understanding of Zn3P2 interfaces, an ideal heterojunction partner has not yet been found. The goal of this thesis is to explore the upper limit of solar conversion efficiency achievable with a Zn3P2 absorber through the design of an optimal heterojunction PV device. To do so, we investigate three key aspects of material growth, interface energetics, and device design. First, the growth of Zn3P2 on GaAs(001) is studied using compound-source molecular-beam epitaxy (MBE). We successfully demonstrate the pseudomorphic growth of Zn3P2 epilayers of controlled orientation and optoelectronic properties. Next, the energy-band alignments of epitaxial Zn3P2 and II-VI and III-V semiconductor interfaces are measured via high-resolution x-ray photoelectron spectroscopy in order to determine the most appropriate heterojunction partner. From this work, we identify ZnSe as a nearly ideal n-type emitter for a Zn3P 2 PV device. Finally, various II-VI/Zn3P2 heterojunction solar cells designs are

  13. The rational design of biological complexity: a deceptive metaphor.

    Science.gov (United States)

    Van Regenmortel, Marc H V

    2007-03-01

    Biologists often claim that they follow a rational design strategy when their research is based on molecular knowledge of biological systems. This claim implies that their knowledge of the innumerable causal connections present in biological systems is sufficient to allow them to deduce and predict the outcome of their experimental interventions. The design metaphor is shown to originate in human intentionality and in the anthropomorphic fallacy of interpreting objects, events, and the behavior of all living organisms in terms of goals and purposes. Instead of presenting rational design as an effective research strategy, it would be preferable to acknowledge that advances in biomedicine are nearly always derived from empirical observations based on trial and error experimentation. The claim that rational design is an effective research strategy was tested in the case of current attempts to develop synthetic vaccines, in particular against human immunodeficiency virus. It was concluded that in this field of biomedicine, trial and error experimentation is more likely to succeed than a rational design approach. Current developments in systems biology may give us eventually a better understanding of the immune system and this may enable us in the future to develop improved vaccines.

  14. Rational Design of Metal Ion Sequestering Agents

    Energy Technology Data Exchange (ETDEWEB)

    Raymond, Kenneth N.

    2000-09-30

    The discriminate bonding of metal ions is a challenge to the synthetic chemist and a phenomenon of considerable practical importance.1 An important feature of many technical applications is the specific or preferential binding of a single metal ion in the presence of many metals. Examples range from large-volume uses (e.g. ferric EDTA as a plant food, calcium complexing agents as water softeners or anticaking formulations) to very high technology applications (technetium complexation in radiopharmaceuticals, synthetic metalloenzymes). We are interested in efficient and discriminate binding of actinides for waste stream remediation. Actinides represent a major and long-lived contaminant in nuclear waste. While the separation of actinides from other radioactive components of waste, such as Sr and Cs, is relatively well established, the separation of actinides from each other and in complex solutions (e.g. those found in tank wastes) is not as well resolved. The challenge of designing metal-specific (actinide) ligands is facilitated by examples from nature. Bacteria synthesize Fe(III)-specific ligands, called siderophores, to sequester Fe(III) from the environment and return it to the cell. The similarities between Fe(III) and Pu(IV) (their charge-to-size ratios and acidity), make the siderophores prototypical for designing actinide-specific ligands. The chelating groups present in siderophores are usually hydroxamic acids and catecholamides. We have developed derivatives of these natural products which have improved properties. The catechol derivatives are the 2,3-dihydroxyterephthalamides (TAMs), and 3,4-dihydroxysulfonamides (SFAMs), and the hydroxamic acid derivatives are three isomers of hydroxypyridinones, 1,2- HOPO, 3,2-HOPO, and 3,4-HOPO. All of these ligands are attached to molecular backbones by amides and a very important feature of HOPO and CAM ligands is a strong hydrogen bonds formed between the amide proton and the adjacent phenolic oxygen in the metal

  15. A rational approach for ω-transaminase-catalyzed process design

    DEFF Research Database (Denmark)

    T. Gundersen, Maria; Lloyd, Richard; Tufvesson, Pär;

    Herein we describe a novel rational approach to the design of a ω-transaminase process such that it will fulfill criteria necessary for industrial use. By first determining the fundamental properties of the reaction system, it is possible to suggest appropriate process strategies that may be used...

  16. On Rational Design of Double Hull Tanker Structures against Collision

    DEFF Research Database (Denmark)

    Paik, Jeom Kee; Chung, Jang Young; Choe, Ich Hung

    1999-01-01

    in the present study were (i) developing a framework for the collision design procedure for double hull tanker structures, (ii) experimental investigation of the structural crashworthiness of the collided vessels in collision or stranding, using double skinned structural models, (iii) validation of the special...... be useful for the rational design of new double hull tanker side structures against ship collision to reduced the risk of oil pollution and for the collision resistance evaluation of existing double hull tanker structures....

  17. Rational Design of a Structural and Functional Nitric Oxide Reductase

    Energy Technology Data Exchange (ETDEWEB)

    Yeung, N.; Lin, Y; Gao, Y; Zhao, X; Russell, B; Lei, L; Miner, L; Robinson, H; Lu, Y

    2009-01-01

    Protein design provides a rigorous test of our knowledge about proteins and allows the creation of novel enzymes for biotechnological applications. Whereas progress has been made in designing proteins that mimic native proteins structurally, it is more difficult to design functional proteins. In comparison to recent successes in designing non-metalloproteins, it is even more challenging to rationally design metalloproteins that reproduce both the structure and function of native metalloenzymes. This is because protein metal-binding sites are much more varied than non-metal-containing sites, in terms of different metal ion oxidation states, preferred geometry and metal ion ligand donor sets. Because of their variability, it has been difficult to predict metal-binding site properties in silico, as many of the parameters, such as force fields, are ill-defined. Therefore, the successful design of a structural and functional metalloprotein would greatly advance the field of protein design and our understanding of enzymes. Here we report a successful, rational design of a structural and functional model of a metalloprotein, nitric oxide reductase (NOR), by introducing three histidines and one glutamate, predicted as ligands in the active site of NOR, into the distal pocket of myoglobin. A crystal structure of the designed protein confirms that the minimized computer model contains a haem/non-haem FeB centre that is remarkably similar to that in the crystal structure. This designed protein also exhibits NO reduction activity, and so models both the structure and function of NOR, offering insight that the active site glutamate is required for both iron binding and activity. These results show that structural and functional metalloproteins can be rationally designed in silico.

  18. Rational SOFC material design: new advances and tools

    Directory of Open Access Journals (Sweden)

    Meilin Liu

    2011-11-01

    Full Text Available Solid oxide fuel cells (SOFCs offer great prospects for the most efficient and cost-effective utilization of a wide variety of fuels. However, their commercialization hinges on the rational design of low cost materials with exceptional functionalities. This article highlights some recent progress in probing and mapping surface species and incipient phases relevant to electrode reactions using in situ Raman spectroscopy, synchrotron based x-ray analysis, and multi-scale modeling of charge and mass transport. The combination of in situ characterization and multi-scale modeling is imperative to unraveling the mechanisms of chemical and energy transformation: a vital step for the rational design of next generation SOFC materials.

  19. Rational design and nanofabrication of gecko-inspired fibrillar adhesives.

    Science.gov (United States)

    Hu, Shihao; Xia, Zhenhai

    2012-08-20

    Gecko feet integrate many intriguing functions such as strong adhesion, easy detachment, and self-cleaning. Mimicking gecko toe pad structure leads to the development of new types of fibrillar adhesives useful for various applications. In this Concept article, in addition to the design of adhesive mimics by replicating gecko geometric features, we show a new trend of rational design by adding other physical, chemical, and biological principles on to the geometric merits, for enhancing robustness, responsive control, and durability. Current challenges and future directions are highlighted in the design and nanofabrication of biomimetic fibrillar adhesives.

  20. Rational principles of compound selection for combinatorial library design.

    Science.gov (United States)

    Tropsha, Alexander; Zheng, Weifan

    2002-03-01

    It is practically impossible in a short period of time to synthesize and test all compounds in any large exhaustive chemical library. We discuss rational approaches to selecting representative subsets of virtual libraries that help direct experimental synthetic efforts for both targeted and diverse library design. For targeted library design, we consider principles based on the similarity to lead molecules. In the case of diverse library design, we discuss algorithms aimed at the selection of both diverse and representative subsets of the entire chemical library space. We illustrate methodologies with several practical examples.

  1. Rational design of semiconductors for photoelectrochemical water splitting

    Science.gov (United States)

    Wei, Su-Huai

    2013-12-01

    Using first-principles method as a tool, we discuss the general strategies for the rational design of semiconductors to simultaneously meet all of requirements for high-efficiency, solar-driven photoelectrochemical (PEC) water-splitting devices. Our studies demonstrate that theoretical calculations, which provided deep understanding of the underlying physics behind these PEC materials, can greatly accelerate scientific discovery of new PEC materials in this exciting field.

  2. Host defense mechanism-based rational design of live vaccine.

    Directory of Open Access Journals (Sweden)

    Yo Han Jang

    Full Text Available Live attenuated vaccine (LAV, mimicking natural infection, provides an excellent protection against microbial infection. The development of LAV, however, still remains highly empirical and the rational design of clinically useful LAV is scarcely available. Apoptosis and caspase activation are general host antiviral responses in virus-infected cells. Utilizing these tightly regulated host defense mechanisms, we present a novel apoptosis-triggered attenuation of viral virulence as a rational design of live attenuated vaccine with desired levels of safety, efficacy, and productivity. Mutant influenza viruses carrying caspase recognition motifs in viral NP and the interferon-antagonist NS1 proteins were highly attenuated both in vitro and in vivo by caspase-mediated cleavage of those proteins in infected cells. Both viral replication and interferon-resistance were substantially reduced, resulting in a marked attenuation of virulence of the virus. Despite pronounced attenuation, the viruses demonstrated high growth phenotype in embryonated eggs at lower temperature, ensuring its productivity. A single dose vaccination with the mutant virus elicited high levels of systemic and mucosal antibody responses and provided complete protection against both homologous and heterologous lethal challenges in mouse model. While providing a practical means to generate seasonal or pandemic influenza live vaccines, the sensitization of viral proteins to pathogen-triggered apoptotic signals presents a potentially universal, mechanism-based rational design of live vaccines against many viral infections.

  3. Host defense mechanism-based rational design of live vaccine.

    Science.gov (United States)

    Jang, Yo Han; Byun, Young Ho; Lee, Kwang-Hee; Park, Eun-Sook; Lee, Yun Ha; Lee, Yoon-Jae; Lee, Jinhee; Kim, Kyun-Hwan; Seong, Baik Lin

    2013-01-01

    Live attenuated vaccine (LAV), mimicking natural infection, provides an excellent protection against microbial infection. The development of LAV, however, still remains highly empirical and the rational design of clinically useful LAV is scarcely available. Apoptosis and caspase activation are general host antiviral responses in virus-infected cells. Utilizing these tightly regulated host defense mechanisms, we present a novel apoptosis-triggered attenuation of viral virulence as a rational design of live attenuated vaccine with desired levels of safety, efficacy, and productivity. Mutant influenza viruses carrying caspase recognition motifs in viral NP and the interferon-antagonist NS1 proteins were highly attenuated both in vitro and in vivo by caspase-mediated cleavage of those proteins in infected cells. Both viral replication and interferon-resistance were substantially reduced, resulting in a marked attenuation of virulence of the virus. Despite pronounced attenuation, the viruses demonstrated high growth phenotype in embryonated eggs at lower temperature, ensuring its productivity. A single dose vaccination with the mutant virus elicited high levels of systemic and mucosal antibody responses and provided complete protection against both homologous and heterologous lethal challenges in mouse model. While providing a practical means to generate seasonal or pandemic influenza live vaccines, the sensitization of viral proteins to pathogen-triggered apoptotic signals presents a potentially universal, mechanism-based rational design of live vaccines against many viral infections.

  4. Rational design and synthesis of semi-conducting polymers.

    Energy Technology Data Exchange (ETDEWEB)

    Wong, Bryan Matthew; Reeder, Craig; Cordaro, Joseph Gabriel

    2010-12-01

    A rational approach was used to design polymeric materials for thin-film electronics applications, whereby theoretical modeling was used to determine synthetic targets. Time-dependent density functional theory calculations were used as a tool to predict the electrical properties of conjugated polymer systems. From these results, polymers with desirable energy levels and band-gaps were designed and synthesized. Measurements of optoelectronic properties were performed on the synthesized polymers and the results were compared to those of the theoretical model. From this work, the efficacy of the model was evaluated and new target polymers were identified.

  5. Rational design of inorganic dielectric materials with expected permittivity

    Science.gov (United States)

    Xie, Congwei; Oganov, Artem R.; Dong, Dong; Liu, Ning; Li, Duan; Debela, Tekalign Terfa

    2015-11-01

    Techniques for rapid design of dielectric materials with appropriate permittivity for many important technological applications are urgently needed. It is found that functional structure blocks (FSBs) are helpful in rational design of inorganic dielectrics with expected permittivity. To achieve this, coordination polyhedra are parameterized as FSBs and a simple empirical model to evaluate permittivity based on these FSB parameters is proposed. Using this model, a wide range of examples including ferroelectric, high/low permittivity materials are discussed, resulting in several candidate materials for experimental follow-up.

  6. Shape Designing of Engineering Images Using Rational Spline Interpolation

    Directory of Open Access Journals (Sweden)

    Muhammad Sarfraz

    2015-01-01

    Full Text Available In modern days, engineers encounter a remarkable range of different engineering problems like study of structure, structure properties, and designing of different engineering images, for example, automotive images, aerospace industrial images, architectural designs, shipbuilding, and so forth. This paper purposes an interactive curve scheme for designing engineering images. The purposed scheme furnishes object designing not just in the area of engineering, but it is equally useful for other areas including image processing (IP, Computer Graphics (CG, Computer-Aided Engineering (CAE, Computer-Aided Manufacturing (CAM, and Computer-Aided Design (CAD. As a method, a piecewise rational cubic spline interpolant, with four shape parameters, has been purposed. The method provides effective results together with the effects of derivatives and shape parameters on the shape of the curves in a local and global manner. The spline method, due to its most generalized description, recovers various existing rational spline methods and serves as an alternative to various other methods including v-splines, gamma splines, weighted splines, and beta splines.

  7. Designing a Rational Distribution Network for Trading Companies

    Directory of Open Access Journals (Sweden)

    Dybskaya V. V.

    2017-09-01

    Full Text Available This article considers the modern methods and approaches to design the company’s distribution network. The authors point out the relevance of this problem for the modern trading and manufacturing companies, give examples of the strategic goal setting of the company in the logistics network reorganization, and the benchmarks of possible economic effects of its conduction. The work reviews the scientific articles of contemporary American, European and Russian authors devoted to the approaches, concerning the implementation of projects for designing a distribution network, methods and models for its optimization. The article concludes that there is no single “language” and an approach to design the logistics networks, with a proper level of detail that takes into account the strategic features and industry specificity of the certain company. The authors propose an algorithm for designing a rational distribution network.

  8. Rational design approach for landfill liner protective soil cover

    Energy Technology Data Exchange (ETDEWEB)

    Ruetten, M.G. [STS Consultants Ltd., Green Bay, WI (United States); Bandi, S.R. [Rust Environment & Infrastructure, Livonia, MI (United States); Reddy, K.R. [Univ. of Illinois, Chicago, IL (United States)

    1995-12-31

    This paper presents a rational approach for designing protective soil cover for landfill geomembrane liners in order to prevent damage to the liners. The present practice involves using a combination of geotextile and soil layer as protective cover. The geotextile is placed directly over the geomembrane and then a protective soil is placed on the geotextile. The protective soil layer generally consists of a free-draining granular soil which also serves as a drainage layer for the leachate collection and removal system. The degree of protection offered to the geomembrane depends on the type of geotextile, and the composition and thickness of the protective soil used.

  9. Rational design of nanoparticles for biomedical imaging and photovoltaic applications

    OpenAIRE

    QIN, HAIYAN

    2011-01-01

    This thesis aims to rationally design nanoparticles and promote their applications in biomedical imaging and photovoltaic cells. Quantum dots (QDs) are promising fluorescent probes for biomedical imaging. We have fabricated two types of MSA capped QDs: CdTe/ZnSe core/shell QDs synthesized via an aqueous method and CdTe QDs via a hydrothermal method. They present high quantum yields (QYs), narrow emission band widths, high photo- and pH-stability, and low cytotoxicity. QD-IgG probes were produ...

  10. Recent trends in library design: 'rational design' revisited.

    Science.gov (United States)

    Schnur, Dora M

    2008-05-01

    Diversity has historically played a critical role in the design of combinatorial libraries, screening sets and corporate collections for lead discovery. Large library design dominated the field of lead discovery in the 1990s, with design methods ranging from arbitrary and property-based reagent selection to product-based approaches. Over time, however, there has been a downward trend in library size as the genomics revolution and the increasing availability of target protein structures from X-ray crystallography and homology modeling have increased the volume of information concerning desired targets. Concurrently, computing grids and CPU clusters have facilitated the development of structure-based tools that are able to screen hundreds of thousands of molecules. Smaller, 'smarter' combinatorial and focused parallel libraries have replaced the unfocused large libraries in the drug design paradigm of the 21st century. While diversity continues to play a role in lead discovery, the focus of current library design methods has shifted to scaffold design and bio-isostere searching, with a greatly needed emphasis on synthetic feasibility.

  11. Tailoring recombinant protein quality by rational media design.

    Science.gov (United States)

    Brühlmann, David; Jordan, Martin; Hemberger, Jürgen; Sauer, Markus; Stettler, Matthieu; Broly, Hervé

    2015-01-01

    Clinical efficacy and safety of recombinant proteins are closely associated with their structural characteristics. The major quality attributes comprise glycosylation, charge variants (oxidation, deamidation, and C- & N-terminal modifications), aggregates, low-molecular-weight species (LMW), and misincorporation of amino acids in the protein backbone. Cell culture media design has a great potential to modulate these quality attributes due to the vital role of medium in mammalian cell culture. The purpose of this review is to provide an overview of the way both classical cell culture medium components and novel supplements affect the quality attributes of recombinant therapeutic proteins expressed in mammalian hosts, allowing rational and high-throughput optimization of mammalian cell culture media. A selection of specific and/or potent inhibitors and activators of oligosaccharide processing as well as components affecting multiple quality attributes are presented. Extensive research efforts in this field show the feasibility of quality engineering through media design, allowing to significantly modulate the protein function.

  12. Using Fitness Landscapes for Rational Hepatitis C Immunogen Design

    Science.gov (United States)

    Hart, Gregory; Ferguson, Andrew

    2015-03-01

    Hepatitis C virus afflicts 170 million people worldwide, 2-3% of the global population. Prophylactic vaccination offers the most realistic and cost effective hope of controlling this epidemic, particularly in the developing world where expensive drug therapies are unavailable. Despite 20 years of research, the high mutability of the virus, and lack of knowledge of what constitutes effective immune responses, have impeded development of an effective vaccine. Coupling data mining of sequence databases with the Potts model, we have developed a computational approach to systematically identify viral vulnerabilities and perform rational design of vaccine immunogens. We applied our approach to the nonstructural proteins NS3, NSA, NSA, and NSB which are crucial for viral replication.The predictions of our model are in good accord with experimental measurements and clinical observations, and we have used our model to design immunogen candidates to elicit T-cell responses against vulnerable regions of theseviral proteins.

  13. The application of rational design on phospholipase A(2) inhibitors.

    Science.gov (United States)

    Mouchlis, V D; Barbayianni, E; Mavromoustakos, T M; Kokotos, G

    2011-01-01

    The phospholipase A(2) (PLA(2)) superfamily consists of different groups of enzymes which are characterized by their ability to catalyze the hydrolysis of the sn-2 ester bond in a variety of phospholipid molecules. The products of PLA(2s) activity play divergent roles in a variety of physiological processes. There are four main types of PLA(2s): the secreted PLA(2s) (sPLA(2s)), the cytosolic PLA(2s) (cPLA(2s)), the calcium-independent PLA(2s) (iPLA(2)) and the lipoprotein-associated PLA(2s) (LpPLA(2s)). Various potent and selective PLA2 inhibitors have been reported up to date and have provided outstanding support in understanding the mechanism of action and elucidating the function of these enzymes. The current review focuses on the implementation of rational design through computer-aided drug design (CADD) on the discovery and development of new PLA(2) inhibitors.

  14. Rational Design of Competitive Electrocatalysts for Hydrogen Fuel Cells.

    Science.gov (United States)

    Stolbov, Sergey; Alcántara Ortigoza, Marisol

    2012-02-16

    The large-scale application of one of the most promising clean and renewable sources of energy, hydrogen fuel cells, still awaits efficient and cost-effective electrocatalysts for the oxygen reduction reaction (ORR) occurring on the cathode. We demonstrate that truly rational design renders electrocatalysts possessing both qualities. By unifying the knowledge on surface morphology, composition, electronic structure, and reactivity, we solve that trimetallic sandwich-like structures are an excellent choice for optimization. Their constituting species are expected to couple synergistically yielding reaction-environment stability, cost-effectiveness, and tunable reactivity. This cooperative-action concept enabled us to predict two advantageous ORR electrocatalysts: Pd/Fe/W(110) and Au/Ru/W(110). Density functional theory calculations of the reaction free-energy diagrams suggest that these materials are more active toward ORR than the so-far best Pt-based catalysts. Our designing concept advances also a general approach for engineering advanced materials.

  15. Structure-based, rational design of T cell receptors

    Directory of Open Access Journals (Sweden)

    Vincent eZoete

    2013-09-01

    Full Text Available Adoptive cell transfer using engineered T cells is emerging as a promising treatment for metastatic melanoma. Such an approach allows one to introduce TCR modifications that, while maintaining the specificity for the targeted antigen, can enhance the binding and kinetic parameters for the interaction pMHC. Using the well-characterized 2C TCR/SIYR/H-2K(b structure as a model system, we demonstrated that a binding free energy decomposition based on the MM-GBSA approach provides a detailed and reliable description of the TCR/pMHC interactions at the structural and thermodynamic levels. Starting from this result, we developed a new structure-based approach, to rationally design new TCR sequences, and applied it to the BC1 TCR targeting the HLA-A2 restricted NY-ESO-1157-165 cancer-testis epitope. 54% of the designed sequence replacements exhibited improved pMHC-binding as compared to the native TCR, with up to 150 fold increase in affinity, while preserving specificity. Genetically-engineered CD8+ T cells expressing these modified TCRs showed an improved functional activity compared to those expressing BC1 TCR. We measured maximum levels of activities for TCRs within the upper limit of natural affinity. Beyond the affinity threshold at KD < 1 μM we observed an attenuation in cellular function. We have also developed a homology modeling-based approach, TCRep 3D, to obtain accurate structural models of any TCR-pMHC complexes. We have complemented the approach with a simplified rigid method to predict the TCR orientation over pMHC. These methods potentially extend the use of our TCR engineering method to entire TCR repertoires for which no X-ray structure is available. We have also performed a steered molecular dynamics study of the unbinding of the TCR-pMHC complex to get a better understanding of how TCRs interact with pMHCs. This entire rational TCR design pipeline is now being used to produce rationally optimized TCRs for adoptive cell therapies of

  16. Theoretically Rational Designs of Transport Organic Semiconductors Based on Heteroacenes

    Institute of Scientific and Technical Information of China (English)

    HE,Yuan-Hang; HUI,Ren-Jie; YI,Yuan-Ping; SHUAI,Zhi-Gang

    2008-01-01

    A Marcus electron transfer theory coupled with an incoherent polaron hopping and charge diffusion model in combining with first-principle quantum chemistry calculation was applied to investigating the effects of heteroatom on the intermolecular charge transfer rate for a seres of heteroacene molecules.The influences of intermolecular packing and charge reorganization energy were discussed.It was found that the sulphur and nitrogen substituted heteroacenes were intrinsically hole-transporting materials due to the reduced hole reorganization energy and the enhanced overlap between HOMOs.For the oxygen-substituted heteroacene,it was found that both the electronic couplings and the reorganization energies for holes and electrons were comparative,indicating the application potential of ambipolar devices.Most interestingly,for the boron-substituted heteroacenes,theoretical calculations predicted a promising electron-transport material,which is rare for organic materials.These findings provide insights into rationally designing organic semiconductors with specific properties.

  17. Artificial intelligence approaches for rational drug design and discovery.

    Science.gov (United States)

    Duch, Włodzisław; Swaminathan, Karthikeyan; Meller, Jarosław

    2007-01-01

    Pattern recognition, machine learning and artificial intelligence approaches play an increasingly important role in rational drug design, screening and identification of candidate molecules and studies on quantitative structure-activity relationships (QSAR). In this review, we present an overview of basic concepts and methodology in the fields of machine learning and artificial intelligence (AI). An emphasis is put on methods that enable an intuitive interpretation of the results and facilitate gaining an insight into the structure of the problem at hand. We also discuss representative applications of AI methods to docking, screening and QSAR studies. The growing trend to integrate computational and experimental efforts in that regard and some future developments are discussed. In addition, we comment on a broader role of machine learning and artificial intelligence approaches in biomedical research.

  18. Rational design of the exchange-spring permanent magnet.

    Science.gov (United States)

    Jiang, J S; Bader, S D

    2014-02-12

    The development of the optimal exchange-spring permanent magnet balances exchange hardening, magnetization enhancement, and the feasibility of scalable fabrication. These requirements can be met with a rational design of the microstructural characteristics. The magnetization processes in several model exchange-spring structures with different geometries have been analyzed with both micromagnetic simulations and nucleation theory. The multilayer geometry and the soft-cylinders-in-hard-matrix geometry have the highest achievable figure of merit (BH)max, while the soft-spheres-in-hard-matrix geometry has the lowest upper limit for (BH)max. The cylindrical geometry permits the soft phase to be larger and does not require strict size control. Exchange-spring permanent magnets based on the cylindrical geometry may be amenable to scaled-up fabrication.

  19. New generation adjuvants--from empiricism to rational design.

    Science.gov (United States)

    O'Hagan, Derek T; Fox, Christopher B

    2015-06-08

    Adjuvants are an essential component of modern vaccine development. Despite many decades of development, only a few types of adjuvants are currently included in vaccines approved for human use. In order to better understand the reasons that development of some adjuvants succeeded while many others failed, we discuss some of the common attributes of successful first generation adjuvants. Next, we evaluate current trends in the development of second generation adjuvants, including the potential advantages of rationally designed synthetic immune potentiators appropriately formulated. Finally, we discuss desirable attributes of next generation adjuvants. Throughout, we emphasize that the importance of formulation and analytical characterization in all aspects of vaccine adjuvant development is often underappreciated. We highlight the formulation factors that must be evaluated in order to optimize interactions between vaccine antigens, immune potentiators, and particulate formulations, and the resulting effects on safety, biological activity, manufacturability, and stability. Copyright © 2015 Elsevier Ltd. All rights reserved.

  20. Rational design of Rho GTPase-targeting inhibitors.

    Science.gov (United States)

    Shang, Xun; Zheng, Yi

    2012-01-01

    Rho GTPases have been implicated in diverse cellular functions and are potential therapeutic targets in inflammation, cancer, and neurologic diseases. Virtual screening of compounds that fit into surface grooves of RhoA known to be critical for guanine nucleotide exchange factor (GEF) interaction produced chemical candidates with minimized docking energy. Subsequent screening for inhibitory activity of RhoA binding to the Rho-GEF, LARG, identified a Rho-specific inhibitor as a lead compound capable of blocking RhoA-LARG interaction and RhoA activation by LARG specifically and dose dependently. A microscale thermophoresis analysis was applied to directly quantify the binding interaction of the lead inhibitor with RhoA target. The lead inhibitor highlights the principle that rational targeting of subfamily members of Rho GTPases is feasible and potentially useful in future drug design effort.

  1. Rational design of functional and tunable oscillating enzymatic networks

    Science.gov (United States)

    Semenov, Sergey N.; Wong, Albert S. Y.; van der Made, R. Martijn; Postma, Sjoerd G. J.; Groen, Joost; van Roekel, Hendrik W. H.; de Greef, Tom F. A.; Huck, Wilhelm T. S.

    2015-02-01

    Life is sustained by complex systems operating far from equilibrium and consisting of a multitude of enzymatic reaction networks. The operating principles of biology's regulatory networks are known, but the in vitro assembly of out-of-equilibrium enzymatic reaction networks has proved challenging, limiting the development of synthetic systems showing autonomous behaviour. Here, we present a strategy for the rational design of programmable functional reaction networks that exhibit dynamic behaviour. We demonstrate that a network built around autoactivation and delayed negative feedback of the enzyme trypsin is capable of producing sustained oscillating concentrations of active trypsin for over 65 h. Other functions, such as amplification, analog-to-digital conversion and periodic control over equilibrium systems, are obtained by linking multiple network modules in microfluidic flow reactors. The methodology developed here provides a general framework to construct dissipative, tunable and robust (bio)chemical reaction networks.

  2. Rational Co-Design of Polymer Dielectrics for Energy Storage.

    Science.gov (United States)

    Mannodi-Kanakkithodi, Arun; Treich, Gregory M; Huan, Tran Doan; Ma, Rui; Tefferi, Mattewos; Cao, Yang; Sotzing, Gregory A; Ramprasad, Rampi

    2016-08-01

    Although traditional materials discovery has historically benefited from intuition-driven experimental approaches and serendipity, computational strategies have risen in prominence and proven to be a powerful complement to experiments in the modern materials research environment. It is illustrated here how one may harness a rational co-design approach-involving synergies between high-throughput computational screening and experimental synthesis and testing-with the example of polymer dielectrics design for electrostatic energy storage applications. Recent co-design efforts that can potentially enable going beyond present-day "standard" polymer dielectrics (such as biaxially oriented polypropylene) are highlighted. These efforts have led to the identification of several new organic polymer dielectrics within known generic polymer subclasses (e.g., polyurea, polythiourea, polyimide), and the recognition of the untapped potential inherent in entirely new and unanticipated chemical subspaces offered by organometallic polymers. The challenges that remain and the need for additional methodological developments necessary to further strengthen the co-design concept are then presented.

  3. Mesoscopic spatial designs of nano- and microfiber meshes for tissue-engineering matrix and scaffold based on newly devised multilayering and mixing electrospinning techniques.

    Science.gov (United States)

    Kidoaki, Satoru; Kwon, Il Kuen; Matsuda, Takehisa

    2005-01-01

    To design a mesoscopically ordered structure of the matrices and scaffolds composed of nano- and microscale fiber meshes for artificial and tissue-engineering devices, two new electrospinning techniques are proposed: multilayering electrospinning and mixing electrospinning. First, the following four kinds of component polymers were individually electrospun to determine the conditions for producing stable nano- and microfibers by optimizing the formulation parameters (solvent and polymer concentration) and operation parameters (voltage, air gap, and flow rate) for each polymer: (a) type I collagen, (b) styrenated gelatin (ST-gelatin), (c) segmented polyurethane (SPU), and (d) poly(ethylene oxide). A trilayered electrospun mesh, in which individual fiber meshes (type I collagen, ST-gelatin, and SPU) were deposited layer by layer, was formed by sequential electrospinning; this was clearly visualized by confocal laser scanning microscopy. The mixed electrospun-fiber mesh composed of SPU and PEO was prepared by simultaneous electrospinning on a stainless-steel mandrel with high-speed rotation and traverse movement. A bilayered tubular construct composed of a thick SPU microfiber mesh as an outer layer and a thin type I collagen nanofiber mesh as an inner layer was fabricated as a prototype scaffold of artificial grafts, and visualized by scanning electron microscopy.

  4. Rational Design of CXCR4 Specific Antibodies with Elongated CDRs

    Science.gov (United States)

    2015-01-01

    The bovine antibody (BLV1H12) which has an ultralong heavy chain complementarity determining region 3 (CDRH3) provides a novel scaffold for antibody engineering. By substituting the extended CDRH3 of BLV1H12 with modified CXCR4 binding peptides that adopt a β-hairpin conformation, we generated antibodies specifically targeting the ligand binding pocket of CXCR4 receptor. These engineered antibodies selectively bind to CXCR4 expressing cells with binding affinities in the low nanomolar range. In addition, they inhibit SDF-1-dependent signal transduction and cell migration in a transwell assay. Finally, we also demonstrate that a similar strategy can be applied to other CDRs and show that a CDRH2-peptide fusion binds CXCR4 with a Kd of 0.9 nM. This work illustrates the versatility of scaffold-based antibody engineering and could greatly expand the antibody functional repertoire in the future. PMID:25041362

  5. Rational Co-Design of Polymer Dielectrics for Energy Storage

    Science.gov (United States)

    Mannodi-Kanakkithodi, Arun; Tran, Huan; Pilania, Ghanshyam; Lookman, Turab; Ramprasad, Rampi

    While intuition-driven experiments and serendipity have guided traditional materials discovery, computational strategies have become increasingly important and a powerful complement to experiments in modern day materials research. With the example of polymer dielectrics for electrostatic energy storage applications, we demonstrate how a rational co-design approach--involving synergies between high-throughput computational screening and experimental synthesis and testing--can be harnessed for quick and efficient discovery. We highlight recent co-design efforts that can potentially lead to replacement of present-day ``standard'' polymer dielectrics (such as biaxially oriented polypropylene) not only by new organic polymer candidates within known generic polymer subclasses (e.g., polyurea, polythiourea, polyimide), but also by organometallic polymers, a hitherto untapped but promising chemical subspace. We also discuss the utilization of vast computational data (generated in the aforementioned process) towards the development of statistical learning models for relevant properties of dielectric polymers, which can further accelerate the guidance to experiments and thus the successful discovery of new materials.

  6. Rational design of electrolyte components by ab initio calculations

    Energy Technology Data Exchange (ETDEWEB)

    Johansson, Patrik; Jacobsson, Per [Department of Applied Physics, Chalmers University of Technology, SE-412 96 Goeteborg (Sweden)

    2006-02-28

    This paper is a small review of the use of computer simulations and especially the use of standard quantum-mechanical ab initio electronic structure calculations to rationally design and investigate different choices of chemicals/systems for lithium battery electrolytes. Covered systems and strategies to enhance the performance of electrolytes will range from assisting the interpretation of vibrational spectroscopy experiments over development of potentials for molecular dynamics simulations, to the design of new lithium salts and the lithium ion coordination in liquid, polymer, and gel polymer electrolytes. Examples of studied properties include the vibrational spectra of anions and ion pairs to characterize the nature and extent of the interactions present, the lithium ion affinities of anions, important for the salt solvation and the ability to provide a high concentration of charge carriers, the HOMO energies of the anions to estimate the stability versus oxidation, the anion volumes that correlate to the anion mobility, the lithium ion coordination and dynamics to reveal the limiting steps of lithium ion transport, etc. (author)

  7. Towards Rational Design of Nanoparticle Catalysis in Ionic Liquids

    Directory of Open Access Journals (Sweden)

    Ning Yan

    2013-06-01

    Full Text Available This feature article introduces the strategies on the design of highly efficient nanoparticle (NP catalytic systems in ionic liquids (ILs. The employment of functional ILs as the media for NP preparation and catalysis could prove advantageous in terms of enhancing both NP stability and catalytic activity. Hydroxyl group functionalized ILs, in particular, exhibited a remarkable promotion effect on a variety of reactions catalyzed by NPs, such as hydrogenation over Rh NPs, hydrodehalogenation over Pt NPs and Suzuki reaction over Pd NPs. In some cases, tailor-made stabilizer is used in addition to keep the NPs sufficiently stable. For example, a carboxylic group modified polyvinylpyrrolidone endows NPs three-fold stabilization, including steric, electrostatic and ligand stabilizations, which leads to excellent stability of the NPs. The catalytic activities of these NPs, on the other hand, are not compromised, as each of these stabilizations is not too strong. Following that, the article describes our recent work on the rational design of bimetallic NPs in ILs and the development of multifunctional systems involving NPs for a tandem reaction sequence that convert lignin-derived phenolic compounds into fuels.

  8. Rational design of nanoparticles for biomedical imaging and photovoltaic applications

    Energy Technology Data Exchange (ETDEWEB)

    Qin, Haiyan

    2011-07-01

    This thesis aims to rationally design nanoparticles and promote their applications in biomedical imaging and photovoltaic cells. Quantum dots (QDs) are promising fluorescent probes for biomedical imaging. We have fabricated two types of MSA capped QDs: CdTe/ZnSe core/shell QDs synthesized via an aqueous method and CdTe QDs via a hydrothermal method. They present high quantum yields (QYs), narrow emission band widths, high photo- and pH-stability, and low cytotoxicity. QD-IgG probes were produced and applied for labeling breast cancer marker HER2 proteins on MCF-7 cells. For the purpose of single molecule tracking using QDs as fluorescent probes, we use small affibodies instead of antibodies to produce QD-affibody probes. Smaller QD-target protein complexes are obtained using a direct immunofluorescence approach. These QD-affibody probes are developed to study the dynamic motion of single HER2 proteins on A431 cell membranes. Fluorescence blinking in single QDs is harmful for dynamic tracking due to information loss. We have experimentally studied the blinking phenomenon and the mechanism behind. We have discovered an emission bunching effect that two nearby QDs tend to emit light synchronously. The long-range Coulomb potential induced by the negative charge on the QD surface is found to be the major cause for the single QD blinking and the emission bunching in QD pairs. We have studied the in vitro cytotoxicity of CdTe QDs to human umbilical vein endothelial cells (HUVECs). The QDs treatment increases the intracellular reactive oxygen species (ROS) level and disrupts the mitochondrial membrane potential. The protein expression levels indicate that the mitochondria apoptosis is the main cause of HUVCEs apoptosis induced by CdTe QDs. Gold nanorods (GNRs) are scattering probes due to their tunable surface plasmon resonance (SPR) enhanced scattering spectrum. In order to control the yield and morphology of GNRs, we have systematically studied the effects of composition

  9. Rational design and synthesis of excavated trioctahedral Au nanocrystals

    Science.gov (United States)

    Chen, Qiaoli; Jia, Yanyan; Shen, Wei; Xie, Shuifen; Yang, Yanan; Cao, Zhenming; Xie, Zhaoxiong; Zheng, Lansun

    2015-06-01

    Excavated polyhedral nanostructures, possessing the features of high surface area and well-defined surface structure with a specific crystal facet and avoidance of aggregation, could be one of the best choices for the purpose of reducing consumption and improving performance of noble metals in many application fields. However, the formation of the excavated structures is thermodynamically unfavourable and its rational synthesis is far beyond our knowledge. In this work, taking overgrowth of Pd onto trioctahedral Au nanocrystals as a model, we present a deep insight study for synthesizing an excavated structure relying on the protection role of surfactants under suitable crystal growth kinetics. Based on the abovementioned understanding, we designed a simple and effective strategy to synthesize Au nanocrystals with excavated trioctahedral structure in one step. Due to the novel feature of the excavated structure and exposed high energy {110} facets, excavated trioctahedral Au NCs exhibited optical extinction at the near-infrared region and showed high catalytic activity towards the reduction of p-nitrophenol. Moreover, the synthetic strategy can be extended to the synthesis of excavated Au-Pd alloys.Excavated polyhedral nanostructures, possessing the features of high surface area and well-defined surface structure with a specific crystal facet and avoidance of aggregation, could be one of the best choices for the purpose of reducing consumption and improving performance of noble metals in many application fields. However, the formation of the excavated structures is thermodynamically unfavourable and its rational synthesis is far beyond our knowledge. In this work, taking overgrowth of Pd onto trioctahedral Au nanocrystals as a model, we present a deep insight study for synthesizing an excavated structure relying on the protection role of surfactants under suitable crystal growth kinetics. Based on the abovementioned understanding, we designed a simple and effective

  10. Rationally designed polyimides for high-energy density capacitor applications.

    Science.gov (United States)

    Ma, Rui; Baldwin, Aaron F; Wang, Chenchen; Offenbach, Ido; Cakmak, Mukerrem; Ramprasad, Rampi; Sotzing, Gregory A

    2014-07-01

    Development of new dielectric materials is of great importance for a wide range of applications for modern electronics and electrical power systems. The state-of-the-art polymer dielectric is a biaxially oriented polypropylene (BOPP) film having a maximal energy density of 5 J/cm(3) and a high breakdown field of 700 MV/m, but with a limited dielectric constant (∼2.2) and a reduced breakdown strength above 85 °C. Great effort has been put into exploring other materials to fulfill the demand of continuous miniaturization and improved functionality. In this work, a series of polyimides were investigated as potential polymer materials for this application. Polyimide with high dielectric constants of up to 7.8 that exhibits low dissipation factors (<1%) and high energy density around 15 J/cm(3), which is 3 times that of BOPP, was prepared. Our syntheses were guided by high-throughput density functional theory calculations for rational design in terms of a high dielectric constant and band gap. Correlations of experimental and theoretical results through judicious variations of polyimide structures allowed for a clear demonstration of the relationship between chemical functionalities and dielectric properties.

  11. Rational Design of Coordination Polymers with Flexible Oxyethylene Side Chains

    Energy Technology Data Exchange (ETDEWEB)

    Choi, Eun Young; Gao, Chunji; Lee, Suck Hyun; Kwon, O Pil [Ajou University, Suwon (Korea, Republic of)

    2012-04-15

    We rationally designed and synthesized metallopolymers with organic 1,4-benzenedicarboxylic acid (BDC) linkers with different lengths of oxyethylene side chains in order to examine the influence of side chains on the coordination characteristics. While in a previous report the BDC linkers with alkyl side chains were found to form three-dimensional (3D) isoreticular metal-organic framework (IRMOF) structures or one-dimensional (1D) coordination polymeric structures with short -O(CH{sub 2}){sub 6}CH{sub 3} or long -O(CH{sub 2}){sub 9}CH{sub 3} side chains, respectively, new BDC linkers with oxyethylene side chains of the same lengths, -(OCH{sub 2}CH{sub 2}){sub 2}CH{sub 3} and -(OCH{sub 2}CH{sub 2}){sub 3}CH{sub 3}, form only 3D IRMOF structures. This result is attributed to the higher flexibility and smaller volume of oxyethylene side chains compared to alkyl side chains

  12. Rational design of enhanced photoresistance in a photoswitchable fluorescent protein

    Science.gov (United States)

    Duan, Chenxi; Byrdin, Martin; El Khatib, Mariam; Henry, Xavier; Adam, Virgile; Bourgeois, Dominique

    2015-03-01

    Fluorescent proteins are particularly susceptible to photobleaching, the permanent loss of fluorescence emission resulting from photodestruction of the chromophore. In the case of Reversibly Switchable Fluorescent Proteins (RSFPs), which can be switched back and forth between a non-fluorescent and a fluorescent state, the achievable number of switching cycles is limited by photobleaching, a process known as photofatigue. Photofatigue has become a crucial limitation in a number of advanced applications based on repeated photoswitching of RSFPs, notably in the field of super-resolution fluorescence microscopy. Here, based on our previous structural investigation of photobleaching mechanisms in IrisFP, an RSFP also capable of green-to-red photoconversion, we present the rational design of a single-mutant IrisFP-M159A that displays considerably enhanced photostability. The results suggest that, under moderate illumination intensities, photobleaching of IrisFP-like Anthozoan fluorescent proteins such as EosFP, Dendra or Dronpa derivatives is mainly driven by an oxygen-dependent mechanism resulting in the irreversible sulfoxidation of methionine 159. The photofatigue decay profiles of IrisFP and its photoresistant mutant IrisFP-M159A were investigated in different experimental conditions, in vitro and in cellulo. Although the performance of the mutant was found to be always superior, the results showed switching behaviors strongly dependent on the nanoenvironment. Thus, in general, assessment of photostability and switching properties of RSFPs should be carried out in real experimental conditions.

  13. A thermostable exo-β-fructosidase immobilised through rational design.

    Science.gov (United States)

    Martínez, Duniesky; Cutiño-Avila, Bessy; Pérez, Enrique Rosendo; Menéndez, Carmen; Hernández, Lázaro; Del Monte-Martínez, Alberto

    2014-02-15

    Thermotoga maritima exo-β-fructosidase (BfrA) secreted by a recombinant Pichia pastoris strain was optimally immobilised on Glyoxyl-Sepharose CL 4B using the Rational Design of Immobilised Derivatives (RDID) strategy. Covalent attachment of the N-glycosylated BfrA onto the activated support at pH 10 allowed total recovery of the loaded enzyme and its activity. The immobilisation process caused no variation in the catalytic properties of the enzyme and allowed further enhancement of the thermal stability. Complete inversion of cane sugar (2.04 M) in a batch stirred tank reactor at 60 °C was achieved with a productivity of 22.2 g of substrate hydrolysed/gram of biocatalyst/hour. Half-life of the immobilised enzyme of 5 days at 60 °C was determined in a continuously operated fixed-bed column reactor. Our results promote the applicability of the BfrA-immobilised biocatalyst for the complete hydrolysis of concentrated sucrose solutions under industrial conditions, especially at a high reaction temperature.

  14. In silico ADME/T modelling for rational drug design.

    Science.gov (United States)

    Wang, Yulan; Xing, Jing; Xu, Yuan; Zhou, Nannan; Peng, Jianlong; Xiong, Zhaoping; Liu, Xian; Luo, Xiaomin; Luo, Cheng; Chen, Kaixian; Zheng, Mingyue; Jiang, Hualiang

    2015-11-01

    In recent decades, in silico absorption, distribution, metabolism, excretion (ADME), and toxicity (T) modelling as a tool for rational drug design has received considerable attention from pharmaceutical scientists, and various ADME/T-related prediction models have been reported. The high-throughput and low-cost nature of these models permits a more streamlined drug development process in which the identification of hits or their structural optimization can be guided based on a parallel investigation of bioavailability and safety, along with activity. However, the effectiveness of these tools is highly dependent on their capacity to cope with needs at different stages, e.g. their use in candidate selection has been limited due to their lack of the required predictability. For some events or endpoints involving more complex mechanisms, the current in silico approaches still need further improvement. In this review, we will briefly introduce the development of in silico models for some physicochemical parameters, ADME properties and toxicity evaluation, with an emphasis on the modelling approaches thereof, their application in drug discovery, and the potential merits or deficiencies of these models. Finally, the outlook for future ADME/T modelling based on big data analysis and systems sciences will be discussed.

  15. Rationally designed, heterologous S. cerevisiae transcripts expose novel expression determinants

    Science.gov (United States)

    Ben-Yehezkel, Tuval; Atar, Shimshi; Zur, Hadas; Diament, Alon; Goz, Eli; Marx, Tzipy; Cohen, Rafael; Dana, Alexandra; Feldman, Anna; Shapiro, Ehud; Tuller, Tamir

    2015-01-01

    Deducing generic causal relations between RNA transcript features and protein expression profiles from endogenous gene expression data remains a major unsolved problem in biology. The analysis of gene expression from heterologous genes contributes significantly to solving this problem, but has been heavily biased toward the study of the effect of 5′ transcript regions and to prokaryotes. Here, we employ a synthetic biology driven approach that systematically differentiates the effect of different regions of the transcript on gene expression up to 240 nucleotides into the ORF. This enabled us to discover new causal effects between features in previously unexplored regions of transcripts, and gene expression in natural regimes. We rationally designed, constructed, and analyzed 383 gene variants of the viral HRSVgp04 gene ORF, with multiple synonymous mutations at key positions along the transcript in the eukaryote S. cerevisiae. Our results show that a few silent mutations at the 5′UTR can have a dramatic effect of up to 15 fold change on protein levels, and that even synonymous mutations in positions more than 120 nucleotides downstream from the ORF 5′end can modulate protein levels up to 160%–300%. We demonstrate that the correlation between protein levels and folding energy increases with the significance of the level of selection of the latter in endogenous genes, reinforcing the notion that selection for folding strength in different parts of the ORF is related to translation regulation. Our measured protein abundance correlates notably(correlation up to r = 0.62 (p=0.0013)) with mean relative codon decoding times, based on ribosomal densities (Ribo-Seq) in endogenous genes, supporting the conjecture that translation elongation and adaptation to the tRNA pool can modify protein levels in a causal/direct manner. This report provides an improved understanding of transcript evolution, design principles of gene expression regulation, and suggests simple

  16. Quantum Dot Superlattice Enabled Rational Design in Optoelectronics and Hydrogen Generation

    Science.gov (United States)

    2014-11-25

    Final 3. DATES COVERED (From - To) 22-April-2013 to 21-April-2014 4. TITLE AND SUBTITLE Quantum Dot Superlattice Enabled Rational Design...15. SUBJECT TERMS Quantum Dots , Optoelectronic Applications, Charge Transfer, Superlattices, Density Functional Theory, Coupling...FA2386-13-1-4074 “ Quantum Dot Superlattice Enabled Rational Design in Optoelectronics and Hydrogen Generation” April 21, 2014 PI and Co-PI

  17. Harvesting bioenergy with rationally designed complex functional materials

    Science.gov (United States)

    Kuang, Liangju

    A key challenge in renewable energy is to capture, convert and store solar power with earth-abundant materials and environmentally benign technologies. The goal of this thesis is to develop rationally designed complex functional materials for bio-renewable energy applications. On one hand, photoconversion membrane proteins (MPs) are nature's nanoengineering feats for renewable energy management. Harnessing their functions in synthetic systems could help understand, predict, and ultimately control matter and energy at the nanoscale. This is particularly enticing in the post-genome era as recombinant or cell-free expression of many MPs with high yields becomes possible. However, the labile nature of lipid bilayers renders them unsuitable for use in a broad range of engineered systems. A knowledge gap exists about how to design robust synthetic nanomembranes as lipid-bilayer-mimics to support MP functions and how to direct hierarchical MP reconstitution into those membranes to form 2-D or 3-D ordered proteomembrane arrays. Our studies on proteorhodopsin (PR) and bacterial reaction center (BRC), the two light-harvesting MPs, reveal that a charge-interaction-directed reconstitution (CIDR) mechanism induces spontaneous reconstitution of detergent-solubilized MPs into various amphiphilic block copolymer membranes, many of which have far superior stability than lipid bilayers. Our preliminary data also suggest MPs are not enslaved by the biological membranes they derive from; rather, the chemically nonspecific material properties of MP-supporting membranes may act as allosteric regulators. Versatile chemical designs are possible to modulate the conformational energetics of MPs, hence their transport performance in synthetic systems. On the other hand, microalgae are widely regarded as a sustainable feedstock for biofuel production. Microalgae-derived biofuels have not been commercialized yet because current technologies for microalgae dewatering add a huge cost to the

  18. Rational design of protamine nanocapsules as antigen delivery carriers.

    Science.gov (United States)

    González-Aramundiz, José Vicente; Presas, Elena; Dalmau-Mena, Inmaculada; Martínez-Pulgarín, Susana; Alonso, Covadonga; Escribano, José M; Alonso, María J; Csaba, Noemi Stefánia

    2017-01-10

    Current challenges in global immunization indicate the demand for new delivery strategies, which could be applied to the development of new vaccines against emerging diseases, as well as to improve safety and efficacy of currently existing vaccine formulations. Here, we report a novel antigen nanocarrier consisting of an oily core and a protamine shell, further stabilized with pegylated surfactants. These nanocarriers, named protamine nanocapsules, were rationally designed to promote the intracellular delivery of antigens to immunocompetent cells and to trigger an efficient and long-lasting immune response. Protamine nanocapsules have nanometric size, positive zeta potential and high association capacity for H1N1 influenza hemagglutinin, a protein that was used here as a model antigen. The new formulation shows an attractive stability profile both, as an aqueous suspension or a freeze-dried powder formulation. In vitro studies showed that protamine nanocapsules were efficiently internalized by macrophages without eliciting significant toxicity. In vivo studies indicate that antigen-loaded nanocapsules trigger immune responses comparable to those achieved with alum, even when using significantly lower antigen doses, thus indicating their adjuvant properties. These promising in vivo data, alongside with their versatility for the loading of different antigens and oily immunomodulators and their excellent stability profile, make these nanocapsules a promising platform for the delivery of antigens. Protamine sulphate (PubChem SID: 7849283), Sodium Cholate (PubChem CID: 23668194), Miglyol (PubChem CID: 53471835), α tocopherol (PubChem CID: 14985), Tween® 20(PubChem CID: 443314), Tween® 80(PubChem CID: 5281955), TPGS (PubChem CID: 71406). Copyright © 2016 Elsevier B.V. All rights reserved.

  19. Achieving nano-gold stability through rational design.

    Science.gov (United States)

    Barrett, Dean H; Scurrell, Michael S; Rodella, Cristiane B; Diaz, Beatriz; Billing, David G; Franklyn, Paul J

    2016-11-18

    When Au is subdivided to the nanoscale its reactivity changes from an inert nature to one of incredible reactivity which is not replicated by other catalysts. When dispersed onto metal oxides such as TiO2, nano-Au has shown high reactivities for a multitude of reduction and oxidation reactions of industrial importance with potential and current uses such as, CO oxidation, NO x reduction, purification of hydrogen for fuel cells, water gas shift reactions, abatement of volatile organic compounds (VOC's) as well as pollution and emission control systems such as autocatalysts. However, many industrially important reactions and applications operate under harsh conditions where the catalyst is exposed to high temperatures and further needs to operate for extended periods of time. These conditions cause Au nanoparticle sintering whereby small, highly active clusters form large clusters which are catalytically inactive. For this reason, research into stabilizing Au nanoparticles has abounded with a goal of producing durable, thermally stable catalysts for industrial applications. Here we show a durable, thermally stable Au-TiO2 catalyst which has been developed by rational design. The catalyst exhibits a 3-dimensional, radially aligned nanorod structure, already locked into the thermodynamically stable polymorph, via a scalable and facile synthesis, with Au nanoparticles isolated on the support structure. As the Au nanoparticles are highly stable the new catalyst is able to maintain light-off for CO oxidation below 115 °C even after multiple cycles at 800 °C. This ability of the catalyst to resist multiple thermal cycles to high temperature while remaining active at low temperatures shows promise for various industrial applications. The thermal stability of the catalyst is investigated and characterized through morphological and structural studies.

  20. Toward the Rational Design of Asymmetric Catalysts using Attractive Non-Covalent Interactions and Design Elements

    OpenAIRE

    Neel, Andrew James

    2016-01-01

    Throughout my doctoral studies, I have endeavored to address the question of how to rationally design chiral catalysts to control enantioselectivity in a predictable fashion. To approach this problem, I have focused on the strategic implementation of attractive non-covalent interactions between catalysts and their substrates at the enantiodetermining transition state. A significant portion of this work involved the development of an approach to elucidating the structural origins of selectiv...

  1. A biphasic scaffold based on silk and bioactive ceramic with stratified properties for osteochondral tissue regeneration.

    Science.gov (United States)

    Li, Jiao Jiao; Kim, Kyungsook; Roohani-Esfahani, Seyed-Iman; Guo, Jin; Kaplan, David L; Zreiqat, Hala

    2015-07-14

    Significant clinical challenges encountered in the effective long-term treatment of osteochondral defects have inspired advancements in scaffold-based tissue engineering techniques to aid repair and regeneration. This study reports the development of a biphasic scaffold produced via a rational combination of silk fibroin and bioactive ceramic with stratified properties to satisfy the complex and diverse regenerative requirements of osteochondral tissue. Structural examination showed that the biphasic scaffold contained two phases with different pore morphologies to match the cartilage and bone segments of osteochondral tissue, which were joined at a continuous interface. Mechanical assessment showed that the two phases of the biphasic scaffold imitated the load-bearing behaviour of native osteochondral tissue and matched its compressive properties. In vitro testing showed that different compositions in the two phases of the biphasic scaffold could direct the preferential differentiation of human mesenchymal stem cells towards the chondrogenic or osteogenic lineage. By featuring simple and reproducible fabrication and a well-integrated interface, the biphasic scaffold strategy established in this study circumvented the common problems experienced with integrated scaffold designs and could provide an effective approach for the regeneration of osteochondral tissue.

  2. Rational design of metal-organic frameworks with anticipated porosities and functionalities

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, MW; Bosch, M; Gentle, T; Zhou, HC

    2014-01-01

    Metal-organic frameworks have emerged as a new category of porous materials that have intriguing structures and diverse applications. Even though the early discovery of new MOFs appears to be serendipitous, much effort has been made to reveal their structure-property relationships for the purpose of rationally designing novel frameworks with expected properties. Until now, much progress has been made to rationalize the design and synthesis of MOFs. This highlight review will outline the recent advances on this topic from both our and other groups and provide a systematic overview of different methods for the rational design of MOFs with desired porosities and functionalities. In this review, we will categorize the recent efforts for rational MOF design into two different approaches: a structural approach and a functional approach.

  3. Does decision documentation help junior designers rationalize their decisions? A comparative multiple-case study

    NARCIS (Netherlands)

    Heesch, U. van; Avgeriou, P.; Tang, A.

    2013-01-01

    Software architecture design is challenging, especially for junior software designers. Lacking practice and experience, junior designers need process support in order to make rational architecture decisions. In this paper, we present the results of a comparative multiple-case study conducted to find

  4. Rational design, synthesis, and pharmacological evaluation of 2-azanorbornane-3-exo,5-endo-dicarboxylic acid

    DEFF Research Database (Denmark)

    Bunch, Lennart; Liljefors, Tommy; Greenwood, Jeremy R

    2003-01-01

    The design and synthesis of conformationally restricted analogues of alpha-amino acids is an often used strategy in medicinal chemistry research. Here we present the rational design, synthesis, and pharmacological evaluation of 2-azanorbornane-3-exo,5-endo-dicarboxylic acid (1), a novel conformat......The design and synthesis of conformationally restricted analogues of alpha-amino acids is an often used strategy in medicinal chemistry research. Here we present the rational design, synthesis, and pharmacological evaluation of 2-azanorbornane-3-exo,5-endo-dicarboxylic acid (1), a novel...

  5. From bricolage to BioBricks™: Synthetic biology and rational design.

    Science.gov (United States)

    Lewens, Tim

    2013-12-01

    Synthetic biology is often described as a project that applies rational design methods to the organic world. Although humans have influenced organic lineages in many ways, it is nonetheless reasonable to place synthetic biology towards one end of a continuum between purely 'blind' processes of organic modification at one extreme, and wholly rational, design-led processes at the other. An example from evolutionary electronics illustrates some of the constraints imposed by the rational design methodology itself. These constraints reinforce the limitations of the synthetic biology ideal, limitations that are often freely acknowledged by synthetic biology's own practitioners. The synthetic biology methodology reflects a series of constraints imposed on finite human designers who wish, as far as is practicable, to communicate with each other and to intervene in nature in reasonably targeted and well-understood ways. This is better understood as indicative of an underlying awareness of human limitations, rather than as expressive of an objectionable impulse to mastery over nature.

  6. Application of Absorption Modeling in Rational Design of Drug Product Under Quality-by-Design Paradigm.

    Science.gov (United States)

    Kesisoglou, Filippos; Mitra, Amitava

    2015-09-01

    Physiologically based absorption models can be an important tool in understanding product performance and hence implementation of Quality by Design (QbD) in drug product development. In this report, we show several case studies to demonstrate the potential application of absorption modeling in rational design of drug product under the QbD paradigm. The examples include application of absorption modeling—(1) prior to first-in-human studies to guide development of a formulation with minimal sensitivity to higher gastric pH and hence reduced interaction when co-administered with PPIs and/or H2RAs, (2) design of a controlled release formulation with optimal release rate to meet trough plasma concentrations and enable QD dosing, (3) understanding the impact of API particle size distribution on tablet bioavailability and guide formulation design in late-stage development, (4) assess impact of API phase change on product performance to guide specification setting, and (5) investigate the effect of dissolution rate changes on formulation bioperformance and enable appropriate specification setting. These case studies are meant to highlight the utility of physiologically based absorption modeling in gaining a thorough understanding of the product performance and the critical factors impacting performance to drive design of a robust drug product that would deliver the optimal benefit to the patients.

  7. Rational design of a robust diesel particulate filter

    Energy Technology Data Exchange (ETDEWEB)

    Van Gulijk, C.

    2002-09-19

    is added. The emphasis in chapter 6 and 7 is on diesel soot filtering by ceramic foam filters; wall-flow monoliths are only included for comparison. In chapter 8 the information from chapter 6 and 7 is combined to give an engineering model for the Modified Turbulent Precipitator. Simulations, experiments, and case studies test the engineering model. Chapter 9 treats the wrap-up of the thesis, which includes a summary, and recommendations for future work. It also introduces a conceptual filter material based on the rationalization of the findings in the thesis.

  8. Rational Design of Cancer-Targeted Benzoselenadiazole by RGD Peptide Functionalization for Cancer Theranostics.

    Science.gov (United States)

    Yang, Liye; Li, Wenying; Huang, Yanyu; Zhou, Yangliang; Chen, Tianfeng

    2015-09-01

    A cancer-targeted conjugate of the selenadiazole derivative BSeC (benzo[1,2,5] selenadiazole-5-carboxylic acid) with RGD peptide as targeting molecule and PEI (polyethylenimine) as a linker is rationally designed and synthesized in the present study. The results show that RGD-PEI-BSeC forms nanoparticles in aqueous solution with a core-shell nanostructure and high stability under physiological conditions. This rational design effectively enhances the selective cellular uptake and cellular retention of BSeC in human glioma cells, and increases its selectivity between cancer and normal cells. The nanoparticles enter the cells through receptor-mediated endocytosis via clathrin-mediated and nystatin-dependent lipid raft-mediated pathways. Internalized nanoparticles trigger glioma cell apoptosis by activation of ROS-mediated p53 phosphorylation. Therefore, this study provides a strategy for the rational design of selenium-containing cancer-targeted theranostics.

  9. Rational, computer-enabled peptide drug design: principles, methods, applications and future directions.

    Science.gov (United States)

    Diller, David J; Swanson, Jon; Bayden, Alexander S; Jarosinski, Mark; Audie, Joseph

    2015-01-01

    Peptides provide promising templates for developing drugs to occupy a middle space between small molecules and antibodies and for targeting 'undruggable' intracellular protein-protein interactions. Importantly, rational or in cerebro design, especially when coupled with validated in silico tools, can be used to efficiently explore chemical space and identify islands of 'drug-like' peptides to satisfy diverse drug discovery program objectives. Here, we consider the underlying principles of and recent advances in rational, computer-enabled peptide drug design. In particular, we consider the impact of basic physicochemical properties, potency and ADME/Tox opportunities and challenges, and recently developed computational tools for enabling rational peptide drug design. Key principles and practices are spotlighted by recent case studies. We close with a hypothetical future case study.

  10. Rational design of an organometallic glutathione transferase inhibitor

    Energy Technology Data Exchange (ETDEWEB)

    Ang, W.H.; Parker, L.J.; De Luca, A.; Juillerat-Jeanneret, L.; Morton, C.J.; LoBello, M.; Parker, M.W.; Dyson, P.J.; (ISIC)

    2010-08-17

    A hybrid organic-inorganic (organometallic) inhibitor was designed to target glutathione transferases. The metal center is used to direct protein binding, while the organic moiety acts as the active-site inhibitor. The mechanism of inhibition was studied using a range of biophysical and biochemical methods.

  11. Rational design of mirror-like peptides with alanine regulation.

    Science.gov (United States)

    Li, Weizhong; Tan, Tingting; Xu, Wei; Xu, Lin; Dong, Na; Ma, Deying; Shan, Anshan

    2016-02-01

    To generate effective antimicrobial peptides (AMPs) with good antimicrobial activities and cell selectivity, many synthetic strategies have been implemented to facilitate the development of AMPs. However, these synthetic strategies represent only a small proportion of the methods used for the development of AMPs and are not optimal with the requirements needed for the design of AMPs. In this investigation, we designed a mirror-like structure with a lower charge and a higher number of hydrophobic amino acids. The amino acid sequence of the designed mirror-like peptides was XXYXXXYXXXYXX [X represents L (Leu) and/or A (Ala); Y represents K (Lys)]. These mirror-like peptides displayed antimicrobial activity against both Gram-positive and Gram-negative bacteria. Hemolysis activity and cytotoxicity, detected by using human red blood cells (hRBCs) and human embryonic kidney cells (HEK293), respectively, demonstrated that the frequency of Ala residues in this structure had a regulatory effect on the high hydrophobic region. In particular, KL4A6 showed a greater antimicrobial potency than the other three mirror-like peptides, folded into an α-helical structure, and displayed the highest therapeutic index, suggesting its good cell selectivity. Observations from fluorescence spectroscopy, flow cytometry, and electron microscopy experiments indicated that KL4A6 exhibited good membrane penetration potential by inducing membrane blebbing, disruption and lysis. Therefore, generating mirror-like peptides is a promising strategy for designing effective AMPs with regions of high hydrophobicity.

  12. Rationally designed porous silicon as platform for optical biosensors

    Energy Technology Data Exchange (ETDEWEB)

    Priano, G. [INQUIMAE, DQIAyQF, FCEN, Universidad de Buenos Aires, Ciudad Universitaria, Pabellon 2 (C1428EHA) Buenos Aires (Argentina); Acquaroli, L.N.; Lasave, L.C. [Instituto De Desarrollo Tecnologico Para La Industria Quimica, UNL, CONICET, Gueemes 3450 (S3000GLN) Santa Fe (Argentina); Battaglini, F. [INQUIMAE, DQIAyQF, FCEN, Universidad de Buenos Aires, Ciudad Universitaria, Pabellon 2 (C1428EHA) Buenos Aires (Argentina); Arce, R.D., E-mail: rarce@intec.unl.edu.ar [Instituto De Desarrollo Tecnologico Para La Industria Quimica, UNL, CONICET, Gueemes 3450 (S3000GLN) Santa Fe (Argentina); Departamento De Materiales, Facultad De Ingenieria Quimica, UNL, Santiago del Estero 2829 (S3000) Santa Fe (Argentina); Koropecki, R.R. [Instituto De Desarrollo Tecnologico Para La Industria Quimica, UNL, CONICET, Gueemes 3450 (S3000GLN) Santa Fe (Argentina); Departamento De Materiales, Facultad De Ingenieria Quimica, UNL, Santiago del Estero 2829 (S3000) Santa Fe (Argentina)

    2012-08-01

    Optical porous silicon multilayer structures are able to work as sensitive chemical sensors or biosensors based in their optical response. An algorithm to simulate the optical response of these multilayers was developed, considering the optical properties of the individual layers. The algorithm allows designing and customizing the porous silicon structures according to a given application. The results obtained by the simulation were experimentally verified; for this purpose different photonic structures were prepared, such as Bragg reflectors and microcavities. Some of these structures have been derivatized by the introduction of aminosilane groups on the porous silicon surface. The algorithm also permits to simulate the effects produced by a non uniform derivatization of the multilayer. - Highlights: Black-Right-Pointing-Pointer Mesoporous silicon structure Black-Right-Pointing-Pointer Functionalization of mesoporous silicon as sensors Black-Right-Pointing-Pointer Design of the one-dimensional photonic crystal Black-Right-Pointing-Pointer Simulation of non-uniformity in covering the sensor structure.

  13. Rational design and evaluation of mammalian ribonuclease cytotoxins.

    Science.gov (United States)

    Lomax, Jo E; Eller, Chelcie H; Raines, Ronald T

    2012-01-01

    Mammalian pancreatic-type ribonucleases (ptRNases) comprise an enzyme family that is remarkably well suited for therapeutic exploitation. ptRNases are robust and prodigious catalysts of RNA cleavage that can naturally access the cytosol. Instilling cytotoxic activity requires endowing them with the ability to evade a cytosolic inhibitor protein while retaining other key attributes. These efforts have informed our understanding of ptRNase-based cytotoxins, as well as the action of protein-based drugs with cytosolic targets. Here, we address the most pressing problems encountered in the design of cytotoxic ptRNases, along with potential solutions. In addition, we describe assays that can be used to evaluate a successful design in vitro, in cellulo, and in vivo. The emerging information validates the continuing development of ptRNases as chemotherapeutic agents.

  14. Rational design of binary halide scintillators via data mining

    Energy Technology Data Exchange (ETDEWEB)

    Kong, Chang Sun [Department of Materials Science and Engineering, Iowa State University, 2220 Hoover Hall, Ames, Iowa 50011-2300 (United States); Rajan, Krishna, E-mail: krajan@iastate.edu [Department of Materials Science and Engineering, Iowa State University, 2220 Hoover Hall, Ames, Iowa 50011-2300 (United States)

    2012-07-11

    We introduce a new search strategy for the development of novel inorganic scintillators. For designing new scintillation host media having the improved properties, the potential candidate materials were chosen by using a chemical selection scheme based on a multi-dimensional similarity metric. For the quantitative assessment of the chosen materials, predictive models based on informatics were built by correlating a set of key parameters which reflect the features of the host materials with the performance of inorganic scintillators. The resulting design rules generated from the relationships serve as a guide to identify HfI{sub 4} and TaI{sub 5} as two new host lattices with high light yield. The method we have outlined here serves as a new computational template based statistical learning method to search for new inorganic scintillators with targeted properties.

  15. Emergence of protein fold families through rational design.

    Directory of Open Access Journals (Sweden)

    Feng Ding

    2006-07-01

    Full Text Available Diverse proteins with similar structures are grouped into families of homologs and analogs, if their sequence similarity is higher or lower, respectively, than 20%-30%. It was suggested that protein homologs and analogs originate from a common ancestor and diverge in their distinct evolutionary time scales, emerging as a consequence of the physical properties of the protein sequence space. Although a number of studies have determined key signatures of protein family organization, the sequence-structure factors that differentiate the two evolution-related protein families remain unknown. Here, we stipulate that subtle structural changes, which appear due to accumulating mutations in the homologous families, lead to distinct packing of the protein core and, thus, novel compositions of core residues. The latter process leads to the formation of distinct families of homologs. We propose that such differentiation results in the formation of analogous families. To test our postulate, we developed a molecular modeling and design toolkit, Medusa, to computationally design protein sequences that correspond to the same fold family. We find that analogous proteins emerge when a backbone structure deviates only 1-2 angstroms root-mean-square deviation from the original structure. For close homologs, core residues are highly conserved. However, when the overall sequence similarity drops to approximately 25%-30%, the composition of core residues starts to diverge, thereby forming novel families of protein homologs. This direct observation of the formation of protein homologs within a specific fold family supports our hypothesis. The conservation of amino acids in designed sequences recapitulates that of the naturally occurring sequences, thereby validating our computational design methodology.

  16. Rational Design of Proteasome Inhibitors as Antimalarial Drugs.

    Science.gov (United States)

    Le Chapelain, Camille; Groll, Michael

    2016-05-23

    One life, two strategies: Crucial structural differences between the human and the Plasmodium falciparum proteasomes were recently identified. A combination of cryo-EM and functional characterization enabled the design of a selective antimalarial proteasome inhibitor that shows low toxicity in the host. When used with artemisinin, this ligand offers a new approach for the efficient treatment of malaria at all stages of the parasite lifecycle.

  17. Numerical simulation and rational design of optically anisotropic columnar films

    Science.gov (United States)

    Leontyev, Viktor A.; Hawkeye, Matthew M.; Wakefield, Nicholas G.; Tabunshchyk, Kyrylo; Sit, Jeremy C.; Kovalenko, Andriy; Brett, Michael J.

    2011-03-01

    Optical anisotropy is an inherent property of columnar dielectric films, such as those fabricated by the glancing angle deposition (GLAD) technique. This process utilizes physical vapor deposition combined with computer-controlled substrate motion to finely tune the direction of column growth and vital morphological parameters such as column cross-section and inter-columnar spacing. Control over the anisotropic properties of the porous film provides an opportunity to design polarization-selective photonic devices and films with improved band gap properties. Anisotropic defects in multilayer films also result in a polarization-sensitive position of resonant transmission modes. We employed the finite-difference time-domain and frequency-domain methods to theoretically analyze and design columnar films with unique band-gap properties. The following morphologies were considered: (i) S-shaped columnar films with polarization-dependent band-gap position and width. Using numerical simulations we have shown that the competitive effect of different sources of anisotropy can be used to engineer photonic band gaps with strong selectivity to linearly-polarized light; (ii) Rugate thin films with an anisotropic defect, which exhibit resonant mode splitting. Optical devices were fabricated using titanium dioxide because it has good transparency in the visible range of the optical spectrum and a large bulk refractive index. Experimental results were compared to simulations to verify the designs and understand the limitations of the fabrication process.

  18. Rational Design of Glucose-Responsive Insulin Using Pharmacokinetic Modeling.

    Science.gov (United States)

    Bakh, Naveed A; Bisker, Gili; Lee, Michael A; Gong, Xun; Strano, Michael S

    2017-08-25

    A glucose responsive insulin (GRI) is a therapeutic that modulates its potency, concentration, or dosing of insulin in relation to a patient's dynamic glucose concentration, thereby approximating aspects of a normally functioning pancreas. Current GRI design lacks a theoretical basis on which to base fundamental design parameters such as glucose reactivity, dissociation constant or potency, and in vivo efficacy. In this work, an approach to mathematically model the relevant parameter space for effective GRIs is induced, and design rules for linking GRI performance to therapeutic benefit are developed. Well-developed pharmacokinetic models of human glucose and insulin metabolism coupled to a kinetic model representation of a freely circulating GRI are used to determine the desired kinetic parameters and dosing for optimal glycemic control. The model examines a subcutaneous dose of GRI with kinetic parameters in an optimal range that results in successful glycemic control within prescribed constraints over a 24 h period. Additionally, it is demonstrated that the modeling approach can find GRI parameters that enable stable glucose levels that persist through a skipped meal. The results provide a framework for exploring the parameter space of GRIs, potentially without extensive, iterative in vivo animal testing. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Rational Design of Antirheumatic Prodrugs Specific for Sites of Inflammation

    Science.gov (United States)

    Onuoha, Shimobi C.; Ferrari, Mathieu; Sblattero, Daniele

    2015-01-01

    Objective Biologic drugs, such as the anti–tumor necrosis factor (anti‐TNF) antibody adalimumab, have represented a breakthrough in the treatment of rheumatoid arthritis. Yet, concerns remain over their lack of efficacy in a sizable proportion of patients and their potential for systemic side effects such as infection. Improved biologic prodrugs specifically targeted to the site of inflammation have the potential to alleviate current concerns surrounding biologic anticytokine therapies. The purpose of this study was to design, construct, and evaluate in vitro and ex vivo the targeting and antiinflammatory capacity of activatable bispecific antibodies. Methods Activatable dual variable domain (aDVD) antibodies were designed and constructed to target intercellular adhesion molecule 1 (ICAM‐1), which is up‐regulated at sites of inflammation, and anti‐TNF antibodies (adalimumab and infliximab). These bispecific molecules included an external arm that targets ICAM‐1 and an internal arm that comprises the therapeutic domain of an anti‐TNF antibody. Both arms were linked to matrix metalloproteinase (MMP)–cleavable linkers. The constructs were tested for their ability to bind and neutralize both in vitro and ex vivo targets. Results Intact aDVD constructs demonstrated significantly reduced binding and anti‐TNF activity in the prodrug formulation as compared to the parent antibodies. Human synovial fluid and physiologic concentrations of MMP enzyme were capable of cleaving the external domain of the antibody, revealing a fully active molecule. Activated antibodies retained the same binding and anti‐TNF inhibitory capacities as the parent molecules. Conclusion The design of a biologic prodrug with enhanced specificity for sites of inflammation (synovium) and reduced specificity for off‐target TNF is described. This construct has the potential to form a platform technology that is capable of enhancing the therapeutic index of drugs for the treatment of

  20. Rational design of diagnostic and vaccination strategies for tuberculosis

    Directory of Open Access Journals (Sweden)

    Sibele Borsuk

    Full Text Available The development of diagnostic tests which can readily differentiate between vaccinated and tuberculosis-infected individuals is crucial for the wider utilization of bacillus Calmette-Guérin (BCG as vaccine in humans and animals. BCG_0092 is an antigen that elicits specific delayed type hypersensitivity reactions similar in size and morphological aspects to that elicited by purified protein derivative, in both animals and humans infected with the tubercle bacilli. We carried out bioinformatics analyses of the BCG_0092 and designed a diagnostic test by using the predicted MHC class I epitopes. In addition, we performed a knockout of this gene by homologous recombination in the BCG vaccine strain to allow differentiation of vaccinated from infected individuals. For that, the flanking sequences of the target gene (BCG_0092were cloned into a suicide vector. Spontaneous double crossovers, which result in wild type revertants or knockouts were selected using SacB. BCG_0092 is present only in members of the Mycobacterium tuberculosis complex. Eight predicted MHC class I epitopes with potential for immunological diagnosis were defined, allowing the design of a specific diagnostic test. The strategy used to delete the (BCG_0092 gene from BCG was successful. The knockout genotype was confirmed by PCR and by Southern blot. The mutant BCG strain has the potential of inducing protection against tuberculosis without interfering with the diagnostic test based on the use of selected epitopes from BCG_0092.

  1. Rational design of diagnostic and vaccination strategies for tuberculosis

    Directory of Open Access Journals (Sweden)

    Sibele Borsuk

    2012-02-01

    Full Text Available The development of diagnostic tests which can readily differentiate between vaccinated and tuberculosis-infected individuals is crucial for the wider utilization of bacillus Calmette-Guérin (BCG as vaccine in humans and animals. BCG_0092 is an antigen that elicits specific delayed type hypersensitivity reactions similar in size and morphological aspects to that elicited by purified protein derivative, in both animals and humans infected with the tubercle bacilli. We carried out bioinformatics analyses of the BCG_0092 and designed a diagnostic test by using the predicted MHC class I epitopes. In addition, we performed a knockout of this gene by homologous recombination in the BCG vaccine strain to allow differentiation of vaccinated from infected individuals. For that, the flanking sequences of the target gene (BCG_0092were cloned into a suicide vector. Spontaneous double crossovers, which result in wild type revertants or knockouts were selected using SacB. BCG_0092 is present only in members of the Mycobacterium tuberculosis complex. Eight predicted MHC class I epitopes with potential for immunological diagnosis were defined, allowing the design of a specific diagnostic test. The strategy used to delete the (BCG_0092 gene from BCG was successful. The knockout genotype was confirmed by PCR and by Southern blot. The mutant BCG strain has the potential of inducing protection against tuberculosis without interfering with the diagnostic test based on the use of selected epitopes from BCG_0092.

  2. Approaches to the rational design of selective melanocortin receptor antagonists

    Science.gov (United States)

    Hruby, Victor J; Cai, Minying; Nyberg, Joel; Muthu, Dhanasekaran

    2015-01-01

    Introduction When establishing the physiological roles of specific receptors in normal and disease states, it is critical to have selective antagonist ligands for each receptor in a receptor system with several subtypes. The melanocortin receptors have five subtypes referred to as the melanocortin 1 receptor, melanocortin 2 receptor, melanocortin 3 receptor, melanocortin 4 receptor and melanocortin 5 receptor, and they are of critical importance for many aspects of human health and disease. Areas covered This article reviews the current efforts to design selective antagonistic ligands for the five human melanocortin receptors summarizing the currently published orthosteric and allosteric antagonists for each of these receptors. Expert opinion Though there has been progress, there are still few drugs available that address the many significant biological activities and diseases that are associated with these receptors, which is possibly due to the lack of receptor selectivity that these designed ligands are currently showing. The authors believe that further studies into the antagonists’ 3D conformational and topographical properties in addition to future mutagenesis studies will provide greater insight into these ligands which could play a role in the treatment of various diseases in the future. PMID:22646078

  3. Rational design of fluorophores for in vivo applications.

    Science.gov (United States)

    Ptaszek, Marcin

    2013-01-01

    Several classes of small organic molecules exhibit properties that make them suitable for fluorescence in vivo imaging. The most promising candidates are cyanines, squaraines, boron dipyrromethenes, porphyrin derivatives, hydroporphyrins, and phthalocyanines. The recent designing and synthetic efforts have been dedicated to improving their optical properties (shift the absorption and emission maxima toward longer wavelengths and increase the brightness) as well as increasing their stability and water solubility. The most notable advances include development of encapsulated cyanine dyes with increased stability and water solubility, squaraine rotaxanes with increased stability, long-wavelength-absorbing boron dipyrromethenes, long-wavelength-absorbing porphyrin and hydroporphyrin derivatives, and water-soluble phthalocyanines. Recent advances in luminescence and bioluminescence have made self-illuminating fluorophores available for in vivo applications. Development of new types of hydroporphyrin energy-transfer dyads gives the promise for further advances in in vivo multicolor imaging.

  4. Rational Design of Calpain Inhibitors Based on Calpastatin Peptidomimetics.

    Science.gov (United States)

    Low, Kristin E; Ler, Spencer; Chen, Kevin J; Campbell, Robert L; Hickey, Jennifer L; Tan, Joanne; Scully, Conor C G; Davies, Peter L; Yudin, Andrei K; Zaretsky, Serge

    2016-06-01

    Our previously reported structures of calpain bound to its endogenous inhibitor calpastatin have motivated the use of aziridine aldehyde-mediated peptide macrocyclization toward the design of cyclic peptides and peptidomimetics as calpain inhibitors. Inspired by nature's hint that a β-turn loop within calpastatin forms a broad interaction around calpain's active site cysteine, we have constructed and tested a library of 45 peptidic compounds based on this loop sequence. Four molecules have shown reproducibly low micromolar inhibition of calpain-2. Further systematic sequence changes led to the development of probes that displayed increased potency and specificity of inhibition against calpain over other cysteine proteases. Calculated Ki values were in the low micromolar range, rivaling other peptidomimetic calpain inhibitors and presenting an improved selectivity profile against other therapeutically relevant proteases. Competitive and mixed inhibition against calpain-2 was observed, and an allosteric inhibition site on the enzyme was identified for a noncompetitive inhibitor.

  5. DNA vaccines: a rational design against parasitic diseases.

    Science.gov (United States)

    Carvalho, Joana A; Rodgers, Jean; Atouguia, Jorge; Prazeres, Duarte M F; Monteiro, Gabriel A

    2010-02-01

    Parasitic diseases are one of the most devastating causes of morbidity and mortality worldwide. Although immunization against these infections would be an ideal solution, the development of effective vaccines has been hampered by specific challenges posed by parasitic pathogens. Plasmid-based DNA vaccines may prove to be promising immunization tools in this area because vectors can be designed to integrate several antigens from different stages of the parasite life cycle or different subspecies; vaccines, formulations and immunization protocols can be tuned to match the immune response that offers protective immunity; and DNA vaccination is an affordable platform for developing countries. Partial and full protective immunity have been reported following DNA vaccination against the most significant parasitic diseases in the world.

  6. Kinetic resolution of oxazinones: rational exploration of chemical space through the design of experiments.

    Science.gov (United States)

    Renzi, Polyssena; Kronig, Christel; Carlone, Armando; Eröksüz, Serap; Berkessel, Albrecht; Bella, Marco

    2014-09-08

    The organocatalytic kinetic resolution of 4-substituted oxazinones has been optimised (selectivity factor S up to 98, chiral oxazinone ee values up to 99.6 % (1 a-g) and product ee values up to 90 % (3 a-g)) in a rational way by applying the Design of Experiments (DoE) approach.

  7. Utilizing interfaces: One-step forward for rational design of heterogeneous catalysts

    Energy Technology Data Exchange (ETDEWEB)

    Kim H. Y.

    2013-06-20

    As far as heterogeneous catalysts are a composite material, physicochemical properties of the interfaces between individual components should be extensively studied for rational design of catalysts with desired properties. Here, I will present recent computational achievements in following three heterogeneous catalysts where the interface between composing materials plays a critical role

  8. Plasmonic Solar Cells: From Rational Design to Mechanism Overview.

    Science.gov (United States)

    Jang, Yoon Hee; Jang, Yu Jin; Kim, Seokhyoung; Quan, Li Na; Chung, Kyungwha; Kim, Dong Ha

    2016-12-28

    Plasmonic effects have been proposed as a solution to overcome the limited light absorption in thin-film photovoltaic devices, and various types of plasmonic solar cells have been developed. This review provides a comprehensive overview of the state-of-the-art progress on the design and fabrication of plasmonic solar cells and their enhancement mechanism. The working principle is first addressed in terms of the combined effects of plasmon decay, scattering, near-field enhancement, and plasmonic energy transfer, including direct hot electron transfer and resonant energy transfer. Then, we summarize recent developments for various types of plasmonic solar cells based on silicon, dye-sensitized, organic photovoltaic, and other types of solar cells, including quantum dot and perovskite variants. We also address several issues regarding the limitations of plasmonic nanostructures, including their electrical, chemical, and physical stability, charge recombination, narrowband absorption, and high cost. Next, we propose a few potentially useful approaches that can improve the performance of plasmonic cells, such as the inclusion of graphene plasmonics, plasmon-upconversion coupling, and coupling between fluorescence resonance energy transfer and plasmon resonance energy transfer. This review is concluded with remarks on future prospects for plasmonic solar cell use.

  9. Rational design of a split-Cas9 enzyme complex

    Science.gov (United States)

    Wright, Addison V.; Sternberg, Samuel H.; Taylor, David W.; Staahl, Brett T.; Bardales, Jorge A.; Kornfeld, Jack E.; Doudna, Jennifer A.

    2015-01-01

    Cas9, an RNA-guided DNA endonuclease found in clustered regularly interspaced short palindromic repeats (CRISPR) bacterial immune systems, is a versatile tool for genome editing, transcriptional regulation, and cellular imaging applications. Structures of Streptococcus pyogenes Cas9 alone or bound to single-guide RNA (sgRNA) and target DNA revealed a bilobed protein architecture that undergoes major conformational changes upon guide RNA and DNA binding. To investigate the molecular determinants and relevance of the interlobe rearrangement for target recognition and cleavage, we designed a split-Cas9 enzyme in which the nuclease lobe and α-helical lobe are expressed as separate polypeptides. Although the lobes do not interact on their own, the sgRNA recruits them into a ternary complex that recapitulates the activity of full-length Cas9 and catalyzes site-specific DNA cleavage. The use of a modified sgRNA abrogates split-Cas9 activity by preventing dimerization, allowing for the development of an inducible dimerization system. We propose that split-Cas9 can act as a highly regulatable platform for genome-engineering applications. PMID:25713377

  10. Rational design of an optical sensing system for multivalent proteins

    Energy Technology Data Exchange (ETDEWEB)

    Song, X.; Swanson, B.I. [Los Alamos National Lab., NM (United States). Chemical Science and Technology Div.

    1999-07-06

    A generic design principle for detection of multivalent interactions is described. A phospholipid bilayer consisting of natural and pyrene-derivatized phosphatidylcholines is used as both a supporting biomimetic surface and part of a signal transduction element. The pyrene excimer formed in the surface can act as fluorescence donor, and DABCY/BODIPY-FL covalently attached to receptor (GM1) can act as acceptors. Aggregation of the acceptor-tagged receptors resulting from multivalent binding of CT induces a decrease in efficiency of fluorescence quenching of the pyrene excimer by DABCY or energy transfer from pyrene excimer to BODIPY-FL. In the case using fluorescent acceptors that can undergo distance-dependent fluorescence self-quenching, combination of the lower energy transfer efficiency from the excimer and the acceptor`s self-quenching capability make acceptor fluorescence go down even further by the binding. This scheme can achieve signal amplification and high surface density of the optical transduction elements, which, in return, require relatively small surface area.

  11. Rational design of new materials for energy storage

    Energy Technology Data Exchange (ETDEWEB)

    Vegge, T.; Andreasen, A.; Pedersen, A.S. [Risoe National Lab., Materials Research Dept., Roskilde (Denmark)

    2005-06-01

    Diversity of energy supply has become a mantra in the industrialized countries over the last years, which has only become louder by the resent surge in oil prices. Hydrogen is widely considered as a prominent energy carrier for the future, particularly for use in the transport sector; although a suitable storage medium still remains to be developed. Synthesis of novel storage materials is often time-consuming and expensive, but recent advances in theoretical modeling and improved insight at the nano-scale can provide a shortcut. Here, we illustrate the potential and possibilities of state-of-the-art in experimental and theoretical methods with particular emphasis on the obtainable synergy of an integrated approach. At the Materials Research Department (MRD) at Risoe National Laboratory we combine density-functional calculations with in situ X-ray diffraction, synchrotron/neutron radiation, and advanced materials testing in an attempt to expedite the design and development of new materials. We focus primarily on obtaining improved nanoscale and structural knowledge to guide our search, as exemplified in this paper. (au)

  12. Multi-Step Usage of in Vivo Models During Rational Drug Design and Discovery

    OpenAIRE

    Williams, Charles H.; Hong, Charles C.

    2011-01-01

    In this article we propose a systematic development method for rational drug design while reviewing paradigms in industry, emerging techniques and technologies in the field. Although the process of drug development today has been accelerated by emergence of computational methodologies, it is a herculean challenge requiring exorbitant resources; and often fails to yield clinically viable results. The current paradigm of target based drug design is often misguided and tends to yield compounds t...

  13. Rational Design of Plasmonic Nanoparticles for Enhanced Cavitation and Cell Perforation.

    Science.gov (United States)

    Lachaine, Rémi; Boutopoulos, Christos; Lajoie, Pierre-Yves; Boulais, Étienne; Meunier, Michel

    2016-05-11

    Metallic nanoparticles are routinely used as nanoscale antenna capable of absorbing and converting photon energy with subwavelength resolution. Many applications, notably in nanomedicine and nanobiotechnology, benefit from the enhanced optical properties of these materials, which can be exploited to image, damage, or destroy targeted cells and subcellular structures with unprecedented precision. Modern inorganic chemistry enables the synthesis of a large library of nanoparticles with an increasing variety of shapes, composition, and optical characteristic. However, identifying and tailoring nanoparticles morphology to specific applications remains challenging and limits the development of efficient nanoplasmonic technologies. In this work, we report a strategy for the rational design of gold plasmonic nanoshells (AuNS) for the efficient ultrafast laser-based nanoscale bubble generation and cell membrane perforation, which constitute one of the most crucial challenges toward the development of effective gene therapy treatments. We design an in silico rational design framework that we use to tune AuNS morphology to simultaneously optimize for the reduction of the cavitation threshold while preserving the particle structural integrity. Our optimization procedure yields optimal AuNS that are slightly detuned compared to their plasmonic resonance conditions with an optical breakdown threshold 30% lower than randomly selected AuNS and 13% lower compared to similarly optimized gold nanoparticles (AuNP). This design strategy is validated using time-resolved bubble spectroscopy, shadowgraphy imaging and electron microscopy that confirm the particle structural integrity and a reduction of 51% of the cavitation threshold relative to optimal AuNP. Rationally designed AuNS are finally used to perforate cancer cells with an efficiency of 61%, using 33% less energy compared to AuNP, which demonstrate that our rational design framework is readily transferable to a cell environment

  14. Rational design of metal oxide nanocomposite anodes for advanced lithium ion batteries

    Science.gov (United States)

    Li, Yong; Yu, Shenglan; Yuan, Tianzhi; Yan, Mi; Jiang, Yinzhu

    2015-05-01

    Metal-oxide anodes represent a significant future direction for advanced lithium ion batteries. However, their practical applications are still seriously hampered by electrode disintegration and capacity fading during cycling. Here, we report a rational design of 3D-staggered metal-oxide nanocomposite electrode directly fabricated by pulsed spray evaporation chemical vapor deposition, where various oxide nanocomponents are in a staggered distribution uniformly along three dimensions and across the whole electrode. Such a special design of nanoarchitecture combines the advantages of nanoscale materials in volume change and Li+/electron conduction as well as uniformly staggered and compact structure in atom migration during lithiation/delithiation, which exhibits high specific capacity, good cycling stability and excellent rate capability. The rational design of metal-oxide nanocomposite electrode opens up new possibilities for high performance lithium ion batteries.

  15. Rational design of new electrolyte materials for electrochemical double layer capacitors

    Science.gov (United States)

    Schütter, Christoph; Husch, Tamara; Viswanathan, Venkatasubramanian; Passerini, Stefano; Balducci, Andrea; Korth, Martin

    2016-09-01

    The development of new electrolytes is a centerpiece of many strategies to improve electrochemical double layer capacitor (EDLC) devices. We present here a computational screening-based rational design approach to find new electrolyte materials. As an example application, the known chemical space of almost 70 million compounds is investigated in search of electrochemically more stable solvents. Cyano esters are identified as especially promising new compound class. Theoretical predictions are validated with subsequent experimental studies on a selected case. These studies show that based on theoretical predictions only, a previously untested, but very well performing compound class was identified. We thus find that our rational design strategy is indeed able to successfully identify completely new materials with substantially improved properties.

  16. Design of a Discrete Tracking Controller for a Magnetic Levitation System: A Nonlinear Rational Model Approach

    Directory of Open Access Journals (Sweden)

    Fernando Gómez-Salas

    2015-01-01

    Full Text Available This work proposes a discrete-time nonlinear rational approximate model for the unstable magnetic levitation system. Based on this model and as an application of the input-output linearization technique, a discrete-time tracking control design will be derived using the corresponding classical state space representation of the model. A simulation example illustrates the efficiency of the proposed methodology.

  17. A systems biology perspective on rational design of peptide vaccine against virus infections.

    Science.gov (United States)

    Chen, Jiajia; Wang, Ying; Guo, Deyin; Shen, Bairong

    2012-01-01

    With the recent onset of influenza A (H1N1) pandemic, the need for improved vaccines against virus infections has become an international priority. Strategies for vaccine development have changed over time, from whole-virus to immunogenic proteins and further to antigenic viral peptides. Various algorithms and bioinformatics tools have been developed to predict immunogenic peptide regions in an antigenic protein sequence. Recent advances in next-generation sequencing technologies, as represented by real time DNA sequencing, provide increased throughput and yield of data on viral pathogens and host cells. This enables us to 'mine' the genomic sequence for putative vaccine candidates or targets, allowing a more rational approach to the peptide vaccine design. This review first describes current computational tools available for the rational design of peptide vaccines and then addresses recent attempts to define pathogenic peptides at '- omics' level. As there are interplay between antibody and T cells, as well as intersection between viruses and hosts, the vaccine-mediated immunity are orchestrated by multiple factors within an interaction network. Therefore, single viral peptide alone fails to provide optimal immunity. Systems biology offers a systems-level perspective of how the various arms of the immune response are integrated to give immune response, as well as how host and virus interact, thereby providing an integrated approach to select the most promising candidates for peptide vaccines development. We highlight in this article the system-level application of rational peptide vaccine design, which may be a general paradigm for future viral vaccine development.

  18. The Development of CK2 Inhibitors: From Traditional Pharmacology to in Silico Rational Drug Design.

    Science.gov (United States)

    Cozza, Giorgio

    2017-02-20

    Casein kinase II (CK2) is an ubiquitous and pleiotropic serine/threonine protein kinase able to phosphorylate hundreds of substrates. Being implicated in several human diseases, from neurodegeneration to cancer, the biological roles of CK2 have been intensively studied. Upregulation of CK2 has been shown to be critical to tumor progression, making this kinase an attractive target for cancer therapy. Several CK2 inhibitors have been developed so far, the first being discovered by "trial and error testing". In the last decade, the development of in silico rational drug design has prompted the discovery, de novo design and optimization of several CK2 inhibitors, active in the low nanomolar range. The screening of big chemical libraries and the optimization of hit compounds by Structure Based Drug Design (SBDD) provide telling examples of a fruitful application of rational drug design to the development of CK2 inhibitors. Ligand Based Drug Design (LBDD) models have been also applied to CK2 drug discovery, however they were mainly focused on methodology improvements rather than being critical for de novo design and optimization. This manuscript provides detailed description of in silico methodologies whose applications to the design and development of CK2 inhibitors proved successful and promising.

  19. Rational design of carbon nitride photocatalysts by identification of cyanamide defects as catalytically relevant sites

    Science.gov (United States)

    Lau, Vincent Wing-Hei; Moudrakovski, Igor; Botari, Tiago; Weinberger, Simon; Mesch, Maria B.; Duppel, Viola; Senker, Jürgen; Blum, Volker; Lotsch, Bettina V.

    2016-07-01

    The heptazine-based polymer melon (also known as graphitic carbon nitride, g-C3N4) is a promising photocatalyst for hydrogen evolution. Nonetheless, attempts to improve its inherently low activity are rarely based on rational approaches because of a lack of fundamental understanding of its mechanistic operation. Here we employ molecular heptazine-based model catalysts to identify the cyanamide moiety as a photocatalytically relevant `defect'. We exploit this knowledge for the rational design of a carbon nitride polymer populated with cyanamide groups, yielding a material with 12 and 16 times the hydrogen evolution rate and apparent quantum efficiency (400 nm), respectively, compared with the unmodified melon. Computational modelling and material characterization suggest that this moiety improves coordination (and, in turn, charge transfer kinetics) to the platinum co-catalyst and enhances the separation of the photogenerated charge carriers. The demonstrated knowledge transfer for rational catalyst design presented here provides the conceptual framework for engineering high-performance heptazine-based photocatalysts.

  20. Chemical engineering in the electronics industry: progress towards the rational design of organic semiconductor heterojunctions

    KAUST Repository

    Clancy, Paulette

    2012-05-01

    We review the current status of heterojunction design for combinations of organic semiconductor materials, given its central role in affecting the device performance for electronic devices and solar cell applications. We provide an emphasis on recent progress towards the rational design of heterojunctions that may lead to higher performance of charge separation and mobility. We also play particular attention to the role played by computational approaches and its potential to help define the best choice of materials for solar cell development in the future. We report the current status of the field with respect to such goals. © 2012 Elsevier Ltd.

  1. Inactivation of TNF Signaling by Rationally Designed Dominant-Negative TNF Variants

    Science.gov (United States)

    Steed, Paul M.; Tansey, Malú G.; Zalevsky, Jonathan; Zhukovsky, Eugene A.; Desjarlais, John R.; Szymkowski, David E.; Abbott, Christina; Carmichael, David; Chan, Cheryl; Cherry, Lisa; Cheung, Peter; Chirino, Arthur J.; Chung, Hyo H.; Doberstein, Stephen K.; Eivazi, Araz; Filikov, Anton V.; Gao, Sarah X.; Hubert, René S.; Hwang, Marian; Hyun, Linus; Kashi, Sandhya; Kim, Alice; Kim, Esther; Kung, James; Martinez, Sabrina P.; Muchhal, Umesh S.; Nguyen, Duc-Hanh T.; O'Brien, Christopher; O'Keefe, Donald; Singer, Karen; Vafa, Omid; Vielmetter, Jost; Yoder, Sean C.; Dahiyat, Bassil I.

    2003-09-01

    Tumor necrosis factor (TNF) is a key regulator of inflammatory responses and has been implicated in many pathological conditions. We used structure-based design to engineer variant TNF proteins that rapidly form heterotrimers with native TNF to give complexes that neither bind to nor stimulate signaling through TNF receptors. Thus, TNF is inactivated by sequestration. Dominant-negative TNFs represent a possible approach to anti-inflammatory biotherapeutics, and experiments in animal models show that the strategy can attenuate TNF-mediated pathology. Similar rational design could be used to engineer inhibitors of additional TNF superfamily cytokines as well as other multimeric ligands.

  2. Rational drug design of antineoplastic agents using 3D-QSAR, cheminformatic, and virtual screening approaches.

    Science.gov (United States)

    Vucicevic, Jelica; Nikolic, Katarina; Mitchell, John B O

    2017-07-12

    Computer-Aided Drug Design has strongly accelerated the development of novel antineoplastic agents by helping in the hit identification, optimization, and evaluation. Computational approaches such as cheminformatic search, virtual screening, pharmacophore modeling, molecular docking and dynamics have been developed and applied to explain the activity of bioactive molecules, design novel agents, increase the success rate of drug research, and decrease the total costs of drug discovery. Similarity searches and virtual screening are used to identify molecules with an increased probability to interact with drug targets of interest, while the other computational approaches are applied for the design and evaluation of molecules with enhanced activity and improved safety profile. In this review are described the main in silico techniques used in rational drug design of antineoplastic agents and presented optimal combinations of computational methods for design of more efficient antineoplastic drugs. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  3. Testing the limits of rational design by engineering pH sensitivity into membrane active peptides

    Science.gov (United States)

    Wiedman, Gregory

    2015-01-01

    In this work, we sought to rationally design membrane active peptides that are triggered by low pH to form macromolecular-sized pores in lipid bilayers. Such peptides could have broad utility in biotechnology and in nanomedicine as cancer therapeutics or drug delivery vehicles that promote release of macromolecules from endosomes. Our approach to rational design was to combine the properties of a pH-independent peptide, MelP5, which forms large pores allowing passage of macromolecules, with the properties of two pH-dependent membrane active peptides, pHlip and GALA. We created two hybrid sequences, MelP5_Δ4 and MelP5_Δ6 by using the distribution of acidic residues on pHlip and GALA as a guide to insert acidic amino acids into the amphipathic helix of MelP5. We show that the new peptides bind to lipid bilayers and acquire secondary structure in a pH-dependent manner. The peptides also destabilize bilayers in a pH-dependent manner, such that lipid vesicles release the small molecules ANTS/DPX at low pH only. Thus, we were successful in designing pH-triggered pore-forming peptides. However, no macro-molecular release was observed under any conditions. Therefore, we abolished the unique macromolecular poration properties of MelP5 by introducing pH-sensitivity into its sequence. We conclude that the properties of pHlip, GALA and MelP5 are additive, but only partially so. We propose that this lack of additivity is a limitation in the rational design of novel membrane active peptides, and that high-throughput approaches to discovery will be critical for continued progress in the field. PMID:25572997

  4. Rational Design of Hyperbranched Nanowire Systems for Tunable Superomniphobic Surfaces Enabled by Atomic Layer Deposition

    Energy Technology Data Exchange (ETDEWEB)

    Bielinski, Ashley R.; Boban, Mathew; He, Yang; Kazyak, Eric; Lee, Duck Hyun; Wang, Chongmin; Tuteja, Anish; Dasgupta, Neil P.

    2017-01-24

    A method for tunable control of geometry in hyperbranched ZnO nanowire (NW) systems is reported, which enables the rational design and fabrication of superomniphobic surfaces. Branched NWs with tunable density and orientation were grown via a sequential hydrothermal process, in which atomic layer deposition (ALD) was used for NW seeding, disruption of epitaxy, and selective blocking of NW nucleation. This approach allows for the rational design and optimization of three-level hierarchical structures, in which the geometric parameters of each level of hierarchy can be individually controlled. We demonstrate the coupled relationships between geometry and contact angle for a variety of liquids, which is supported by mathematical models of structural superomniphobicity. The highest performing superomniphobic surface was designed with three levels of hierarchy and achieved the following advancing/receding contact angles, water: 172°/170°, hexadecane: 166°/156°, octane: 162°/145°, and heptane: 160°/130°. Low surface tension liquids were shown to bounce off the surface from a height of 7 cm without breaking through and wetting. This approach demonstrates the power of ALD as an enabling technique for hierarchical materials by design, spanning the macro, micro, and nano length scales.

  5. Recent Advances in the Rational Design and Optimization of Antibacterial Agents.

    Science.gov (United States)

    Jones, Jesse A; Virga, Kristopher G; Gumina, Giuseppe; Hevener, Kirk E

    2016-09-01

    This review discusses next-generation antibacterial agents developed using rational, or targeted, drug design strategies. The focus of this review is on small-molecule compounds that have been designed to bypass developing bacterial resistance, improve the antibacterial spectrum of activity, and/or to optimize other properties, including physicochemical and pharmacokinetic properties. Agents are discussed that affect known antibacterial targets, such as the bacterial ribosome, nucleic acid binding proteins, and proteins involved in cell-wall biosynthesis; as well as some affecting novel bacterial targets which do not have currently marketed agents. The discussion of the agents focuses on the rational design strategies employed and the synthetic medicinal chemistry and structure-based design techniques utilized by the scientists involved in the discoveries, including such methods as ligand- and structure-based strategies, structure-activity relationship (SAR) expansion strategies, and novel synthetic organic chemistry methods. As such, the discussion is limited to small-molecule therapeutics that have confirmed macromolecular targets and encompasses only a fraction of all antibacterial agents recently approved or in late-stage clinical trials. The antibacterial agents selected have been recently approved for use on the U.S. or European markets or have shown promising results in phase 2 or phase 3 U.S.

  6. Multi-Step Usage of in Vivo Models During Rational Drug Design and Discovery

    Directory of Open Access Journals (Sweden)

    Charles H. Williams

    2011-04-01

    Full Text Available In this article we propose a systematic development method for rational drug design while reviewing paradigms in industry, emerging techniques and technologies in the field. Although the process of drug development today has been accelerated by emergence of computational methodologies, it is a herculean challenge requiring exorbitant resources; and often fails to yield clinically viable results. The current paradigm of target based drug design is often misguided and tends to yield compounds that have poor absorption, distribution, metabolism, and excretion, toxicology (ADMET properties. Therefore, an in vivo organism based approach allowing for a multidisciplinary inquiry into potent and selective molecules is an excellent place to begin rational drug design. We will review how organisms like the zebrafish and Caenorhabditis elegans can not only be starting points, but can be used at various steps of the drug development process from target identification to pre-clinical trial models. This systems biology based approach paired with the power of computational biology; genetics and developmental biology provide a methodological framework to avoid the pitfalls of traditional target based drug design.

  7. Multi-step usage of in vivo models during rational drug design and discovery.

    Science.gov (United States)

    Williams, Charles H; Hong, Charles C

    2011-01-01

    In this article we propose a systematic development method for rational drug design while reviewing paradigms in industry, emerging techniques and technologies in the field. Although the process of drug development today has been accelerated by emergence of computational methodologies, it is a herculean challenge requiring exorbitant resources; and often fails to yield clinically viable results. The current paradigm of target based drug design is often misguided and tends to yield compounds that have poor absorption, distribution, metabolism, and excretion, toxicology (ADMET) properties. Therefore, an in vivo organism based approach allowing for a multidisciplinary inquiry into potent and selective molecules is an excellent place to begin rational drug design. We will review how organisms like the zebrafish and Caenorhabditis elegans can not only be starting points, but can be used at various steps of the drug development process from target identification to pre-clinical trial models. This systems biology based approach paired with the power of computational biology; genetics and developmental biology provide a methodological framework to avoid the pitfalls of traditional target based drug design.

  8. Impact of Binding Site Comparisons on Medicinal Chemistry and Rational Molecular Design.

    Science.gov (United States)

    Ehrt, Christiane; Brinkjost, Tobias; Koch, Oliver

    2016-05-12

    Modern rational drug design not only deals with the search for ligands binding to interesting and promising validated targets but also aims to identify the function and ligands of yet uncharacterized proteins having impact on different diseases. Additionally, it contributes to the design of inhibitors with distinct selectivity patterns and the prediction of possible off-target effects. The identification of similarities between binding sites of various proteins is a useful approach to cope with those challenges. The main scope of this perspective is to describe applications of different protein binding site comparison approaches to outline their applicability and impact on molecular design. The article deals with various substantial application domains and provides some outstanding examples to show how various binding site comparison methods can be applied to promote in silico drug design workflows. In addition, we will also briefly introduce the fundamental principles of different protein binding site comparison methods.

  9. Rational Design of Novel Enzymes%酶的理性设计

    Institute of Scientific and Technical Information of China (English)

    陈勇; 王淑珍; 陈依军

    2011-01-01

    酶作为一种重要的生物催化剂,广泛应用于医药、化工等领域,但由于新酶以及酶的新用途开发速度的不足使得其应用受到了限制.酶的理性设计是新酶发现的一个重要来源,对于扩大酶的应用范围发挥重要作用.近年来,采用传统基于实验结果的设计的方法已取得了可喜的进展.然而,随着计算机技术的发展,计算机辅助设计和从头设计的方法和策略得到了更为迅猛的发展,已成为理性设计新酶的有力工具和新的研究前沿.文章就各种理性设计方法和策略以及未来发展趋势进行简要介绍和讨论.%As important biocatalyst, enzyme is widely used in pharmaceutical, chemical and other fields. However, the low-speed exploitation of novelenzymes or the limited uses of developed enzymes greatly restrict the applications of enzymes. Rational design of enzyme is an important approach for the discovery of new enzymes to enlarge the scope of their applications. In recent years, although the traditional methods of experimental design have made tremendous accomplishments, the emerging development of information technology has also promoted the rapid advancements in enzyme design by computational design, which is a powerful new tool and research frontier. As a part of computational design, de novo design, due to itsgreat and promising success, emerges in the field of rational design of novel enzymes, providing new ideas and options for the enzyme designers. In this review, currently available strategies, methods and development trends on enzyme rational design are briefly introduced and discussed.

  10. Crystals of Human Serum Albumin for Use in Genetic Engineering and Rational Drug Design

    Science.gov (United States)

    Carter, Daniel C. (Inventor)

    1994-01-01

    This invention pertains to crystals of serum albumin and processes for growing them. The purpose of the invention is to provide crystals of serum albumin which can be studied to determine binding sites for drugs. Form 2 crystals grow in the monoclinic space P2(sub 1), and possesses the following unit cell constraints: a = 58.9 +/- 7, b = 88.3 +/- 7, c = 60.7 +/- 7, Beta = 101.0 +/- 2 degrees. One advantage of the invention is that it will allow rational drug design

  11. Recent advances in the rational design of silica-based nanoparticles for gene therapy.

    Science.gov (United States)

    Niut, Yuting; Popatt, Amirali; Yu, Meihua; Karmakar, Surajit; Gu, Wenyi; Yu, Chengzhong

    2012-10-01

    Gene therapy has attracted much attention in modern society and provides a promising approach for treating genetic disorders, diseases and cancers. Safe and effective vectors are vital tools to deliver genetic molecules to cells. This review summarizes recent advances in the rational design of silica-based nanoparticles and their applications in gene therapy. An overview of different types of genetic agents available for gene therapy is provided. The engineering of various silica nanoparticles is described, which can be used as versatile complexation tools for genetic agents and advanced gene therapy. Several challenges are raised and future research directions in the area of gene therapy using silica-based nanoparticles are proposed.

  12. Control over Catenation in Metal−Organic Frameworks via Rational Design of the Organic Building Block

    Energy Technology Data Exchange (ETDEWEB)

    Farha, Omar K.; Malliakas, Christos D.; Kanatzidis, Mercouri G.; Hupp, Joseph T. (NWU)

    2010-02-19

    Metal-organic frameworks (MOFs), a hybrid class of materials comprising inorganic nodes and organic struts, have potential application in many areas due to their high surface areas and uniform pores and channels. One of the key challenges to be overcome in MOF synthesis is the strong propensity for catenation (growth of multiple independent networks within a given crystal), as catenation reduces cavity sizes and diminishes porosity. Here we demonstrate that rational design of organic building blocks, which act as strut-impervious scaffolds, can be exploited to generate highly desired noncatenated materials in a controlled fashion.

  13. Rationalization and Design of the Complementarity Determining Region Sequences in an Antibody-Antigen Recognition Interface

    Science.gov (United States)

    Chen, Ing-Chien; Lee, Yu-Ching; Chen, Jun-Bo; Tsai, Keng-Chang; Chen, Ching-Tai; Chang, Jeng-Yih; Yang, Ei-Wen; Hsu, Po-Chiang; Jian, Jhih-Wei; Hsu, Hung-Ju; Chang, Hung-Ju; Hsu, Wen-Lian; Huang, Kai-Fa; Ma, Alex Che; Yang, An-Suei

    2012-01-01

    Protein-protein interactions are critical determinants in biological systems. Engineered proteins binding to specific areas on protein surfaces could lead to therapeutics or diagnostics for treating diseases in humans. But designing epitope-specific protein-protein interactions with computational atomistic interaction free energy remains a difficult challenge. Here we show that, with the antibody-VEGF (vascular endothelial growth factor) interaction as a model system, the experimentally observed amino acid preferences in the antibody-antigen interface can be rationalized with 3-dimensional distributions of interacting atoms derived from the database of protein structures. Machine learning models established on the rationalization can be generalized to design amino acid preferences in antibody-antigen interfaces, for which the experimental validations are tractable with current high throughput synthetic antibody display technologies. Leave-one-out cross validation on the benchmark system yielded the accuracy, precision, recall (sensitivity) and specificity of the overall binary predictions to be 0.69, 0.45, 0.63, and 0.71 respectively, and the overall Matthews correlation coefficient of the 20 amino acid types in the 24 interface CDR positions was 0.312. The structure-based computational antibody design methodology was further tested with other antibodies binding to VEGF. The results indicate that the methodology could provide alternatives to the current antibody technologies based on animal immune systems in engineering therapeutic and diagnostic antibodies against predetermined antigen epitopes. PMID:22457753

  14. Rationalization and design of the complementarity determining region sequences in an antibody-antigen recognition interface.

    Directory of Open Access Journals (Sweden)

    Chung-Ming Yu

    Full Text Available Protein-protein interactions are critical determinants in biological systems. Engineered proteins binding to specific areas on protein surfaces could lead to therapeutics or diagnostics for treating diseases in humans. But designing epitope-specific protein-protein interactions with computational atomistic interaction free energy remains a difficult challenge. Here we show that, with the antibody-VEGF (vascular endothelial growth factor interaction as a model system, the experimentally observed amino acid preferences in the antibody-antigen interface can be rationalized with 3-dimensional distributions of interacting atoms derived from the database of protein structures. Machine learning models established on the rationalization can be generalized to design amino acid preferences in antibody-antigen interfaces, for which the experimental validations are tractable with current high throughput synthetic antibody display technologies. Leave-one-out cross validation on the benchmark system yielded the accuracy, precision, recall (sensitivity and specificity of the overall binary predictions to be 0.69, 0.45, 0.63, and 0.71 respectively, and the overall Matthews correlation coefficient of the 20 amino acid types in the 24 interface CDR positions was 0.312. The structure-based computational antibody design methodology was further tested with other antibodies binding to VEGF. The results indicate that the methodology could provide alternatives to the current antibody technologies based on animal immune systems in engineering therapeutic and diagnostic antibodies against predetermined antigen epitopes.

  15. Experimental and Theoretical Investigations of CB8-:Towards Rational Design of Hypercoordinated Planar Chemical Species

    Energy Technology Data Exchange (ETDEWEB)

    Averkiev, Boris B.; Wang, Leiming; Huang, Wei; Wang, Lai S.; Boldyrev, Alexander I.

    2009-11-01

    We demonstrated in our joint photoelectron spectroscopic and ab initio study that wheel-type structures with a boron ring are not appropriate for designing planar molecules with a hypercoordinate central carbon on the example of CB8, and CB8 clusters. According to our chemical bonding model, in the wheel type structures the central atom is involved in delocalized bonding, while peripheral atoms are involved in both delocalized bonding and 2c-2e -bonding. Since carbon is more electronegative than boron it favors peripheral positions where it can participate in 2c-2e -bonding. To design a chemical species with a central hypercoordinate carbon atom, one should consider electropositive ligands, which would have lone pairs instead of 2c-2e peripheral bonds. We presented a chemical bonding model capable of rationalizing and predicting structures either with a boron ring or a central planar carbon. This represents the first step toward rational design of nano- and subnano-structures with tailored properties.

  16. Rational design of mass diffusion metamaterial concentrators based on coordinate transformations

    Science.gov (United States)

    Restrepo-Flórez, Juan Manuel; Maldovan, Martin

    2016-08-01

    Recent advances in coordinate transformations of Fick's equation have paved the way for the design of metamaterial devices that can manipulate mass diffusion flux. The control of diffusion paths has a great potential for the design of novel catalytic and separation systems in chemical and biomolecular engineering. In order to explore these new applications, it is necessary to understand mass diffusion in coordinate transformation metamaterial devices. In this work, we present a comprehensive study on the impact of structure and material properties on the resultant physical properties of mass concentrator metamaterial shells. The concentration gradient at the core, the total mass flow rate towards the core, and the disturbance of the external concentration field are systematically examined in order to provide guidelines for the rational design and fabrication of metamaterial mass concentrators. A practical case is also presented where the concentration of oxygen diffusing in a polymeric system is studied.

  17. Rational Design of a Fusion Protein to Exhibit Disulfide-Mediated Logic Gate Behavior

    Science.gov (United States)

    2015-01-01

    Synthetic cellular logic gates are primarily built from gene circuits owing to their inherent modularity. Single proteins can also possess logic gate functions and offer the potential to be simpler, quicker, and less dependent on cellular resources than gene circuits. However, the design of protein logic gates that are modular and integrate with other cellular components is a considerable challenge. As a step toward addressing this challenge, we describe the design, construction, and characterization of AND, ORN, and YES logic gates built by introducing disulfide bonds into RG13, a fusion of maltose binding protein and TEM-1 β-lactamase for which maltose is an allosteric activator of enzyme activity. We rationally designed these disulfide bonds to manipulate RG13’s allosteric regulation mechanism such that the gating had maltose and reducing agents as input signals, and the gates could be toggled between different gating functions using redox agents, although some gates performed suboptimally. PMID:25144732

  18. Rational design of the column of a heavy multipurpose machining center

    Science.gov (United States)

    Atapin, V. V.; Kurlaev, N. V.

    2016-04-01

    The main purpose in the design of supporting constructions of heavy multipurpose machining center is the reduction of mass at the given precision and productivity of machining. Accomplish these ends the technology of rational design of supporting constructions is offered. This technology is based on the decomposition method and the finite elements method in the combination with optimization methods. The technology has four stages: 1) calculation of external forces and loads, 2) as a result the boundary conditions (force, kinematics) for individual supporting constructions are formed, 3) a problem about final optimal distribution of a material by the individual supporting constructions with the real cross-section is solved; 4) dynamic analysis. By the example of design of the column of a heavy multipurpose machining center the main stages of rational design of the individual supporting constructions are shown. At a design stage of the carrying system consisting of load-bearing structures with simplified geometry, optimum overall dimensions of the column are identified. For the admitted system of preferences, it is necessary to accept the fact that the carrying system with the column with the sizes of cross section of 1.8 m (along x axis) and 2.6 m (along y axis) is the best. The analysis of the work of the column under the torsion condition with the use of method of mechanics shows that the column with square cross sections = 2.46·2.46 m which rigidity on torsion is 26 % higher in comparison with a production version is the best. The results of calculation show that a production-release design of the column with longitudinal and transverse edges of rigidity is 24 % heavier than the column with the edges located on a diagonally at equal rigidity.

  19. Rationally designed small molecules that target both the DNA and RNA causing myotonic dystrophy type 1.

    Science.gov (United States)

    Nguyen, Lien; Luu, Long M; Peng, Shaohong; Serrano, Julio F; Chan, H Y Edwin; Zimmerman, Steven C

    2015-11-11

    Single-agent, single-target therapeutic approaches are often limited by a complex disease pathobiology. We report rationally designed, multi-target agents for myotonic dystrophy type 1 (DM1). DM1 originates in an abnormal expansion of CTG repeats (CTG(exp)) in the DMPK gene. The resultant expanded CUG transcript (CUG(exp)) identified as a toxic agent sequesters important proteins, such as muscleblind-like proteins (MBNL), undergoes repeat-associated non-ATG (RAN) translation, and potentially causes microRNA dysregulation. We report rationally designed small molecules that target the DM1 pathobiology in vitro in three distinct ways by acting simultaneously as transcription inhibitors, by inhibiting aberrant protein binding to the toxic RNA, and by acting as RNase mimics to degrade the toxic RNA. In vitro, the agents are shown to (1) bind CTG(exp) and inhibit formation of the CUG(exp) transcript, (2) bind CUG(exp) and inhibit sequestration of MBNL1, and (3) cleave CUG(exp) in an RNase-like manner. The most potent compounds are capable of reducing the levels of CUG(exp) in DM1 model cells, and one reverses two separate CUG(exp)-induced phenotypes in a DM1 Drosophila model.

  20. Rational design and synthesis of freestanding photoelectric nanodevices as highly efficient photocatalysts.

    Science.gov (United States)

    Qu, Yongquan; Liao, Lei; Cheng, Rui; Wang, Yue; Lin, Yung-Chen; Huang, Yu; Duan, Xiangfeng

    2010-05-12

    Photocatalysts are of significant interest in solar energy harvesting and conversion into chemical energy. However, the photocatalysts available to date are limited by either poor efficiency in the visible light range or insufficient photoelectrochemical stability. Here we report the rational design of a new generation of freestanding photoelectric nanodevices as highly efficient and stable photocatalysts by integrating a nanoscale photodiode with two redox catalysts in a single nanowire heterostructure. We show that a platinum-silicon-silver nanowire heterostructure can be synthesized to integrate a nanoscale metal-semiconductor Schottky diode encased in a protective insulating shell with two exposed metal catalysts. We further demonstrated that the Schottky diodes exhibited a pronounced photovoltaic effect with nearly unity internal quantum efficiency and that the integrated nanowire heterostructures could be used as highly efficient photocatalysts for a wide range of thermodynamically downhill and uphill reactions including the photocatalytic degradation of organic dyes and the reduction of metal ions and carbon dioxide using visible light. Our studies for the first time demonstrated the integration of multiple distinct functional components into a single nanostructure to form a standalone active nanosystem and for the first time successfully realized a photoelectric nanodevice that is both highly efficient and highly stable throughout the entire solar spectrum. It thus opens a rational avenue to the design and synthesis of a new generation of photoelectric nanosystems with unprecedented efficiency and stability and will have a broad impact in areas including environmental remediation, artificial photosynthesis and solar fuel production.

  1. Rational Basis for Designing Horizontal-Flow Anaerobic Immobilized Sludge (HAIS Reactor for Wastewater Treatment

    Directory of Open Access Journals (Sweden)

    M. Zaiat

    1997-03-01

    Full Text Available The conception and development on a rational basis of a new configuration of anaerobic fixed-bed bioreactor for wastewater treatment, the horizontal-flow anaerobic immobilized sludge (HAIS reactor, is presented. Such a reactor containing immobilized sludge in polyurethane foam matrices was first assayed for treating paper industry wastewater. A very short start-up period was observed and the reactor achieved stable operation by the eighth day. Afterwards, fundamental aspects of the process were investigated in order to obtain a rational basis for HAIS reactor design. A sequence of experiments was carried out for evaluating the cell wash-out from polyurethane foam matrices, the liquid-phase mass transfer coefficient and the intrinsic kinetic parameters, besides the hydrodynamic flow pattern of the reactor. The knowledge of such fundamental phenomena is useful for improving the reactor’s design and operation. Besides, these fundamental studies are essential to provide parameters for simulation and optimization of processes that make use of immobilized biomass

  2. Rational design of metal nitride redox materials for solar-driven ammonia synthesis

    Science.gov (United States)

    Michalsky, Ronald; Pfromm, Peter H.; Steinfeld, Aldo

    2015-01-01

    Fixed nitrogen is an essential chemical building block for plant and animal protein, which makes ammonia (NH3) a central component of synthetic fertilizer for the global production of food and biofuels. A global project on artificial photosynthesis may foster the development of production technologies for renewable NH3 fertilizer, hydrogen carrier and combustion fuel. This article presents an alternative path for the production of NH3 from nitrogen, water and solar energy. The process is based on a thermochemical redox cycle driven by concentrated solar process heat at 700–1200°C that yields NH3 via the oxidation of a metal nitride with water. The metal nitride is recycled via solar-driven reduction of the oxidized redox material with nitrogen at atmospheric pressure. We employ electronic structure theory for the rational high-throughput design of novel metal nitride redox materials and to show how transition-metal doping controls the formation and consumption of nitrogen vacancies in metal nitrides. We confirm experimentally that iron doping of manganese nitride increases the concentration of nitrogen vacancies compared with no doping. The experiments are rationalized through the average energy of the dopant d-states, a descriptor for the theory-based design of advanced metal nitride redox materials to produce sustainable solar thermochemical ammonia. PMID:26052421

  3. Rational design of metal nitride redox materials for solar-driven ammonia synthesis.

    Science.gov (United States)

    Michalsky, Ronald; Pfromm, Peter H; Steinfeld, Aldo

    2015-06-01

    Fixed nitrogen is an essential chemical building block for plant and animal protein, which makes ammonia (NH3) a central component of synthetic fertilizer for the global production of food and biofuels. A global project on artificial photosynthesis may foster the development of production technologies for renewable NH3 fertilizer, hydrogen carrier and combustion fuel. This article presents an alternative path for the production of NH3 from nitrogen, water and solar energy. The process is based on a thermochemical redox cycle driven by concentrated solar process heat at 700-1200°C that yields NH3 via the oxidation of a metal nitride with water. The metal nitride is recycled via solar-driven reduction of the oxidized redox material with nitrogen at atmospheric pressure. We employ electronic structure theory for the rational high-throughput design of novel metal nitride redox materials and to show how transition-metal doping controls the formation and consumption of nitrogen vacancies in metal nitrides. We confirm experimentally that iron doping of manganese nitride increases the concentration of nitrogen vacancies compared with no doping. The experiments are rationalized through the average energy of the dopant d-states, a descriptor for the theory-based design of advanced metal nitride redox materials to produce sustainable solar thermochemical ammonia.

  4. Rational design of 13C-labeling experiments for metabolic flux analysis in mammalian cells

    Directory of Open Access Journals (Sweden)

    Crown Scott B

    2012-05-01

    Full Text Available Abstract Background 13C-Metabolic flux analysis (13C-MFA is a standard technique to probe cellular metabolism and elucidate in vivo metabolic fluxes. 13C-Tracer selection is an important step in conducting 13C-MFA, however, current methods are restricted to trial-and-error approaches, which commonly focus on an arbitrary subset of the tracer design space. To systematically probe the complete tracer design space, especially for complex systems such as mammalian cells, there is a pressing need for new rational approaches to identify optimal tracers. Results Recently, we introduced a new framework for optimal 13C-tracer design based on elementary metabolite units (EMU decomposition, in which a measured metabolite is decomposed into a linear combination of so-called EMU basis vectors. In this contribution, we applied the EMU method to a realistic network model of mammalian metabolism with lactate as the measured metabolite. The method was used to select optimal tracers for two free fluxes in the system, the oxidative pentose phosphate pathway (oxPPP flux and anaplerosis by pyruvate carboxylase (PC. Our approach was based on sensitivity analysis of EMU basis vector coefficients with respect to free fluxes. Through efficient grouping of coefficient sensitivities, simple tracer selection rules were derived for high-resolution quantification of the fluxes in the mammalian network model. The approach resulted in a significant reduction of the number of possible tracers and the feasible tracers were evaluated using numerical simulations. Two optimal, novel tracers were identified that have not been previously considered for 13C-MFA of mammalian cells, specifically [2,3,4,5,6-13C]glucose for elucidating oxPPP flux and [3,4-13C]glucose for elucidating PC flux. We demonstrate that 13C-glutamine tracers perform poorly in this system in comparison to the optimal glucose tracers. Conclusions In this work, we have demonstrated that optimal tracer design does not

  5. Rational Design of an Epstein-Barr Virus Vaccine Targeting the Receptor-Binding Site.

    Science.gov (United States)

    Kanekiyo, Masaru; Bu, Wei; Joyce, M Gordon; Meng, Geng; Whittle, James R R; Baxa, Ulrich; Yamamoto, Takuya; Narpala, Sandeep; Todd, John-Paul; Rao, Srinivas S; McDermott, Adrian B; Koup, Richard A; Rossmann, Michael G; Mascola, John R; Graham, Barney S; Cohen, Jeffrey I; Nabel, Gary J

    2015-08-27

    Epstein-Barr virus (EBV) represents a major global health problem. Though it is associated with infectious mononucleosis and ∼200,000 cancers annually worldwide, a vaccine is not available. The major target of immunity is EBV glycoprotein 350/220 (gp350) that mediates attachment to B cells through complement receptor 2 (CR2/CD21). Here, we created self-assembling nanoparticles that displayed different domains of gp350 in a symmetric array. By focusing presentation of the CR2-binding domain on nanoparticles, potent neutralizing antibodies were elicited in mice and non-human primates. The structurally designed nanoparticle vaccine increased neutralization 10- to 100-fold compared to soluble gp350 by targeting a functionally conserved site of vulnerability, improving vaccine-induced protection in a mouse model. This rational approach to EBV vaccine design elicited potent neutralizing antibody responses by arrayed presentation of a conserved viral entry domain, a strategy that can be applied to other viruses.

  6. Rational Design and Adaptive Management of Combination Therapies for Hepatitis C Virus Infection.

    Directory of Open Access Journals (Sweden)

    Ruian Ke

    2015-06-01

    Full Text Available Recent discoveries of direct acting antivirals against Hepatitis C virus (HCV have raised hopes of effective treatment via combination therapies. Yet rapid evolution and high diversity of HCV populations, combined with the reality of suboptimal treatment adherence, make drug resistance a clinical and public health concern. We develop a general model incorporating viral dynamics and pharmacokinetics/ pharmacodynamics to assess how suboptimal adherence affects resistance development and clinical outcomes. We derive design principles and adaptive treatment strategies, identifying a high-risk period when missing doses is particularly risky for de novo resistance, and quantifying the number of additional doses needed to compensate when doses are missed. Using data from large-scale resistance assays, we demonstrate that the risk of resistance can be reduced substantially by applying these principles to a combination therapy of daclatasvir and asunaprevir. By providing a mechanistic framework to link patient characteristics to the risk of resistance, these findings show the potential of rational treatment design.

  7. Rational Design and Adaptive Management of Combination Therapies for Hepatitis C Virus Infection

    Science.gov (United States)

    Ke, Ruian; Loverdo, Claude; Qi, Hangfei; Sun, Ren; Lloyd-Smith, James O.

    2015-01-01

    Recent discoveries of direct acting antivirals against Hepatitis C virus (HCV) have raised hopes of effective treatment via combination therapies. Yet rapid evolution and high diversity of HCV populations, combined with the reality of suboptimal treatment adherence, make drug resistance a clinical and public health concern. We develop a general model incorporating viral dynamics and pharmacokinetics/ pharmacodynamics to assess how suboptimal adherence affects resistance development and clinical outcomes. We derive design principles and adaptive treatment strategies, identifying a high-risk period when missing doses is particularly risky for de novo resistance, and quantifying the number of additional doses needed to compensate when doses are missed. Using data from large-scale resistance assays, we demonstrate that the risk of resistance can be reduced substantially by applying these principles to a combination therapy of daclatasvir and asunaprevir. By providing a mechanistic framework to link patient characteristics to the risk of resistance, these findings show the potential of rational treatment design. PMID:26125950

  8. Rational design of crystalline supermicroporous covalent organic frameworks with triangular topologies

    Science.gov (United States)

    Dalapati, Sasanka; Addicoat, Matthew; Jin, Shangbin; Sakurai, Tsuneaki; Gao, Jia; Xu, Hong; Irle, Stephan; Seki, Shu; Jiang, Donglin

    2015-07-01

    Covalent organic frameworks (COFs) are an emerging class of highly ordered porous polymers with many potential applications. They are currently designed and synthesized through hexagonal and tetragonal topologies, limiting the access to and exploration of new structures and properties. Here, we report that a triangular topology can be developed for the rational design and synthesis of a new class of COFs. The triangular topology features small pore sizes down to 12 Å, which is among the smallest pores for COFs reported to date, and high π-column densities of up to 0.25 nm-2, which exceeds those of supramolecular columnar π-arrays and other COF materials. These crystalline COFs facilitate π-cloud delocalization and are highly conductive, with a hole mobility that is among the highest reported for COFs and polygraphitic ensembles.

  9. Rational design of a β-glycosidase with high regiospecificity for triterpenoid tailoring.

    Science.gov (United States)

    Park, Sang Jin; Choi, Jung Min; Kyeong, Hyun-Ho; Kim, Song-Gun; Kim, Hak-Sung

    2015-03-23

    Triterpenoids with desired glycosylation patterns have attracted considerable attention as potential therapeutics for inflammatory diseases and various types of cancer. Sugar-hydrolyzing enzymes with high substrate specificity would be far more efficient than other methods for the synthesis of such specialty triterpenoids, but they are yet to be developed. Here we present a strategy to rationally design a β-glycosidase with high regiospecificity for triterpenoids. A β-glycosidase with broad substrate specificity was isolated, and its crystal structure was determined at 2.0 Å resolution. Based on the product profiles and substrate docking simulations, we modeled the substrate binding modes of the enzyme. From the model, the substrate binding cleft of the enzyme was redesigned in a manner that preferentially hydrolyzes glycans at specific glycosylation sites of triterpenoids. The designed mutants were shown to produce a variety of specialty triterpenoids with high purity.

  10. From G Protein-coupled Receptor Structure Resolution to Rational Drug Design.

    Science.gov (United States)

    Jazayeri, Ali; Dias, Joao M; Marshall, Fiona H

    2015-08-07

    A number of recent technical solutions have led to significant advances in G protein-coupled receptor (GPCR) structural biology. Apart from a detailed mechanistic view of receptor activation, the new structures have revealed novel ligand binding sites. Together, these insights provide avenues for rational drug design to modulate the activities of these important drug targets. The application of structural data to GPCR drug discovery ushers in an exciting era with the potential to improve existing drugs and discover new ones. In this review, we focus on technical solutions that have accelerated GPCR crystallography as well as some of the salient findings from structures that are relevant to drug discovery. Finally, we outline some of the approaches used in GPCR structure based drug design.

  11. Rational design of capillary-driven flows for paper-based microfluidics.

    Science.gov (United States)

    Elizalde, Emanuel; Urteaga, Raúl; Berli, Claudio L A

    2015-05-21

    The design of paper-based assays that integrate passive pumping requires a precise programming of the fluid transport, which has to be encoded in the geometrical shape of the substrate. This requirement becomes critical in multiple-step processes, where fluid handling must be accurate and reproducible for each operation. The present work theoretically investigates the capillary imbibition in paper-like substrates to better understand fluid transport in terms of the macroscopic geometry of the flow domain. A fluid dynamic model was derived for homogeneous porous substrates with arbitrary cross-sectional shapes, which allows one to determine the cross-sectional profile required for a prescribed fluid velocity or mass transport rate. An extension of the model to slit microchannels is also demonstrated. Calculations were validated by experiments with prototypes fabricated in our lab. The proposed method constitutes a valuable tool for the rational design of paper-based assays.

  12. More rational design of bubble columns; Kihoto sekkei no genjo to kadai

    Energy Technology Data Exchange (ETDEWEB)

    Kawase, Y.; Shimizu, K. [Toyo University, Saitama (Japan)

    1998-04-05

    Design and scale-up of bubble columns are not easy even at present. For not the conventional empirical design and scale-up by 1-D dispersion model or vessel line model but more rational approach, simulation is essential. This paper outlines approaches to design and scale-up of bubble columns from the viewpoints of gas dispersion as an important factor for design of bubble columns, and flow analysis of bubble columns. A large part of the design and scale-up of bubble columns is dependent on previous experiences. However, for more precise design and scale-up of bubble columns, those should be conducted through simulation. More precise simulation should be based on simultaneous solution of a motion equation on flow in gas-liquid two-phase system, a diffusion equation of mass transfer including a reaction term, and a heat transmission equation on heat transfer, reducing participation of an empirical correlation equation as much as possible. The importance of simulation will surely increase in the future. 14 refs., 5 figs.

  13. Rational design of small molecule inhibitors targeting the Ras GEF, SOS1

    Science.gov (United States)

    Evelyn, Chris R.; Duan, Xin; Biesiada, Jacek; Seibel, William L.; Meller, Jaroslaw; Zheng, Yi

    2014-01-01

    Summary Ras GTPases regulate intracellular signaling involved in cell proliferation. Elevated Ras signaling activity has been associated with human cancers. Ras activation is catalyzed by guanine-nucleotide exchange factors (GEFs), of which SOS1 is a major member that transduces receptor tyrosine kinase signaling to Ras. We have developed a rational approach coupling virtual screening with experimental screening in identifying small-molecule inhibitors targeting the catalytic site of SOS1 and SOS1-regulated Ras activity. A lead inhibitor, NSC-658497, is found to bind to SOS1, competitively suppresses SOS1-Ras interaction, and dose-dependently inhibits SOS1 GEF activity. Mutagenesis and structure-activity relationship studies map the NSC-658497 site of action to the SOS1 catalytic site, and define the chemical moieties in the inhibitor essential for the activity. NSC-658497 showed dose-dependent efficacy in inhibiting Ras, downstream signaling activities, and associated cell proliferation. These studies establish a proof of principle for rational design of small-molecule inhibitors targeting Ras GEF enzymatic activity. PMID:25455859

  14. Rational design of small molecule inhibitors targeting the Ras GEF, SOS1.

    Science.gov (United States)

    Evelyn, Chris R; Duan, Xin; Biesiada, Jacek; Seibel, William L; Meller, Jaroslaw; Zheng, Yi

    2014-12-18

    Ras GTPases regulate intracellular signaling involved in cell proliferation. Elevated Ras signaling activity has been associated with human cancers. Ras activation is catalyzed by guanine nucleotide exchange factors (GEFs), of which SOS1 is a major member that transduces receptor tyrosine kinase signaling to Ras. We have developed a rational approach coupling virtual screening with experimental screening in identifying small-molecule inhibitors targeting the catalytic site of SOS1 and SOS1-regulated Ras activity. A lead inhibitor, NSC-658497, was found to bind to SOS1, competitively suppress SOS1-Ras interaction, and dose-dependently inhibit SOS1 GEF activity. Mutagenesis and structure-activity relationship studies map the NSC-658497 site of action to the SOS1 catalytic site, and define the chemical moieties in the inhibitor essential for the activity. NSC-658497 showed dose-dependent efficacy in inhibiting Ras, downstream signaling activities, and associated cell proliferation. These studies establish a proof of principle for rational design of small-molecule inhibitors targeting Ras GEF enzymatic activity.

  15. Rational design of antibodies targeting specific epitopes within intrinsically disordered proteins

    Science.gov (United States)

    Sormanni, Pietro; Aprile, Francesco A.; Vendruscolo, Michele

    2015-01-01

    Antibodies are powerful tools in life sciences research, as well as in diagnostic and therapeutic applications, because of their ability to bind given molecules with high affinity and specificity. Using current methods, however, it is laborious and sometimes difficult to generate antibodies to target specific epitopes within a protein, in particular if these epitopes are not effective antigens. Here we present a method to rationally design antibodies to enable them to bind virtually any chosen disordered epitope in a protein. The procedure consists in the sequence-based design of one or more complementary peptides targeting a selected disordered epitope and the subsequent grafting of such peptides on an antibody scaffold. We illustrate the method by designing six single-domain antibodies to bind different epitopes within three disease-related intrinsically disordered proteins and peptides (α-synuclein, Aβ42, and IAPP). Our results show that all these designed antibodies bind their targets with good affinity and specificity. As an example of an application, we show that one of these antibodies inhibits the aggregation of α-synuclein at substoichiometric concentrations and that binding occurs at the selected epitope. Taken together, these results indicate that the design strategy that we propose makes it possible to obtain antibodies targeting given epitopes in disordered proteins or protein regions. PMID:26216991

  16. Rational design of antibodies targeting specific epitopes within intrinsically disordered proteins.

    Science.gov (United States)

    Sormanni, Pietro; Aprile, Francesco A; Vendruscolo, Michele

    2015-08-11

    Antibodies are powerful tools in life sciences research, as well as in diagnostic and therapeutic applications, because of their ability to bind given molecules with high affinity and specificity. Using current methods, however, it is laborious and sometimes difficult to generate antibodies to target specific epitopes within a protein, in particular if these epitopes are not effective antigens. Here we present a method to rationally design antibodies to enable them to bind virtually any chosen disordered epitope in a protein. The procedure consists in the sequence-based design of one or more complementary peptides targeting a selected disordered epitope and the subsequent grafting of such peptides on an antibody scaffold. We illustrate the method by designing six single-domain antibodies to bind different epitopes within three disease-related intrinsically disordered proteins and peptides (α-synuclein, Aβ42, and IAPP). Our results show that all these designed antibodies bind their targets with good affinity and specificity. As an example of an application, we show that one of these antibodies inhibits the aggregation of α-synuclein at substoichiometric concentrations and that binding occurs at the selected epitope. Taken together, these results indicate that the design strategy that we propose makes it possible to obtain antibodies targeting given epitopes in disordered proteins or protein regions.

  17. Sleeping Beauty transposase structure allows rational design of hyperactive variants for genetic engineering.

    Science.gov (United States)

    Voigt, Franka; Wiedemann, Lisa; Zuliani, Cecilia; Querques, Irma; Sebe, Attila; Mátés, Lajos; Izsvák, Zsuzsanna; Ivics, Zoltán; Barabas, Orsolya

    2016-03-30

    Sleeping Beauty (SB) is a prominent Tc1/mariner superfamily DNA transposon that provides a popular genome engineering tool in a broad range of organisms. It is mobilized by a transposase enzyme that catalyses DNA cleavage and integration at short specific sequences at the transposon ends. To facilitate SB's applications, here we determine the crystal structure of the transposase catalytic domain and use it to model the SB transposase/transposon end/target DNA complex. Together with biochemical and cell-based transposition assays, our structure reveals mechanistic insights into SB transposition and rationalizes previous hyperactive transposase mutations. Moreover, our data enables us to design two additional hyperactive transposase variants. Our work provides a useful resource and proof-of-concept for structure-based engineering of tailored SB transposases.

  18. Spin models inferred from patient data faithfully describe HIV fitness landscapes and enable rational vaccine design

    CERN Document Server

    Shekhar, Karthik; Ferguson, Andrew L; Barton, John P; Kardar, Mehran; Chakraborty, Arup K

    2013-01-01

    Mutational escape from vaccine induced immune responses has thwarted the development of a successful vaccine against AIDS, whose causative agent is HIV, a highly mutable virus. Knowing the virus' fitness as a function of its proteomic sequence can enable rational design of potent vaccines, as this information can focus vaccine induced immune responses to target mutational vulnerabilities of the virus. Spin models have been proposed as a means to infer intrinsic fitness landscapes of HIV proteins from patient-derived viral protein sequences. These sequences are the product of non-equilibrium viral evolution driven by patient-specific immune responses, and are subject to phylogenetic constraints. How can such sequence data allow inference of intrinsic fitness landscapes? We combined computer simulations and variational theory \\'{a} la Feynman to show that, in most circumstances, spin models inferred from patient-derived viral sequences reflect the correct rank order of the fitness of mutant viral strains. Our f...

  19. Rational design of multifunctional devices based on molybdenum disulfide and graphene hybrid nanostructures

    Science.gov (United States)

    Lim, Yi Rang; Lee, Young Bum; Kim, Seong Ku; Kim, Seong Jun; Kim, Yooseok; Jeon, Cheolho; Song, Wooseok; Myung, Sung; Lee, Sun Sook; An, Ki-Seok; Lim, Jongsun

    2017-01-01

    We rationally designed a new type of hybrid materials, molybdenum disulfide (MoS2) synthesized by Mo pre-deposition followed by subsequent sulfurization process directly on thermal chemical vapor deposition (TCVD)-grown graphene, for applications in a multifunctional device. The synthesis of stoichiometric and uniform multilayer MoS2 and high-crystalline monolayer graphene was evaluated by X-ray photoelectron spectroscopy and Raman spectroscopy. To examine the electrical transport and photoelectrical properties of MoS2-graphene hybrid films, field effect transistors (FETs) and visible-light photodetectors based on MoS2-graphene were both fabricated. As a result, the extracted mobility for MoS2-graphene hybrid FETs was two times higher than that of MoS2 FETs. In addition, the MoS2-graphene photodetectors revealed a significant photocurrent with abrupt switching behavior under periodic illumination.

  20. Evolving serodiagnostics by rationally designed peptide arrays: the Burkholderia paradigm in Cystic Fibrosis

    Science.gov (United States)

    Peri, Claudio; Gori, Alessandro; Gagni, Paola; Sola, Laura; Girelli, Daniela; Sottotetti, Samantha; Cariani, Lisa; Chiari, Marcella; Cretich, Marina; Colombo, Giorgio

    2016-09-01

    Efficient diagnosis of emerging and novel bacterial infections is fundamental to guide decisions on therapeutic treatments. Here, we engineered a novel rational strategy to design peptide microarray platforms, which combines structural and genomic analyses to predict the binding interfaces between diverse protein antigens and antibodies against Burkholderia cepacia complex infections present in the sera of Cystic Fibrosis (CF) patients. The predicted binding interfaces on the antigens are synthesized in the form of isolated peptides and chemically optimized for controlled orientation on the surface. Our platform displays multiple Burkholderia-related epitopes and is shown to diagnose infected individuals even in presence of superinfections caused by other prevalent CF pathogens, with limited cost and time requirements. Moreover, our data point out that the specific patterns determined by combined probe responses might provide a characterization of Burkholderia infections even at the subtype level (genomovars). The method is general and immediately applicable to other bacteria.

  1. Rational design of metallic nanocavities for resonantly enhanced four-wave mixing

    CERN Document Server

    Almeida, Euclides

    2015-01-01

    Optimizing the shape of nanostructures and nano antennas for specific optical properties has evolved to be a very fruitful activity. With modern fabrication tools a large variety of possibilities is available for shaping both nanoparticles and nanocavities; in particular nanocavities in thin metal films have emerged as attractive candidates for new metamaterials and strong linear and nonlinear optical systems. Here we rationally design metallic nanocavities to boost their Four Wave Mixing response by resonating the optical plasmonic resonances with the incoming and generated beams. The linear and nonlinear optical responses as well as the propagation of the electric fields inside the cavities are derived from the solution of Maxwell equations by using the 3D finite-differences time domain method. The observed conversion-efficiency of near infra-red to visible light equals or surpasses that of BBO of equivalent thickness. Implications to further optimization for efficient and broadband ultrathin nonlinear opti...

  2. Rational design of metallic nanocavities for resonantly enhanced four-wave mixing

    Science.gov (United States)

    Almeida, Euclides; Prior, Yehiam

    2015-01-01

    Optimizing the shape of nanostructures and nano-antennas for specific optical properties has evolved to be a very fruitful activity. With modern fabrication tools a large variety of possibilities is available for shaping both nanoparticles and nanocavities; in particular nanocavities in thin metal films have emerged as attractive candidates for new metamaterials and strong linear and nonlinear optical systems. Here we rationally design metallic nanocavities to boost their Four-Wave Mixing response by resonating the optical plasmonic resonances with the incoming and generated beams. The linear and nonlinear optical responses as well as the propagation of the electric fields inside the cavities are derived from the solution of Maxwell’s equations by using the 3D finite-differences time domain method. The observed conversion-efficiency of near-infrared to visible light equals or surpasses that of BBO of equivalent thickness. Implications to further optimization for efficient and broadband ultrathin nonlinear optical materials are discussed. PMID:25974175

  3. Understanding Amino Acid Mutations in Hepatitis B Virus Proteins for Rational Design of Vaccines and Drugs.

    Science.gov (United States)

    Shen, Ke; Shen, Li; Wang, Jing; Jiang, Zhi; Shen, Bairong

    2015-01-01

    The hepatitis B virus (HBV) genome encodes four proteins, i.e., DNA polymerase, surface protein, X, and core proteins. HBV undergoes different selective pressures for drug resistance and immune/vaccine escape and mutations are common for the HBV proteins. We here collected all the reported amino acid mutations happened in these four HBV proteins and studied their patterns. The relationship between the mutations and epitopic functions are investigated with bioinformatics tools, based on their sequence information. Some interesting results are observed for the mutation patterns, such as we found the serine and threonine are both for frequently mutated residues and mutant residues, while the tryptophan and methionine have low mutability. The results provide important information for the understanding of the molecular mechanism of virus evolution and therefore will facilitate the future rational design of HBV vaccines or drugs.

  4. Rational design of a structure-switching DNA aptamer for potassium ions

    Science.gov (United States)

    Catherine, Andrew T.; Shishido, Stephanie N.; Robbins-Welty, Gregg A.; Diegelman-Parente, Amy

    2014-01-01

    Structure-switching molecules provide a unique means for analyte detection, generating a response to analyte concentration through a binding-specific conformational change between non-binding and binding-competent states. While most ligand-binding molecules are not structure switching by default, many can be engineered to be so through the introduction of an alternative non-binding (and thus non-signalling) conformation. This population-shift mechanism is particularly effective with oligonucleotides and has led to the creation of structure-switching aptamers for many target ligands. Here, we report the rational design of structure-switching DNA aptamers, based on the thrombin binding aptamer (TBA), that bind potassium with affinities that bridge the gap between previously reported weak-binding and strong-binding aptamers. We also demonstrate a correlation between the free energy of the experimentally determined binding affinity for potassium and the computationally estimated free energy of the alternative (non-binding) structure. PMID:25352996

  5. From empiricism to rational design: a personal perspective of the evolution of vaccine development.

    Science.gov (United States)

    De Gregorio, Ennio; Rappuoli, Rino

    2014-07-01

    Vaccination, which is the most effective medical intervention that has ever been introduced, originated from the observation that individuals who survived a plague or smallpox would not get the disease twice. To mimic the protective effects of natural infection, Jenner - and later Pasteur - inoculated individuals with attenuated or killed disease-causing agents. This empirical approach inspired a century of vaccine development and the effective prophylaxis of many infectious diseases. From the 1980s, several waves of new technologies have enabled the development of novel vaccines that would not have been possible using the empirical approach. The technological revolution in the field of vaccination is now continuing, and it is delivering novel and safer vaccines. In this Timeline article, we provide our views on the transition from empiricism to rational vaccine design.

  6. ShearLab: A Rational Design of a Digital Parabolic Scaling Algorithm

    CERN Document Server

    Kutyniok, Gitta; Zhuang, Xiaosheng

    2011-01-01

    Multivariate problems are typically governed by anisotropic features such as edges in images. A common bracket of most of the various directional representation systems which have been proposed to deliver sparse approximations of such features is the utilization of parabolic scaling. One prominent example is the shearlet system. Our objective in this paper is three-fold: We firstly develop a digital shearlet theory which is rationally designed in the sense that it is the digitization of the existing shearlet theory for continuous data. This implicates that shearlet theory provides a unified treatment of both the continuum and digital realm. Secondly, we analyze the utilization of pseudo-polar grids and the pseudo-polar Fourier transform for digital implementations of parabolic scaling algorithms. We derive an isometric pseudo-polar Fourier transform by careful weighting of the pseudo-polar grid, allowing exploitation of its adjoint for the inverse transform. This leads to a digital implementation of the shear...

  7. Rational Design of Multi-Stimuli-Responsive Nanoparticles for Precise Cancer Therapy.

    Science.gov (United States)

    An, Xiaonan; Zhu, Aijun; Luo, Huanhuan; Ke, Hengte; Chen, Huabing; Zhao, Youliang

    2016-06-28

    Stimuli-responsive nanoparticles with target capacity are of great interest in drug delivery for cancer therapy. However, the challenge is to achieve highly smart release with precise spatiotemporal control for cancer therapy. Herein, we report the preparation and properties of multi-stimuli-responsive nanoparticles through the co-assembly of a 3-arm star quaterpolymer with a near-infrared (NIR) photothermal agent and chemotherapeutic compound. The nanoparticles can exhibit NIR light/pH/reduction-responsive drug release and intracellular drug translocation in cancer cells, which further integrate photoinduced hyperthermia for synergistic anticancer efficiency, thereby leading to tumor ablation without tumor regrowth. Thus, this rational design of nanoparticles with multiple responsiveness represents a versatile strategy to provide smart drug delivery paradigms for cancer therapy.

  8. Sleeping Beauty transposase structure allows rational design of hyperactive variants for genetic engineering

    Science.gov (United States)

    Voigt, Franka; Wiedemann, Lisa; Zuliani, Cecilia; Querques, Irma; Sebe, Attila; Mátés, Lajos; Izsvák, Zsuzsanna; Ivics, Zoltán; Barabas, Orsolya

    2016-01-01

    Sleeping Beauty (SB) is a prominent Tc1/mariner superfamily DNA transposon that provides a popular genome engineering tool in a broad range of organisms. It is mobilized by a transposase enzyme that catalyses DNA cleavage and integration at short specific sequences at the transposon ends. To facilitate SB's applications, here we determine the crystal structure of the transposase catalytic domain and use it to model the SB transposase/transposon end/target DNA complex. Together with biochemical and cell-based transposition assays, our structure reveals mechanistic insights into SB transposition and rationalizes previous hyperactive transposase mutations. Moreover, our data enables us to design two additional hyperactive transposase variants. Our work provides a useful resource and proof-of-concept for structure-based engineering of tailored SB transposases. PMID:27025571

  9. Rational design of Nb-based alloys for hydrogen separation: A first principles study

    Directory of Open Access Journals (Sweden)

    Byungki Ryu

    2013-02-01

    Full Text Available We have investigated the effect of alloying metal elements on hydrogen solubility and mechanical integrity of Nb-based alloys, Nb15M1 (where M = Ca–Zn, Ge, using first principles-based calculations. In general, the chemical interaction between the interstitial H and metal is weakened as the alloying element is changed from an early to a late transition metal, leading to lower H solubility and higher resistance to H embrittlement. This effect becomes more pronounced when a smaller alloying element is used due to stronger elastic interaction between interstitial H and metal atoms. These finding may provide scientific basis for rational design of Nb-based hydrogen separation membranes with tailored H solubility to effectively suppress H embrittlement while maintaining excellent hydrogen permeation rate.

  10. Engineering of isoamylase: improvement of protein stability and catalytic efficiency through semi-rational design.

    Science.gov (United States)

    Li, Youran; Zhang, Liang; Ding, Zhongyang; Gu, Zhenghua; Shi, Guiyang

    2016-01-01

    Isoamylase catalyzes the hydrolysis of α-1,6-glycosidic linkages in glycogen, amylopectin and α/β-limit dextrins. A semi-rational design strategy was performed to improve catalytic properties of isoamylase from Bacillus lentus. Three residues in vicinity of the essential residues, Arg505, Asn513, and Gly608, were chosen as the mutation sites and were substituted by Ala, Pro, Glu, and Lys, respectively. Thermal stability of the mutant R505P and acidic stability of the mutant R505E were enhanced. The k cat /K m values of the mutant G608V have been promoted by 49%, and the specific activity increased by 33%. This work provides an effective strategy for improving the catalytic activity and stability of isoamylase, and the results obtained here may be useful for the improvement of catalytic properties of other α/β barrel enzymes.

  11. Rational design of aggregation-resistant bioactive peptides: reengineering human calcitonin.

    Science.gov (United States)

    Fowler, Susan B; Poon, Stephen; Muff, Roman; Chiti, Fabrizio; Dobson, Christopher M; Zurdo, Jesús

    2005-07-19

    A high propensity to aggregate into intractable deposits is a common problem limiting the production and use of many peptides and proteins in a wide range of biotechnological and pharmaceutical applications. Many therapeutic polypeptides are frequently abandoned at an early stage in their development because of problems with stability and aggregation. It has been shown recently that parameters describing the physicochemical properties of polypeptides can be used as predictors of protein aggregation. Here we demonstrate that these and similar tools can be applied to the rational redesign of bioactive molecules with a significantly reduced aggregation propensity without loss of physiological activity. This strategy has been exemplified by designing variants of the hormone calcitonin that show a significantly reduced aggregation propensity, yet maintain, or even increase, their potency when compared to the current therapeutic forms. The results suggest that this approach could be used successfully to enhance the solubility and efficacy of a wide range of other peptide and protein therapeutics.

  12. Rational design of metallic nanocavities for resonantly enhanced four-wave mixing.

    Science.gov (United States)

    Almeida, Euclides; Prior, Yehiam

    2015-05-14

    Optimizing the shape of nanostructures and nano-antennas for specific optical properties has evolved to be a very fruitful activity. With modern fabrication tools a large variety of possibilities is available for shaping both nanoparticles and nanocavities; in particular nanocavities in thin metal films have emerged as attractive candidates for new metamaterials and strong linear and nonlinear optical systems. Here we rationally design metallic nanocavities to boost their Four-Wave Mixing response by resonating the optical plasmonic resonances with the incoming and generated beams. The linear and nonlinear optical responses as well as the propagation of the electric fields inside the cavities are derived from the solution of Maxwell's equations by using the 3D finite-differences time domain method. The observed conversion-efficiency of near-infrared to visible light equals or surpasses that of BBO of equivalent thickness. Implications to further optimization for efficient and broadband ultrathin nonlinear optical materials are discussed.

  13. Rational design of DNA-actuated enzyme nanoreactors guided by single molecule analysis

    Science.gov (United States)

    Dhakal, Soma; Adendorff, Matthew R.; Liu, Minghui; Yan, Hao; Bathe, Mark; Walter, Nils G.

    2016-01-01

    The control of enzymatic reactions using nanoscale DNA devices offers a powerful application of DNA nanotechnology uniquely derived from actuation. However, previous characterization of enzymatic reaction rates using bulk biochemical assays reported suboptimal function of DNA devices such as tweezers. To gain mechanistic insight into this deficiency and to identify design rules to improve their function, here we exploit the synergy of single molecule imaging and computational modeling to characterize the three-dimensional structures and catalytic functions of DNA tweezer-actuated nanoreactors. Our analysis revealed two important deficiencies - incomplete closure upon actuation and conformational heterogeneity. Upon rational redesign of the Holliday junctions located at their hinge and arms, we found that the DNA tweezers could be more completely and uniformly closed. A novel single molecule enzyme assay was developed to demonstrate that our design improvements yield significant, independent enhancements in the fraction of active enzyme nanoreactors and their individual substrate turnover frequencies. The sequence-level design strategies explored here may aid more broadly in improving the performance of DNA-based nanodevices including biological and chemical sensors.The control of enzymatic reactions using nanoscale DNA devices offers a powerful application of DNA nanotechnology uniquely derived from actuation. However, previous characterization of enzymatic reaction rates using bulk biochemical assays reported suboptimal function of DNA devices such as tweezers. To gain mechanistic insight into this deficiency and to identify design rules to improve their function, here we exploit the synergy of single molecule imaging and computational modeling to characterize the three-dimensional structures and catalytic functions of DNA tweezer-actuated nanoreactors. Our analysis revealed two important deficiencies - incomplete closure upon actuation and conformational

  14. Design for Additive Bio-Manufacturing: From Patient-Specific Medical Devices to Rationally Designed Meta-Biomaterials

    Directory of Open Access Journals (Sweden)

    Amir A. Zadpoor

    2017-07-01

    Full Text Available Recent advances in additive manufacturing (AM techniques in terms of accuracy, reliability, the range of processable materials, and commercial availability have made them promising candidates for production of functional parts including those used in the biomedical industry. The complexity-for-free feature offered by AM means that very complex designs become feasible to manufacture, while batch-size-indifference enables fabrication of fully patient-specific medical devices. Design for AM (DfAM approaches aim to fully utilize those features for development of medical devices with substantially enhanced performance and biomaterials with unprecedented combinations of favorable properties that originate from complex geometrical designs at the micro-scale. This paper reviews the most important approaches in DfAM particularly those applicable to additive bio-manufacturing including image-based design pipelines, parametric and non-parametric designs, metamaterials, rational and computationally enabled design, topology optimization, and bio-inspired design. Areas with limited research have been identified and suggestions have been made for future research. The paper concludes with a brief discussion on the practical aspects of DfAM and the potential of combining AM with subtractive and formative manufacturing processes in so-called hybrid manufacturing processes.

  15. Design for Additive Bio-Manufacturing: From Patient-Specific Medical Devices to Rationally Designed Meta-Biomaterials.

    Science.gov (United States)

    Zadpoor, Amir A

    2017-07-25

    Recent advances in additive manufacturing (AM) techniques in terms of accuracy, reliability, the range of processable materials, and commercial availability have made them promising candidates for production of functional parts including those used in the biomedical industry. The complexity-for-free feature offered by AM means that very complex designs become feasible to manufacture, while batch-size-indifference enables fabrication of fully patient-specific medical devices. Design for AM (DfAM) approaches aim to fully utilize those features for development of medical devices with substantially enhanced performance and biomaterials with unprecedented combinations of favorable properties that originate from complex geometrical designs at the micro-scale. This paper reviews the most important approaches in DfAM particularly those applicable to additive bio-manufacturing including image-based design pipelines, parametric and non-parametric designs, metamaterials, rational and computationally enabled design, topology optimization, and bio-inspired design. Areas with limited research have been identified and suggestions have been made for future research. The paper concludes with a brief discussion on the practical aspects of DfAM and the potential of combining AM with subtractive and formative manufacturing processes in so-called hybrid manufacturing processes.

  16. Design for Additive Bio-Manufacturing: From Patient-Specific Medical Devices to Rationally Designed Meta-Biomaterials

    Science.gov (United States)

    Zadpoor, Amir A.

    2017-01-01

    Recent advances in additive manufacturing (AM) techniques in terms of accuracy, reliability, the range of processable materials, and commercial availability have made them promising candidates for production of functional parts including those used in the biomedical industry. The complexity-for-free feature offered by AM means that very complex designs become feasible to manufacture, while batch-size-indifference enables fabrication of fully patient-specific medical devices. Design for AM (DfAM) approaches aim to fully utilize those features for development of medical devices with substantially enhanced performance and biomaterials with unprecedented combinations of favorable properties that originate from complex geometrical designs at the micro-scale. This paper reviews the most important approaches in DfAM particularly those applicable to additive bio-manufacturing including image-based design pipelines, parametric and non-parametric designs, metamaterials, rational and computationally enabled design, topology optimization, and bio-inspired design. Areas with limited research have been identified and suggestions have been made for future research. The paper concludes with a brief discussion on the practical aspects of DfAM and the potential of combining AM with subtractive and formative manufacturing processes in so-called hybrid manufacturing processes. PMID:28757572

  17. Rational design of an enzyme mutant for anti-cocaine therapeutics

    Science.gov (United States)

    Zheng, Fang; Zhan, Chang-Guo

    2008-09-01

    (-)-Cocaine is a widely abused drug and there is no available anti-cocaine therapeutic. The disastrous medical and social consequences of cocaine addiction have made the development of an effective pharmacological treatment a high priority. An ideal anti-cocaine medication would be to accelerate (-)-cocaine metabolism producing biologically inactive metabolites. The main metabolic pathway of cocaine in body is the hydrolysis at its benzoyl ester group. Reviewed in this article is the state-of-the-art computational design of high-activity mutants of human butyrylcholinesterase (BChE) against (-)-cocaine. The computational design of BChE mutants have been based on not only the structure of the enzyme, but also the detailed catalytic mechanisms for BChE-catalyzed hydrolysis of (-)-cocaine and (+)-cocaine. Computational studies of the detailed catalytic mechanisms and the structure-and-mechanism-based computational design have been carried out through the combined use of a variety of state-of-the-art techniques of molecular modeling. By using the computational insights into the catalytic mechanisms, a recently developed unique computational design strategy based on the simulation of the rate-determining transition state has been employed to design high-activity mutants of human BChE for hydrolysis of (-)-cocaine, leading to the exciting discovery of BChE mutants with a considerably improved catalytic efficiency against (-)-cocaine. One of the discovered BChE mutants (i.e., A199S/S287G/A328W/Y332G) has a ˜456-fold improved catalytic efficiency against (-)-cocaine. The encouraging outcome of the computational design and discovery effort demonstrates that the unique computational design approach based on the transition-state simulation is promising for rational enzyme redesign and drug discovery.

  18. Rationally designed squaryldiamides - a novel class of sugar-nucleotide mimics?

    Science.gov (United States)

    Niewiadomski, Sven; Beebeejaun, Zeenat; Denton, Helen; Smith, Terry K; Morris, Richard J; Wagner, Gerd K

    2010-08-07

    Sugar-nucleotides such as GDP-mannose, GDP-fucose and UDP-glucose are important biomolecules with a central role in carbohydrate and glycoconjugate biosynthesis, metabolism and cell signalling. Analogues and mimics of naturally occurring sugar-nucleotides are sought after as chemical tools and inhibitor candidates for sugar-nucleotide-dependent enzymes including glycosyltransferases. Many sugar-nucleotides bind to their target glycosyltransferases via coordination of the diphosphate group to a divalent metal cofactor in the active site. The identification of uncharged, chemically stable surrogates for the diphosphate group, with the ability to coordinate to a divalent metal, is therefore an important design criteria for the development of sugar-nucleotide mimics. Here, we describe the rational design and synthesis of a novel class of sugar-nucleotide mimics based on a squaryldiamide scaffold, an uncharged phosphate isostere. We demonstrate by comprehensive NMR titration experiments that the new sugar-nucleotide mimics coordinate efficiently to Mg(2+), and provide results from biological studies with a therapeutically relevant mannosyltransferase from Trypanosoma brucei. Our findings suggest that squaryldiamides are a promising template for the development of sugar-nucleotide mimics, and illustrate the considerable potential of the squarylamide group as a fragment for inhibitor design.

  19. Rational design of modular circuits for gene transcription: A test of the bottom-up approach

    Directory of Open Access Journals (Sweden)

    Giordano Emanuele

    2010-11-01

    Full Text Available Abstract Background Most of synthetic circuits developed so far have been designed by an ad hoc approach, using a small number of components (i.e. LacI, TetR and a trial and error strategy. We are at the point where an increasing number of modular, inter-changeable and well-characterized components is needed to expand the construction of synthetic devices and to allow a rational approach to the design. Results We used interchangeable modular biological parts to create a set of novel synthetic devices for controlling gene transcription, and we developed a mathematical model of the modular circuits. Model parameters were identified by experimental measurements from a subset of modular combinations. The model revealed an unexpected feature of the lactose repressor system, i.e. a residual binding affinity for the operator site by induced lactose repressor molecules. Once this residual affinity was taken into account, the model properly reproduced the experimental data from the training set. The parameters identified in the training set allowed the prediction of the behavior of networks not included in the identification procedure. Conclusions This study provides new quantitative evidences that the use of independent and well-characterized biological parts and mathematical modeling, what is called a bottom-up approach to the construction of gene networks, can allow the design of new and different devices re-using the same modular parts.

  20. Rational protein design: developing next-generation biological therapeutics and nanobiotechnological tools.

    Science.gov (United States)

    Wilson, Corey J

    2015-01-01

    Proteins are the most functionally diverse macromolecules observed in nature, participating in a broad array of catalytic, biosensing, transport, scaffolding, and regulatory functions. Fittingly, proteins have become one of the most promising nanobiotechnological tools to date, and through the use of recombinant DNA and other laboratory methods we have produced a vast number of biological therapeutics derived from human genes. Our emerging ability to rationally design proteins (e.g., via computational methods) holds the promise of significantly expanding the number and diversity of protein therapies and has opened the gateway to realizing true and uncompromised personalized medicine. In the last decade computational protein design has been transformed from a set of fundamental strategies to stringently test our understanding of the protein structure-function relationship, to practical tools for developing useful biological processes, nano-devices, and novel therapeutics. As protein design strategies improve (i.e., in terms of accuracy and efficiency) clinicians will be able to leverage individual genetic data and biological metrics to develop and deliver personalized protein therapeutics with minimal delay.

  1. Theory and simulation of DNA-coated colloids: a guide for rational design

    Science.gov (United States)

    Angioletti-Uberti, Stefano; Mognetti, Bortolo M.; Frenkel, Daan

    By exploiting the exquisite selectivity of DNA hybridization, DNA-Coated Colloids (DNACCs) can be made to self-assemble in a wide variety of structures. The beauty of this system stems largely from its exceptional versatility and from the fact that a proper choice of the grafted DNA sequences yields fine control over the colloidal interactions. Theory and simulations have an important role to play in the optimal design of self- assembling DNACCs. At present, the powerful model-based design tools are not widely used, because the theoretical literature is fragmented and the connection between different theories is often not evident. In this Perspective, we aim to discuss the similarities and differences between the different models that have been described in the literature, their underlying assumptions, their strengths and their weaknesses. Using the tools described in the present Review, it should be possible to move towards a more rational design of novel self-assembling structures of DNACCs and, more generally, of systems where ligand-receptors bonds are used to control interactions.

  2. Rational Design of Peptide Vaccines Against Multiple Types of Human Papillomavirus.

    Science.gov (United States)

    Dey, Sumanta; De, Antara; Nandy, Ashesh

    2016-01-01

    Human papillomavirus (HPV) occurs in many types, some of which cause cervical, genital, and other cancers. While vaccination is available against the major cancer-causing HPV types, many others are not covered by these preventive measures. Herein, we present a bioinformatics study for the designing of multivalent peptide vaccines against multiple HPV types as an alternative strategy to the virus-like particle vaccines being used now. Our technique of rational design of peptide vaccines is expected to ensure stability of the vaccine against many cycles of mutational changes, elicit immune response, and negate autoimmune possibilities. Using the L1 capsid protein sequences, we identified several peptides for potential vaccine design for HPV 16, 18, 33, 35, 45, and 11 types. Although there are concerns about the epitope-binding affinities for the peptides identified in this process, the technique indicates possibilities of multivalent, adjuvanted, peptide vaccines against a wider range of HPV types, and tailor-made different combinations of the peptides to address frequency variations of types over different population groups as required for prophylaxis and at lower cost than are in use at the present time.

  3. Rational design of Nd(3+)-sensitized multifunctional nanoparticles with highly dominant red emission.

    Science.gov (United States)

    Xu, Xia; Lei, Pengpeng; Dong, Lile; Liu, Xiuling; Su, Yue; Song, Shuyan; Feng, Jing; Zhang, Hongjie

    2016-05-28

    Controlling excitation and emission wavelengths on demand is very significant in bioimaging. Up-conversion nanoparticles (UCNPs) emit visible light upon near-infrared (NIR) light excitation and are well studied in bioimaging. Red emission is usually preferred to green due to its higher tissue penetration depth in bioimaging. Herein, dominant red emission has been achieved under 808 nm excitation based on the designed α-NaYbF4:Mn(2+)/Er(3+)@NaLuF4:Mn(2+)/Yb(3+)@NaNdF4:Yb(3+)@NaGdF4 (C@S1@S2@S3) nanostructure. The rationally designed interlayer shell NaLuF4:Mn(2+)/Yb(3+) could efficiently filter unwanted energy back-transfer from Er(3+) to Nd(3+) and the outmost shell NaGdF4 could prevent excitation energy from surface-related quenching. The lifetime of (4)F9/2→(4)I15/2 transition of Er(3+) could be as high as 0.7 ms. Moreover, C@S1@S2@S3 UCNPs also possess effective contrast efficiency for both X-ray computed tomography (CT) and magnetic resonance (MR) imaging. The designed multifunctional UCNPs could be used as a potential multimodal bioprobe in bioimaging applications.

  4. Rationally designed BCL6 inhibitors target activated B cell diffuse large B cell lymphoma.

    Science.gov (United States)

    Cardenas, Mariano G; Yu, Wenbo; Beguelin, Wendy; Teater, Matthew R; Geng, Huimin; Goldstein, Rebecca L; Oswald, Erin; Hatzi, Katerina; Yang, Shao-Ning; Cohen, Joanna; Shaknovich, Rita; Vanommeslaeghe, Kenno; Cheng, Huimin; Liang, Dongdong; Cho, Hyo Je; Abbott, Joshua; Tam, Wayne; Du, Wei; Leonard, John P; Elemento, Olivier; Cerchietti, Leandro; Cierpicki, Tomasz; Xue, Fengtian; MacKerell, Alexander D; Melnick, Ari M

    2016-09-01

    Diffuse large B cell lymphomas (DLBCLs) arise from proliferating B cells transiting different stages of the germinal center reaction. In activated B cell DLBCLs (ABC-DLBCLs), a class of DLBCLs that respond poorly to current therapies, chromosomal translocations and amplification lead to constitutive expression of the B cell lymphoma 6 (BCL6) oncogene. The role of BCL6 in maintaining these lymphomas has not been investigated. Here, we designed small-molecule inhibitors that display higher affinity for BCL6 than its endogenous corepressor ligands to evaluate their therapeutic efficacy for targeting ABC-DLBCL. We used an in silico drug design functional-group mapping approach called SILCS to create a specific BCL6 inhibitor called FX1 that has 10-fold greater potency than endogenous corepressors and binds an essential region of the BCL6 lateral groove. FX1 disrupted formation of the BCL6 repression complex, reactivated BCL6 target genes, and mimicked the phenotype of mice engineered to express BCL6 with corepressor binding site mutations. Low doses of FX1 induced regression of established tumors in mice bearing DLBCL xenografts. Furthermore, FX1 suppressed ABC-DLBCL cells in vitro and in vivo, as well as primary human ABC-DLBCL specimens ex vivo. These findings indicate that ABC-DLBCL is a BCL6-dependent disease that can be targeted by rationally designed inhibitors that exceed the binding affinity of natural BCL6 ligands.

  5. Intrinsic disorder as a generalizable strategy for the rational design of highly responsive, allosterically cooperative receptors

    Science.gov (United States)

    Simon, Anna J.; Vallée-Bélisle, Alexis; Ricci, Francesco; Plaxco, Kevin W.

    2014-01-01

    Control over the sensitivity with which biomolecular receptors respond to small changes in the concentration of their target ligand is critical for the proper function of many cellular processes. Such control could likewise be of utility in artificial biotechnologies, such as biosensors, genetic logic gates, and “smart” materials, in which highly responsive behavior is of value. In nature, the control of molecular responsiveness is often achieved using “Hill-type” cooperativity, a mechanism in which sequential binding events on a multivalent receptor are coupled such that the first enhances the affinity of the next, producing a steep, higher-order dependence on target concentration. Here, we use an intrinsic-disorder–based mechanism that can be implemented without requiring detailed structural knowledge to rationally introduce this potentially useful property into several normally noncooperative biomolecules. To do so, we fabricate a tandem repeat of the receptor that is destabilized (unfolded) via the introduction of a long, unstructured loop. The first binding event requires the energetically unfavorable closing of this loop, reducing its affinity relative to that of the second binding event, which, in contrast occurs at a preformed site. Using this approach, we have rationally introduced cooperativity into three unrelated DNA aptamers, achieving in the best of these a Hill coefficient experimentally indistinguishable from the theoretically expected maximum. The extent of cooperativity and thus the steepness of the binding transition are, moreover, well modeled as simple functions of the energetic cost of binding-induced folding, speaking to the quantitative nature of this design strategy. PMID:25288724

  6. On rationally supported surfaces

    DEFF Research Database (Denmark)

    Gravesen, Jens; Juttler, B.; Sir, Z.

    2008-01-01

    We analyze the class of surfaces which are equipped with rational support functions. Any rational support function can be decomposed into a symmetric (even) and an antisymmetric (odd) part. We analyze certain geometric properties of surfaces with odd and even rational support functions....... In particular it is shown that odd rational support functions correspond to those rational surfaces which can be equipped with a linear field of normal vectors, which were discussed by Sampoli et al. (Sampoli, M.L., Peternell, M., Juttler, B., 2006. Rational surfaces with linear normals and their convolutions...... with rational surfaces. Comput. Aided Geom. Design 23, 179-192). As shown recently, this class of surfaces includes non-developable quadratic triangular Bezier surface patches (Lavicka, M., Bastl, B., 2007. Rational hypersurfaces with rational convolutions. Comput. Aided Geom. Design 24, 410426; Peternell, M...

  7. Adapting Rational Unified Process (RUP) approach in designing a secure e-Tendering model

    Science.gov (United States)

    Mohd, Haslina; Robie, Muhammad Afdhal Muhammad; Baharom, Fauziah; Darus, Norida Muhd; Saip, Mohamed Ali; Yasin, Azman

    2016-08-01

    e-Tendering is an electronic processing of the tender document via internet and allow tenderer to publish, communicate, access, receive and submit all tender related information and documentation via internet. This study aims to design the e-Tendering system using Rational Unified Process approach. RUP provides a disciplined approach on how to assign tasks and responsibilities within the software development process. RUP has four phases that can assist researchers to adjust the requirements of various projects with different scope, problem and the size of projects. RUP is characterized as a use case driven, architecture centered, iterative and incremental process model. However the scope of this study only focusing on Inception and Elaboration phases as step to develop the model and perform only three of nine workflows (business modeling, requirements, analysis and design). RUP has a strong focus on documents and the activities in the inception and elaboration phases mainly concern the creation of diagrams and writing of textual descriptions. The UML notation and the software program, Star UML are used to support the design of e-Tendering. The e-Tendering design based on the RUP approach can contribute to e-Tendering developers and researchers in e-Tendering domain. In addition, this study also shows that the RUP is one of the best system development methodology that can be used as one of the research methodology in Software Engineering domain related to secured design of any observed application. This methodology has been tested in various studies in certain domains, such as in Simulation-based Decision Support, Security Requirement Engineering, Business Modeling and Secure System Requirement, and so forth. As a conclusion, these studies showed that the RUP one of a good research methodology that can be adapted in any Software Engineering (SE) research domain that required a few artifacts to be generated such as use case modeling, misuse case modeling, activity

  8. Rationally designed small molecules targeting the RNA that causes myotonic dystrophy type 1 are potently bioactive.

    Science.gov (United States)

    Childs-Disney, Jessica L; Hoskins, Jason; Rzuczek, Suzanne G; Thornton, Charles A; Disney, Matthew D

    2012-05-18

    RNA is an important drug target, but it is difficult to design or discover small molecules that modulate RNA function. In the present study, we report that rationally designed, modularly assembled small molecules that bind the RNA that causes myotonic dystrophy type 1 (DM1) are potently bioactive in cell culture models. DM1 is caused when an expansion of r(CUG) repeats, or r(CUG)(exp), is present in the 3' untranslated region (UTR) of the dystrophia myotonica protein kinase (DMPK) mRNA. r(CUG)(exp) folds into a hairpin with regularly repeating 5'CUG/3'GUC motifs and sequesters muscleblind-like 1 protein (MBNL1). A variety of defects are associated with DM1, including (i) formation of nuclear foci, (ii) decreased translation of DMPK mRNA due to its nuclear retention, and (iii) pre-mRNA splicing defects due to inactivation of MBNL1, which controls the alternative splicing of various pre-mRNAs. Previously, modularly assembled ligands targeting r(CUG)(exp) were designed using information in an RNA motif-ligand database. These studies showed that a bis-benzimidazole (H) binds the 5'CUG/3'GUC motif in r(CUG)(exp.) Therefore, we designed multivalent ligands to bind simultaneously multiple copies of this motif in r(CUG)(exp). Herein, we report that the designed compounds improve DM1-associated defects including improvement of translational and pre-mRNA splicing defects and the disruption of nuclear foci. These studies may establish a foundation to exploit other RNA targets in genomic sequence.

  9. Study of rationalized safety design based on the seismic PSA for an LMFBR

    Energy Technology Data Exchange (ETDEWEB)

    Nakai, Ryodai; Yamaguchi, Akira

    1998-12-01

    Seismic PSA was carried out for a typical liquid metal cooled fast breeder reactor (LMFBR) in order to study the rationalized seismic design, maintaining and/or improving safety during seismic event. The seismic sequence quantification identifies the dominant structures, systems and components (SSCs) to the seismic core damage frequency (CDF). The sensitivity analyses by reducing or increasing the seismic capacity for SSCs are used to examine the optimized seismic design in view of safety and economical aspects. The LMFBR-specific risk-significant SSCs are reactor coolant boundary, decay heat removal coolant path and reactor control rod, which are different from those of light water reactors (LWRs). The electrical power supply system has a minor contribution to the seismic CDF. The sensitivity study shows that passive safety features of LMFBRs are important to maintain and/or enhance seismic capacity. The passive safety includes the decay heat removal capability via natural circulation and safety measures without depending on the support systems such as alternating current (AC) electrical power, for example. On the course of seismic sequence quantification, a methodology to evaluate the probability of seismic-induced multiple failure has been developed and applied to the decay heat removal function. The results suggest the multiplicity of the triply redundant system is to be considered for the significant components such as the decay heat removal path when one considers the difference in the seismic response.

  10. Rationally Designing Aptamer Sequences with Reduced Affinity for Controlled Sensor Performance

    Directory of Open Access Journals (Sweden)

    Lauren R. Schoukroun-Barnes

    2015-03-01

    Full Text Available The relative ease of predicting the secondary structure of nucleic acid sequences lends itself to the design of sequences to perform desired functions. Here, we combine the utility of nucleic acid aptamers with predictable control over the secondary structure to rationally design sequences with controlled affinity towards a target analyte when employed as the recognition element in an electrochemical sensor. Specifically, we present a method to modify an existing high-gain aptamer sequence to create sequences that, when employed in an electrochemical, aptamer-based sensor, exhibit reduced affinity towards a small molecule analyte tobramycin. Sensors fabricated with the high-gain parent sequence saturate at concentrations much below the therapeutic window for tobramycin (7–18 µM. Accordingly, the rationale behind modifying this high-gain sequence to reduce binding affinity was to tune sensor performance for optimal sensitivity in the therapeutic window. Using secondary structure predictions and analysis of the NMR structure of an aminoglycoside RNA aptamer bound to tobramycin, we are able to successfully modify the aptamer sequence to tune the dissociation constants of electrochemical aptamer-based sensors between 0.17 and 3 µM. The guidelines we present represent a general strategy to lessening binding affinity of sensors employing aptamer-modified electrodes.

  11. Rational Design of Porous Conjugated Polymers and Roles of Residual Palladium for Photocatalytic Hydrogen Production.

    Science.gov (United States)

    Li, Lianwei; Cai, Zhengxu; Wu, Qinghe; Lo, Wai-Yip; Zhang, Na; Chen, Lin X; Yu, Luping

    2016-06-22

    Developing highly efficient photocatalyts for water splitting is one of the grand challenges in solar energy conversion. Here, we report the rational design and synthesis of porous conjugated polymer (PCP) that photocatalytically generates hydrogen from water splitting. The design mimics natural photosynthetics systems with conjugated polymer component to harvest photons and the transition metal part to facilitate catalytic activities. A series of PCPs have been synthesized with different light harvesting chromophores and transition metal binding bipyridyl (bpy) sites. The photocatalytic activity of these bpy-containing PCPs can be greatly enhanced due to the improved light absorption, better wettability, local ordering structure, and the improved charge separation process. The PCP made of strong and fully conjugated donor chromophore DBD (M4) shows the highest hydrogen production rate at ∼33 μmol/h. The results indicate that copolymerization between a strong electron donor and weak electron acceptor into the same polymer chain is a useful strategy for developing efficient photocatalysts. This study also reveals that the residual palladium in the PCP networks plays a key role for the catalytic performance. The hydrogen generation activity of PCP photocatalyst can be further enhanced to 164 μmol/h with an apparent quantum yield of 1.8% at 350 nm by loading 2 wt % of extra platinum cocatalyst.

  12. Rational design and validation of a vanilloid-sensitive TRPV2 ion channel.

    Science.gov (United States)

    Yang, Fan; Vu, Simon; Yarov-Yarovoy, Vladimir; Zheng, Jie

    2016-06-28

    Vanilloids activation of TRPV1 represents an excellent model system of ligand-gated ion channels. Recent studies using cryo-electron microcopy (cryo-EM), computational analysis, and functional quantification revealed the location of capsaicin-binding site and critical residues mediating ligand-binding and channel activation. Based on these new findings, here we have successfully introduced high-affinity binding of capsaicin and resiniferatoxin to the vanilloid-insensitive TRPV2 channel, using a rationally designed minimal set of four point mutations (F467S-S498F-L505T-Q525E, termed TRPV2_Quad). We found that binding of resiniferatoxin activates TRPV2_Quad but the ligand-induced open state is relatively unstable, whereas binding of capsaicin to TRPV2_Quad antagonizes resiniferatoxin-induced activation likely through competition for the same binding sites. Using Rosetta-based molecular docking, we observed a common structural mechanism underlying vanilloids activation of TRPV1 and TRPV2_Quad, where the ligand serves as molecular "glue" that bridges the S4-S5 linker to the S1-S4 domain to open these channels. Our analysis revealed that capsaicin failed to activate TRPV2_Quad likely due to structural constraints preventing such bridge formation. These results not only validate our current working model for capsaicin activation of TRPV1 but also should help guide the design of drug candidate compounds for this important pain sensor.

  13. Structure-based rational design of streptavidin mutants with pseudo-catalytic activity.

    Science.gov (United States)

    Pazy, Yael; Raboy, Bilha; Matto, Meirav; Bayer, Edward A; Wilchek, Meir; Livnah, Oded

    2003-02-28

    Introduction of enzymatic activity into proteins or other types of polymers by rational design is a major objective in the life sciences. To date, relatively low levels of enzymatic activity could be introduced into antibodies by using transition-state analogues of haptens. In the present study, we identify the structural elements that contribute to the observed hydrolytic activity in egg white avidin, which promote the cleavage of active biotin esters (notably biotinyl p-nitrophenyl ester). The latter elements were then incorporated into bacterial streptavidin via genetic engineering. The streptavidin molecule was thus converted from a protector to an enhancer of hydrolysis of biotin esters. The conversion was accomplished by the combined replacement of a "lid-like loop" (L3,4) and a leucine-to-arginine point mutation in streptavidin. Interestingly, neither of these elements play a direct role in the hydrolytic reaction. The latter features were thus shown to be responsible for enhanced substrate hydrolysis. This work indicates that structural and non-catalytic elements of a protein can be modified to promote the induced fit of a substrate for subsequent interaction with either a catalytic residue or water molecules. This approach complements the conventional design of active sites that involves direct modifications of catalytic residues.

  14. Rational design of ornithine decarboxylase with high catalytic activity for the production of putrescine.

    Science.gov (United States)

    Choi, Hyang; Kyeong, Hyun-Ho; Choi, Jung Min; Kim, Hak-Sung

    2014-09-01

    Putrescine finds wide industrial applications in the synthesis of polymers, pharmaceuticals, agrochemicals, and surfactants. Owing to economic and environmental concerns, the microbial production of putrescine has attracted a great deal of attention, and ornithine decarboxylase (ODC) is known to be a key enzyme in the biosynthetic pathway. Herein, we present the design of ODC from Escherichia coli with high catalytic efficiency using a structure-based rational approach. Through a substrate docking into the model structure of the enzyme, we first selected residues that might lead to an increase in catalytic activity. Of the selected residues that are located in the α-helix and the loops constituting the substrate entry site, a mutational analysis of the single mutants identified two key residues, I163 and E165. A combination of two single mutations resulted in a 62.5-fold increase in the catalytic efficiency when compared with the wild-type enzyme. Molecular dynamics simulations of the best mutant revealed that the substrate entry site becomes more flexible through mutations, while stabilizing the formation of the dimeric interface of the enzyme. Our approach can be applied to the design of other decarboxylases with high catalytic efficiency for the production of various chemicals through bio-based processes.

  15. Rational design of aptazyme riboswitches for efficient control of gene expression in mammalian cells

    Science.gov (United States)

    Zhong, Guocai; Wang, Haimin; Bailey, Charles C; Gao, Guangping; Farzan, Michael

    2016-01-01

    Efforts to control mammalian gene expression with ligand-responsive riboswitches have been hindered by lack of a general method for generating efficient switches in mammalian systems. Here we describe a rational-design approach that enables rapid development of efficient cis-acting aptazyme riboswitches. We identified communication-module characteristics associated with aptazyme functionality through analysis of a 32-aptazyme test panel. We then developed a scoring system that predicts an aptazymes’s activity by integrating three characteristics of communication-module bases: hydrogen bonding, base stacking, and distance to the enzymatic core. We validated the power and generality of this approach by designing aptazymes responsive to three distinct ligands, each with markedly wider dynamic ranges than any previously reported. These aptayzmes efficiently regulated adeno-associated virus (AAV)-vectored transgene expression in cultured mammalian cells and mice, highlighting one application of these broadly usable regulatory switches. Our approach enables efficient, protein-independent control of gene expression by a range of small molecules. DOI: http://dx.doi.org/10.7554/eLife.18858.001 PMID:27805569

  16. Towards a rational design of solid drug nanoparticles with optimised pharmacological properties

    Science.gov (United States)

    Martin, Phillip; Smith, Darren; Curley, Paul; McDonald, Tom; Giardiello, Marco; Liptrott, Neill; Rannard, Steve; Owen, Andrew

    2016-01-01

    Abstract Solid drug nanoparticles (SDNs) are a nanotechnology with favourable characteristics to enhance drug delivery and improve the treatment of several diseases, showing benefit for improved oral bioavailability and injectable long‐acting medicines. The physicochemical properties and composition of nanoformulations can influence the absorption, distribution, and elimination of nanoparticles; consequently, the development of nanoparticles for drug delivery should consider the potential role of nanoparticle characteristics in the definition of pharmacokinetics. The aim of this study was to investigate the pharmacological behaviour of efavirenz SDNs and the identification of optimal nanoparticle properties and composition. Seventy‐seven efavirenz SDNs were included in the analysis. Cellular accumulation was evaluated in HepG2 (hepatic) and Caco‐2 (intestinal), CEM (lymphocyte), THP1 (monocyte), and A‐THP1 (macrophage) cell lines. Apparent intestinal permeability (Papp) was measured using a monolayer of Caco‐2 cells. The Papp values were used to evaluate the potential benefit on pharmacokinetics using a physiologically based pharmacokinetic model. The generated SDNs had an enhanced intestinal permeability and accumulation in different cell lines compared to the traditional formulation of efavirenz. Nanoparticle size and excipient choice influenced efavirenz apparent permeability and cellular accumulation, and this appeared to be cell line dependent. These findings represent a valuable platform for the design of SDNs, giving an empirical background for the selection of optimal nanoparticle characteristics and composition. Understanding how nanoparticle components and physicochemical properties influence pharmacological patterns will enable the rational design of SDNs with desirable pharmacokinetics. PMID:27774308

  17. Glycolipid-based TLR4 Modulators and Fluorescent Probes: Rational Design, Synthesis, and Biological Properties.

    Science.gov (United States)

    Ciaramelli, Carlotta; Calabrese, Valentina; Sestito, Stefania E; Pérez-Regidor, Lucia; Klett, Javier; Oblak, Alja; Jerala, Roman; Piazza, Matteo; Martín-Santamaría, Sonsoles; Peri, Francesco

    2016-08-01

    The cationic glycolipid IAXO-102, a potent TLR4 antagonist targeting both MD-2 and CD14 co-receptors, has been used as scaffold to design new potential TLR4 modulators and fluorescent labels for the TLR4 receptor complex (membrane TLR4.MD-2 dimer and CD14). The primary amino group of IAXO-102, not involved in direct interaction with MD-2 and CD14 receptors, has been exploited to covalently attach a fluorescein (molecules 1 and 2) or to link two molecules of IAXO-102 through diamine and diammonium spacers, obtaining 'dimeric' molecules 3 and 4. The structure-based rational design of compounds 1-4 was guided by the optimization of MD-2 and CD14 binding. Compounds 1 and 2 inhibited TLR4 activation, in a concentration-dependent manner, and signaling in HEK-Blue TLR4 cells. The fluorescent labeling of murine macrophages by molecule 1 was inhibited by LPS and was also abrogated when cell surface proteins were digested by trypsin, thus suggesting an interaction of fluorescent probe 1 with membrane proteins of the TLR4 receptor system.

  18. Rational Design of Biomolecular Templates for Synthesizing Multifunctional Noble Metal Nanoclusters toward Personalized Theranostic Applications.

    Science.gov (United States)

    Yu, Yong; Mok, Beverly Y L; Loh, Xian Jun; Tan, Yen Nee

    2016-08-01

    Biomolecule-templated or biotemplated metal nanoclusters (NCs) are ultrasmall (<2 nm) metal (Au, Ag) particles stabilized by a certain type of biomolecular template (e.g., peptides, proteins, and DNA). Due to their unique physiochemical properties, biotemplated metal NCs have been widely used in sensing, imaging, delivery and therapy. The overwhelming applications in these individual areas imply the great promise of harnessing biotemplated metal NCs in more advanced biomedical aspects such as theranostics. Although applications of biotemplated metal NCs as theranostic agents are trending, the rational design of biomolecular templates suitable for the synthesis of multifunctional metal NCs for theranostics is comparatively underexplored. This progress report first identifies the essential attributes of biotemplated metal NCs for theranostics by reviewing the state-of-art applications in each of the four modalities of theranostics, namely sensing, imaging, delivery and therapy. To achieve high efficacy in these modalities, we elucidate the design principles underlying the use of biomolecules (proteins, peptides and nucleic acids) to control the NC size, emission color and surface chemistries for post-functionalization of therapeutic moieties. We then propose a unified strategy to engineer biomolecular templates that combine all these modalities to produce multifunctional biotemplated metal NCs that can serve as the next-generation personalized theranostic agents.

  19. Tuning Cellular Uptake of Molecular Probes by Rational Design of Their Assembly into Supramolecular Nanoprobes.

    Science.gov (United States)

    Lock, Lye Lin; Reyes, Claudia D; Zhang, Pengcheng; Cui, Honggang

    2016-03-16

    Intracellular sensing of pathologically relevant biomolecules could provide essential information for accurate evaluation of disease staging and progression, yet the poor cellular uptake of water-soluble molecular probes limits their use as protease sensors. In other cases such as extracellular sensing, cellular uptake should be effectively inhibited. Self-assembly of molecular probes into supramolecular nanoprobes presents a potential strategy to alter their interaction mechanisms with cells to promote or reduce their cellular uptake. Here, we report on the design, synthesis, and assembly of peptide-based molecular beacons into supramolecular protease sensors of either spherical or filamentous shapes. We found that positively charged spherical nanobeacons demonstrate much higher cellular uptake efficiency than its monomeric form, thus making them most suitable for intracellular sensing of the lysosomal protease cathepsin B. Our results also suggest that assembly into filamentous nanobeacons significantly reduces their internalization by cancer cells, an important property that can be utilized for probing extracellular protease activities. These studies provide important guiding principles for rational design of supramolecular nanoprobes with tunable cellular uptake characteristics.

  20. An approach to rational ligand-design based on a thermodynamic analysis.

    Science.gov (United States)

    Ui, Mihoko; Tsumoto, Kouhei

    2010-11-01

    Thermodynamic analysis is an effective tool in screening of lead-compounds for development of potential drug candidates. In most cases, a ligand achieve high affinity and specificity to a target protein by means of both favorable enthalpy and entropy terms, which can be reflected in binding profiles of Isothermal Titration Calorimetry (ITC). A favorable enthalpy change suggests the contribution of noncovalent contacts such as hydrogen bonding and van der Waals interaction between a ligand and its target protein. In general, optimization of binding enthalpy is more difficult than that of entropies in ligand-design; therefore, it is desirable to choose firstly a lead-compound based on its binding enthalpic gain. In this paper, we demonstrate the utility of thermodynamic approach to ligand screening using anti-ciguatoxin antibody 10C9 as a model of a target protein which possesses a large hydrophobic pocket. As a result of this screening, we have identified three compounds that could bind to the antigen-binding pocket of 10C9 with a few kcal/mol of favorable binding enthalpy. Comparison of their structure with the proper antigen ciguatoxin CTX3C revealed that 10C9 rigorously identifies their cyclic structure and a characteristic hydroxyl group. ITC measurement might be useful and powerful for a rational ligand screening and the optimization of the ligand; the enthalpic gain is an effective index for ligand-design studies.

  1. Rational design equations for the Aeolian vibration of overhead power lines

    Energy Technology Data Exchange (ETDEWEB)

    Lu, M.L.; Chopra, N. [BC Hydro, Burnaby, BC (Canada)

    2008-07-01

    Aeolian vibration must be considered when designing overhead power transmission lines because of its potential risk of causing fatigue failure to the conductor, hardware, and tower members. Aeolian vibration is caused by the alternate shedding of Karman vortices from the top and bottom of the line's conductor when the conductor is exposed to a side wind. This paper presented a novel approach to analytically predict the vortex-induced vibration (i.e. Aeolian vibration) of an overhead power line's single conductor due to wind. The paper described the derivation of an analytical solution to the basic problem of the Aeolian vibration of a conductor span with equivalent supports on both ends by using the energy balance principle as well as the semi-empirical equations for the wind power input and the self damping of a conductor. The paper noted that a wind's turbulence effect may also be taken into account by using a previously found analytical solution. Simple, pragmatic design equations were established for undamped conductor spans by curve-fitting the numerical data from analytical solutions. It was concluded that the complicated problem of Aeolian vibration of a single conductor without damper or with multiple dampers could be easily solved by using the analytical solutions developed in this paper and that simple, yet rational design equations have been established for the Aeolian vibration of undamped conductor spans to bridge the gap between the apparently complicated theory and the often overly simplified actual design practice. 13 refs., 1 tab., 4 figs.

  2. Rational Design of Small Molecules Targeting Oncogenic Noncoding RNAs from Sequence.

    Science.gov (United States)

    Disney, Matthew D; Angelbello, Alicia J

    2016-12-20

    The discovery of RNA catalysis in the 1980s and the dissemination of the human genome sequence at the start of this century inspired investigations of the regulatory roles of noncoding RNAs in biology. In fact, the Encyclopedia of DNA Elements (ENCODE) project has shown that only 1-2% of the human genome encodes protein, yet 75% is transcribed into RNA. Functional studies both preceding and following the ENCODE project have shown that these noncoding RNAs have important roles in regulating gene expression, developmental timing, and other critical functions. RNA's diverse roles are often a consequence of the various folds that it adopts. The single-stranded nature of the biopolymer enables it to adopt intramolecular folds with noncanonical pairings to lower its free energy. These folds can be scaffolds to bind proteins or to form frameworks to interact with other RNAs. Not surprisingly, dysregulation of certain noncoding RNAs has been shown to be causative of disease. Given this as the background, it is easy to see why it would be useful to develop methods that target RNA and manipulate its biology in rational and predictable ways. The antisense approach has afforded strategies to target RNAs via Watson-Crick base pairing and has typically focused on targeting partially unstructured regions of RNA. Small molecule strategies to target RNA would be desirable not only because compounds could be lead optimized via medicinal chemistry but also because structured regions within an RNA of interest could be targeted to directly interfere with RNA folds that contribute to disease. Additionally, small molecules have historically been the most successful drug candidates. Until recently, the ability to design small molecules that target non-ribosomal RNAs has been elusive, creating the perception that they are "undruggable". In this Account, approaches to demystify targeting RNA with small molecules are described. Rather than bulk screening for compounds that bind to singular

  3. Rationally designed fluorescence turn-on sensors: a new design strategy based on orbital control.

    Science.gov (United States)

    Jung, Hyo Sung; Ko, Kyoung Chul; Lee, Jae Hong; Kim, Sang Hoon; Bhuniya, Sankarprasad; Lee, Jin Yong; Kim, Youngmee; Kim, Sung Jin; Kim, Jong Seung

    2010-09-20

    Herein, we explore a new strategy in the chemo-sensor field for fluorescence amplification upon binding with metal ions based on controlled participation of the nitrogen lone pair orbital. The basic architecture of the sensor entails a fluorophore, the sp(2) hybridized nitrogen lone pair (-C═N-), and a chelator site referred to as the control part. Though nonplanar and nonfluorescent, compound IC1 achieved pseudo planarity from binding with Zn(2+) as indicated by the increased fluorescence signal. Its other analogue (IC2) is also planar, and unlike IC1-Zn(2+) was fluorescent with a lack of binding affinity to metal ions. The time-dependent density functional theory (TDDFT) calculations revealed that the fluorescence amplification was due to the blocking of the nitrogen lone pair orbital; unlikely geometrical rearrangements were insignificant. This could indicate a breakthrough concept in the future design of fluorescent turn-on sensors.

  4. Rationally designed donor-acceptor scheme based molecules for applications in opto-electronic devices.

    Science.gov (United States)

    Subash Sundar, T; Sen, R; Johari, P

    2016-04-07

    Several donor (D)-acceptor (A) based molecules are rationally designed by adopting three different schemes in which the conjugation length, strength of the donor and acceptor moieties, and planarity of the molecules are varied. These variations are made by introducing a π-conjugated linkage unit, terminating the ends of the moieties by different electron donating and accepting functional groups, and fusing the donor and acceptor moieties, respectively. Our DFT and TDDFT based calculations reveal that using the above-mentioned design schemes, the electronic and optical properties of the D-A based molecules can be largely tuned. While introduction of a linkage and fusing of moieties enhance the π-π interaction, addition of electron donating groups (-CH3, -OH, and -NH2) and electron accepting groups (-CF3, -CN, -NO2, and -NH3(+)) varies the strength of the donor and acceptor moieties. These factors lead to modulation of the HOMO and LUMO energy levels and facilitate the engineering of the HOMO-LUMO gap and the optical gap over a wide range of ∼0.7-3.7 eV. Moreover, on the basis of calculated ionization potential and reorganization energy, most of the investigated molecules are predicted to be air stable and to exhibit high electron mobility, with the possibility of the presence of ambipolar characteristics in a few of them. The results of our calculations not only demonstrate the examined molecules to be the potential materials for organic opto-electronic devices, but also establish an understanding of the composition-structure-property correlation, which will provide guidelines for designing and synthesizing new materials of choice.

  5. Rational design of a structure-switching DNA aptamer for potassium ions

    Directory of Open Access Journals (Sweden)

    Andrew T. Catherine

    2014-01-01

    Full Text Available Structure-switching molecules provide a unique means for analyte detection, generating a response to analyte concentration through a binding-specific conformational change between non-binding and binding-competent states. While most ligand-binding molecules are not structure switching by default, many can be engineered to be so through the introduction of an alternative non-binding (and thus non-signalling conformation. This population-shift mechanism is particularly effective with oligonucleotides and has led to the creation of structure-switching aptamers for many target ligands. Here, we report the rational design of structure-switching DNA aptamers, based on the thrombin binding aptamer (TBA, that bind potassium with affinities that bridge the gap between previously reported weak-binding and strong-binding aptamers. We also demonstrate a correlation between the free energy of the experimentally determined binding affinity for potassium and the computationally estimated free energy of the alternative (non-binding structure.

  6. Biomimetics: From Bioinformatics to Rational Design of Dendrimers as Gene Carriers

    Science.gov (United States)

    Araya-Durán, Ingrid; Varas-Concha, Ignacio; Almonacid, Daniel Eduardo; González-Nilo, Fernando Danilo

    2015-01-01

    Biomimetics, or the use of principles of Nature for developing new materials, is a paradigm that could help Nanomedicine tremendously. One of the current challenges in Nanomedicine is the rational design of new efficient and safer gene carriers. Poly(amidoamine) (PAMAM) dendrimers are a well-known class of nanoparticles, extensively used as non-viral nucleic acid carriers, due to their positively charged end-groups. Yet, there are still several aspects that can be improved for their successful application in in vitro and in vivo systems, including their affinity for nucleic acids as well as lowering their cytotoxicity. In the search of new functional groups that could be used as new dendrimer-reactive groups, we followed a biomimetic approach to determine the amino acids with highest prevalence in protein-DNA interactions. Then we introduced them individually as terminal groups of dendrimers, generating a new class of nanoparticles. Molecular dynamics studies of two systems: PAMAM-Arg and PAMAM-Lys were also performed in order to describe the formation of complexes with DNA. Results confirmed that the introduction of amino acids as terminal groups in a dendrimer increases their affinity for DNA and the interactions in the complexes were characterized at atomic level. We end up by briefly discussing additional modifications that can be made to PAMAM dendrimers to turned them into promising new gene carriers. PMID:26382062

  7. Biomimetics: From Bioinformatics to Rational Design of Dendrimers as Gene Carriers.

    Directory of Open Access Journals (Sweden)

    Valeria Márquez-Miranda

    Full Text Available Biomimetics, or the use of principles of Nature for developing new materials, is a paradigm that could help Nanomedicine tremendously. One of the current challenges in Nanomedicine is the rational design of new efficient and safer gene carriers. Poly(amidoamine (PAMAM dendrimers are a well-known class of nanoparticles, extensively used as non-viral nucleic acid carriers, due to their positively charged end-groups. Yet, there are still several aspects that can be improved for their successful application in in vitro and in vivo systems, including their affinity for nucleic acids as well as lowering their cytotoxicity. In the search of new functional groups that could be used as new dendrimer-reactive groups, we followed a biomimetic approach to determine the amino acids with highest prevalence in protein-DNA interactions. Then we introduced them individually as terminal groups of dendrimers, generating a new class of nanoparticles. Molecular dynamics studies of two systems: PAMAM-Arg and PAMAM-Lys were also performed in order to describe the formation of complexes with DNA. Results confirmed that the introduction of amino acids as terminal groups in a dendrimer increases their affinity for DNA and the interactions in the complexes were characterized at atomic level. We end up by briefly discussing additional modifications that can be made to PAMAM dendrimers to turned them into promising new gene carriers.

  8. Rational Design of Cathode Structure for High Rate Performance Lithium-Sulfur Batteries.

    Science.gov (United States)

    Chen, Hongwei; Wang, Changhong; Dai, Yafei; Qiu, Shengqiang; Yang, Jinlong; Lu, Wei; Chen, Liwei

    2015-08-12

    Practical applications of Li-S batteries require not only high specific capacities and long cycle lifetimes but also high rate performance. We report a rationally designed Li-S cathode, which consists of a freestanding composite thin film assembled from S nanoparticles, reduced graphene oxide (rGO), and a multifunctional additive poly(anthraquinonyl sulfide) (PAQS). The S nanoparticles provide a high initial specific capacity, and the layered and porous rGO structure provides electron and ion transport paths and restricts polysulfide shuttling. PAQS is not only a highly efficient sulfide trapping agent but also an excellent Li(+) conductor, which benefits the battery reaction kinetics at a high rate. The resulting cathode exhibits an initial specific capacity of 1255 mAh g(-1) with a decay rate as low as 0.046% per cycles over 1200 cycles. Importantly, it displays a reversible capacity of 615 mAh g(-1) when discharged at a high rate of 8 C (13.744 A g(-1)).

  9. Rational Design of Thermally Stable Novel Biocatalytic Nanomaterials: Enzyme Stability in Restricted Spatial Dimensions

    Science.gov (United States)

    Mudhivarthi, Vamsi K.

    Enzyme stability is of intense interest in bio-materials science as biocatalysts, and as sensing platforms. This is essentially because the unique properties of DNA, RNA, PAA can be coupled with the interesting and novel properties of proteins to produce systems with unprecedented control over their properties. In this article, the very first examples of enzyme/NA/inorganic hybrid nanomaterials and enzyme-Polyacrylic acid conjugates will be presented. The basic principles of design, synthesis and control of properties of these hybrid materials will be presented first, and this will be followed by a discussion of selected examples from our recent research findings. Data show that key properties of biological catalysts are improved by the inorganic framework especially when the catalyst is co-embedded with DNA. Several examples of such studies with various enzymes and proteins, including horseradish peroxidase (HRP), glucose oxidase (GO), cytochrome c (Cyt c), met-hemoglobin (Hb) and met-myoglobin (Mb) will be discussed. Additionally, key insights obtained by the standard methods of materials science including XRD, SEM and TEM as well as biochemical, calorimetric and spectroscopic methods will be discussed. Furthermore, improved structure and enhanced activities of the biocatalysts in specific cases will be demonstrated along with the potential stabilization mechanisms. Our hypothesis is that nucleic acids provide an excellent control over the enzyme-solid interactions as well as rational assembly of nanomaterials. These novel nanobiohybrid materials may aid in engineering more effective synthetic materials for gene-delivery, RNA-delivery and drug delivery applications.

  10. Engineering of genetic control tools in Synechocystis sp. PCC 6803 using rational design techniques.

    Science.gov (United States)

    Albers, Stevan C; Gallegos, Victor A; Peebles, Christie A M

    2015-12-20

    Cyanobacteria show promise as photosynthetic microbial factories capable of harnessing sunlight and CO2 to produce valuable end products, but few genetic control tools have been characterized and utilized in these organisms. To develop a suite of control elements capable of gene control at a variety of expression strengths, a library of 10 promoter-constructs were developed and built via rational design techniques by adding individual nucleotides in a step-wise manner within the -10 and -35 cis-acting regions of the tac promoter. This suite produced a dynamic range of expression strength, exhibiting a 78 fold change between the lowest expressing promoter, Psca8- and the highest expressing promoter, Psca3-2 when tested within Synechocystis sp. PCC 6803. Additionally, this study details the construction of a chemically inducible construct for use in Synechocystis that is based on the tac repressor system most commonly used in Escherichia coli. This research demonstrates the construction of a highly expressed inducible promoter that is also capable of high levels of gene repression. Upon chemical induction with IPTG, this same mutant strain was capable of exhibiting an average 24X increase in GFP expression over that of the repressed state.

  11. Rational design of CPP-based drug delivery systems: considerations from pharmacokinetics.

    Science.gov (United States)

    Mickan, Arite; Sarko, Dikran; Haberkorn, Uwe; Mier, Walter

    2014-01-01

    Therapeutics are restricted from cellular internalization due to the biological barrier formed by the cell membrane. Especially for therapeutics with high molecular weight, strategies are required to enable delivery to intracellular targets. Cell-penetrating peptides (CPPs) represent a powerful tool to mediate the entry of large cargos such as proteins, siRNA and nanoparticles. The high diversity of CPPs is the prerequisite to use this class of carriers for various applications. However, therapies based on CPPs are hampered by their unfavorable pharmacokinetics, mainly dominated by their rapid renal clearance and their lack of specificity. Rational design is required to overcome these disadvantages and thereby exploits the actual potential of CPPs. We summarize and highlight the current state of knowledge with special emphasis on pharmacokinetics. The unclear internalization pathways of CPPs remain one of the main obstacles and therefore have been in the focus of research. In this review, several promising strategies such as the combination with targeting sequences, activatable CPPs and adjustment of the molecular weight are described. In addition, new absorption pathways such as nasal, pulmonary or transdermal uptake expand the applicability of CPPs and may be a promising prospect for clinical application.

  12. Surface Termination of M1 Phase and Rational Design of Propane Ammoxidation Catalysts

    Energy Technology Data Exchange (ETDEWEB)

    Guliants, Vadim

    2015-02-16

    This final report describes major accomplishments in this research project which has demonstrated that the M1 phase is the only crystalline phase required for propane ammoxidation to acrylonitrile and that a surface monolayer terminating the ab planes of the M1 phase is responsible for their activity and selectivity in this reaction. Fundamental studies of the topmost surface chemistry and mechanism of propane ammoxidation over the Mo-V-(Te,Sb)-(Nb,Ta)-O M1 and M2 phases resulted in the development of quantitative understanding of the surface molecular structure – reactivity relationships for this unique catalytic system. These oxides possess unique catalytic properties among mixed metal oxides, because they selectively catalyze three alkane transformation reactions, namely propane ammoxidation to acrylonitrile, propane oxidation to acrylic acid and ethane oxidative dehydrogenation, all of considerable economic significance. Therefore, the larger goal of this research was to expand this catalysis to other alkanes of commercial interest, and more broadly, demonstrate successful approaches to rational design of improved catalysts that can be applied to other selective (amm)oxidation processes.

  13. Tools for the rational design of bivalent microtubule-targeting drugs.

    Science.gov (United States)

    Marangon, Jacopo; Christodoulou, Michael S; Casagrande, Fancesca V M; Tiana, Guido; Dalla Via, Lisa; Aliverti, Alessandro; Passarella, Daniele; Cappelletti, Graziella; Ricagno, Stefano

    2016-10-01

    Microtubule (MT) dynamic behaviour is an attractive drug target for chemotherapy, whose regulation by MT-stabilizing and destabilizing agents has been fruitfully applied in treating several types of cancers. MT-stabilizing agents are also emerging as potential remedies for neurodegenerative conditions, such as Alzheimer's and Parkinson's disease, although single-target drugs are not expected to fully cure these complex pathologies. Drug combination often displays enhanced efficacy with respect to mono-therapies. In particular, MT-targeting bivalent compounds (MTBCs) represent a promising class of molecules; however, surprisingly, the majority of MTBCs reported so far exhibit equal if not less efficacy than their building monomers. In order to shed light on MTBCs poor performance, we characterised through a set of complementary approaches thiocolchine (TH) and two bivalent TH-homodimers as prototype molecules. First, the binding affinities of these three molecules were assessed, then we obtained the crystallographic structure of a tubulin-TH complex. The binding affinities were interpreted in light of structural data and of molecular dynamics simulations. Finally, their effects on MT cytoskeleton and cell survival were validated on HeLa cells. The ensemble of these data provides chemical and structural considerations on how a successful rational design of MTBCs should be conceived.

  14. Rational design of novel cathode materials in solid oxide fuel cells using first-principles simulations

    Energy Technology Data Exchange (ETDEWEB)

    Choi, YongMan; Liu, Meilin [Center for Innovative Fuel Cell and Battery Technologies, School of Materials Science and Engineering, Georgia Institute of Technology, 771 Ferst Drive, N.W., Atlanta, GA 30332 (United States); Lin, M.C. [Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322 (United States); Center for Interdisciplinary Molecular Science, National Chiao Tung University, Hsinchu 30010 (China)

    2010-03-01

    The search for clean and renewable sources of energy represents one of the most vital challenges facing us today. Solid oxide fuel cells (SOFCs) are among the most promising technologies for a clean and secure energy future due to their high energy efficiency and excellent fuel flexibility (e.g., direct utilization of hydrocarbons or renewable fuels). To make SOFCs economically competitive, however, development of new materials for low-temperature operation is essential. Here we report our results on a computational study to achieve rational design of SOFC cathodes with fast oxygen reduction kinetics and rapid ionic transport. Results suggest that surface catalytic properties are strongly correlated with the bulk transport properties in several material systems with the formula of La{sub 0.5}Sr{sub 0.5}BO{sub 2.75} (where B = Cr, Mn, Fe, or Co). The predictions seem to agree qualitatively with available experimental results on these materials. This computational screening technique may guide us to search for high-efficiency cathode materials for a new generation of SOFCs. (author)

  15. Recovery of red fluorescent protein chromophore maturation deficiency through rational design.

    Directory of Open Access Journals (Sweden)

    Matthew M Moore

    Full Text Available Red fluorescent proteins (RFPs derived from organisms in the class Anthozoa have found widespread application as imaging tools in biological research. For most imaging experiments, RFPs that mature quickly to the red chromophore and produce little or no green chromophore are most useful. In this study, we used rational design to convert a yellow fluorescent mPlum mutant to a red-emitting RFP without reverting any of the mutations causing the maturation deficiency and without altering the red chromophore's covalent structure. We also created an optimized mPlum mutant (mPlum-E16P that matures almost exclusively to the red chromophore. Analysis of the structure/function relationships in these proteins revealed two structural characteristics that are important for efficient red chromophore maturation in DsRed-derived RFPs. The first is the presence of a lysine residue at position 70 that is able to interact directly with the chromophore. The second is an absence of non-bonding interactions limiting the conformational flexibility at the peptide backbone that is oxidized during red chromophore formation. Satisfying or improving these structural features in other maturation-deficient RFPs may result in RFPs with faster and more complete maturation to the red chromophore.

  16. Tuning calcite morphology and growth acceleration by a rational design of highly stable protein-mimetics

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Chunlong; Qi, Jiahui; Tao, Jinhui; Zuckermann, Ronald; De Yoreo, James J.

    2014-09-05

    In nature, proteins play a significant role in biomineral formation. One of the ultimate goals of bioinspired materials science is to develop highly stable synthetic molecules that mimic the function of these natural proteins by controlling crystal formation. Here, we demonstrate that both the morphology and the degree of acceleration or inhibition observed during growth of calcite in the presence of peptoids can be rationally tuned by balancing the electrostatic interactions (EI) and hydrophobic interactions (HI), with HI playing the dominant role. While either strong EI or HI inhibit growth and suppress (104) face expression, correlations between peptoid-crystal binding energies and observed changes in calcite growth indicate moderate EI allow peptoids to weakly adsorb while moderate HI cause disruption of surface-adsorbed water layers, leading to growth acceleration with retained expression of (104) faces. This study provides fundamental principles for designing peptoids as crystallization promoters, and offers a straightforward screening method based on macroscopic crystal morphology. Because peptoids are sequence-specific, highly stable, and easily synthesized, peptoid-enhanced crystallization offers a broad range of potential applications.

  17. Staphylococcus aureus in continuous culture: a tool for the rational design of antibiotic treatment protocols.

    Directory of Open Access Journals (Sweden)

    Klas I Udekwu

    Full Text Available In vitro measures of the pharmacodynamics of antibiotics that account for the factors anticipated for bacteria in infected patients are central to the rational design of antibiotic treatment protocols. We consider whether or not continuous culture devices are a way to obtain these measures. Staphylococcus aureus PS80 in high-density continuous cultures were exposed to oxacillin, ciprofloxacin, vancomycin, gentamicin, daptomycin and linezolid. Contrary to results from low density retentostats as well as to predictions of traditional PK/MIC ratios, daily dosing with up to 100× MIC did not clear these cultures. The densities of S. aureus in these cultures oscillated with constant amplitude and never fell below 10(5 CFU per ml. Save for daptomycin "treated" populations, the densities of bacteria in these cultures remained significantly below that of similar antibiotic-free cultures. Although these antibiotics varied in their pharmacodynamic properties there were only modest differences in their mean densities. Mathematical models and experiments suggest that the dominant factor preventing clearance was wall-adhering subpopulations reseeding the planktonic population which can be estimated and corrected for. Continuous cultures provide a way to evaluate the potential efficacy of antibiotic treatment regimes in vitro under conditions that are more clinically realistic and comprehensive than traditional in vitro PK/PD indices.

  18. Rational Design of Transcranial Current Stimulation (TCS through Mechanistic Insights into Cortical Network Dynamics

    Directory of Open Access Journals (Sweden)

    Flavio eFrohlich

    2013-11-01

    Full Text Available Transcranial current stimulation (TCS is a promising method of non-invasive brain stimulation to modulate cortical network dynamics. Preliminary studies have demonstrated the ability of TCS to enhance cognition and reduce symptoms in both neurological and psychiatric illnesses. Despite the encouraging results of these studies, the mechanisms by which TCS and endogenous network dynamics interact remain poorly understood. Here, we propose that the development of the next generation of TCS paradigms with increased efficacy requires such mechanistic understanding of how weak electric fields imposed by TCS interact with the nonlinear dynamics of large-scale cortical networks. We highlight key recent advances in the study of the interaction dynamics between TCS and cortical network activity. In particular, we demonstrate the opportunities provided by an interdisciplinary approach that bridges neurobiology and electrical engineering. We discuss the use of (1 hybrid biological-electronic experimental approaches to disentangle feedback interactions, (2 large-scale computer simulations for the study of weak global perturbations imposed by TCS, and (3 optogenetic manipulations informed by dynamics systems theory to probe network dynamics. Together, we here provide the foundation for the use of rational design for the development of the next generation of TCS neurotherapeutics.

  19. Rational design and controlled synthesis of Te/Bi2Te3 heterostructure nanostring composites

    Science.gov (United States)

    Zhang, Yuzhuo; Chen, Hong; Li, Zhiliang; Huang, Ting; Zheng, Shuqi

    2015-07-01

    Te/Bi2Te3 heterostructure nanostring composites composed of several Bi2Te3 nanoplates, which were perpendicularly strung together by Te nanorod, were rationally designed and synthesized via a facile solvothermal method on a large scale. The X-ray diffraction (XRD) characterization demonstrated that the Bi2Te3 nanoplates were rhombohedral phase and the Te nanorods were trigonal phase. The uniform nanostring morphologies were well characterized by scanning electron microscope (SEM) and transmission electron microscope (TEM). Detailed heterostructures were proved via energy dispersive spectrometer (EDS) and high-resolution transmission electron microscope (HRTEM). The morphology transformation from Bi2Te3 nanoplates to Te/Bi2Te3 heterostructure nanostrings could be controlled by adjusting the ratio of bismuth oxide to tellurium oxide. NaOH, serving as catalytic reduction agent and morphology controlling agent, played an important role in the synthesis of Te/Bi2Te3 heterostructure nanostrings. The reaction mechanism was also proposed to explain the formation process of the composites and the specific function of reagents in this reaction system.

  20. Tuning calcite morphology and growth acceleration by a rational design of highly stable protein-mimetics

    Science.gov (United States)

    Chen, Chun-Long; Qi, Jiahui; Tao, Jinhui; Zuckermann, Ronald N.; Deyoreo, James J.

    2014-09-01

    In nature, proteins play a significant role in biomineral formation. One of the ultimate goals of bioinspired materials science is to develop highly stable synthetic molecules that mimic the function of these natural proteins by controlling crystal formation. Here, we demonstrate that both the morphology and the degree of acceleration or inhibition observed during growth of calcite in the presence of peptoids can be rationally tuned by balancing the electrostatic and hydrophobic interactions, with hydrophobic interactions playing the dominant role. While either strong electrostatic or hydrophobic interactions inhibit growth and reduces expression of the {104} faces, correlations between peptoid-crystal binding energies and observed changes in calcite growth indicate moderate electrostatic interactions allow peptoids to weakly adsorb while moderate hydrophobic interactions cause disruption of surface-adsorbed water layers, leading to growth acceleration with retained expression of the {104} faces. This study provides fundamental principles for designing peptoids as crystallization promoters, and offers a straightforward screening method based on macroscopic crystal morphology. Because peptoids are sequence-specific, highly stable, and easily synthesized, peptoid-enhanced crystallization offers a broad range of potential applications.

  1. Development of bright fluorescent quadracyclic adenine analogues: TDDFT-calculation supported rational design

    Science.gov (United States)

    Foller Larsen, Anders; Dumat, Blaise; Wranne, Moa S.; Lawson, Christopher P.; Preus, Søren; Bood, Mattias; Gradén, Henrik; Marcus Wilhelmsson, L.; Grøtli, Morten

    2015-07-01

    Fluorescent base analogues (FBAs) comprise a family of increasingly important molecules for the investigation of nucleic acid structure and dynamics. We recently reported the quantum chemical calculation supported development of four microenvironment sensitive analogues of the quadracyclic adenine (qA) scaffold, the qANs, with highly promising absorptive and fluorescence properties that were very well predicted by TDDFT calculations. Herein, we report on the efficient synthesis, experimental and theoretical characterization of nine novel quadracyclic adenine derivatives. The brightest derivative, 2-CNqA, displays a 13-fold increased brightness (ɛΦF = 4500) compared with the parent compound qA and has the additional benefit of being a virtually microenvironment-insensitive fluorophore, making it a suitable candidate for nucleic acid incorporation and use in quantitative FRET and anisotropy experiments. TDDFT calculations, conducted on the nine novel qAs a posteriori, successfully describe the relative fluorescence quantum yield and brightness of all qA derivatives. This observation suggests that the TDDFT-based rational design strategy may be employed for the development of bright fluorophores built up from a common scaffold to reduce the otherwise costly and time-consuming screening process usually required to obtain useful and bright FBAs.

  2. SMET: systematic multiple enzyme targeting - a method to rationally design optimal strains for target chemical overproduction.

    Science.gov (United States)

    Flowers, David; Thompson, R Adam; Birdwell, Douglas; Wang, Tsewei; Trinh, Cong T

    2013-05-01

    Identifying multiple enzyme targets for metabolic engineering is very critical for redirecting cellular metabolism to achieve desirable phenotypes, e.g., overproduction of a target chemical. The challenge is to determine which enzymes and how much of these enzymes should be manipulated by adding, deleting, under-, and/or over-expressing associated genes. In this study, we report the development of a systematic multiple enzyme targeting method (SMET), to rationally design optimal strains for target chemical overproduction. The SMET method combines both elementary mode analysis and ensemble metabolic modeling to derive SMET metrics including l-values and c-values that can identify rate-limiting reaction steps and suggest which enzymes and how much of these enzymes to manipulate to enhance product yields, titers, and productivities. We illustrated, tested, and validated the SMET method by analyzing two networks, a simple network for concept demonstration and an Escherichia coli metabolic network for aromatic amino acid overproduction. The SMET method could systematically predict simultaneous multiple enzyme targets and their optimized expression levels, consistent with experimental data from the literature, without performing an iterative sequence of single-enzyme perturbation. The SMET method was much more efficient and effective than single-enzyme perturbation in terms of computation time and finding improved solutions.

  3. Atomic force microscopy as a nanoscience tool in rational food design.

    Science.gov (United States)

    Morris, Victor J; Woodward, Nicola C; Gunning, Allan P

    2011-09-01

    Atomic force microscopy (AFM) is a nanoscience tool that has been used to provide new information on the molecular structure of food materials. As an imaging tool it has led to solutions to previously intractable problems in food science. This type of information can provide a basis for tailoring food structures to optimise functional behaviour. Such an approach will be illustrated by indicating how a basic understanding of the role of interfacial stability in complex foods systems can be extended to understand how such interfacial structures behave on digestion, and how this in turn suggests routes for the rational design of processed food structures to modify lipolysis and control fat intake. As a force transducer AFM can be used to probe interactions between food structures such as emulsion droplets at the colloidal level. This use of force spectroscopy will be illustrated through showing how it allows the effect of the structural modification of interfacial structures on colloidal interactions to be probed in model emulsion systems. Direct studies on interactions between colliding soft, deformable droplets reveal new types of interactions unique to deformable particles that can be exploited to manipulate the behaviour of processed or natural emulsion structures involved in digestion processes. Force spectroscopy can be adapted to probe specific intermolecular interactions, and this application of the technique will be illustrated through its use to test molecular hypotheses for the bioactivity of modified pectin molecules.

  4. Specific noncovalent interactions at protein-ligand interface: implications for rational drug design.

    Science.gov (United States)

    Zhou, P; Huang, J; Tian, F

    2012-01-01

    Specific noncovalent interactions that are indicative of attractive, directional intermolecular forces have always been of key interest to medicinal chemists in their search for the "glue" that holds drugs and their targets together. With the rapid increase in the number of solved biomolecular structures as well as the performance enhancement of computer hardware and software in recent years, it is now possible to give more comprehensive insight into the geometrical characteristics and energetic landscape of certain sophisticated noncovalent interactions present at the binding interface of protein receptors and small ligands based on accumulated knowledge gaining from the combination of two quite disparate but complementary approaches: crystallographic data analysis and quantum-mechanical ab initio calculation. In this perspective, we survey massive body of published works relating to structural characterization and theoretical investigation of three kinds of strong, specific, direct, enthalpy-driven intermolecular forces, including hydrogen bond, halogen bond and salt bridge, involved in the formation of protein-ligand complex architecture in order to characterize their biological functions in conferring affinity and specificity for ligand recognition by host protein. In particular, the biomedical implications of raised knowledge are discussed with respect to potential applications in rational drug design.

  5. Rational design of didodecyldimethylammonium bromide-based nanoassemblies for gene delivery.

    Science.gov (United States)

    Jin, Yiguang; Wang, Shuangmiao; Tong, Li; Du, Lina

    2015-02-01

    Nonviral gene vectors are a hot topic for gene delivery. High cost and low transfection efficiency hinder the application of them. The aim of this study was to find out the optimal gene vectors with lower cost and more effective gene delivery than commonly used gene vectors. A cheap cationic lipid, didodecyldimethylammonium bromide (DDAB) was the basic component and the other components included oleic acid (OA), cholesterol (Chol), cholesteryl succinyl poly(ethylene glycol) 1500 (CHS-PEG), poly(D,L-lactide-co-glycolide)-methoxy-poly(ethylene glycol) (PLGA-PEG). The combinations of DDAB/OA/Chol, DDAB/OA/CHS-PEG and DDAB/PLGA-PEG were adopted to prepare the nanoassemblies named CNA, CPNA and PPNA, respectively. The optimal component ratios were screened out according to their Langmuir monolayer behavior. The optimal preparation method of nanoassemblies involved firstly compressing DNA or siRNA with the cationic lipid (DDAB) and secondly being coated with the helper lipids (OA and CHS-PEG) or the helper polymer (PLGA-PEG). The complexes of genes and cationic lipids were encapsulated into the core of CPNA and PPNA. The optimal gene vectors (CPNA and PPNA) with small sizes, low negative surface charges and non-exposure of cationic lipids were achieved. They had the advantages of no cytotoxicity, high transfection efficiency and low cost. More importantly, CPNA and PPNA were not sensitive to serum and showed the similar or higher transfection efficiency of pDNA and siRNA compared to Lipofectamine 2000. CPNA could mainly enter cell plasma based on endocytosis. The rational design method is useful for the design and optimization of DDAB-based gene carriers and other cationic lipid-based carriers.

  6. Rational design of the gram-scale synthesis of nearly monodisperse semiconductor nanocrystals

    Directory of Open Access Journals (Sweden)

    Renard Olivier

    2011-01-01

    Full Text Available Abstract We address two aspects of general interest for the chemical synthesis of colloidal semiconductor nanocrystals: (1 the rational design of the synthesis protocol aiming at the optimization of the reaction parameters in a minimum number of experiments; (2 the transfer of the procedure to the gram scale, while maintaining a low size distribution and maximizing the reaction yield. Concerning the first point, the design-of-experiment (DOE method has been applied to the synthesis of colloidal CdSe nanocrystals. We demonstrate that 16 experiments, analyzed by means of a Taguchi L16 table, are sufficient to optimize the reaction parameters for controlling the mean size of the nanocrystals in a large range while keeping the size distribution narrow (5-10%. The DOE method strongly reduces the number of experiments necessary for the optimization as compared to trial-and-error approaches. Furthermore, the Taguchi table analysis reveals the degree of influence of each reaction parameter investigated (e.g., the nature and concentration of reagents, the solvent, the reaction temperature and indicates the interactions between them. On the basis of these results, the synthesis has been scaled up by a factor of 20. Using a 2-L batch reactor combined with a high-throughput peristaltic pump, different-sized samples of CdSe nanocrystals with yields of 2-3 g per synthesis have been produced without sacrificing the narrow size distribution. In a similar setup, the gram-scale synthesis of CdSe/CdS/ZnS core/shell/shell nanocrystals exhibiting a fluorescence quantum yield of 81% and excellent resistance of the photoluminescence in presence of a fluorescent quencher (aromatic thiol has been achieved. PACS: 81.20.Ka, 81.07.Bc, 78.67.Bf

  7. Intensive mutagenesis of the nisin hinge leads to the rational design of enhanced derivatives.

    Directory of Open Access Journals (Sweden)

    Brian Healy

    Full Text Available Nisin A is the most extensively studied lantibiotic and has been used as a preservative by the food industry since 1953. This 34 amino acid peptide contains three dehydrated amino acids and five thioether rings. These rings, resulting from one lanthionine and four methyllanthionine bridges, confer the peptide with its unique structure. Nisin A has two mechanisms of action, with the N-terminal domain of the peptide inhibiting cell wall synthesis through lipid II binding and the C-terminal domain responsible for pore-formation. The focus of this study is the three amino acid 'hinge' region (N 20, M 21 and K 22 which separates these two domains and allows for conformational flexibility. As all lantibiotics are gene encoded, novel variants can be generated through manipulation of the corresponding gene. A number of derivatives in which the hinge region was altered have previously been shown to possess enhanced antimicrobial activity. Here we take this approach further by employing simultaneous, indiscriminate site-saturation mutagenesis of all three hinge residues to create a novel bank of nisin derivative producers. Screening of this bank revealed that producers of peptides with hinge regions consisting of AAK, NAI and SLS displayed enhanced bioactivity against a variety of targets. These and other results suggested a preference for small, chiral amino acids within the hinge region, leading to the design and creation of producers of peptides with hinges consisting of AAA and SAA. These producers, and the corresponding peptides, exhibited enhanced bioactivity against Lactococcus lactis HP, Streptococcus agalactiae ATCC 13813, Mycobacterium smegmatis MC2155 and Staphylococcus aureus RF122 and thus represent the first example of nisin derivatives that possess enhanced activity as a consequence of rational design.

  8. Rational design of the gram-scale synthesis of nearly monodisperse semiconductor nanocrystals

    Science.gov (United States)

    Protière, Myriam; Nerambourg, Nicolas; Renard, Olivier; Reiss, Peter

    2011-07-01

    We address two aspects of general interest for the chemical synthesis of colloidal semiconductor nanocrystals: (1) the rational design of the synthesis protocol aiming at the optimization of the reaction parameters in a minimum number of experiments; (2) the transfer of the procedure to the gram scale, while maintaining a low size distribution and maximizing the reaction yield. Concerning the first point, the design-of-experiment (DOE) method has been applied to the synthesis of colloidal CdSe nanocrystals. We demonstrate that 16 experiments, analyzed by means of a Taguchi L16 table, are sufficient to optimize the reaction parameters for controlling the mean size of the nanocrystals in a large range while keeping the size distribution narrow (5-10%). The DOE method strongly reduces the number of experiments necessary for the optimization as compared to trial-and-error approaches. Furthermore, the Taguchi table analysis reveals the degree of influence of each reaction parameter investigated (e.g., the nature and concentration of reagents, the solvent, the reaction temperature) and indicates the interactions between them. On the basis of these results, the synthesis has been scaled up by a factor of 20. Using a 2-L batch reactor combined with a high-throughput peristaltic pump, different-sized samples of CdSe nanocrystals with yields of 2-3 g per synthesis have been produced without sacrificing the narrow size distribution. In a similar setup, the gram-scale synthesis of CdSe/CdS/ZnS core/shell/shell nanocrystals exhibiting a fluorescence quantum yield of 81% and excellent resistance of the photoluminescence in presence of a fluorescent quencher (aromatic thiol) has been achieved. PACS: 81.20.Ka, 81.07.Bc, 78.67.Bf

  9. Rational design of hierarchically nanostructured electrodes for solid oxide fuel cells

    Science.gov (United States)

    Çelikbilek, Ӧzden; Jauffrès, David; Siebert, Elisabeth; Dessemond, Laurent; Burriel, Mónica; Martin, Christophe L.; Djurado, Elisabeth

    2016-11-01

    Understanding, controlling and optimizing the mechanisms of electrode reactions need to be addressed for high performance energy and storage conversion devices. Hierarchically structured porous films of mixed ionic electronic conductors (MIECs) and their composites with ionic conductors offer unique properties. However, correlating the intrinsic properties of electrode components to microstructural features remains a challenging task. Here, La0.6Sr0.4Co0.2Fe0.8O3-δ (LSCF) and La0.6Sr0.4Co0.2Fe0.8O3-δ: Ce0.9Gd0.1O2-δ (LSCF:CGO) composite cathodes with hierarchical porosity from nano to micro range are fabricated. The LSCF film exhibits exceptional electrode performance with area specific resistance values of 0.021 and 0.065 Ω cm2 at 650 and 600 °C respectively, whereas LSCF:CGO composite is only slightly superior than pure LSCF below 450 °C. We report for the first time a numerical 3D Finite Element Model (FEM) comprising real micro/nanostructural parameters from 3D reconstructions into a simple geometry similar to experimentally observed columnar features. The model demonstrates that heterogeneities in porosity within the film thickness and percolation of the ionically conducting phase significantly impact bulk transport at low temperatures. Design guidelines relating performance to microstructure and bulk material properties in relation to experimental results are proposed. Our model has potential to be extended for rational design of larger, regular and heterogeneous microstructures.

  10. Rational drug design approach for overcoming drug resistance: application to pyrimethamine resistance in malaria.

    Science.gov (United States)

    McKie, J H; Douglas, K T; Chan, C; Roser, S A; Yates, R; Read, M; Hyde, J E; Dascombe, M J; Yuthavong, Y; Sirawaraporn, W

    1998-04-23

    Pyrimethamine acts by selectively inhibiting malarial dihydrofolate reductase-thymidylate synthase (DHFR-TS). Resistance in the most important human parasite, Plasmodium falciparum, initially results from an S108N mutation in the DHFR domain, with additional mutation (most commonly C59R or N51I or both) imparting much greater resistance. From a homology model of the 3-D structure of DHFR-TS, rational drug design techniques have been used to design and subsequently synthesize inhibitors able to overcome malarial pyrimethamine resistance. Compared to pyrimethamine (Ki 1.5 nM) with purified recombinant DHFR fromP. falciparum, the Ki value of the m-methoxy analogue of pyrimethamine was 1.07 nM, but against the DHFR bearing the double mutation (C59R + S108N), the Ki values for pyrimethamine and the m-methoxy analogue were 71.7 and 14.0 nM, respectively. The m-chloro analogue of pyrimethamine was a stronger inhibitor of both wild-type DHFR (with Ki 0.30 nM) and the doubly mutant (C59R +S108N) purified enzyme (with Ki 2.40 nM). Growth of parasite cultures of P. falciparum in vitro was also strongly inhibited by these compounds with 50% inhibition of growth occurring at 3.7 microM for the m-methoxy and 0.6 microM for the m-chloro compounds with the K1 parasite line bearing the double mutation (S108N + C59R), compared to 10.2 microM for pyrimethamine. These inhibitors were also found in preliminary studies to retain antimalarial activity in vivo in P. berghei-infected mice.

  11. Rational Design of Orthogonal Multipolar Interactions with Fluorine in Protein–Ligand Complexes

    Science.gov (United States)

    2015-01-01

    Multipolar interactions involving fluorine and the protein backbone have been frequently observed in protein–ligand complexes. Such fluorine–backbone interactions may substantially contribute to the high affinity of small molecule inhibitors. Here we found that introduction of trifluoromethyl groups into two different sites in the thienopyrimidine class of menin–MLL inhibitors considerably improved their inhibitory activity. In both cases, trifluoromethyl groups are engaged in short interactions with the backbone of menin. In order to understand the effect of fluorine, we synthesized a series of analogues by systematically changing the number of fluorine atoms, and we determined high-resolution crystal structures of the complexes with menin. We found that introduction of fluorine at favorable geometry for interactions with backbone carbonyls may improve the activity of menin–MLL inhibitors as much as 5- to 10-fold. In order to facilitate the design of multipolar fluorine–backbone interactions in protein–ligand complexes, we developed a computational algorithm named FMAP, which calculates fluorophilic sites in proximity to the protein backbone. We demonstrated that FMAP could be used to rationalize improvement in the activity of known protein inhibitors upon introduction of fluorine. Furthermore, FMAP may also represent a valuable tool for designing new fluorine substitutions and support ligand optimization in drug discovery projects. Analysis of the menin–MLL inhibitor complexes revealed that the backbone in secondary structures is particularly accessible to the interactions with fluorine. Considering that secondary structure elements are frequently exposed at protein interfaces, we postulate that multipolar fluorine–backbone interactions may represent a particularly attractive approach to improve inhibitors of protein–protein interactions. PMID:26288158

  12. Rational design of allosteric-inhibition sites in classical protein tyrosine phosphatases

    Science.gov (United States)

    Chio, Cynthia M.; Yu, Xiaoling; Bishop, Anthony C.

    2015-01-01

    Protein tyrosine phosphatases (PTPs), which catalyze the dephosphorylation of phosphotyrosine in protein substrates, are critical regulators of metazoan cell signaling and have emerged as potential drug targets for a range of human diseases. Strategies for chemically targeting the function of individual PTPs selectively could serve to elucidate the signaling roles of these enzymes and would potentially expedite validation of the therapeutic promise of PTP inhibitors. Here we report a novel strategy for the design of non-natural allosteric-inhibition sites in PTPs; these sites, which can be introduced into target PTPs through protein engineering, serve to sensitize target PTPs to potent and selective inhibition by a biarsenical small molecule. Building on the recent discovery of a naturally occurring cryptic allosteric site in wild-type Src-homology-2 domain containing PTP (Shp2) that can be targeted by biarsenical compounds, we hypothesized that Shp2’s unusual sensitivity to biarsenicals could be strengthened through rational design and that the Shp2-specific site could serve as a blueprint for the introduction of non-natural inhibitor sensitivity in other PTPs. Indeed, we show here that the strategic introduction of a cysteine residue at a position removed from the Shp2 active site can serve to increase the potency and selectivity of the interaction between Shp2’s allosteric site and the biarsenical inhibitor. Moreover, we find that “Shp2-like” allosteric sites can be installed de novo in PTP enzymes that do not possess naturally occurring sensitivity to biarsenical compounds. Using primary-sequence alignments to guide our enzyme engineering, we have successfully introduced allosteric-inhibition sites in four classical PTPs—PTP1B, PTPH-1, FAP-1, and HePTP—from four different PTP subfamilies, suggesting that our sensitization approach can likely be applied widely across the classical PTP family to generate biarsenical-responsive PTPs. PMID:25828055

  13. Rational design, synthesis, purification, and activation of metal-organic framework materials.

    Science.gov (United States)

    Farha, Omar K; Hupp, Joseph T

    2010-08-17

    The emergence of metal-organic frameworks (MOFs) as functional ultrahigh surface area materials is one of the most exciting recent developments in solid-state chemistry. Now constituting thousands of distinct examples, MOFs are an intriguing class of hybrid materials that exist as infinite crystalline lattices with inorganic vertices and molecular-scale organic connectors. Useful properties such as large internal surface areas, ultralow densities, and the availability of uniformly structured cavities and portals of molecular dimensions characterize functional MOFs. Researchers have effectively exploited these unusual properties in applications such as hydrogen and methane storage, chemical separations, and selective chemical catalysis. In principle, one of the most attractive features of MOFs is the simplicity of their synthesis. Typically they are obtained via one-pot solvothermal preparations. However, with the simplicity come challenges. In particular, MOF materials, especially more complex ones, can be difficult to obtain in pure form and with the optimal degree of catenation, the interpenetration or interweaving of identical independent networks. Once these two issues are satisfied, the removal of the guest molecules (solvent from synthesis) without damaging the structural integrity of the material is often an additional challenge. In this Account, we review recent advances in the synthetic design, purification, and activation of metal-organic framework materials. We describe the rational design of a series of organic struts to limit framework catenation and thereby produce large pores. In addition, we demonstrate the rapid separation of desired MOFs from crystalline and amorphous contaminants cogenerated during synthesis based on their different densities. Finally, we discuss the mild and efficient activation of initially solvent-filled pores with supercritical carbon dioxide, yielding usable channels and high internal surface areas. We expect that the

  14. Recent progress on pyrazole scaffold-based antimycobacterial agents.

    Science.gov (United States)

    Keri, Rangappa S; Chand, Karam; Ramakrishnappa, Thippeswamy; Nagaraja, Bhari Mallanna

    2015-05-01

    New and reemerging infectious diseases will continue to pose serious global health threats well into the 21st century and according to the World Health Organization report, these are still the leading cause of death among humans worldwide. Among infectious diseases, tuberculosis claims approximately 2 million deaths per year worldwide. Also, agents that reduce the duration and complexity of the current therapy would have a major impact on the overall cure rate. Due to the development of resistance to conventional antibiotics there is a need for new therapeutic strategies to combat Mycobacterium tuberculosis. Subsequently, there is an urgent need for the development of new drug candidates with newer targets and alternative mechanism of action. In this perspective, pyrazole, one of the most important classes of heterocycles, has been the topic of research for thousands of researchers all over the world because of its wide spectrum of biological activities. To pave the way for future research, there is a need to collect the latest information in this promising area. In the present review, we have collated published reports on the pyrazole core to provide an insight so that its full therapeutic potential can be utilized for the treatment of tuberculosis. In this article, the possible structure-activity relationship of pyrazole analogs for designing better antituberculosis (anti-TB) agents has been discussed and is also helpful for new thoughts in the quest for rational designs of more active and less toxic pyrazole-based anti-TB drugs.

  15. Fundamental Investigations and Rational Design of Durable High-Performance SOFC Cathodes

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Yu [Georgia Inst. of Technology, Atlanta, GA (United States); Ding, Dong [Georgia Inst. of Technology, Atlanta, GA (United States); Wei, Tao [Georgia Inst. of Technology, Atlanta, GA (United States); Liu, Meilin [Georgia Inst. of Technology, Atlanta, GA (United States)

    2016-03-31

    The main objective of this project is to unravel the degradation mechanism of LSCF cathodes under realistic operating conditions with different types of contaminants, aiming towards the rational design of cathodes with high-performance and enhanced durability by combining a porous backbone (such as LSCF) with a thin catalyst coating. The mechanistic understanding will help us to optimize the composition and morphology of the catalyst layer and microstructure of the LSCF backbone for better performance and durability. More specifically, the technical objectives include: (1) to unravel the degradation mechanism of LSCF cathodes under realistic operating conditions with different types of contaminants using in situ and ex situ measurements performed on specially-designed cathodes; (2) to examine the microstructural and compositional evolution of LSCF cathodes as well as the cathode/electrolyte interfaces under realistic operating conditions; (3) to correlate the fuel cell performance instability and degradation with the microstructural and morphological evolution and surface chemistry change of the cathode under realistic operating conditions; (4) to explore new catalyst materials and electrode structures to enhance the stability of the LSCF cathode under realistic operating conditions; and (5) to validate the long term stability of the modified LSCF cathode in commercially available cells under realistic operating conditions. We have systematically evaluated LSCF cathodes in symmetrical cells and anode supported cells under realistic conditions with different types of contaminants such as humidity, CO2, and Cr. Electrochemical models for the design of test cells and understanding of mechanisms have been developed for the exploration of fundamental properties of electrode materials. It is demonstrated that the activity and stability of LSCF cathodes can be degraded by the introduction of contaminants. The microstructural and compositional evolution of LSCF

  16. Rational design of surface/interface chemistry for quantitative in vivo monitoring of brain chemistry.

    Science.gov (United States)

    Zhang, Meining; Yu, Ping; Mao, Lanqun

    2012-04-17

    To understand the molecular basis of brain functions, researchers would like to be able to quantitatively monitor the levels of neurochemicals in the extracellular fluid in vivo. However, the chemical and physiological complexity of the central nervous system (CNS) presents challenges for the development of these analytical methods. This Account describes the rational design and careful construction of electrodes and nanoparticles with specific surface/interface chemistry for quantitative in vivo monitoring of brain chemistry. We used the redox nature of neurochemicals at the electrode/electrolyte interface to establish a basis for monitoring specific neurochemicals. Carbon nanotubes provide an electrode/electrolyte interface for the selective oxidation of ascorbate, and we have developed both in vivo voltammetry and an online electrochemical detecting system for continuously monitoring this molecule in the CNS. Although Ca(2+) and Mg(2+) are involved in a number of neurochemical signaling processes, they are still difficult to detect in the CNS. These divalent cations can enhance electrocatalytic oxidation of NADH at an electrode modified with toluidine blue O. We used this property to develop online electrochemical detection systems for simultaneous measurements of Ca(2+) and Mg(2+) and for continuous selective monitoring of Mg(2+) in the CNS. We have also harnessed biological schemes for neurosensing in the brain to design other monitoring systems. By taking advantage of the distinct reaction properties of dopamine (DA), we have developed a nonoxidative mechanism for DA sensing and a system that can potentially be used for continuously sensing of DA release. Using "artificial peroxidase" (Prussian blue) to replace a natural peroxidase (horseradish peroxidase, HRP), our online system can simultaneously detect basal levels of glucose and lactate. By substituting oxidases with dehydrogenases, we have used enzyme-based biosensing schemes to develop a physiologically

  17. Rational design of a flavivirus vaccine by abolishing viral RNA 2'-O methylation.

    Science.gov (United States)

    Li, Shi-Hua; Dong, Hongping; Li, Xiao-Feng; Xie, Xuping; Zhao, Hui; Deng, Yong-Qiang; Wang, Xiao-Yu; Ye, Qing; Zhu, Shun-Ya; Wang, Hong-Jiang; Zhang, Bo; Leng, Qi-Bin; Zuest, Roland; Qin, E-De; Qin, Cheng-Feng; Shi, Pei-Yong

    2013-05-01

    Viruses that replicate in the cytoplasm cannot access the host nuclear capping machinery. These viruses have evolved viral methyltransferase(s) to methylate N-7 and 2'-O cap of their RNA; alternatively, they "snatch" host mRNA cap to form the 5' end of viral RNA. The function of 2'-O methylation of viral RNA cap is to mimic cellular mRNA and to evade host innate immune restriction. A cytoplasmic virus defective in 2'-O methylation is replicative, but its viral RNA lacks 2'-O methylation and is recognized and eliminated by the host immune response. Such a mutant virus could be rationally designed as a live attenuated vaccine. Here, we use Japanese encephalitis virus (JEV), an important mosquito-borne flavivirus, to prove this novel vaccine concept. We show that JEV methyltransferase is responsible for both N-7 and 2'-O cap methylations as well as evasion of host innate immune response. Recombinant virus completely defective in 2'-O methylation was stable in cell culture after being passaged for >30 days. The mutant virus was attenuated in mice, elicited robust humoral and cellular immune responses, and retained the engineered mutation in vivo. A single dose of immunization induced full protection against lethal challenge with JEV strains in mice. Mechanistically, the attenuation phenotype was attributed to the enhanced sensitivity of the mutant virus to the antiviral effects of interferon and IFIT proteins. Collectively, the results demonstrate the feasibility of using 2'-O methylation-defective virus as a vaccine approach; this vaccine approach should be applicable to other flaviviruses and nonflaviviruses that encode their own viral 2'-O methyltransferases.

  18. Rational Design of a Flavivirus Vaccine by Abolishing Viral RNA 2′-O Methylation

    Science.gov (United States)

    Li, Shi-Hua; Dong, Hongping; Li, Xiao-Feng; Xie, Xuping; Zhao, Hui; Deng, Yong-Qiang; Wang, Xiao-Yu; Ye, Qing; Zhu, Shun-Ya; Wang, Hong-Jiang; Zhang, Bo; Leng, Qi-Bin; Zuest, Roland; Qin, E-De

    2013-01-01

    Viruses that replicate in the cytoplasm cannot access the host nuclear capping machinery. These viruses have evolved viral methyltransferase(s) to methylate N-7 and 2′-O cap of their RNA; alternatively, they “snatch” host mRNA cap to form the 5′ end of viral RNA. The function of 2′-O methylation of viral RNA cap is to mimic cellular mRNA and to evade host innate immune restriction. A cytoplasmic virus defective in 2′-O methylation is replicative, but its viral RNA lacks 2′-O methylation and is recognized and eliminated by the host immune response. Such a mutant virus could be rationally designed as a live attenuated vaccine. Here, we use Japanese encephalitis virus (JEV), an important mosquito-borne flavivirus, to prove this novel vaccine concept. We show that JEV methyltransferase is responsible for both N-7 and 2′-O cap methylations as well as evasion of host innate immune response. Recombinant virus completely defective in 2′-O methylation was stable in cell culture after being passaged for >30 days. The mutant virus was attenuated in mice, elicited robust humoral and cellular immune responses, and retained the engineered mutation in vivo. A single dose of immunization induced full protection against lethal challenge with JEV strains in mice. Mechanistically, the attenuation phenotype was attributed to the enhanced sensitivity of the mutant virus to the antiviral effects of interferon and IFIT proteins. Collectively, the results demonstrate the feasibility of using 2′-O methylation-defective virus as a vaccine approach; this vaccine approach should be applicable to other flaviviruses and nonflaviviruses that encode their own viral 2′-O methyltransferases. PMID:23487465

  19. Towards Rational Design of a Toxoid Vaccine against the Heat-Stable Toxin of Escherichia coli

    Science.gov (United States)

    Taxt, Arne M.; Diaz, Yuleima; Aasland, Rein; Clements, John D.; Nataro, James P.; Sommerfelt, Halvor

    2016-01-01

    Enterotoxigenic Escherichia coli (ETEC) is an important cause of diarrheal disease and death in children <5 years old. ETEC strains that express the heat-stable toxin (ST), with or without the heat-labile toxin, are among the four most important diarrhea-causing pathogens. This makes ST an attractive target for an ETEC vaccine. An ST vaccine should be nontoxic and elicit an immune response that neutralizes native ST without cross-reacting with the human endogenous guanylate cyclase C receptor ligands. To identify variants of ST with no or low toxicity, we screened a library of all 361 possible single-amino-acid mutant forms of ST by using the T84 cell assay. Moreover, we identified mutant variants with intact epitopes by screening for the ability to bind neutralizing anti-ST antibodies. ST mutant forms with no or low toxicity and intact epitopes are termed toxoid candidates, and the top 30 candidates all had mutations of residues A14, N12, and L9. The identification of nontoxic variants of L9 strongly suggests that it is a novel receptor-interacting residue, in addition to the previously identified N12, P13, and A14 residues. The screens also allowed us to map the epitopes of three neutralizing monoclonal antibodies, one of which cross-reacts with the human ligand uroguanylin. The common dominant epitope residue for all non-cross-reacting antibodies was Y19. Our results suggest that it should be possible to rationally design ST toxoids that elicit neutralizing immune responses against ST with minimal risk of immunological cross-reactivity. PMID:26883587

  20. Rational design of on-chip refractive index sensors based on lattice plasmon resonances (Presentation Recording)

    Science.gov (United States)

    Lin, Linhan; Zheng, Yuebing

    2015-08-01

    Lattice plasmon resonances (LPRs), which originate from the plasmonic-photonic coupling in gold or silver nanoparticle arrays, possess ultra-narrow linewidth by suppressing the radiative damping and provide the possibility to develop the plasmonic sensors with high figure of merit (FOM). However, the plasmonic-photonic coupling is greatly suppressed when the nanoparticles are immobilized on substrates because the diffraction orders are cut off at the nanoparticle-substrate interfaces. Here, we develop the rational design of LPR structures for the high-performance, on-chip plasmonic sensors based on both orthogonal and parallel coupling. Our finite-difference time-domain simulations in the core/shell SiO2/Au nanocylinder arrays (NCAs) reveal that new modes of localized surface plasmon resonances (LSPRs) show up when the aspect ratio of the NCAs is increased. The height-induced LSPRs couple with the superstrate diffraction orders to generate the robust LPRs in asymmetric environment. The high wavelength sensitivity and narrow linewidth in these LPRs lead to the plasmonic sensors with high FOM and high signal-to-noise ratio (SNR). Wide working wavelengths from visible to near-infrared are also achieved by tuning the parameters of the NCAs. Moreover, the wide detection range of refractive index is obtained in the parallel LPR structure. The electromagnetic field distributions in the NCAs demonstrate the height-enabled tunability of the plasmonic "hot spots" at the sub-nanoparticles resolution and the coupling between these "hot spots" with the superstrate diffraction waves, which are responsible for the high performance LPRs-based on-chip refractive index sensors.

  1. Improving the Thermostability of Acidic Pullulanase from Bacillus naganoensis by Rational Design

    Science.gov (United States)

    Lv, Jinzhi; Li, Qingbin; Tian, Jian; Wu, Ningfeng

    2016-01-01

    Pullulanase (EC 3.2.1.41) plays an important role in the specific hydrolysis of branch points in amylopectin. Enhancing its thermostability is required for its industrial application. In this study, rational protein design was used to improve the thermostability of PulB from Bacillus naganoensis (AB231790.1), which has strong enzymatic properties. Three positive single-site mutants (PulB-D328H, PulB-N387D, and PulB-A414P) were selected from six mutants. After incubation at 65°C for 5 min, the residual activities of PulB-D328H, PulB-N387D, and PulB-A414P were 4.5-, 1.7-, and 1.47-fold higher than PulB-WT, and their Tm values (the temperature at which half protein molecule denature) were 1.8°C, 0.4°C, and 0.9°C higher than PulB-WT, respectively. Then the final combined mutant PulB-328/387/414 was constructed. The t1/2 of it was 12.9-fold longer than that of PulB-WT at 65°C and the total increase in Tm of it (5.0°C) was almost 60% greater than the sum of individual increases (3.1°C). In addition, kinetic studies revealed that the kcat and the kcat/Km of PulB-328/387/414 increased by 38.8% and 12.9%. The remarkable improvement in thermostability and the high catalytic efficiency of PulB-328/387/414 make it suitable for industrial applications. PMID:27764201

  2. A rationally designed tyrosine hydroxylase DNA vaccine induces specific antineuroblastoma immunity.

    Science.gov (United States)

    Huebener, Nicole; Fest, Stefan; Strandsby, Anne; Michalsky, Elke; Preissner, Robert; Zeng, Yan; Gaedicke, Gerhard; Lode, Holger N

    2008-07-01

    Therapeutic vaccination against tumor antigens without induction of autoimmunity remains a major challenge in cancer immunotherapy. Here, we show for the first time effective therapeutic vaccination followed by suppression of established spontaneous neuroblastoma metastases using a tyrosine hydroxylase (TH) DNA minigene vaccine. We identified three novel mouse TH (mTH3) derived peptides with high predicted binding affinity to MHC class I antigen H2-K(k) according to the prediction program SYFPEITHI and computer modeling of epitopes into the MHC class I antigen binding groove. Subsequently, a DNA minigene vaccine was generated based on the expression vector pCMV-F3Ub encoding mutated ubiquitin (Gly(76) to Ala(76)) and mTH3. Prophylactic and therapeutic efficacies of this vaccine were established following oral delivery with attenuated Salmonella typhimurium SL7207. Only mice immunized with mTH3 were free of spontaneous liver metastases. This effect was clearly dependent on ubiquitin and high affinity of the mTH epitopes to MHC class I antigens. Specifically, we showed a crucial role for minigene expression as a stable ubiquitin-Ala(76) fusion peptide for vaccine efficacy. The immune response following the mTH3 DNA minigene vaccination was mediated by CD8(+) T cells as indicated by infiltration of primary tumors and TH-specific cytolytic activity in vitro. Importantly, no cell infiltration was detectable in TH-expressing adrenal medulla, indicating the absence of autoimmunity. In summary, we show effective therapeutic vaccination against neuroblastoma with a novel rationally designed TH minigene vaccine without induction of autoimmunity providing an important baseline for future clinical application of this strategy.

  3. Rational Ligand Design for U(VI) and Pu(IV)

    Energy Technology Data Exchange (ETDEWEB)

    Szigethy, Geza [Univ. of California, Berkeley, CA (United States)

    2009-08-12

    Nuclear power is an attractive alternative to hydrocarbon-based energy production at a time when moving away from carbon-producing processes is widely accepted as a significant developmental need. Hence, the radioactive actinide power sources for this industry are necessarily becoming more widespread, which is accompanied by the increased risk of exposure to both biological and environmental systems. This, in turn, requires the development of technology designed to remove such radioactive threats efficiently and selectively from contaminated material, whether that be contained nuclear waste streams or the human body. Raymond and coworkers (University of California, Berkeley) have for decades investigated the interaction of biologically-inspired, hard Lewis-base ligands with high-valent, early-actinide cations. It has been established that such ligands bind strongly to the hard Lewis-acidic early actinides, and many poly-bidentate ligands have been developed and shown to be effective chelators of actinide contaminants in vivo. Work reported herein explores the effect of ligand geometry on the linear U(IV) dioxo dication (uranyl, UO2 2+). The goal is to utilize rational ligand design to develop ligands that exhibit shape selectivity towards linear dioxo cations and provides thermodynamically favorable binding interactions. The uranyl complexes with a series of tetradentate 3-hydroxy-pyridin-2-one (3,2-HOPO) ligands were studied in both the crystalline state as well as in solution. Despite significant geometric differences, the uranyl affinities of these ligands vary only slightly but are better than DTPA, the only FDA-approved chelation therapy for actinide contamination. The terepthalamide (TAM) moiety was combined into tris-beidentate ligands with 1,2- and 3,2-HOPO moieties were combined into hexadentate ligands whose structural preferences and solution thermodynamics were measured with the uranyl cation. In addition to achieving coordinative

  4. Rationally Designed Interfacial Peptides Are Efficient In Vitro Inhibitors of HIV-1 Capsid Assembly with Antiviral Activity

    OpenAIRE

    Rebeca Bocanegra; María Nevot; Rosa Doménech; Inmaculada López; Olga Abián; Alicia Rodríguez-Huete; Cavasotto, Claudio N.; Adrián Velázquez-Campoy; Javier Gómez; Miguel Ángel Martínez; José Luis Neira; Mateu, Mauricio G.

    2011-01-01

    Virus capsid assembly constitutes an attractive target for the development of antiviral therapies; a few experimental inhibitors of this process for HIV-1 and other viruses have been identified by screening compounds or by selection from chemical libraries. As a different, novel approach we have undertaken the rational design of peptides that could act as competitive assembly inhibitors by mimicking capsid structural elements involved in intersubunit interfaces. Several discrete interfaces in...

  5. Evolutionary and Comparative Genomics to Drive Rational Drug Design, with Particular Focus on Neuropeptide Seven-Transmembrane Receptors

    OpenAIRE

    Furlong, Michael; Seong, Jae Young

    2017-01-01

    Seven transmembrane receptors (7TMRs), also known as G protein-coupled receptors, are popular targets of drug development, particularly 7TMR systems that are activated by peptide ligands. Although many pharmaceutical drugs have been discovered via conventional bulk analysis techniques the increasing availability of structural and evolutionary data are facilitating change to rational, targeted drug design. This article discusses the appeal of neuropeptide-7TMR systems as drug targets and provi...

  6. 数据库设计工具的选择——Erwin,Power Designer,Rational Rose

    Institute of Scientific and Technical Information of China (English)

    孟令凤; 饶莉莉

    2007-01-01

    随着数据库设计的需要,越来越多的CASE工具出现在我们的视野里,如何选择适合自己的工具就成了当务之急,下面对几种常用的工具Erwin,Power Designer,Rational Rose做以下对比.

  7. A multi-factors rational design strategy for enhancing the thermostability of Escherichia coli AppA phytase.

    Science.gov (United States)

    Fei, Baojin; Xu, Hui; Cao, Yu; Ma, Shuhan; Guo, Hongxiu; Song, Tao; Qiao, Dairong; Cao, Yi

    2013-05-01

    Despite recent advances in our understanding of the importance of protein surface properties for protein thermostability,there are seldom studies on multi-factors rational design strategy, so a more scientific, simple and effective rational strategy is urgent for protein engineering. Here, we first attempted to use a three-factors rational design strategy combining three common structural features, protein flexibility, protein surface, and salt bridges. Escherichia coli AppA phytase was used as a model enzyme to improve its thermostability. Moreover, the structure and enzyme features of the thermostable mutants designed by our strategy were analyzed roundly. For the single mutants, two (Q206E and Y311K), in five exhibited thermostable property with a higher success rate of prediction (40 %). For the multiple mutants, the themostable sites were combined with another site, I427L, we obtained by directed evolution, Q206E/I427L, Y311K/I427L, and Q206E/Y311K/I427L, all exhibited thermostable property. The Y311K/I427L doubled thermostability (61.7 %, and was compared to 30.97 % after being heated at 80 °C for 10 min) and catalytic efficiency (4.46 was compared to 2.37) improved more than the wild-type AppA phytase almost without hampering catalytic activity. These multi-factors of rational design strategy can be applied practically as a thermostabilization strategy instead of the conventional single-factor approach.

  8. Rational design of conformationally constrained cyclopentapeptide antagonists for C-x-C chemokine receptor 4 (CXCR4)

    DEFF Research Database (Denmark)

    Mungalpara, Jignesh; Thiele, Stefanie; Eriksen, Øystein;

    2012-01-01

    In the absence of an experimentally determined binding mode for the cyclopentapeptide CXCR4 antagonists, we have rationally designed conformationally constrained analogues to further probe the small peptide binding pocket of CXCR4. Two different rigidification strategies were employed, both...... resulting in highly potent ligands (9 and 13). The information provided by this cyclopentapeptide ligand series will be very valuable in the development of novel peptidomimetic CXCR4 antagonists....

  9. Rational design of therapeutic mAbs against aggregation through protein engineering and incorporation of glycosylation motifs applied to bevacizumab

    Science.gov (United States)

    Courtois, Fabienne; Agrawal, Neeraj J; Lauer, Timothy M; Trout, Bernhardt L

    2016-01-01

    The aggregation of biotherapeutics is a major hindrance to the development of successful drug candidates; however, the propensity to aggregate is often identified too late in the development phase to permit modification to the protein's sequence. Incorporating rational design for the stability of proteins in early discovery has numerous benefits. We engineered out aggregation-prone regions on the Fab domain of a therapeutic monoclonal antibody, bevacizumab, to rationally design a biobetter drug candidate. With the purpose of stabilizing bevacizumab with respect to aggregation, 2 strategies were undertaken: single point mutations of aggregation-prone residues and engineering a glycosylation site near aggregation-prone residues to mask these residues with a carbohydrate moiety. Both of these approaches lead to comparable decreases in aggregation, with an up to 4-fold reduction in monomer loss. These single mutations and the new glycosylation pattern of the Fab domain do not modify binding to the target. Biobetters with increased stability against aggregation can therefore be generated in a rational manner, by either removing or masking the aggregation-prone region or crowding out protein-protein interactions. PMID:26514585

  10. Rational design of therapeutic mAbs against aggregation through protein engineering and incorporation of glycosylation motifs applied to bevacizumab.

    Science.gov (United States)

    Courtois, Fabienne; Agrawal, Neeraj J; Lauer, Timothy M; Trout, Bernhardt L

    2016-01-01

    The aggregation of biotherapeutics is a major hindrance to the development of successful drug candidates; however, the propensity to aggregate is often identified too late in the development phase to permit modification to the protein's sequence. Incorporating rational design for the stability of proteins in early discovery has numerous benefits. We engineered out aggregation-prone regions on the Fab domain of a therapeutic monoclonal antibody, bevacizumab, to rationally design a biobetter drug candidate. With the purpose of stabilizing bevacizumab with respect to aggregation, 2 strategies were undertaken: single point mutations of aggregation-prone residues and engineering a glycosylation site near aggregation-prone residues to mask these residues with a carbohydrate moiety. Both of these approaches lead to comparable decreases in aggregation, with an up to 4-fold reduction in monomer loss. These single mutations and the new glycosylation pattern of the Fab domain do not modify binding to the target. Biobetters with increased stability against aggregation can therefore be generated in a rational manner, by either removing or masking the aggregation-prone region or crowding out protein-protein interactions.

  11. The Report on Rational Matrix Rational Diagonalization Algorithm and Program Design%有理矩阵有理对角化问题的算法及程序设计研究报告

    Institute of Scientific and Technical Information of China (English)

    周腾锦; 王纯

    2013-01-01

    Matrix is an important mathematical method of diagonalization, but because of its computational complexity, it has caused great difficulties on the application, The mathematical software has the function of processing of diagonalization, but for rational matrix diagonalization problem in the field of rational number the result is not satisfactory. So the study of rational matrix over the rational number field similarity diagonalization diagonalization, contract and orthogonal diagonalization algorithm and program project, design to realize rational matrices over the field of rational numbers on the diagonalization of utility software, solves the rational matrices over the field of rational numbers on the diagonalization of the accurate determination and computation problem.%  矩阵对角化是重要的数学方法,但因其计算复杂却造成了应用上的极大困难,虽然已有的数学软件具有处理对角化功能,但对有理矩阵在有理数域上的对角化问题的计算结果却不尽人意。所以提出了研究有理矩阵在有理数域上相似对角化、合同对角化以及正交对角化的算法与程序课题,设计出能够实现有理矩阵在有理数域上对角化的实用软件,解决了有理矩阵在有理数域上对角化的精确判定与计算问题。

  12. Scaffold-based Drug Delivery for Cartilage Tissue Regeneration.

    Science.gov (United States)

    Shalumon, K T; Chen, Jyh-Ping

    2015-01-01

    in scaffold based cartilage tissue regeneration.

  13. Testing the limits of rational design by engineering pH sensitivity into membrane-active peptides.

    Science.gov (United States)

    Wiedman, Gregory; Wimley, William C; Hristova, Kalina

    2015-04-01

    In this work, we sought to rationally design membrane-active peptides that are triggered by low pH to form macromolecular-sized pores in lipid bilayers. Such peptides could have broad utility in biotechnology and in nanomedicine as cancer therapeutics or drug delivery vehicles that promote release of macromolecules from endosomes. Our approach to rational design was to combine the properties of a pH-independent peptide, MelP5, which forms large pores allowing passage of macromolecules, with the properties of two pH-dependent membrane-active peptides, pHlip and GALA. We created two hybrid sequences, MelP5_Δ4 and MelP5_Δ6, by using the distribution of acidic residues on pHlip and GALA as a guide to insert acidic amino acids into the amphipathic helix of MelP5. We show that the new peptides bind to lipid bilayers and acquire secondary structure in a pH-dependent manner. The peptides also destabilize bilayers in a pH-dependent manner, such that lipid vesicles release the small molecules ANTS/DPX at low pH only. Thus, we were successful in designing pH-triggered pore-forming peptides. However, no macromolecular release was observed under any conditions. Therefore, we abolished the unique macromolecular poration properties of MelP5 by introducing pH sensitivity into its sequence. We conclude that the properties of pHlip, GALA, and MelP5 are additive, but only partially so. We propose that this lack of additivity is a limitation in the rational design of novel membrane-active peptides, and that high-throughput approaches to discovery will be critical for continued progress in the field.

  14. Rational Design of Spur Gears Directed to Increase Efficiency and Decrease Loss by Friction

    Directory of Open Access Journals (Sweden)

    Gonzalo González Rey

    2010-10-01

    Full Text Available External parallel-axis cylindrical gears are considered as very efficient means for transmitting mechanical power, but for requirements of maximum efficiency in the current machines and equipments a precision in the procedures of calculation of power losses is necessary. In this sense, the Technical Report ISO / TR 14179-1:2001 offers formulas with empirical and theoretical bases to evaluate the gear efficiency considering gear mesh losses, windage and churning losses, and losses by bearings and seals. In particular, this article presents some results derived from a study of ISO/TR 14179-1:2001 and mathematical models described the interrelation of gear geometry, working parameters and efficiency. The results offer solution to the problem of increasing gear efficiency through a convenient relationship between the load, speed and rational gear geometry. Finally, through multiple regression a new formulation was estimated for the calculation of gear efficiency as a function of the load density, module, speed, gear ration and number of pinion teeth.

  15. Rational Suicide?

    Science.gov (United States)

    Mayo, David J.

    1998-01-01

    The rational suicide paradigm is contrasted with the traditional view of the mental health professions. Historical background on suicide in western civilization is supplied and the concept of rationality elucidated. Parallels between the questions of refusing life-prolonging therapy and rational suicide are discussed, as are reasons for suicide.…

  16. A Rational Design Strategy for the Selective Activity Enhancement of a Molecular Chaperone toward a Target Substrate.

    Science.gov (United States)

    Aprile, Francesco A; Sormanni, Pietro; Vendruscolo, Michele

    2015-08-18

    Molecular chaperones facilitate the folding and assembly of proteins and inhibit their aberrant aggregation. They thus offer several opportunities for biomedical and biotechnological applications, as for example they can often prevent protein aggregation more effectively than other therapeutic molecules, including small molecules and antibodies. Here we present a method of designing molecular chaperones with enhanced activity against specific amyloidogenic substrates while leaving unaltered their functions toward other substrates. The method consists of grafting onto a molecular chaperone a peptide designed to bind specifically an epitope in the target substrate. We illustrate this strategy by describing Hsp70 variants with increased affinities for α-synuclein and Aβ42 but otherwise unaltered affinities for other substrates. These designed variants inhibit protein aggregation and disaggregate preformed fibrils significantly more effectively than wild-type Hsp70 indicating that the strategy presented here provides a possible route for tailoring rationally molecular chaperones for specific purposes.

  17. Converting bulk sugars into prebiotics: semi-rational design of a transglucosylase with controlled selectivity.

    Science.gov (United States)

    Verhaeghe, Tom; De Winter, Karel; Berland, Magali; De Vreese, Rob; D'hooghe, Matthias; Offmann, Bernard; Desmet, Tom

    2016-03-01

    Despite the growing importance of prebiotics in nutrition and gastroenterology, their structural variety is currently still very limited. The lack of straightforward procedures to gain new products in sufficient amounts often hampers application testing and further development. Although the enzyme sucrose phosphorylase can be used to produce the rare disaccharide kojibiose (α-1,2-glucobiose) from the bulk sugars sucrose and glucose, the target compound is only a side product that is difficult to isolate. Accordingly, for this biocatalyst to become economically attractive, the formation of other glucobioses should be avoided and therefore we applied semi-rational mutagenesis and low-throughput screening, which resulted in a double mutant (L341I_Q345S) with a selectivity of 95% for kojibiose. That way, an efficient and scalable production process with a yield of 74% could be established, and with a simple yeast treatment and crystallization step over a hundred grams of highly pure kojibiose (>99.5%) was obtained.

  18. Elementary Mode Analysis for the Rational Design of Efficient Succinate Conversion from Glycerol by Escherichia coli

    Directory of Open Access Journals (Sweden)

    Zhen Chen

    2010-01-01

    Full Text Available By integrating the restriction of oxygen and redox sensing/regulatory system, elementary mode analysis was used to predict the metabolic potential of glycerol for succinate production by E. coli under either anaerobic or aerobic conditions. It was found that although the theoretical maximum succinate yields under both anaerobic and aerobic conditions are 1.0 mol/mol glycerol, the aerobic condition was considered to be more favorable for succinate production. Although increase of the oxygen concentration would reduce the succinate yield, the calculation suggests that controlling the molar fraction of oxygen to be under 0.65 mol/mol would be beneficial for increasing the succinate productivity. Based on the elementary mode analysis, the rational genetic modification strategies for efficient succinate production under aerobic and anaerobic conditions were obtained, respectively. Overexpressing the phosphoenolpyruvate carboxylase or heterogonous pyruvate carboxylase is considered to be the most efficient strategy to increase the succinate yield.

  19. Protein engineering of Bacillus acidopullulyticus pullulanase for enhanced thermostability using in silico data driven rational design methods.

    Science.gov (United States)

    Chen, Ana; Li, Yamei; Nie, Jianqi; McNeil, Brian; Jeffrey, Laura; Yang, Yankun; Bai, Zhonghu

    2015-10-01

    Thermostability has been considered as a requirement in the starch processing industry to maintain high catalytic activity of pullulanase under high temperatures. Four data driven rational design methods (B-FITTER, proline theory, PoPMuSiC-2.1, and sequence consensus approach) were adopted to identify the key residue potential links with thermostability, and 39 residues of Bacillus acidopullulyticus pullulanase were chosen as mutagenesis targets. Single mutagenesis followed by combined mutagenesis resulted in the best mutant E518I-S662R-Q706P, which exhibited an 11-fold half-life improvement at 60 °C and a 9.5 °C increase in Tm. The optimum temperature of the mutant increased from 60 to 65 °C. Fluorescence spectroscopy results demonstrated that the tertiary structure of the mutant enzyme was more compact than that of the wild-type (WT) enzyme. Structural change analysis revealed that the increase in thermostability was most probably caused by a combination of lower stability free-energy and higher hydrophobicity of E518I, more hydrogen bonds of S662R, and higher rigidity of Q706P compared with the WT. The findings demonstrated the effectiveness of combined data-driven rational design approaches in engineering an industrial enzyme to improve thermostability.

  20. Rationally designed interfacial peptides are efficient in vitro inhibitors of HIV-1 capsid assembly with antiviral activity.

    Directory of Open Access Journals (Sweden)

    Rebeca Bocanegra

    Full Text Available Virus capsid assembly constitutes an attractive target for the development of antiviral therapies; a few experimental inhibitors of this process for HIV-1 and other viruses have been identified by screening compounds or by selection from chemical libraries. As a different, novel approach we have undertaken the rational design of peptides that could act as competitive assembly inhibitors by mimicking capsid structural elements involved in intersubunit interfaces. Several discrete interfaces involved in formation of the mature HIV-1 capsid through polymerization of the capsid protein CA were targeted. We had previously designed a peptide, CAC1, that represents CA helix 9 (a major part of the dimerization interface and binds the CA C-terminal domain in solution. Here we have mapped the binding site of CAC1, and shown that it substantially overlaps with the CA dimerization interface. We have also rationally modified CAC1 to increase its solubility and CA-binding affinity, and designed four additional peptides that represent CA helical segments involved in other CA interfaces. We found that peptides CAC1, its derivative CAC1M, and H8 (representing CA helix 8 were able to efficiently inhibit the in vitro assembly of the mature HIV-1 capsid. Cocktails of several peptides, including CAC1 or CAC1M plus H8 or CAI (a previously discovered inhibitor of CA polymerization, or CAC1M+H8+CAI, also abolished capsid assembly, even when every peptide was used at lower, sub-inhibitory doses. To provide a preliminary proof that these designed capsid assembly inhibitors could eventually serve as lead compounds for development of anti-HIV-1 agents, they were transported into cultured cells using a cell-penetrating peptide, and tested for antiviral activity. Peptide cocktails that drastically inhibited capsid assembly in vitro were also able to efficiently inhibit HIV-1 infection ex vivo. This study validates a novel, entirely rational approach for the design of capsid

  1. Transitioning Rationally Designed Catalytic Materials to Real 'Working' Catalysts Produced at Commercial Scale: Nanoparticle Materials

    Energy Technology Data Exchange (ETDEWEB)

    Schaidle, Joshua A.; Habas, Susan E.; Baddour, Frederick G.; Farberow, Carrie A.; Ruddy, Daniel A.; Hensley, Jesse E.; Brutchey, Richard L.; Malmstadt, Noah; Robota, Heinz

    2017-02-01

    Catalyst design, from idea to commercialization, requires multi-disciplinary scientific and engineering research and development over 10-20 year time periods. Historically, the identification of new or improved catalyst materials has largely been an empirical trial-and-error process. However, advances in computational capabilities (new tools and increased processing power) coupled with new synthetic techniques have started to yield rationally-designed catalysts with controlled nano-structures and tailored properties. This technological advancement represents an opportunity to accelerate the catalyst development timeline and to deliver new materials that outperform existing industrial catalysts or enable new applications, once a number of unique challenges associated with the scale-up of nano-structured materials are overcome.

  2. Line width roughness reduction by rational design of photoacid generator for sub-millisecond laser post-exposure bake

    Science.gov (United States)

    Jiang, Jing; Thompson, Michael O.; Ober, Christopher K.

    2014-03-01

    Sub-millisecond laser post-exposure bake (PEB) is an alternative technology to address the excessive acid diffusion for chemically amplified photoresist systems. By rationally designing the resist, laser post-exposure bake is able to improve the resolution and reduce the line width roughness (LWR) compared to patterns exposed under the same conditions but using conventional hotplate PEB. It was found that only the resist with high deprotection activation energy and low diffusion activation energy showed improved performance using laser PEB. Accordingly, a PAG was designed to have low acid diffusivity by binding the counter ions to a molecular glass core while keeping photophysical properties and processing conditions similar to a conventional PAG. By reducing the diffusivity of the counter ions, the PAG was able to further reduce LWR by 60% using laser PEB.

  3. Design and Evaluation of an Energy-Dense, Light-Weight Combat Ration to Sustain Land Forces Involved in High-Intensity, Short-Duration Operations

    Science.gov (United States)

    2015-03-01

    2009). The effects of geography, climate, stress and sleep deprivation are all likely to be detrimental to performance, however they have not been...UNCLASSIFIED UNCLASSIFIED Design and Evaluation of an Energy–Dense, Light– Weight Combat Ration to Sustain Land Forces Involved in High...Evaluation of an Energy–Dense, Light– Weight Combat Ration to Sustain Land Forces Involved in High–Intensity, Short–Duration Operations Executive

  4. Balancing intuition and rationality for improving innovation decision-making: The role of design consultancies

    NARCIS (Netherlands)

    Calabretta, G.; Gemser, G.; Wijnberg, N.M.; Hekkert, P.P.M.

    2013-01-01

    To contain risks and increase the profitability of innovation efforts, firms frequently engage in joint innovation activities with external sources of knowledge, like design consultancies. Innovation literature has given limited consideration to the strategic role that design consultancies can play

  5. A rational account of parasitic elements of the electronic modules in their design .

    Directory of Open Access Journals (Sweden)

    Nikolaenko O. V.

    2003-10-01

    Full Text Available The paper presents two approaches to ensure the functional properties of the designed electronic modules for different purposes, taking into account the influence of parasitic elements of their design implementation. The first of these approaches uses an iterative design process of adjustment based on circuit analysis in the CxCAD environment. In the second approach, the design limitations based on such analysis are previously worked out. It is also possible to combine the two approaches.

  6. Rational design of temperature swing adsorption cycles for post-combustion CO2 capture

    NARCIS (Netherlands)

    Joss, Lisa; Gazzani, Matteo|info:eu-repo/dai/nl/412517361; Mazzotti, Marco

    2017-01-01

    The design of temperature swing adsorption (TSA) cycles aimed at recovering the heavy product at high purity is investigated by model-based design and applied to the capture of CO2 from flue gases. This model based design strategy and an extensive parametric analysis enables gaining an understanding

  7. Rational design of reduced graphene oxide for superior performance of supercapacitor electrodes

    KAUST Repository

    Rasul, Shahid

    2016-10-24

    Strategies to synthesize reduced graphene oxide (rGO) abound but, in most studies, research teams select one particular oxidation-reduction method without providing a methodic reasoning for doing so. Herein, it is analyzed how diverse oxidation-reduction strategies commonly used can result in considerable performance differences of rGO for supercapacitor applications. Depending on the graphite oxidation method followed, the surface chemistry analysis of the products confirms that there is a marked disparity in the degree of oxidation and the nature of the oxygen functional groups present. Subsequent reduction of the oxidized graphite (using three different methods) showed that the maximum specific capacitance of rGOs produced from the classical Hummers\\' method was 128 F g−1 whereas an analogous material obtained from an improved Hummers\\' method reached ∼274 F g−1 (both via an hydrothermal reduction route). Besides showing that the improved oxidation method results in superior capacitance performance, explained by the higher number of structural defects allied to a surface chemistry where residual hydroxyl and epoxy functional groups predominate, this study highlights the need to rationalize the oxidation-reduction strategies followed when investigating applications of rGO materials.

  8. Rational design of MgB2 conductors toward practical applications

    Science.gov (United States)

    Patel, Dipak; Hossain, Md Shahriar Al; Motaman, Ashkan; Barua, Shaon; Shahabuddin, Mohammed; Kim, Jung Ho

    2014-09-01

    We report the research progress that has been made on developing rational MgB2 superconducting conductors toward practical applications. Owing to the poor performance of the critical current density (Jc) of bare MgB2, various techniques have been developed to overcome this obstacle. Among these, chemical doping has proved to be the most effective way to enhance the superconducting properties, such as Jc and the irreversibility field (Birr). More than a hundred different forms of dopants have been investigated over the past 13 years. Among these, the most effective dopants have been identified to be silicon carbide, carbon, and malic acid. The best results, Birr of 22 T and Jc of 40,000 A cm-2 at 4.2 K and 10 T, have been reported for malic acid treated MgB2 conductors, which have matched the benchmark performance of commercial low temperature superconductor wire such as Nb-Ti. This work will review and discuss the progress on MgB2 conductor development over the past few years at the University of Wollongong and Hyper Tech Research, Inc.

  9. Rational Design of Methodology-Independent Metal Parameters Using a Nonbonded Dummy Model.

    Science.gov (United States)

    Jiang, Yang; Zhang, Haiyang; Tan, Tianwei

    2016-07-12

    A nonbonded dummy model for metal ions is highly imperative for the computation of complex biological systems with for instance multiple metal centers. Here we present nonbonded dummy parameters of 11 divalent metallic cations, namely, Mg(2+), V(2+), Cr(2+), Mn(2+), Fe(2+), Co(2+), Ni(2+), Zn(2+), Cd(2+), Sn(2+), and Hg(2+), that are optimized to be compatible with three widely used water models (TIP3P, SPC/E, and TIP4P-EW). The three sets of metal parameters reproduce simultaneously the solvation free energies (ΔGsol), the ion-oxygen distance in the first solvation shell (IOD), and coordination numbers (CN) in explicit water with a relative error less than 1%. The main sources of errors to ΔGsol that arise from the boundary conditions and treatment of electrostatic interactions are corrected rationally, which ensures the independence of the proposed parameters on the methodology used in the calculation. This work will be of great value for the computational study of metal-containing biological systems.

  10. Activity improvement of a Kluyveromyces lactis aldo-keto reductase KlAKR via rational design.

    Science.gov (United States)

    Luo, Xi; Wang, Ya-Jun; Shen, Wei; Zheng, Yu-Guo

    2016-04-20

    Optically pure t-butyl 6-cyano-(3R, 5R)-dihydroxyhexanoate ((R)-1b) is the key chiral precursor for atorvastatin calcium, the most widely used cholesterol-lowering drug. Wild-type aldo-keto reductase KlAKR from Kluyveromyces lactis has ideal diastereoselectivity toward t-butyl 6-cyano-(5R)-hydroxy-3-oxohexanoate (1a, dep>99.5%) but poor activity. A rational engineering was used to improve the KlAKR activity. Based on homology modeling and molecular docking, two amino acid residues (295 and 296) were selected as mutation sites, and two rounds of site-saturation mutagenesis were performed. Among the mutants, KlAKR-Y295W/W296L exhibited the highest catalytic efficiency (kcat/Km) toward 1a up to 12.37s(-1)mM(-1), which was 11.25-fold higher than that of wild-type KlAKR. Moreover, the majority of mutations have no negative impact on stereoselectivity. Using KlAKR-Y295W/W296L coupled with Exiguobacterium sibiricum glucose dehydrogenase (EsGDH) for cofactor regeneration, (R)-1b was accumulated up to 162.7mM with dep value above 99.5%. KlAKR-Y295W/W296L represents a robust tool for (R)-1b synthesis.

  11. A rational approach to the design and synthesis of a new bradykinin B(1) receptor antagonist.

    Science.gov (United States)

    Bedos, P; Amblard, M; Subra, G; Dodey, P; Luccarini, J M; Paquet, J L; Pruneau, D; Aumelas, A; Martinez, J

    2000-06-15

    We have previously synthesized a potent and selective B(1) bradykinin receptor antagonist, JMV1645 (H-Lys-Arg-Pro-Hyp-Gly-Igl-Ser-D-BT-OH), containing a dipeptide mimetic ((3S)-amino-5-carbonylmethyl-2,3-dihydro-1, 5-benzothiazepin-4(5H)-one (D-BT) moiety) at the C-terminal. Analogues of this potent B(1) bradykinin receptor antagonist in which the central Pro(2)-Hyp(3)-Gly(4)-Igl(5) tetrapeptide has been replaced by constrained N-1-substituted-1,3,8-triazaspiro¿4. 5decan-4-one ring system were synthesized. Among these analogues, compound JMV1640 (1) was found to have an affinity of 24.10 +/- 9.48 nM for the human cloned B(1) receptor. It antagonized the ¿des-Arg(10)-kallidin-induced contraction of the human umbilical vein (pA(2) = 6.1 +/- 0.1). Compound 1 was devoid of agonist activity at the kinin B(1) receptor. Moreover, it did not bind to the human cloned B(2) receptor. Therefore, JMV1640 constitutes a lead compound for the rational search of nonpeptide B(1) receptor analogues based on the BK sequence.

  12. Rational design of broad spectrum antibacterial activity based on a clinically relevant enoyl-acyl carrier protein (ACP) reductase inhibitor.

    Science.gov (United States)

    Schiebel, Johannes; Chang, Andrew; Shah, Sonam; Lu, Yang; Liu, Li; Pan, Pan; Hirschbeck, Maria W; Tareilus, Mona; Eltschkner, Sandra; Yu, Weixuan; Cummings, Jason E; Knudson, Susan E; Bommineni, Gopal R; Walker, Stephen G; Slayden, Richard A; Sotriffer, Christoph A; Tonge, Peter J; Kisker, Caroline

    2014-06-06

    Determining the molecular basis for target selectivity is of particular importance in drug discovery. The ideal antibiotic should be active against a broad spectrum of pathogenic organisms with a minimal effect on human targets. CG400549, a Staphylococcus-specific 2-pyridone compound that inhibits the enoyl-acyl carrier protein reductase (FabI), has recently been shown to possess human efficacy for the treatment of methicillin-resistant Staphylococcus aureus infections, which constitute a serious threat to human health. In this study, we solved the structures of three different FabI homologues in complex with several pyridone inhibitors, including CG400549. Based on these structures, we rationalize the 65-fold reduced affinity of CG400549 toward Escherichia coli versus S. aureus FabI and implement concepts to improve the spectrum of antibacterial activity. The identification of different conformational states along the reaction coordinate of the enzymatic hydride transfer provides an elegant visual depiction of the relationship between catalysis and inhibition, which facilitates rational inhibitor design. Ultimately, we developed the novel 4-pyridone-based FabI inhibitor PT166 that retained favorable pharmacokinetics and efficacy in a mouse model of S. aureus infection with extended activity against Gram-negative and mycobacterial organisms. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  13. Rational Design of Broad Spectrum Antibacterial Activity Based on a Clinically Relevant Enoyl-Acyl Carrier Protein (ACP) Reductase Inhibitor*

    Science.gov (United States)

    Schiebel, Johannes; Chang, Andrew; Shah, Sonam; Lu, Yang; Liu, Li; Pan, Pan; Hirschbeck, Maria W.; Tareilus, Mona; Eltschkner, Sandra; Yu, Weixuan; Cummings, Jason E.; Knudson, Susan E.; Bommineni, Gopal R.; Walker, Stephen G.; Slayden, Richard A.; Sotriffer, Christoph A.; Tonge, Peter J.; Kisker, Caroline

    2014-01-01

    Determining the molecular basis for target selectivity is of particular importance in drug discovery. The ideal antibiotic should be active against a broad spectrum of pathogenic organisms with a minimal effect on human targets. CG400549, a Staphylococcus-specific 2-pyridone compound that inhibits the enoyl-acyl carrier protein reductase (FabI), has recently been shown to possess human efficacy for the treatment of methicillin-resistant Staphylococcus aureus infections, which constitute a serious threat to human health. In this study, we solved the structures of three different FabI homologues in complex with several pyridone inhibitors, including CG400549. Based on these structures, we rationalize the 65-fold reduced affinity of CG400549 toward Escherichia coli versus S. aureus FabI and implement concepts to improve the spectrum of antibacterial activity. The identification of different conformational states along the reaction coordinate of the enzymatic hydride transfer provides an elegant visual depiction of the relationship between catalysis and inhibition, which facilitates rational inhibitor design. Ultimately, we developed the novel 4-pyridone-based FabI inhibitor PT166 that retained favorable pharmacokinetics and efficacy in a mouse model of S. aureus infection with extended activity against Gram-negative and mycobacterial organisms. PMID:24739388

  14. Rational design and validation of an anti-protein kinase C active-state specific antibody based on conformational changes

    Science.gov (United States)

    Pena, Darlene Aparecida; Andrade, Victor Piana de; Silva, Gabriela Ávila Fernandes; Neves, José Ivanildo; Oliveira, Paulo Sergio Lopes de; Alves, Maria Julia Manso; Devi, Lakshmi A.; Schechtman, Deborah

    2016-01-01

    Protein kinase C (PKC) plays a regulatory role in key pathways in cancer. However, since phosphorylation is a step for classical PKC (cPKC) maturation and does not correlate with activation, there is a lack of tools to detect active PKC in tissue samples. Here, a structure-based rational approach was used to select a peptide to generate an antibody that distinguishes active from inactive cPKC. A peptide conserved in all cPKCs, C2Cat, was chosen since modeling studies based on a crystal structure of PKCβ showed that it is localized at the interface between the C2 and catalytic domains of cPKCs in an inactive kinase. Anti-C2Cat recognizes active cPKCs at least two-fold better than inactive kinase in ELISA and immunoprecipitation assays, and detects the temporal dynamics of cPKC activation upon receptor or phorbol stimulation. Furthermore, the antibody is able to detect active PKC in human tissue. Higher levels of active cPKC were observed in the more aggressive triple negative breast cancer tumors as compared to the less aggressive estrogen receptor positive tumors. Thus, this antibody represents a reliable, hitherto unavailable and a valuable tool to study PKC activation in cells and tissues. Similar structure-based rational design strategies can be broadly applied to obtain active-state specific antibodies for other signal transduction molecules. PMID:26911897

  15. Rational design and validation of an anti-protein kinase C active-state specific antibody based on conformational changes.

    Science.gov (United States)

    Pena, Darlene Aparecida; Andrade, Victor Piana de; Silva, Gabriela Ávila Fernandes; Neves, José Ivanildo; Oliveira, Paulo Sergio Lopes de; Alves, Maria Julia Manso; Devi, Lakshmi A; Schechtman, Deborah

    2016-02-25

    Protein kinase C (PKC) plays a regulatory role in key pathways in cancer. However, since phosphorylation is a step for classical PKC (cPKC) maturation and does not correlate with activation, there is a lack of tools to detect active PKC in tissue samples. Here, a structure-based rational approach was used to select a peptide to generate an antibody that distinguishes active from inactive cPKC. A peptide conserved in all cPKCs, C2Cat, was chosen since modeling studies based on a crystal structure of PKCβ showed that it is localized at the interface between the C2 and catalytic domains of cPKCs in an inactive kinase. Anti-C2Cat recognizes active cPKCs at least two-fold better than inactive kinase in ELISA and immunoprecipitation assays, and detects the temporal dynamics of cPKC activation upon receptor or phorbol stimulation. Furthermore, the antibody is able to detect active PKC in human tissue. Higher levels of active cPKC were observed in the more aggressive triple negative breast cancer tumors as compared to the less aggressive estrogen receptor positive tumors. Thus, this antibody represents a reliable, hitherto unavailable and a valuable tool to study PKC activation in cells and tissues. Similar structure-based rational design strategies can be broadly applied to obtain active-state specific antibodies for other signal transduction molecules.

  16. Rationally designed aberrant kinase-targeted endogenous protein nanomedicine against oncogene mutated/amplified refractory chronic myeloid leukemia.

    Science.gov (United States)

    Retnakumari, Archana P; Hanumanthu, Prasanna Lakshmi; Malarvizhi, Giridharan L; Prabhu, Raghuveer; Sidharthan, Neeraj; Thampi, Madhavan V; Menon, Deepthy; Mony, Ullas; Menon, Krishnakumar; Keechilat, Pavithran; Nair, Shantikumar; Koyakutty, Manzoor

    2012-11-05

    Deregulated protein kinases play a very critical role in tumorigenesis, metastasis, and drug resistance of cancer. Although molecularly targeted small molecule kinase inhibitors (SMI) are effective against many types of cancer, point mutations in the kinase domain impart drug resistance, a major challenge in the clinic. A classic example is chronic myeloid leukemia (CML) caused by BCR-ABL fusion protein, wherein a BCR-ABL kinase inhibitor, imatinib (IM), was highly successful in the early chronic phase of the disease, but failed in the advanced stages due to amplification of oncogene or point mutations in the drug-binding site of kinase domain. Here, by identifying critical molecular pathways responsible for the drug-resistance in refractory CML patient samples and a model cell line, we have rationally designed an endogenous protein nanomedicine targeted to both cell surface receptors and aberrantly activated secondary kinase in the oncogenic network. Molecular diagnosis revealed that, in addition to point mutations and amplification of oncogenic BCR-ABL kinase, relapsed/refractory patients exhibited significant activation of STAT5 signaling with correlative overexpression of transferrin receptors (TfR) on the cell membrane. Accordingly, we have developed a human serum albumin (HSA) based nanomedicine, loaded with STAT5 inhibitor (sorafenib), and surface conjugated the same with holo-transferrin (Tf) ligands for TfR specific delivery. This dual-targeted "transferrin conjugated albumin bound sorafenib" nanomedicine (Tf-nAlb-Soraf), prepared using aqueous nanoprecipitation method, displayed uniform spherical morphology with average size of ∼150 nm and drug encapsulation efficiency of ∼74%. TfR specific uptake and enhanced antileukemic activity of the nanomedicine was found maximum in the most drug resistant patient sample having the highest level of STAT5 and TfR expression, thereby confirming the accuracy of our rational design and potential of dual

  17. The Promiscuity of [beta]-Strand Pairing Allows for Rational Design of [beta]-Sheet Face Inversion

    Energy Technology Data Exchange (ETDEWEB)

    Makabe, Koki; Koide, Shohei (UC)

    2009-06-17

    Recent studies suggest the dominant role of main-chain H-bond formation in specifying {beta}-sheet topology. Its essentially sequence-independent nature implies a large degree of freedom in designing {beta}-sheet-based nanomaterials. Here we show rational design of {beta}-sheet face inversions by incremental deletions of {beta}-strands from the single-layer {beta}-sheet of Borrelia outer surface protein A. We show that a {beta}-sheet structure can be maintained when a large number of native contacts are removed and that one can design large-scale conformational transitions of a {beta}-sheet such as face inversion by exploiting the promiscuity of strand-strand interactions. High-resolution X-ray crystal structures confirmed the success of the design and supported the importance of main-chain H-bonds in determining {beta}-sheet topology. This work suggests a simple but effective strategy for designing and controlling nanomaterials based on {beta}-rich peptide self-assemblies.

  18. Rational design of a new Trypanosoma rangeli trans-sialidase for efficient sialylation of glycans.

    Directory of Open Access Journals (Sweden)

    Carsten Jers

    Full Text Available This paper reports rational engineering of Trypanosoma rangeli sialidase to develop an effective enzyme for a potentially important type of reactivity: production of sialylated prebiotic glycans. The Trypanosoma cruzi trans-sialidase and the homologous T. rangeli sialidase has previously been used to investigate the structural requirements for trans-sialidase activity. We observed that the T. cruzi trans-sialidase has a seven-amino-acid motif (197-203 at the border of the substrate binding cleft. The motif differs substantially in chemical properties and substitution probability from the homologous sialidase, and we hypothesised that this motif is important for trans-sialidase activity. The 197-203 motif is strongly positively charged with a marked change in hydrogen bond donor capacity as compared to the sialidase. To investigate the role of this motif, we expressed and characterised a T. rangeli sialidase mutant, Tr13. Conditions for efficient trans-sialylation were determined, and Tr13's acceptor specificity demonstrated promiscuity with respect to the acceptor molecule enabling sialylation of glycans containing terminal galactose and glucose and even monomers of glucose and fucose. Sialic acid is important in association with human milk oligosaccharides, and Tr13 was shown to sialylate a number of established and potential prebiotics. Initial evaluation of prebiotic potential using pure cultures demonstrated, albeit not selectively, growth of Bifidobacteria. Since the 197-203 motif stands out in the native trans-sialidase, is markedly different from the wild-type sialidase compared to previous mutants, and is shown here to confer efficient and broad trans-sialidase activity, we suggest that this motif can serve as a framework for future optimization of trans-sialylation towards prebiotic production.

  19. Rationalization of safety factors for breakwater design in hurricane-prone areas

    NARCIS (Netherlands)

    Tsimopoulou, V.; Kanning, W.; Verhagen, H.J.; Vrijling, J.K.

    2011-01-01

    This paper presents the development of a semi-probabilistic method for armour layer design of rubble mound breakwaters, which is based on the use of safety factors. The objective is to introduce an approach that is both attractive to designers and sufficiently reliable when a high degree of uncertai

  20. A Novel Rational Design Method for Laminated Composite Structures Exhibiting Complex Geometrically Nonlinear Buckling Behaviour

    DEFF Research Database (Denmark)

    Lindgaard, Esben; Lund, Erik

    2012-01-01

    This paper presents a novel FEM-based approach for fiber angle optimal design of laminated composite structures exhibiting complicated nonlinear buckling behavior, thus enabling design of lighter and more cost-effective structures. The approach accounts for the geometrically nonlinear behavior...

  1. Rationalization of safety factors for breakwater design in hurricane-prone areas

    NARCIS (Netherlands)

    Tsimopoulou, V.; Kanning, W.; Verhagen, H.J.; Vrijling, J.K.

    2011-01-01

    This paper presents the development of a semi-probabilistic method for armour layer design of rubble mound breakwaters, which is based on the use of safety factors. The objective is to introduce an approach that is both attractive to designers and sufficiently reliable when a high degree of uncertai

  2. Kinetic control over pathway complexity in supramolecular polymerization through modulating the energy landscape by rational molecular design.

    Science.gov (United States)

    Ogi, Soichiro; Fukui, Tomoya; Jue, Melinda L; Takeuchi, Masayuki; Sugiyasu, Kazunori

    2014-12-22

    Far-from-equilibrium thermodynamic systems that are established as a consequence of coupled equilibria are the origin of the complex behavior of biological systems. Therefore, research in supramolecular chemistry has recently been shifting emphasis from a thermodynamic standpoint to a kinetic one; however, control over the complex kinetic processes is still in its infancy. Herein, we report our attempt to control the time evolution of supramolecular assembly in a process in which the supramolecular assembly transforms from a J-aggregate to an H-aggregate over time. The transformation proceeds through a delicate interplay of these two aggregation pathways. We have succeeded in modulating the energy landscape of the respective aggregates by a rational molecular design. On the basis of this understanding of the energy landscape, programming of the time evolution was achieved through adjusting the balance between the coupled equilibria. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Final Report: Rational Design of Wide Band Gap Buffer Layers for High-Efficiency Thin-Film Photovoltaics

    Energy Technology Data Exchange (ETDEWEB)

    Lordi, Vincenzo [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2016-09-30

    The main objective of this project is to enable rational design of wide band gap buffer layer materials for CIGS thin-film PV by building understanding of the correlation of atomic-scale defects in the buffer layer and at the buffer/absorber interface with device electrical properties. Optimized wide band gap buffers are needed to reduce efficiency loss from parasitic absorption in the buffer. The approach uses first-principles materials simulations coupled with nanoscale analytical electron microscopy as well as device electrical characterization. Materials and devices are produced by an industrial partner in a manufacturing line to maximize relevance, with the goal of enabling R&D of new buffer layer compositions or deposition processes to push device efficiencies above 21%. Cadmium sulfide (CdS) is the reference material for analysis, as the prototypical high-performing buffer material.

  4. Comparative study of singlet oxygen production by photosensitiser dyes encapsulated in silicone: towards rational design of anti-microbial surfaces.

    Science.gov (United States)

    Noimark, Sacha; Salvadori, Enrico; Gómez-Bombarelli, Rafael; MacRobert, Alexander J; Parkin, Ivan P; Kay, Christopher W M

    2016-10-12

    Surfaces with built-in antimicrobial activity have the potential to reduce hospital-acquired infections. One promising strategy is to create functionalised surfaces which, following illumination with visible light, are able to generate singlet oxygen under aerobic conditions. In contrast to antibiotics, the mechanism of bacterial kill by species derived from reactions with singlet oxygen is completely unselective, therefore offering little room for evolutionary adaptation. Here we consider five commercially available organic photosensitiser dyes encapsulated in silicone polymer that show varied antimicrobial activity. We correlate density functional theory calculations with UV-Vis spectroscopy, electron paramagnetic resonance spectroscopy and singlet oxygen production measurements in order to define and test the elements required for efficacious antimicrobial activity. Our approach forms the basis for the rational in silico design and spectroscopic screening of simple and efficient self-sterilising surfaces made from cheap, low toxicity photosensitiser dyes encapsulated in silicone.

  5. Rational Design Synthesis and Evaluation of New Selective Inhibitors of Microbial Class II (Zinc Dependent) Fructose Bis-phosphate Aldolases

    Energy Technology Data Exchange (ETDEWEB)

    R Daher; M Coincon; M Fonvielle; P Gest; M Guerin; M Jackson; J Sygusch; M Therisod

    2011-12-31

    We report the synthesis and biochemical evaluation of several selective inhibitors of class II (zinc dependent) fructose bis-phosphate aldolases (Fba). The products were designed as transition-state analogues of the catalyzed reaction, structurally related to the substrate fructose bis-phosphate (or sedoheptulose bis-phosphate) and based on an N-substituted hydroxamic acid, as a chelator of the zinc ion present in active site. The compounds synthesized were tested on class II Fbas from various pathogenic microorganisms and, by comparison, on a mammalian class I Fba. The best inhibitor shows Ki against class II Fbas from various pathogens in the nM range, with very high selectivity (up to 105). Structural analyses of inhibitors in complex with aldolases rationalize and corroborate the enzymatic kinetics results. These inhibitors represent lead compounds for the preparation of new synthetic antibiotics, notably for tuberculosis prophylaxis.

  6. Rational design of a protein that binds integrin αvβ3 outside the ligand binding site

    Science.gov (United States)

    Turaga, Ravi Chakra; Yin, Lu; Yang, Jenny J.; Lee, Hsiauwei; Ivanov, Ivaylo; Yan, Chunli; Yang, Hua; Grossniklaus, Hans E.; Wang, Siming; Ma, Cheng; Sun, Li; Liu, Zhi-Ren

    2016-01-01

    Integrin αvβ3 expression is altered in various diseases and has been proposed as a drug target. Here we use a rational design approach to develop a therapeutic protein, which we call ProAgio, that binds to integrin αvβ3 outside the classical ligand-binding site. We show ProAgio induces apoptosis of integrin αvβ3-expressing cells by recruiting and activating caspase 8 to the cytoplasmic domain of integrin αvβ3. ProAgio also has anti-angiogenic activity and strongly inhibits growth of tumour xenografts, but does not affect the established vasculature. Toxicity analyses demonstrate that ProAgio is not toxic to mice. Our study reports a new integrin-targeting agent with a unique mechanism of action, and provides a template for the development of integrin-targeting therapeutics. PMID:27241473

  7. Rational Design of an α-Ketoamide-Based Near-Infrared Fluorescent Probe Specific for Hydrogen Peroxide in Living Systems.

    Science.gov (United States)

    Xie, Xilei; Yang, Xiu'e; Wu, Tianhong; Li, Yong; Li, Mengmeng; Tan, Qi; Wang, Xu; Tang, Bo

    2016-08-16

    Hydrogen peroxide, an important biomolecule, receives earnest attention because of its physiological and pathological functions. In this Article, we present the rational design, characterization, and biological application of a mitochondria-targetable NIR fluorescent sensor, Mito-NIRHP, for hydrogen peroxide visualization. Mito-NIRHP utilizes a unique reaction switch, α-ketoamide moiety, to turn on a highly specific, sensitive, and rapid fluorescence response toward hydrogen peroxide coupled with the intramolecular charge transfer strategy. Mito-NIRHP is competent to track endogenously produced hydrogen peroxide in both living cells and living animals. In addition, utilizing Mito-NIRHP, overgeneration of hydrogen peroxide during ischemia-reperfusion injury was directly visualized at both cell and organ levels.

  8. Structure-Based Rational Design of Prodrugs To Enable Their Combination with Polymeric Nanoparticle Delivery Platforms for Enhanced Antitumor Efficacy**

    Science.gov (United States)

    Wang, Hangxiang; Xie, Haiyang; Wu, Jiaping; Wei, Xuyong; Zhou, Lin; Xu, Xiao; Zheng, Shusen

    2014-01-01

    Drug-loaded nanoparticles (NPs) are of particular interest for efficient cancer therapy due to their improved drug delivery and therapeutic index in various types of cancer. However, the encapsulation of many chemotherapeutics into delivery NPs is often hampered by their unfavorable physicochemical properties. Here, we employed a drug reform strategy to construct a small library of SN-38 (7-ethyl-10-hydroxycamptothecin)-derived prodrugs, in which the phenolate group was modified with a variety of hydrophobic moieties. This esterification fine-tuned the polarity of the SN-38 molecule and enhanced the lipophilicity of the formed prodrugs, thereby inducing their self-assembly into biodegradable poly(ethylene glycol)-block-poly(d,l-lactic acid) (PEG-PLA) nanoparticulate structures. Our strategy combining the rational engineering of prodrugs with the pre-eminent features of conventionally used polymeric materials should open new avenues for designing more potent drug delivery systems as a therapeutic modality. PMID:25196427

  9. Rational design of a protein that binds integrin αvβ3 outside the ligand binding site.

    Science.gov (United States)

    Turaga, Ravi Chakra; Yin, Lu; Yang, Jenny J; Lee, Hsiauwei; Ivanov, Ivaylo; Yan, Chunli; Yang, Hua; Grossniklaus, Hans E; Wang, Siming; Ma, Cheng; Sun, Li; Liu, Zhi-Ren

    2016-05-31

    Integrin αvβ3 expression is altered in various diseases and has been proposed as a drug target. Here we use a rational design approach to develop a therapeutic protein, which we call ProAgio, that binds to integrin αvβ3 outside the classical ligand-binding site. We show ProAgio induces apoptosis of integrin αvβ3-expressing cells by recruiting and activating caspase 8 to the cytoplasmic domain of integrin αvβ3. ProAgio also has anti-angiogenic activity and strongly inhibits growth of tumour xenografts, but does not affect the established vasculature. Toxicity analyses demonstrate that ProAgio is not toxic to mice. Our study reports a new integrin-targeting agent with a unique mechanism of action, and provides a template for the development of integrin-targeting therapeutics.

  10. Rational design of organophosphorus hydrolase with high catalytic efficiency for detoxifying a V-type nerve agent.

    Science.gov (United States)

    Jeong, Young-Su; Choi, Jung Min; Kyeong, Hyun-Ho; Choi, Jae-Youl; Kim, Eui-Joong; Kim, Hak-Sung

    2014-07-01

    V-type nerve agents, known as VX, are organophosphate (OP) compounds, and show extremely toxic effects on human and animals by causing cholinergic overstimulation of synapses. The bacterial organophosphorus hydrolase (OPH) has attracted much attention for detoxifying V-type agents through hydrolysis of the P-S bond. However, low catalytic efficiency of OPH has limited the practical use of the enzyme. Here we present rational design of OPH with high catalytic efficiency for a V-type nerve agent. Based on the model structure of the enzyme and substrate docking simulation, we predicted the key residues that appear to enhance the access of the substrate to the active site of the enzyme, and constructed numerous OPH mutants. Of them, double mutant, L271/Y309A, was shown to exhibit a 150-fold higher catalytic efficiency for VX than the wild-type.

  11. Controlling resistant bacteria with a novel class of β-lactamase inhibitor peptides: from rational design to in vivo analyses

    Science.gov (United States)

    Mandal, Santi M.; Migliolo, Ludovico; Silva, Osmar N.; Fensterseifer, Isabel C. M.; Faria-Junior, Celio; Dias, Simoni C.; Basak, Amit; Hazra, Tapas K.; Franco, Octávio L.

    2014-01-01

    Peptide rational design was used here to guide the creation of two novel short β-lactamase inhibitors, here named dBLIP-1 and -2, with length of five amino acid residues. Molecular modeling associated with peptide synthesis improved bactericidal efficacy in addition to amoxicillin, ampicillin and cefotaxime. Docked structures were consistent with calorimetric analyses against bacterial β-lactamases. These two compounds were further tested in mice. Whereas commercial antibiotics alone failed to cure mice infected with Staphylococcus aureus and Escherichia coli expressing β-lactamases, infection was cleared when treated with antibiotics in combination with dBLIPs, clearly suggesting that peptides were able to neutralize bacterial resistance. Moreover, immunological assays were also performed showing that dBLIPs were unable to modify mammalian immune response in both models, reducing the risks of collateral effects. In summary, the unusual peptides here described provide leads to overcome β-lactamase-based resistance, a remarkable clinical challenge. PMID:25109311

  12. Rational Design of Diketopyrrolopyrrole-Based Small Moleculesas Donating Materials for Organic Solar Cells

    Directory of Open Access Journals (Sweden)

    Ruifa Jin

    2015-08-01

    Full Text Available A series of diketopyrrolopyrrole-based small molecules have been designed toexplore their optical, electronic, and charge transport properties as organic solar cell(OSCs materials. The calculation results showed that the designed molecules can lowerthe band gap and extend the absorption spectrum towards longer wavelengths.The designed molecules own the large longest wavelength of absorption spectra,the oscillator strength, and absorption region values. The optical, electronic, and chargetransport properties of the designed molecules are affected by the introduction of differentπ-bridges and end groups. We have also predicted the mobility of the designed moleculewith the lowest total energies. Our results reveal that the designed molecules are expectedto be promising candidates for OSC materials. Additionally, the designed molecules areexpected to be promising candidates for electron and/or hole transport materials. On thebasis of our results, we suggest that molecules under investigation are suitable donors for[6,6]-phenyl-C61-butyric acid methyl ester (PCBM and its derivatives as acceptors of OSCs.

  13. Rational Design of Diketopyrrolopyrrole-Based Small Molecules as Donating Materials for Organic Solar Cells

    Science.gov (United States)

    Jin, Ruifa; Wang, Kai

    2015-01-01

    A series of diketopyrrolopyrrole-based small molecules have been designed to explore their optical, electronic, and charge transport properties as organic solar cell (OSCs) materials. The calculation results showed that the designed molecules can lower the band gap and extend the absorption spectrum towards longer wavelengths. The designed molecules own the large longest wavelength of absorption spectra, the oscillator strength, and absorption region values. The optical, electronic, and charge transport properties of the designed molecules are affected by the introduction of different π-bridges and end groups. We have also predicted the mobility of the designed molecule with the lowest total energies. Our results reveal that the designed molecules are expected to be promising candidates for OSC materials. Additionally, the designed molecules are expected to be promising candidates for electron and/or hole transport materials. On the basis of our results, we suggest that molecules under investigation are suitable donors for [6,6]-phenyl-C61-butyric acid methyl ester (PCBM) and its derivatives as acceptors of OSCs. PMID:26343640

  14. Reflections on architectural design education: The return of rationalism in the studio

    Directory of Open Access Journals (Sweden)

    Fathi Bashier

    2014-12-01

    The Department of Architecture and Urban Planning at the Ethiopian Institute of Technology EiT of Mekelle University (MU is currently developing a research program in which the development of and reflection on design methods is a key research area. Within this framework, the present study is intends to be an introductory effort to guide future empirical research. The present study aims to describe the design process of architects, and introduces theoretical and technical frameworks. The integrated design paradigm as a system of inquiry within the spatial relationship strategy is framed.

  15. Rational design and one-step formation of multifunctional gel transducer for simple fabrication of integrated electrochemical biosensors.

    Science.gov (United States)

    Yu, Ping; Zhou, Heng; Cheng, Hanjun; Qian, Qin; Mao, Lanqun

    2011-07-15

    This study demonstrates a new strategy to simplify the biosensor fabrication and thus minimize the biosensor-to-biosensor deviation through rational design and one-step formation of a multifunctional gel electronic transducer integrating all elements necessitated for efficiently transducing the biorecognition events to signal readout, by using glucose dehydrogenase (GDH) based electrochemical biosensor as an example. To meet the requirements for preparing integrated biosensors and retaining electronic and ionic conductivities for electronically transducing process, ionic liquids (ILs) with enzyme cofactor (i.e., oxidized form of nicotinamide adenine dinucleotide) as the anion were synthesized and used to form a bucky gel with single-walled carbon nanotubes, in which methylene green electrocatalyst was stably encapsulated for the oxidation of nicotinamide adenine dinucleotide. With such kind of rationally designed and one-step-formed multifunctional gel as the electronic transducer, the GDH-based electrochemical biosensors were simply fabricated by polishing the electrodes onto the gel followed by enzyme immobilization. This capability greatly simplifies the biosensor fabrication, prolongs the stability of the biosensors, and, more remarkably, minimizes the biosensor-to-biosensor deviation. The relative standard deviations obtained both with one electrode for the repeated measurements of glucose and with the different electrodes prepared with the same method for the concurrent measurements of glucose with the same concentration were 3.30% (n = 7) and 4.70% (n = 6), respectively. These excellent properties of the multifunctional gel-based biosensors substantially enable them to well-satisfy the pressing need of rapid measurements, for example, environmental monitoring, food analysis, and clinical diagnoses.

  16. Model-based rational feedback controller design for closed-loop deep brain stimulation of Parkinson's disease

    Science.gov (United States)

    Gorzelic, P.; Schiff, S. J.; Sinha, A.

    2013-04-01

    Objective. To explore the use of classical feedback control methods to achieve an improved deep brain stimulation (DBS) algorithm for application to Parkinson's disease (PD). Approach. A computational model of PD dynamics was employed to develop model-based rational feedback controller design. The restoration of thalamocortical relay capabilities to patients suffering from PD is formulated as a feedback control problem with the DBS waveform serving as the control input. Two high-level control strategies are tested: one that is driven by an online estimate of thalamic reliability, and another that acts to eliminate substantial decreases in the inhibition from the globus pallidus interna (GPi) to the thalamus. Control laws inspired by traditional proportional-integral-derivative (PID) methodology are prescribed for each strategy and simulated on this computational model of the basal ganglia network. Main Results. For control based upon thalamic reliability, a strategy of frequency proportional control with proportional bias delivered the optimal control achieved for a given energy expenditure. In comparison, control based upon synaptic inhibitory output from the GPi performed very well in comparison with those of reliability-based control, with considerable further reduction in energy expenditure relative to that of open-loop DBS. The best controller performance was amplitude proportional with derivative control and integral bias, which is full PID control. We demonstrated how optimizing the three components of PID control is feasible in this setting, although the complexity of these optimization functions argues for adaptive methods in implementation. Significance. Our findings point to the potential value of model-based rational design of feedback controllers for Parkinson's disease.

  17. Rational Design of Bioelectrochemically Multifunctional Film with Oxidase, Ferrocene, and Graphene Oxide for Development of in Vivo Electrochemical Biosensors.

    Science.gov (United States)

    Wang, Xiuyun; Li, Qian; Xu, Jingjing; Wu, Shuo; Xiao, Tongfang; Hao, Jie; Yu, Ping; Mao, Lanqun

    2016-06-01

    This study demonstrates a new strategy to develop in vivo electrochemical biosensors through rational design and simple formation of bioelectrochemically multifunctional film (BMF). The BMF is rationally designed by first efficiently incorporating oxidase, ferrocene mediator, and graphene oxide into polymaleimidostyrene/polystyrene (PMS/PS) matrix to form a homogeneous mixture and then simply formed by drop-coating the mixture onto solid conducting substrate. By using the as-formed BMF, electrochemical biosensors could be constructed with a technical simplicity and high reproducibility. To illustrate the BMF-based biosensors for in vivo applications, we directly couple the biosensors to in vivo microdialysis to establish an online electrochemical system (OECS) for in vivo monitoring of glucose in rat auditory cortex during salicylate-induced tinnitus model. The OECS with the BMF-based biosensor as the detector shows a linear response toward glucose within a concentration range from 50 to 500 μM with a detection limit of 10 μM (S/N = 3). Additionally, the OECS is stable and does not suffer from the interference from the electroactive species endogenously coexisting in the brain microdialysate. With the BMF-based OECS, the basal level of glucose in the microdialysate continuously sampled from rat auditory cortex is determined to be 120 ± 10 μM (n = 5). After the rats were administrated with salicylate to induce transient tinnitus, the microdialysate glucose concentration in the rat auditory cortex remarkably increased to 433 ± 190 μM (n = 5) at the time point of 1.5 h. This study essentially offers a new, technically simple and reproducible approach to development of in vivo electrochemical biosensors, which is envisaged to be relatively useful for understanding of the molecular basis of brain functions.

  18. Improving the specific activity of β-mannanase from Aspergillus niger BK01 by structure-based rational design.

    Science.gov (United States)

    Huang, Jian-Wen; Chen, Chun-Chi; Huang, Chun-Hsiang; Huang, Ting-Yung; Wu, Tzu-Hui; Cheng, Ya-Shan; Ko, Tzu-Ping; Lin, Cheng-Yen; Liu, Je-Ruei; Guo, Rey-Ting

    2014-03-01

    β-Mannanase has found various biotechnological applications because it is capable of degrading mannans into smaller sugar components. A highly potent example is the thermophilic β-mannanase from Aspergillus niger BK01 (ManBK), which can be efficiently expressed in industrial yeast strains and is thus an attractive candidate for commercial utilizations. In order to understand the molecular mechanism, which helps in strategies to improve the enzyme's performance that would meet industrial demands, 3D-structural information is a great asset. Here, we present the 1.57Å crystal structure of ManBK. The protein adopts a typical (β/α)8 fold that resembles the other GH5 family members. Polysaccharides were subsequently modeled into the substrate binding groove to identify the residues and structural features that may be involved in the catalytic reaction. Based on the structure, rational design was conducted to engineer ManBK in an attempt to enhance its enzymatic activity. Among the 23 mutants that we constructed, the most promising Y216W showed an 18±2.7% increase in specific activity by comparison with the wild type enzyme. The optimal temperature and heat tolerance profiles of Y216W were similar to those of the wild type, manifesting a preserved thermostability. Kinetic studies showed that Y216W has higher kcat values than the wild type enzyme, suggesting a faster turnover rate of catalysis. In this study we applied rational design to ManBK by using its crystal structure as a basis and identified the Y216W mutant that shows great potentials in industrial applications.

  19. Improving a natural CaMKII inhibitor by random and rational design.

    Directory of Open Access Journals (Sweden)

    Steven J Coultrap

    Full Text Available BACKGROUND: CaM-KIIN has evolved to inhibit stimulated and autonomous activity of the Ca(2+/calmodulin (CaM-dependent protein kinase II (CaMKII efficiently, selectively, and potently (IC50 ∼100 nM. The CN class of peptides, derived from the inhibitory region of CaM-KIIN, provides powerful new tools to study CaMKII functions. The goal of this study was to identify the residues required for CaMKII inhibition, and to assess if artificial mutations could further improve the potency achieved during evolution. METHODOLOGY/PRINCIPAL FINDINGS: First, the minimal region with full inhibitory potency was identified (CN19 by determining the effect of truncated peptides on CaMKII activity in biochemical assays. Then, individual residues of CN19 were mutated. Most individual Ala substitutions decreased potency of CaMKII inhibition, however, P3A, K13A, and R14A increased potency. Importantly, this initial Ala scan suggested a specific interaction of the region around R11 with the CaMKII substrate binding site, which was exploited for further rational mutagenesis to generate an optimized pseudo-substrate sequence. Indeed, the potency of the optimized peptide CN19o was >250fold improved (IC50 <0.4 nM, and CN19o has characteristics of a tight-binding inhibitor. The selectivity for CaMKII versus CaMKI was similarly improved (to almost 100,000fold for CN19o. A phospho-mimetic S12D mutation decreased potency, indicating potential for regulation by cellular signaling. Consistent with importance of this residue in inhibition, most other S12 mutations also significantly decreased potency, however, mutation to V or Q did not. CONLUSIONS/SIGNIFICANCE: These results provide improved research tools for studying CaMKII function, and indicate that evolution fine-tuned CaM-KIIN not for maximal potency of CaMKII inhibition, but for lower potency that may be optimal for dynamic regulation of signal transduction.

  20. Insights into the Rational Design of Multi-Functional Fullerene Systems for Application in Blended Heterojunction Organic Solar Cells

    Science.gov (United States)

    Cowart, John S., Jr.

    Elucidating the structure-function relationships of organic semiconductors has been central to the advancement of organic photovoltaics (OPVs). In particular, enhancing the performance of p-type materials in disordered heterojunctions is broadly acknowledged as the principal factor leading to current trends of improved power conversion efficiencies (PCEs). However, two additional factors are crucially important for the next step forward in improving PCEs. First, investigating the influence, design and synthesis of new n-type materials, specifically fullerene acceptors, is of high importance. Second, because fullerene performance is often compromised by the morphological disorder of bulk heterojunctions, developing fullerenes systems that retain fidelity within disordered blends is also of broad interest. In light of these challenges, the field has witnessed a notable shift towards developing a comprehensive understanding of the design rules needed to advance the performance of fullerene acceptors in bulk heterojunctions. This work spotlights two multi-functional fullerene systems designed for blended heterojunctions. First, the synthesis of several novel fullerene-dye adducts with enhanced photon absorption will be presented. The ability of these adducts to absorb visible light in their pure state was evaluated and systematically examined versus their capacity to complement the absorption of low band gap donors and mediate charge transport in bulk heterojunctions. Second, mixed fullerene ternary blends were introduced as a strategy to stabilize the morphology in bulk heterojunctions and prolong operational lifetimes of OPV devices. Combined, these two systems offer unique insight into the rational design of fullerenes for their application in blended systems.

  1. A crystal structure-guided rational design switching non-carbohydrate inhibitors' specificity between two β-GlcNAcase homologs

    Science.gov (United States)

    Liu, Tian; Guo, Peng; Zhou, Yong; Wang, Jing; Chen, Lei; Yang, Huibin; Qian, Xuhong; Yang, Qing

    2014-01-01

    Selective inhibition of function-specific β-GlcNAcase has great potential in terms of drug design and biological research. The symmetrical bis-naphthalimide M-31850 was previously obtained by screening for specificity against human glycoconjugate-lytic β-GlcNAcase. Using protein-ligand co-crystallization and molecular docking, we designed an unsymmetrical dyad of naphthalimide and thiadiazole, Q2, that changes naphthalimide specificity from against a human glycoconjugate-lytic β-GlcNAcase to against insect and bacterial chitinolytic β-GlcNAcases. The crystallographic and in silico studies reveal that the naphthalimide ring can be utilized to bind different parts of these enzyme homologs, providing a new starting point to design specific inhibitors. Moreover, Q2-induced closure of the substrate binding pocket is the structural basis for its 13-fold increment in inhibitory potency. Q2 is the first non-carbohydrate inhibitor against chitinolytic β-GlcNAcases. This study provides a useful example of structure-based rationally designed inhibitors as potential pharmaceuticals or pesticides. PMID:25155420

  2. STRATEGIES FOR PACKAGE WASTE REDUCING THROUGH A RATIONAL AND EFFECTIVE DESIGN

    Directory of Open Access Journals (Sweden)

    Barsan Lucian

    2017-05-01

    Full Text Available The paper presents a number of regulations which should be respected when designing a package. Package represents a large percent of the total waste, therefore we should focus on this ‘type’ of product to reduce the resources used and also to reduce the waste through reusing and recycling. Design is strongly involved in this activity analysing the package lifecycle and trying to respect some rules, which represent the fundaments for a design strategy. Regulations regarding materials choosing, materials combinations, choosing the most adequate process are presented. Either the package is reusable or not, it must be recyclable. The possibility of simply dismantle the package for sorting the materials represent another requirement for the design process. Examples of good practice are presented as a case study.

  3. Fluorescence detection of natural RNA using rationally designed "clickable" oligonucleotide probes

    DEFF Research Database (Denmark)

    Okholm, Anders; Kjems, Jørgen; Astakhova, Kira

    2014-01-01

    Herein a reliable approach to the design of effective fluorescent probes for RNA detection is described. The fluorescence signalling of hybridization by internally positioned polyaromatic hydrocarbons and rhodamine dyes was achieved with a low fluorescence background signal, high fluorescence...

  4. Rational Design of Fluorescent Phthalazinone Derivatives for One- and Two-Photon Imaging.

    Science.gov (United States)

    Yang, Lingfei; Zhu, Yuanjun; Shui, Mengyang; Zhou, Tongliang; Cai, Yuanbo; Wang, Wei; Xu, Fengrong; Niu, Yan; Wang, Chao; Zhang, Jun-Long; Xu, Ping; Yuan, Lan; Liang, Lei

    2016-08-22

    Phthalazinone derivatives were designed as optical probes for one- and two-photon fluorescence microscopy imaging. The design strategy involves stepwise extension and modification of pyridazinone by 1) expansion of pyridazinone to phthalazinone, a larger conjugated system, as the electron acceptor, 2) coupling of electron-donating aromatic groups such as N,N-diethylaminophenyl, thienyl, naphthyl, and quinolyl to the phthalazinone, and 3) anchoring of an alkyl chain to the phthalazinone with various terminal substituents such as triphenylphosphonio, morpholino, triethylammonio, N-methylimidazolio, pyrrolidino, and piperidino. Theoretical calculations were utilized to verify the initial design. The desired fluorescent probes were synthesized by two different routes in considerable yields. Twenty-two phthalazinone derivatives were synthesized and their photophysical properties were measured. Selected compounds were applied in cell imaging, and valuable information was obtained. Furthermore, the designed compounds showed excellent performance in two-photon microscopic imaging of mouse brain slices.

  5. Combined Bioinformatic and Rational Design Approach To Develop Antimicrobial Peptides against Mycobacterium tuberculosis

    Science.gov (United States)

    Pearson, C. Seth; Kloos, Zachary; Murray, Brian; Tabe, Ebot; Gupta, Monica; Kwak, Jun Ha; Karande, Pankaj

    2016-01-01

    Drug-resistant pathogens are a growing problem, and novel strategies are needed to combat this threat. Among the most significant of these resistant pathogens is Mycobacterium tuberculosis, which is an unusually difficult microbial target due to its complex membrane. Here, we design peptides for specific activity against M. tuberculosis using a combination of “database filtering” bioinformatics, protein engineering, and de novo design. Several variants of these peptides are structurally characterized to validate the design process. The designed peptides exhibit potent activity (MIC values as low as 4 μM) against M. tuberculosis and also exhibit broad activity against a host of other clinically relevant pathogenic bacteria such as Gram-positive bacteria (Streptococcus) and Gram-negative bacteria (Escherichia coli). They also display excellent selectivity, with low cytotoxicity against cultured macrophages and lung epithelial cells. These first-generation antimicrobial peptides serve as a platform for the design of antibiotics and for investigating structure-activity relationships in the context of the M. tuberculosis membrane. The antimicrobial peptide design strategy is expected to be generalizable for any pathogen for which an activity database can be created. PMID:26902758

  6. Biophysically Inspired Rational Design of Structured Chimeric Substrates for DNAzyme Cascade Engineering

    Science.gov (United States)

    Lakin, Matthew R.; Brown, Carl W.; Horwitz, Eli K.; Fanning, M. Leigh; West, Hannah E.; Stefanovic, Darko; Graves, Steven W.

    2014-01-01

    The development of large-scale molecular computational networks is a promising approach to implementing logical decision making at the nanoscale, analogous to cellular signaling and regulatory cascades. DNA strands with catalytic activity (DNAzymes) are one means of systematically constructing molecular computation networks with inherent signal amplification. Linking multiple DNAzymes into a computational circuit requires the design of substrate molecules that allow a signal to be passed from one DNAzyme to another through programmed biochemical interactions. In this paper, we chronicle an iterative design process guided by biophysical and kinetic constraints on the desired reaction pathways and use the resulting substrate design to implement heterogeneous DNAzyme signaling cascades. A key aspect of our design process is the use of secondary structure in the substrate molecule to sequester a downstream effector sequence prior to cleavage by an upstream DNAzyme. Our goal was to develop a concrete substrate molecule design to achieve efficient signal propagation with maximal activation and minimal leakage. We have previously employed the resulting design to develop high-performance DNAzyme-based signaling systems with applications in pathogen detection and autonomous theranostics. PMID:25347066

  7. Biophysically inspired rational design of structured chimeric substrates for DNAzyme cascade engineering.

    Science.gov (United States)

    Lakin, Matthew R; Brown, Carl W; Horwitz, Eli K; Fanning, M Leigh; West, Hannah E; Stefanovic, Darko; Graves, Steven W

    2014-01-01

    The development of large-scale molecular computational networks is a promising approach to implementing logical decision making at the nanoscale, analogous to cellular signaling and regulatory cascades. DNA strands with catalytic activity (DNAzymes) are one means of systematically constructing molecular computation networks with inherent signal amplification. Linking multiple DNAzymes into a computational circuit requires the design of substrate molecules that allow a signal to be passed from one DNAzyme to another through programmed biochemical interactions. In this paper, we chronicle an iterative design process guided by biophysical and kinetic constraints on the desired reaction pathways and use the resulting substrate design to implement heterogeneous DNAzyme signaling cascades. A key aspect of our design process is the use of secondary structure in the substrate molecule to sequester a downstream effector sequence prior to cleavage by an upstream DNAzyme. Our goal was to develop a concrete substrate molecule design to achieve efficient signal propagation with maximal activation and minimal leakage. We have previously employed the resulting design to develop high-performance DNAzyme-based signaling systems with applications in pathogen detection and autonomous theranostics.

  8. Combined Bioinformatic and Rational Design Approach To Develop Antimicrobial Peptides against Mycobacterium tuberculosis.

    Science.gov (United States)

    Pearson, C Seth; Kloos, Zachary; Murray, Brian; Tabe, Ebot; Gupta, Monica; Kwak, Jun Ha; Karande, Pankaj; McDonough, Kathleen A; Belfort, Georges

    2016-05-01

    Drug-resistant pathogens are a growing problem, and novel strategies are needed to combat this threat. Among the most significant of these resistant pathogens is Mycobacterium tuberculosis, which is an unusually difficult microbial target due to its complex membrane. Here, we design peptides for specific activity against M. tuberculosis using a combination of "database filtering" bioinformatics, protein engineering, and de novo design. Several variants of these peptides are structurally characterized to validate the design process. The designed peptides exhibit potent activity (MIC values as low as 4 μM) against M. tuberculosis and also exhibit broad activity against a host of other clinically relevant pathogenic bacteria such as Gram-positive bacteria (Streptococcus) and Gram-negative bacteria (Escherichia coli). They also display excellent selectivity, with low cytotoxicity against cultured macrophages and lung epithelial cells. These first-generation antimicrobial peptides serve as a platform for the design of antibiotics and for investigating structure-activity relationships in the context of the M. tuberculosis membrane. The antimicrobial peptide design strategy is expected to be generalizable for any pathogen for which an activity database can be created.

  9. Biophysically inspired rational design of structured chimeric substrates for DNAzyme cascade engineering.

    Directory of Open Access Journals (Sweden)

    Matthew R Lakin

    Full Text Available The development of large-scale molecular computational networks is a promising approach to implementing logical decision making at the nanoscale, analogous to cellular signaling and regulatory cascades. DNA strands with catalytic activity (DNAzymes are one means of systematically constructing molecular computation networks with inherent signal amplification. Linking multiple DNAzymes into a computational circuit requires the design of substrate molecules that allow a signal to be passed from one DNAzyme to another through programmed biochemical interactions. In this paper, we chronicle an iterative design process guided by biophysical and kinetic constraints on the desired reaction pathways and use the resulting substrate design to implement heterogeneous DNAzyme signaling cascades. A key aspect of our design process is the use of secondary structure in the substrate molecule to sequester a downstream effector sequence prior to cleavage by an upstream DNAzyme. Our goal was to develop a concrete substrate molecule design to achieve efficient signal propagation with maximal activation and minimal leakage. We have previously employed the resulting design to develop high-performance DNAzyme-based signaling systems with applications in pathogen detection and autonomous theranostics.

  10. Baseline rationing

    DEFF Research Database (Denmark)

    Hougaard, Jens Leth; Moreno-Ternero, Juan D.; Østerdal, Lars Peter Raahave

    The standard problem of adjudicating conflicting claims describes a situation in which a given amount of a divisible good has to be allocated among agents who hold claims against it exceeding the available amount. This paper considers more general rationing problems in which, in addition to claims......, there exist baselines (to be interpreted as objective entitlements, ideal targets, or past consumption) that might play an important role in the allocation process. The model we present is able to accommodate real-life rationing situations, ranging from resource allocation in the public health care sector...... to international protocols for the reduction of greenhouse emissions, or water distribution in drought periods. We define a family of allocation methods for such general rationing problems - called baseline rationing rules - and provide an axiomatic characterization for it. Any baseline rationing rule within...

  11. Roles of Glutamates and Metal ions in a Rationally Designed Nitric Oxide Reductase Based on Myoglobin

    Energy Technology Data Exchange (ETDEWEB)

    Y Lin; N Yeung; Y Gao; K Miner; S Tian; H Robinson; Y Lu

    2011-12-31

    A structural and functional model of bacterial nitric oxide reductase (NOR) has been designed by introducing two glutamates (Glu) and three histidines (His) in sperm whale myoglobin. X-ray structural data indicate that the three His and one Glu (V68E) residues bind iron, mimicking the putative FeB site in NOR, while the second Glu (I107E) interacts with a water molecule and forms a hydrogen bonding network in the designed protein. Unlike the first Glu (V68E), which lowered the heme reduction potential by {approx}110 mV, the second Glu has little effect on the heme potential, suggesting that the negatively charged Glu has a different role in redox tuning. More importantly, introducing the second Glu resulted in a {approx}100% increase in NOR activity, suggesting the importance of a hydrogen bonding network in facilitating proton delivery during NOR reactivity. In addition, EPR and X-ray structural studies indicate that the designed protein binds iron, copper, or zinc in the FeB site, each with different effects on the structures and NOR activities, suggesting that both redox activity and an intermediate five-coordinate heme-NO species are important for high NOR activity. The designed protein offers an excellent model for NOR and demonstrates the power of using designed proteins as a simpler and more well-defined system to address important chemical and biological issues.

  12. Roles of glutamates and metal ions in a rationally designed nitric oxide reductase based on myoglobin

    Energy Technology Data Exchange (ETDEWEB)

    Lin, Y.W.; Robinson, H.; Yeung, N.; Gao, Y.-G.; Miner, K. D.; Tian, S.; Lu, Y.

    2010-05-11

    A structural and functional model of bacterial nitric oxide reductase (NOR) has been designed by introducing two glutamates (Glu) and three histidines (His) in sperm whale myoglobin. X-ray structural data indicate that the three His and one Glu (V68E) residues bind iron, mimicking the putative FeB site in NOR, while the second Glu (I107E) interacts with a water molecule and forms a hydrogen bonding network in the designed protein. Unlike the first Glu (V68E), which lowered the heme reduction potential by {approx}110 mV, the second Glu has little effect on the heme potential, suggesting that the negatively charged Glu has a different role in redox tuning. More importantly, introducing the second Glu resulted in a {approx}100% increase in NOR activity, suggesting the importance of a hydrogen bonding network in facilitating proton delivery during NOR reactivity. In addition, EPR and X-ray structural studies indicate that the designed protein binds iron, copper, or zinc in the FeB site, each with different effects on the structures and NOR activities, suggesting that both redox activity and an intermediate five-coordinate heme-NO species are important for high NOR activity. The designed protein offers an excellent model for NOR and demonstrates the power of using designed proteins as a simpler and more well-defined system to address important chemical and biological issues.

  13. Standby Gasoline Rationing Plan

    Energy Technology Data Exchange (ETDEWEB)

    None

    1980-06-01

    The final rules adopted by the President for a Standby Gasoline Rationing Plan are presented. The plan provides that eligibility for ration allotments will be determined primarily on the basis of motor vehicle registrations, taking into account historical differences in the use of gasoline among states. The regulations also provide authority for supplemental allotments to firms so that their allotment will equal a specified percentage of gasoline use during a base period. Priority classifications, i.e., agriculture, defense, etc., are established to assure adequate gasoline supplies for designated essential services. Ration rights must be provided by end-users to their suppliers for each gallon sold. DOE will regulate the distribution of gasoline at the wholesale level according to the transfer by suppliers of redeemed ration rights and the gasoline allocation regulations. Ration rights are transferable. A ration banking system is created to facilitate transfers of ration rights. Each state will be provided with a reserve of ration rights to provide for hardship needs and to alleviate inequities. (DC)

  14. A minimal length rigid helical peptide motif allows rational design of modular surfactants

    Science.gov (United States)

    Mondal, Sudipta; Varenik, Maxim; Bloch, Daniel Nir; Atsmon-Raz, Yoav; Jacoby, Guy; Adler-Abramovich, Lihi; Shimon, Linda J. W.; Beck, Roy; Miller, Yifat; Regev, Oren; Gazit, Ehud

    2017-01-01

    Extensive work has been invested in the design of bio-inspired peptide emulsifiers. Yet, none of the formulated surfactants were based on the utilization of the robust conformation and self-assembly tendencies presented by the hydrophobins, which exhibited highest surface activity among all known proteins. Here we show that a minimalist design scheme could be employed to fabricate rigid helical peptides to mimic the rigid conformation and the helical amphipathic organization. These designer building blocks, containing natural non-coded α-aminoisobutyric acid (Aib), form superhelical assemblies as confirmed by crystallography and microscopy. The peptide sequence is amenable to structural modularity and provides the highest stable emulsions reported so far for peptide and protein emulsifiers. Moreover, we establish the ability of short peptides to perform the dual functions of emulsifiers and thickeners, a feature that typically requires synergistic effects of surfactants and polysaccharides. This work provides a different paradigm for the molecular engineering of bioemulsifiers.

  15. Approaching rational epitope vaccine design for hepatitis C virus with meta-server and multivalent scaffolding

    Science.gov (United States)

    He, Linling; Cheng, Yushao; Kong, Leopold; Azadnia, Parisa; Giang, Erick; Kim, Justin; Wood, Malcolm R.; Wilson, Ian A.; Law, Mansun; Zhu, Jiang

    2015-08-01

    Development of a prophylactic vaccine against hepatitis C virus (HCV) has been hampered by the extraordinary viral diversity and the poor host immune response. Scaffolding, by grafting an epitope onto a heterologous protein scaffold, offers a possible solution to epitope vaccine design. In this study, we designed and characterized epitope vaccine antigens for the antigenic sites of HCV envelope glycoproteins E1 (residues 314-324) and E2 (residues 412-423), for which neutralizing antibody-bound structures are available. We first combined six structural alignment algorithms in a “scaffolding meta-server” to search for diverse scaffolds that can structurally accommodate the HCV epitopes. For each antigenic site, ten scaffolds were selected for computational design, and the resulting epitope scaffolds were analyzed using structure-scoring functions and molecular dynamics simulation. We experimentally confirmed that three E1 and five E2 epitope scaffolds bound to their respective neutralizing antibodies, but with different kinetics. We then investigated a “multivalent scaffolding” approach by displaying 24 copies of an epitope scaffold on a self-assembling nanoparticle, which markedly increased the avidity of antibody binding. Our study thus demonstrates the utility of a multi-scale scaffolding strategy in epitope vaccine design and provides promising HCV immunogens for further assessment in vivo.

  16. Computational Protein Engineering: Bridging the Gap between Rational Design and Laboratory Evolution

    Directory of Open Access Journals (Sweden)

    Shina Caroline Lynn Kamerlin

    2012-09-01

    Full Text Available Enzymes are tremendously proficient catalysts, which can be used as extracellular catalysts for a whole host of processes, from chemical synthesis to the generation of novel biofuels. For them to be more amenable to the needs of biotechnology, however, it is often necessary to be able to manipulate their physico-chemical properties in an efficient and streamlined manner, and, ideally, to be able to train them to catalyze completely new reactions. Recent years have seen an explosion of interest in different approaches to achieve this, both in the laboratory, and in silico. There remains, however, a gap between current approaches to computational enzyme design, which have primarily focused on the early stages of the design process, and laboratory evolution, which is an extremely powerful tool for enzyme redesign, but will always be limited by the vastness of sequence space combined with the low frequency for desirable mutations. This review discusses different approaches towards computational enzyme design and demonstrates how combining newly developed screening approaches that can rapidly predict potential mutation “hotspots” with approaches that can quantitatively and reliably dissect the catalytic step can bridge the gap that currently exists between computational enzyme design and laboratory evolution studies.

  17. Rational design of a non-canonical "sticky-ended" collagen triple helix.

    Science.gov (United States)

    Jalan, Abhishek A; Jochim, Katherine A; Hartgerink, Jeffrey D

    2014-05-28

    In a canonical collagen triple helix, three peptides self-assemble into a supercoiled motif with a one-amino-acid offset between the peptide chains. Design of triple helices that contain more than one residue offset is lucrative, as it leaves the non-covalent interactions unsatisfied at the termini and renders the termini "sticky" to further self-assemble into collagen-like nanofibers. Here we use lysine-glutamate axial salt-bridges to design a heterotrimeric collagen triple helix, ABC-1, containing a non-canonical offset of four residues between the peptide chains. The four-residue offset is necessary to prevent aggregation, which would prevent characterization of the non-canonical chain arrangement at the molecular level by NMR spectroscopy. A second heterotrimer, ABC-2, also stabilized by axial salt-bridges, is designed containing a canonical one-amino-acid offset to facilitate comparison of structure and stability by CD and NMR. ABC-1 and ABC-2 demonstrate our ability to modulate chain offset in a collagen triple helix. This lays the groundwork to design longer, and therefore stickier, offsets allowing access to a new class of collagen-related nanostructures.

  18. The dual aptamer approach: rational design of a high-affinity FAD aptamer.

    Science.gov (United States)

    Merkle, T; Holder, I T; Hartig, J S

    2016-01-14

    A design strategy for high-affinity aptamers of complex biomolecules is presented. We developed an RNA with FAD-binding properties by combining known ATP- and FMN-aptamers. Cooperative binding of FAD was shown by SPR spectroscopy and fluorescence assays. The strategy should be transferable to several other biomolecules.

  19. Rational design of ultrastable and reversibly photoswitchable fluorescent proteins for super-resolution imaging of the bacterial periplasm

    Science.gov (United States)

    El Khatib, Mariam; Martins, Alexandre; Bourgeois, Dominique; Colletier, Jacques-Philippe; Adam, Virgile

    2016-01-01

    Phototransformable fluorescent proteins are central to several nanoscopy approaches. As yet however, there is no available variant allowing super-resolution imaging in cell compartments that maintain oxidative conditions. Here, we report the rational design of two reversibly switchable fluorescent proteins able to fold and photoswitch in the bacterial periplasm, rsFolder and rsFolder2. rsFolder was designed by hybridisation of Superfolder-GFP with rsEGFP2, and inherited the fast folding properties of the former together with the rapid switching of the latter, but at the cost of a reduced switching contrast. Structural characterisation of the switching mechanisms of rsFolder and rsEGFP2 revealed different scenarios for chromophore cis-trans isomerisation and allowed designing rsFolder2, a variant of rsFolder that exhibits improved switching contrast and is amenable to RESOLFT nanoscopy. The rsFolders can be efficiently expressed in the E. coli periplasm, opening the door to the nanoscale investigation of proteins localised in hitherto non-observable cellular compartments. PMID:26732634

  20. Rational design of alpha-helical tandem repeat proteins with closed architectures

    Science.gov (United States)

    Doyle, Lindsey; Hallinan, Jazmine; Bolduc, Jill; Parmeggiani, Fabio; Baker, David; Stoddard, Barry L.; Bradley, Philip

    2015-01-01

    Tandem repeat proteins, which are formed by repetition of modular units of protein sequence and structure, play important biological roles as macromolecular binding and scaffolding domains, enzymes, and building blocks for the assembly of fibrous materials1,2. The modular nature of repeat proteins enables the rapid construction and diversification of extended binding surfaces by duplication and recombination of simple building blocks3,4. The overall architecture of tandem repeat protein structures – which is dictated by the internal geometry and local packing of the repeat building blocks – is highly diverse, ranging from extended, super-helical folds that bind peptide, DNA, and RNA partners5–9, to closed and compact conformations with internal cavities suitable for small molecule binding and catalysis10. Here we report the development and validation of computational methods for de novo design of tandem repeat protein architectures driven purely by geometric criteria defining the inter-repeat geometry, without reference to the sequences and structures of existing repeat protein families. We have applied these methods to design a series of closed alpha-solenoid11 repeat structures (alpha-toroids) in which the inter-repeat packing geometry is constrained so as to juxtapose the N- and C-termini; several of these designed structures have been validated by X-ray crystallography. Unlike previous approaches to tandem repeat protein engineering12–20, our design procedure does not rely on template sequence or structural information taken from natural repeat proteins and hence can produce structures unlike those seen in nature. As an example, we have successfully designed and validated closed alpha-solenoid repeats with a left-handed helical architecture that – to our knowledge – is not yet present in the protein structure database21. PMID:26675735

  1. Rational design of α-helical tandem repeat proteins with closed architectures.

    Science.gov (United States)

    Doyle, Lindsey; Hallinan, Jazmine; Bolduc, Jill; Parmeggiani, Fabio; Baker, David; Stoddard, Barry L; Bradley, Philip

    2015-12-24

    Tandem repeat proteins, which are formed by repetition of modular units of protein sequence and structure, play important biological roles as macromolecular binding and scaffolding domains, enzymes, and building blocks for the assembly of fibrous materials. The modular nature of repeat proteins enables the rapid construction and diversification of extended binding surfaces by duplication and recombination of simple building blocks. The overall architecture of tandem repeat protein structures--which is dictated by the internal geometry and local packing of the repeat building blocks--is highly diverse, ranging from extended, super-helical folds that bind peptide, DNA, and RNA partners, to closed and compact conformations with internal cavities suitable for small molecule binding and catalysis. Here we report the development and validation of computational methods for de novo design of tandem repeat protein architectures driven purely by geometric criteria defining the inter-repeat geometry, without reference to the sequences and structures of existing repeat protein families. We have applied these methods to design a series of closed α-solenoid repeat structures (α-toroids) in which the inter-repeat packing geometry is constrained so as to juxtapose the amino (N) and carboxy (C) termini; several of these designed structures have been validated by X-ray crystallography. Unlike previous approaches to tandem repeat protein engineering, our design procedure does not rely on template sequence or structural information taken from natural repeat proteins and hence can produce structures unlike those seen in nature. As an example, we have successfully designed and validated closed α-solenoid repeats with a left-handed helical architecture that--to our knowledge--is not yet present in the protein structure database.

  2. A rational design for the separation of metallic and semiconducting single-walled carbon nanotubes using a magnetic field

    Science.gov (United States)

    Luo, Chengzhi; Wan, Da; Jia, Junji; Li, Delong; Pan, Chunxu; Liao, Lei

    2016-06-01

    The separation of metallic (m-) and semiconducting (s-) single-walled carbon nanotubes (SWNTs) without causing contamination and damage is a major challenge for SWNT-based devices. As a facile and nondestructive tool, the use of a magnetic field could be an ideal strategy to separate m-/s-SWNTs, based on the difference of magnetic susceptibilities. Here, we designed a novel magnetic field-assisted floating catalyst chemical vapor deposition system to separate m-/s-SWNTs. Briefly, m-SWNTs are attracted toward the magnetic pole, leaving s-SWNTs on the substrate. By using this strategy, s-SWNTs with a purity of 99% could be obtained, which is enough to construct high-performance transistors with a mobility of 230 cm2 V-1 s-1 and an on/off ratio of 106. We also established a model to quantitatively calculate the percentage of m-SWNTs on the substrate and this model shows a good match with the experimental data. Furthermore, our rational design also provides a new avenue for the growth of SWNTs with specific chirality and manipulated arrangement due to the difference of magnetic susceptibilities between different diameters, chiralities, and types.The separation of metallic (m-) and semiconducting (s-) single-walled carbon nanotubes (SWNTs) without causing contamination and damage is a major challenge for SWNT-based devices. As a facile and nondestructive tool, the use of a magnetic field could be an ideal strategy to separate m-/s-SWNTs, based on the difference of magnetic susceptibilities. Here, we designed a novel magnetic field-assisted floating catalyst chemical vapor deposition system to separate m-/s-SWNTs. Briefly, m-SWNTs are attracted toward the magnetic pole, leaving s-SWNTs on the substrate. By using this strategy, s-SWNTs with a purity of 99% could be obtained, which is enough to construct high-performance transistors with a mobility of 230 cm2 V-1 s-1 and an on/off ratio of 106. We also established a model to quantitatively calculate the percentage of m

  3. Rationally designed fluorescently labeled sulfate-binding protein mutants: evaluation in the development of a sensing system for sulfate

    Science.gov (United States)

    Shrestha, Suresh; Salins, Lyndon L E.; Mark Ensor, C.; Daunert, Sylvia

    2002-01-01

    Periplasmic binding proteins from E. coli undergo large conformational changes upon binding their respective ligands. By attaching a fluorescent probe at rationally selected unique sites on the protein, these conformational changes in the protein can be monitored by measuring the changes in fluorescence intensity of the probe which allow the development of reagentless sensing systems for their corresponding ligands. In this work, we evaluated several sites on bacterial periplasmic sulfate-binding protein (SBP) for attachment of a fluorescent probe and rationally designed a reagentless sensing system for sulfate. Eight different mutants of SBP were prepared by employing the polymerase chain reaction (PCR) to introduce a unique cysteine residue at a specific location on the protein. The sites Gly55, Ser90, Ser129, Ala140, Leu145, Ser171, Val181, and Gly186 were chosen for mutagenesis by studying the three-dimensional X-ray crystal structure of SBP. An environment-sensitive fluorescent probe (MDCC) was then attached site-specifically to the protein through the sulfhydryl group of the unique cysteine residue introduced. Each fluorescent probe-conjugated SBP mutant was characterized in terms of its fluorescence properties and Ser171 was determined to be the best site for the attachment of the fluorescent probe that would allow for the development of a reagentless sensing system for sulfate. Three different environment-sensitive fluorescent probes (1,5-IAEDANS, MDCC, and acylodan) were studied with the SBP171 mutant protein. A calibration curve for sulfate was constructed using the labeled protein and relating the change in the fluorescence intensity with the amount of sulfate present in the sample. The detection limit for sulfate was found to be in the submicromolar range using this system. The selectivity of the sensing system was demonstrated by evaluating its response to other anions. A fast and selective sensing system with detection limits for sulfate in the

  4. Rational Design of in Vivo Tau Tangle-Selective Near-Infrared Fluorophores: Expanding the BODIPY Universe.

    Science.gov (United States)

    Verwilst, Peter; Kim, Hye-Ri; Seo, Jinho; Sohn, Nak-Won; Cha, Seung-Yun; Kim, Yeongmin; Maeng, Sungho; Shin, Jung-Won; Kwak, Jong Hwan; Kang, Chulhun; Kim, Jong Seung

    2017-09-15

    The elucidation of the cause of Alzheimer's disease remains one of the greatest questions in neurodegenerative research. The lack of highly reliable low-cost sensors to study the structural changes in key proteins during the progression of the disease is a contributing factor to this lack of insight. In the current work, we describe the rational design and synthesis of two fluorescent BODIPY-based probes, named Tau 1 and Tau 2. The probes were evaluated on the molecular surface formed by a fibril of the PHF6 ((306)VQIVYK(311)) tau fragment using molecular docking studies to provide a potential molecular model to rationalize the selectivity of the new probes as compared to a homologous Aβ-selective probe. The probes were synthesized in a few steps from commercially available starting products and could thus prove to be highly cost-effective. We demonstrated the excellent photophysical properties of the dyes, such as a large Stokes shift and emission in the near-infrared window of the electromagnetic spectrum. The probes demonstrated a high selectivity for self-assembled microtubule-associated protein tau (Tau protein), in both solution and cell-based experiments. Moreover, the administration to an acute murine model of tauopathy clearly revealed the staining of self-assembled hyperphosphorylated tau protein in pathologically relevant hippocampal brain regions. Tau 1 demonstrated efficient blood-brain barrier penetrability and demonstrated a clear selectivity for tau tangles over Aβ plaques, as well as the capacity for in vivo imaging in a transgenic mouse model. The current work could open up avenues for the cost-effective monitoring of the tau protein aggregation state in animal models as well as tissue staining. Furthermore, these fluorophores could serve as the basis for the development of clinically relevant sensors, for example based on PET imaging.

  5. Enhanced Photoelectrochemical Performance from Rationally Designed Anatase/Rutile TiO2 Heterostructures.

    Science.gov (United States)

    Cao, Fengren; Xiong, Jie; Wu, Fangli; Liu, Qiong; Shi, Zhiwei; Yu, Yanhao; Wang, Xudong; Li, Liang

    2016-05-18

    In a photoelectrochemical (PEC) cell for water splitting, the critical issue is charge separation and transport, which is usually completed by designing semiconductor heterojunctions. TiO2 anatase-rutile mixed junctions could largely improve photocatalytic properties, but impairs PEC water splitting performance. We designed and prepared two types of TiO2 heterostructures with the anatase thin film and rutile nanowire phases organized in different sequences. The two types of heterostructures were used as PEC photoanodes for water splitting and demonstrated completely opposite results. Rutile nanowires on anatase film demonstrated enhanced photocurrent density and onset potential, whereas strong negative performance was obtained from anatase film on rutile nanowire structures. The mechanism was investigated by photoresponse, light absorption and reflectance, and electrochemical impedance spectra. This work revealed the significant role of phase sequence in performance gain of anatase-rutile TiO2 heterostructured PEC photoanodes.

  6. Rational design and simple chemistry yield a superior, neuroprotective HDAC6 inhibitor, tubastatin A.

    Science.gov (United States)

    Butler, Kyle V; Kalin, Jay; Brochier, Camille; Vistoli, Guilio; Langley, Brett; Kozikowski, Alan P

    2010-08-11

    Structure-based drug design combined with homology modeling techniques were used to develop potent inhibitors of HDAC6 that display superior selectivity for the HDAC6 isozyme compared to other inhibitors. These inhibitors can be assembled in a few synthetic steps, and thus are readily scaled up for in vivo studies. An optimized compound from this series, designated Tubastatin A, was tested in primary cortical neuron cultures in which it was found to induce elevated levels of acetylated alpha-tubulin, but not histone, consistent with its HDAC6 selectivity. Tubastatin A also conferred dose-dependent protection in primary cortical neuron cultures against glutathione depletion-induced oxidative stress. Importantly, when given alone at all concentrations tested, this hydroxamate-containing HDAC6-selective compound displayed no neuronal toxicity, thus, forecasting the potential application of this agent and its analogues to neurodegenerative conditions.

  7. Rational design of metal ion sequestering agents. 1998 annual progress report

    Energy Technology Data Exchange (ETDEWEB)

    Raymond, K.N.

    1998-06-01

    'This project addresses fundamental issues and requirements in developing hazardous metal ion separation technologies needed in the treatment and disposal of radioactive and chemical toxic waste. It encompasses the synthesis of new agents, followed by their characterization and evaluation, with the aim to optimize their metal ion sequestering properties for use in applied technologies. This research is focused on the following key areas: (1) basic design and synthesis of new metal ion specific sequestering ligands; (2) structural and thermodynamic investigations of these ligands and their complexes formed with the targeted metal ions; and (3) development of sequestering agents and their incorporation into systems designed to be prototypes of inexpensive and highly effective materials for hazardous metal ion decontamination. Basic studies of the sequestration of relevant toxic metals are required in order to develop processes that will treat effluents sufficiently well to allow direct release into the environment and minimize the production of secondary wastes.'

  8. Rational Design of a Bisphenol A Aptamer Selective Surface-Enhanced Raman Scattering Nanoprobe

    Science.gov (United States)

    2015-01-01

    Surface-enhanced Raman scattering (SERS) optical nanoprobes offer a number of advantages for ultrasensitive analyte detection. These functionalized colloidal nanoparticles are a multifunctional assay component. providing a platform for conjugation to spectral tags, stabilizing polymers, and biorecognition elements such as aptamers or antibodies. We demonstrate the design and characterization of a SERS-active nanoprobe and investigate the nanoparticles’ biorecognition capabilities for use in a competitive binding assay. Specifically, the nanoprobe is designed for the quantification of bisphenol A (BPA) levels in the blood after human exposure to the toxin in food and beverage plastic packaging. The nanoprobes demonstrated specific affinity to a BPA aptamer with a dissociation constant Kd of 54 nM, and provided a dose-dependent SERS spectra with a limit of detection of 3 nM. Our conjugation approach shows the versatility of colloidal nanoparticles in assay development, acting as detectable spectral tagging elements and biologically active ligands concurrently. PMID:25329684

  9. Rational use of plasma protein and tissue binding data in drug design.

    Science.gov (United States)

    Liu, Xingrong; Wright, Matthew; Hop, Cornelis E C A

    2014-10-23

    It is a commonly accepted assumption that only unbound drug molecules are available to interact with their targets. Therefore, one of the objectives in drug design is to optimize the compound structure to increase in vivo unbound drug concentration. In this review, theoretical analyses and experimental observations are presented to illustrate that low plasma protein binding does not necessarily lead to high in vivo unbound plasma concentration. Similarly, low brain tissue binding does not lead to high in vivo unbound brain tissue concentration. Instead, low intrinsic clearance leads to high in vivo unbound plasma concentration, and low efflux transport activity at the blood-brain barrier leads to high unbound brain concentration. Plasma protein and brain tissue binding are very important parameters in understanding pharmacokinetics, pharmacodynamics, and toxicities of drugs, but these parameters should not be targeted for optimization in drug design.

  10. Rational Design and Enhanced Biocompatibility of a Dry Adhesive Medical Skin Patch

    KAUST Repository

    Kwak, Moon Kyu

    2011-07-28

    A new type of medical skin patch is developed that contains high-density, mushroom-like micropillars. Such dry-adhesive micropillars are highly biocompatible, have minimized side effects, and provide reasonable normal adhesion strength. To arrive at optimal conditions for the dry adhesive skin patch, the proper design of various structural and material parameters of micropillars is investigated. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Rational design of orally-active, pyrrolidine-based progesterone receptor partial agonists

    Energy Technology Data Exchange (ETDEWEB)

    Thompson, Scott K.; Washburn, David G.; Frazee, James S.; Madauss, Kevin P.; Hoang, Tram H.; Lapinski, Leahann; Grygielko, Eugene T.; Glace, Lindsay E.; Trizna, Walter; Williams, Shawn P.; Duraiswami, Chaya; Bray, Jeffrey D.; Laping, Nicholas J.; (GSKNC); (GSKPA)

    2010-09-03

    Using the X-ray crystal structure of an amide-based progesterone receptor (PR) partial agonist bound to the PR ligand binding domain, a novel PR partial agonist class containing a pyrrolidine ring was designed. Members of this class of N-alkylpyrrolidines demonstrate potent and highly selective partial agonism of the progesterone receptor, and one of these analogs was shown to be efficacious upon oral dosing in the OVX rat model of estrogen opposition.

  12. Molding Phonon Flow with Symmetry: Rational Design of Hypersonic Phononic Crystals

    Science.gov (United States)

    Koh, Cheong Yang; Thomas, Edwin L.

    2009-03-01

    Phononic crystals structured at appropriate length scales allow control over the flow of phonons, leading to new possibilities in applications such as heat-management, sound isolation and even energy transfer and conversion. Symmetry provides a unified framework for the interpretation 1D to 3D phononic band structures, allowing utilization of a common set of principles for designing band structures of phononic crystals as well as actual purposeful defects such as waveguide location and boundary termination in finite devices. In this work, we explore the band structure properties of phononic crystals with non-symmorphic space groups, as well as those having quasi-crystalline approximants. We demonstrate gap opening abilities from both anti-crossing and Bragg scattering, as well as unique features like ``sticking'' bands. Symmetry concepts are also powerful means to tune the density of states of the structures. Importantly, we fabricate various theoretical designs and measure their experimental dispersion diagrams for comparison with theoretical calculation. This affords an elegant approach toward a design blueprint for fabricating phononic structures for applications such as opto-acoustic coupling.

  13. Computer-aided rational design of novel EBF analogues with an aromatic ring.

    Science.gov (United States)

    Wang, Shanshan; Sun, Yufeng; Du, Shaoqing; Qin, Yaoguo; Duan, Hongxia; Yang, Xinling

    2016-06-01

    Odorant binding proteins (OBPs) are important in insect olfactory recognition. These proteins bind specifically to insect semiochemicals and induce their seeking, mating, and alarm behaviors. Molecular docking and molecular dynamics simulations were performed to provide computational insight into the interaction mode between AgamOBP7 and novel (E)-β-farnesene (EBF) analogues with an aromatic ring. The ligand-binding cavity in OBP7 was found to be mostly hydrophobic due to the presence of several nonpolar residues. The interactions between the EBF analogues and the hydrophobic residues in the binding cavity increased in strength as the distance between them decreased. The EBF analogues with an N-methyl formamide or ester linkage had higher docking scores than those with an amide linkage. Moreover, delocalized π-π and electrostatic interactions were found to contribute significantly to the binding between the ligand benzene ring and nearby protein residues. To design new compounds with higher activity, four EBF analogues D1-D4 with a benzene ring were synthesized and evaluated based on their docking scores and binding affinities. D2, which had an N-methyl formamide group linkage, exhibited stronger binding than D1, which had an amide linkage. D4 exhibited particularly strong binding due to multiple hydrophobic interactions with the protein. This study provides crucial foundations for designing novel EBF analogues based on the OBP structure. Graphical abstract The design strategy of new EBF analogues based on the OBP7 structure.

  14. Rational design and synthesis of an orally bioavailable peptide guided by NMR amide temperature coefficients

    Science.gov (United States)

    Wang, Conan K.; Northfield, Susan E.; Colless, Barbara; Chaousis, Stephanie; Hamernig, Ingrid; Lohman, Rink-Jan; Nielsen, Daniel S.; Schroeder, Christina I.; Liras, Spiros; Price, David A.; Fairlie, David P.; Craik, David J.

    2014-01-01

    Enhancing the oral bioavailability of peptide drug leads is a major challenge in drug design. As such, methods to address this challenge are highly sought after by the pharmaceutical industry. Here, we propose a strategy to identify appropriate amides for N-methylation using temperature coefficients measured by NMR to identify exposed amides in cyclic peptides. N-methylation effectively caps these amides, modifying the overall solvation properties of the peptides and making them more membrane permeable. The approach for identifying sites for N-methylation is a rapid alternative to the elucidation of 3D structures of peptide drug leads, which has been a commonly used structure-guided approach in the past. Five leucine-rich peptide scaffolds are reported with selectively designed N-methylated derivatives. In vitro membrane permeability was assessed by parallel artificial membrane permeability assay and Caco-2 assay. The most promising N-methylated peptide was then tested in vivo. Here we report a novel peptide (15), which displayed an oral bioavailability of 33% in a rat model, thus validating the design approach. We show that this approach can also be used to explain the notable increase in oral bioavailability of a somatostatin analog. PMID:25416591

  15. Rational approach to polymer-supported catalysts: synergy between catalytic reaction mechanism and polymer design.

    Science.gov (United States)

    Madhavan, Nandita; Jones, Christopher W; Weck, Marcus

    2008-09-01

    Supported catalysis is emerging as a cornerstone of transition metal catalysis, as environmental awareness necessitates "green" methodologies and transition metal resources become scarcer and more expensive. Although these supported systems are quite useful, especially in their capacity for transition metal catalyst recycling and recovery, higher activity and selectivity have been elusive compared with nonsupported catalysts. This Account describes recent developments in polymer-supported metal-salen complexes, which often surpass nonsupported analogues in catalytic activity and selectivity, demonstrating the effectiveness of a systematic, logical approach to designing supported catalysts from a detailed understanding of the catalytic reaction mechanism. Over the past few decades, a large number of transition metal complex catalysts have been supported on a variety of materials ranging from polymers to mesoporous silica. In particular, soluble polymer supports are advantageous because of the development of controlled and living polymerization methods that are tolerant to a wide variety of functional groups, including controlled radical polymerizations and ring-opening metathesis polymerization. These methods allow for tuning the density and structure of the catalyst sites along the polymer chain, thereby enabling the development of structure-property relationships between a catalyst and its polymer support. The fine-tuning of the catalyst-support interface, in combination with a detailed understanding of catalytic reaction mechanisms, not only permits the generation of reusable and recyclable polymer-supported catalysts but also facilitates the design and realization of supported catalysts that are significantly more active and selective than their nonsupported counterparts. These superior supported catalysts are accessible through the optimization of four basic variables in their design: (i) polymer backbone rigidity, (ii) the nature of the linker, (iii) catalyst

  16. Rational Design, Synthesis and Evaluation of Coumarin Derivatives as Protein-protein Interaction Inhibitors.

    Science.gov (United States)

    De Luca, Laura; Agharbaoui, Fatima E; Gitto, Rosaria; Buemi, Maria Rosa; Christ, Frauke; Debyser, Zeger; Ferro, Stefania

    2016-09-01

    Herein we describe the design and synthesis of a new series of coumarin derivatives searching for novel HIV-1 integrase (IN) allosteric inhibitors. All new obtained compounds were tested in order to evaluate their ability to inhibit the interaction between the HIV-1 IN enzyme and the nuclear protein lens epithelium growth factor LEDGF/p75. A combined approach of docking and molecular dynamic simulations has been applied to clarify the activity of the new compounds. Specifically, the binding free energies by using the method of molecular mechanics-generalized Born surface area (MM-GBSA) was calculated, whereas hydrogen bond occupancies were monitored throughout simulations methods.

  17. Rational design of cyclopropane-based chiral PHOX ligands for intermolecular asymmetric Heck reaction

    Directory of Open Access Journals (Sweden)

    Marina Rubina

    2014-07-01

    Full Text Available A novel class of chiral phosphanyl-oxazoline (PHOX ligands with a conformationally rigid cyclopropyl backbone was synthesized and tested in the intermolecular asymmetric Heck reaction. Mechanistic modelling and crystallographic studies were used to predict the optimal ligand structure and helped to design a very efficient and highly selective catalytic system. Employment of the optimized ligands in the asymmetric arylation of cyclic olefins allowed for achieving high enantioselectivities and significantly suppressing product isomerization. Factors affecting the selectivity and the rate of the isomerization were identified. It was shown that the nature of this isomerization is different from that demonstrated previously using chiral diphosphine ligands.

  18. Structural Similarity between Defense Peptide from Wheat and Scorpion Neurotoxin Permits Rational Functional Design*

    Science.gov (United States)

    Berkut, Antonina A.; Usmanova, Dinara R.; Peigneur, Steve; Oparin, Peter B.; Mineev, Konstantin S.; Odintsova, Tatyana I.; Tytgat, Jan; Arseniev, Alexander S.; Grishin, Eugene V.; Vassilevski, Alexander A.

    2014-01-01

    In this study, we present the spatial structure of the wheat antimicrobial peptide (AMP) Tk-AMP-X2 studied using NMR spectroscopy. This peptide was found to adopt a disulfide-stabilized α-helical hairpin fold and therefore belongs to the α-hairpinin family of plant defense peptides. Based on Tk-AMP-X2 structural similarity to cone snail and scorpion potassium channel blockers, a mutant molecule, Tk-hefu, was engineered by incorporating the functionally important residues from κ-hefutoxin 1 onto the Tk-AMP-X2 scaffold. The designed peptide contained the so-called essential dyad of amino acid residues significant for channel-blocking activity. Electrophysiological studies showed that although the parent peptide Tk-AMP-X2 did not present any activity against potassium channels, Tk-hefu blocked Kv1.3 channels with similar potency (IC50 ∼ 35 μm) to κ-hefutoxin 1 (IC50 ∼ 40 μm). We conclude that α-hairpinins are attractive in their simplicity as structural templates, which may be used for functional engineering and drug design. PMID:24671422

  19. Structural similarity between defense peptide from wheat and scorpion neurotoxin permits rational functional design.

    Science.gov (United States)

    Berkut, Antonina A; Usmanova, Dinara R; Peigneur, Steve; Oparin, Peter B; Mineev, Konstantin S; Odintsova, Tatyana I; Tytgat, Jan; Arseniev, Alexander S; Grishin, Eugene V; Vassilevski, Alexander A

    2014-05-16

    In this study, we present the spatial structure of the wheat antimicrobial peptide (AMP) Tk-AMP-X2 studied using NMR spectroscopy. This peptide was found to adopt a disulfide-stabilized α-helical hairpin fold and therefore belongs to the α-hairpinin family of plant defense peptides. Based on Tk-AMP-X2 structural similarity to cone snail and scorpion potassium channel blockers, a mutant molecule, Tk-hefu, was engineered by incorporating the functionally important residues from κ-hefutoxin 1 onto the Tk-AMP-X2 scaffold. The designed peptide contained the so-called essential dyad of amino acid residues significant for channel-blocking activity. Electrophysiological studies showed that although the parent peptide Tk-AMP-X2 did not present any activity against potassium channels, Tk-hefu blocked Kv1.3 channels with similar potency (IC50 ∼ 35 μm) to κ-hefutoxin 1 (IC50 ∼ 40 μm). We conclude that α-hairpinins are attractive in their simplicity as structural templates, which may be used for functional engineering and drug design. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  20. Interface engineering for a rational design of poison-free bimetallic CO oxidation catalysts.

    Science.gov (United States)

    Shin, Kihyun; Zhang, Liang; An, Hyesung; Ha, Hyunwoo; Yoo, Mi; Lee, Hyuck Mo; Henkelman, Graeme; Kim, Hyun You

    2017-04-20

    We use density functional theory calculations of Pt@Cu core@shell nanoparticles (NPs) to design bifunctional poison-free CO oxidation catalysts. By calculating the adsorption chemistry under CO oxidation conditions, we find that the Pt@Cu NPs will be active for CO oxidation with resistance to CO-poisoning. The CO oxidation pathway at the Pt-Cu interface is determined on the Pt NP covered with a full- and partial-shell of Cu. The exposed portion of the Pt core preferentially binds CO and the Cu shell binds O2, supplying oxygen for the reaction. The Pt-Cu interface provides CO-oxidation sites that are not poisoned by either CO or O2. Additional computational screening shows that this separation of reactant binding sites is possible for several other core@shell NPs. Our results indicate that the metal-metal interface within a single NP can be optimized for design of bifunctional catalytic systems with improved performance.

  1. Rational design of inducible CRISPR guide RNAs for de novo assembly of transcriptional programs

    Science.gov (United States)

    Ferry, Quentin R. V.; Lyutova, Radostina; Fulga, Tudor A.

    2017-01-01

    CRISPR-based transcription regulators (CRISPR-TRs) have transformed the current synthetic biology landscape by allowing specific activation or repression of any target gene. Here we report a modular and versatile framework enabling rapid implementation of inducible CRISPR-TRs in mammalian cells. This strategy relies on the design of a spacer-blocking hairpin (SBH) structure at the 5′ end of the single guide RNA (sgRNA), which abrogates the function of CRISPR-transcriptional activators. By replacing the SBH loop with ligand-controlled RNA-cleaving units, we demonstrate conditional activation of quiescent sgRNAs programmed to respond to genetically encoded or externally delivered triggers. We use this system to couple multiple synthetic and endogenous target genes with specific inducers, and assemble gene regulatory modules demonstrating parallel and orthogonal transcriptional programs. We anticipate that this ‘plug and play' approach will be a valuable addition to the synthetic biology toolkit, facilitating the understanding of natural gene circuits and the design of cell-based therapeutic strategies. PMID:28256578

  2. Rational Design of Multiamphiphilic Polymer Compatibilizers: Versatile Solubility and Hybridization of Noncovalently Functionalized CNT Nanocomposites.

    Science.gov (United States)

    Cho, Kie Yong; Yeom, Yong Sik; Seo, Heun Young; Park, Young Hun; Jang, Ha Na; Baek, Kyung-Youl; Yoon, Ho Gyu

    2015-05-13

    The design of amphiphilic polymer compatibilizers for solubility manipulation of CNT composites was systematically generalized in this study. Structurally tailored multiamphiphilic compatibilizer were designed and synthesized by applying simple, high-yield reactions. This multiamphiphilic compatibilizer was applied for noncovalent functionalization of CNTs as well as provided CNTs with outstanding dispersion stability, manipulation of solubility, and hybridization with Ag nanoparticles (NPs). With regard to the dispersion properties, superior records in maximum concentration (2.88-3.10 mg/mL in chloroform), and mass ratio of the compatibilizer for good CNT dispersion (36 wt %) were achieved by MWCNTs functionalized with a multiamphiphilic block copolymer compatibilizer. In particular, the solubility limitations of MWCNT dispersion in solvents ranging from toluene (nonpolar) to aqueous solution (polar) are surprisingly resolved by introducing this multiamphiphilic polymer compatibilizer. Furthermore, this polymer compatibilizer allowed the synthesis of the hybrid CNT nanocomposites with Ag nanoparticles by an in situ nucleation process. As such, the multiamphiphilic compatibilizer candidate as a new concept for the noncovalent functionalization of CNTs can extend their use for a wide range of applications.

  3. A rational design and operating strategy for pipelines traversing unstable slopes

    Energy Technology Data Exchange (ETDEWEB)

    Simmonds, G.R.; Zhou, Z.J. [NOVA Gas Transmission Ltd., Calgary, Alberta (Canada); Samchek, A.T. [Golder Associates Ltd., Calgary, Alberta (Canada)

    1996-12-31

    A common challenge for pipeline designers is the placement and safe operation of pipelines within unstable slopes. Consequently, special design and operation procedures must be created to maintain the integrity of the pipeline through its operating life. Nova Gas Transmission Limited (NGTL) has developed a methodology to monitor pipeline integrity in slow moving (creeping) unstable slopes. This methodology uses Pipeline-Soil Interaction models to produce parameters that are in turn placed in Pipeline Integrity Assessment Techniques such as finite element analysis. For slope movements, pipeline integrity is based on pipeline strain criteria that are established from regulated codes or NGTL`s risk-based criteria. The result is that pipe strain can be estimated over time given a particular soil type and predicted ground movement. The ability to predict when a pipeline is reaching a critical strain allows NGTL to effectively quantify the risk and associated cost for various remedial measured based on a given operating life (life-cycle cost). These remedial measures can take the form of strain relieving outages, re-routing of the pipeline, directional drilling or conventional geotechnical remedial practices (dewatering, slope grading, buttressing, etc.). Two case studies are presented detailing this present state-of-practice methodology at NGTL.

  4. Towards Rational Design Method for Strengthening of Concrete Structures by External Bonding

    Directory of Open Access Journals (Sweden)

    Furuuchi H.

    2012-01-01

    Full Text Available Many infrastructures need to be repaired or strengthened due to various reasons, such as unexpected deterioration and changes in performance requirement. This paper presents the following recent achievements by the authors’ group on design method for flexural strengthening of concrete structures by external bonding; (i fracture characteristics of interface between substrate concrete and cementitious overlay, (ii crack spacing of flexural strengthened beams, which affects debonding strength, (iii strengths of intermediate crack (IC debonding and end peeling, (iv strength of concrete cover separation, and (v effectiveness of strengthening by external bonding. A unified approach for flexural strengthening by steel plate, fiber reinforced polymer lami¬nate and cementitious overlay, for both intermediate crack (IC debonding, including end peeling, and concrete cover separation is pre¬sented with consideration of crack spacing in the streng¬thened members. Appropriate interfacial rough¬¬¬ness to achieve efficient interface bond property is clari¬fied and the concept of effectiveness of strengthen¬ing is proposed for better strengthening design.

  5. Hairpin Ribozyme Genes Curtail Alcohol Drinking: from Rational Design to in vivo Effects in the Rat.

    Science.gov (United States)

    Sapag, Amalia; Irrazábal, Thergiory; Lobos-González, Lorena; Muñoz-Brauning, Carlos R; Quintanilla, María Elena; Tampier, Lutske

    2016-07-12

    Ribozyme genes were designed to reduce voluntary alcohol drinking in a rat model of alcohol dependence. Acetaldehyde generated from alcohol in the liver is metabolized by the mitochondrial aldehyde dehydrogenase (ALDH2) such that diminishing ALDH2 activity leads to the aversive effects of blood acetaldehyde upon alcohol intake. A stepwise approach was followed to design genes encoding ribozymes targeted to the rat ALDH2 mRNA. In vitro studies of accessibility to oligonucleotides identified suitable target sites in the mRNA, one of which fulfilled hammerhead and hairpin ribozyme requirements (CGGUC). Ribozyme genes delivered in plasmid constructs were tested in rat cells in culture. While the hairpin ribozyme reduced ALDH2 activity 56% by cleavage and blockade (P < 0.0001), the hammerhead ribozyme elicited minor effects by blockade. The hairpin ribozyme was tested in vivo by adenoviral gene delivery to UChB alcohol drinker rats. Ethanol intake was curtailed 47% for 34 days (P < 0.0001), while blood acetaldehyde more than doubled upon ethanol administration and ALDH2 activity dropped 25% in liver homogenates, not affecting other ALDH isoforms. Thus, hairpin ribozymes targeted to 16 nt in the ALDH2 mRNA provide durable and specific effects in vivo, representing an improvement on previous work and encouraging development of gene therapy for alcoholism.

  6. Rational design of highly active sgRNAs for CRISPR-Cas9-mediated gene inactivation

    Science.gov (United States)

    Doench, John G.; Hartenian, Ella; Graham, Daniel B.; Tothova, Zuzana; Hegde, Mudra; Smith, Ian; Sullender, Meagan; Ebert, Benjamin L.; Xavier, Ramnik J.; Root, David E.

    2014-01-01

    Components of the prokaryotic clustered regularly interspersed palindromic repeat (CRISPR) loci have recently been repurposed for use in mammalian cells1–6. The Cas9 protein can be programmed with a single guide RNA (sgRNA) to generate site-specific DNA breaks, but there are few known rules governing on-target efficacy of this system7,8. We created a pool of sgRNAs, tiling across all possible target sites of a panel of six endogenous mouse and three endogenous human genes and quantitatively assessed their ability to produce null alleles of their target gene by antibody staining and flow cytometry. We discovered sequence features that improved activity, including a further optimization of the proto-spacer adjacent motif (PAM) of Streptococcus pyogenes Cas9. The results from 1,841 sgRNAs were used to construct a predictive model of sgRNA activity to improve sgRNA design for gene editing and genetic screens. We provide an online tool for the design of highly active sgRNAs for any gene of interest. PMID:25184501

  7. Rational design of self-assembly pathways for complex multicomponent structures

    Science.gov (United States)

    Jacobs, William M.; Reinhardt, Aleks; Frenkel, Daan

    2015-01-01

    The field of complex self-assembly is moving toward the design of multiparticle structures consisting of thousands of distinct building blocks. To exploit the potential benefits of structures with such “addressable complexity,” we need to understand the factors that optimize the yield and the kinetics of self-assembly. Here we use a simple theoretical method to explain the key features responsible for the unexpected success of DNA-brick experiments, which are currently the only demonstration of reliable self-assembly with such a large number of components. Simulations confirm that our theory accurately predicts the narrow temperature window in which error-free assembly can occur. Even more strikingly, our theory predicts that correct assembly of the complete structure may require a time-dependent experimental protocol. Furthermore, we predict that low coordination numbers result in nonclassical nucleation behavior, which we find to be essential for achieving optimal nucleation kinetics under mild growth conditions. We also show that, rather surprisingly, the use of heterogeneous bond energies improves the nucleation kinetics and in fact appears to be necessary for assembling certain intricate 3D structures. This observation makes it possible to sculpt nucleation pathways by tuning the distribution of interaction strengths. These insights not only suggest how to improve the design of structures based on DNA bricks, but also point the way toward the creation of a much wider class of chemical or colloidal structures with addressable complexity. PMID:25941388

  8. Rational Design of Potent and Selective Inhibitors of an Epoxide Hydrolase Virulence Factor from Pseudomonas aeruginosa.

    Science.gov (United States)

    Kitamura, Seiya; Hvorecny, Kelli L; Niu, Jun; Hammock, Bruce D; Madden, Dean R; Morisseau, Christophe

    2016-05-26

    The virulence factor cystic fibrosis transmembrane conductance regulator (CFTR) inhibitory factor (Cif) is secreted by Pseudomonas aeruginosa and is the founding member of a distinct class of epoxide hydrolases (EHs) that triggers the catalysis-dependent degradation of the CFTR. We describe here the development of a series of potent and selective Cif inhibitors by structure-based drug design. Initial screening revealed 1a (KB2115), a thyroid hormone analog, as a lead compound with low micromolar potency. Structural requirements for potency were systematically probed, and interactions between Cif and 1a were characterized by X-ray crystallography. On the basis of these data, new compounds were designed to yield additional hydrogen bonding with residues of the Cif active site. From this effort, three compounds were identified that are 10-fold more potent toward Cif than our first-generation inhibitors and have no detectable thyroid hormone-like activity. These inhibitors will be useful tools to study the pathological role of Cif and have the potential for clinical application.

  9. Rational design of a low-affinity peptide for the detection of cystatin C in a fast homogeneous immunoassay.

    Science.gov (United States)

    Dobslaff, Kristin; Zscharnack, Kristin; Kreisig, Thomas; Zuchner, Thole

    2016-02-01

    Immunoassays play an essential role in current research and diagnostics resulting in a variety of detection principles. Thereby, homogeneous assays are often used for a fast signal response as demanded for example in point-of-care diagnostics. These systems often rely on a competitive assay design where the sample analyte and the corresponding dye-labeled substance are competing for binding sites on an antibody present in limited amounts. Due to the similar affinities of the antibody towards the sample analyte and the competitor, both sensitivity and assay time are limited. As a consequence, a competitor with a slightly reduced affinity towards the antibody can potentially overcome these drawbacks. Here, we present the rational design of a low-affinity peptide (donor peptide) as a specific analyte competitor for a FRET-based homogeneous immunoassay for the analysis of the protein cystatin C. Thereby, the strategy of peptide-induced antibody generation was combined with the selective variation of the immunization sequence in order to achieve a lower affinity towards the antibody. We could show that shortened donor peptides improved the resulting quenching efficiency in the immunoassay. In addition, the substitution of small hydrophobic amino acids by those with a higher steric demand appeared to be the most promising strategy providing a fast assay response for cystatin C of only 90 s.

  10. Urokinase-targeted recombinant bacterial protein toxins-a rationally designed and engineered anticancer agent for cancer therapy

    Institute of Scientific and Technical Information of China (English)

    Yizhen LIU; Shi-Yan LI

    2009-01-01

    Urokinase-targeted recombinant bacterial protein toxins are a sort of rationally designed and engineered anticancer recombinant fusion proteins representing a novel class of agents for cancer therapy.Bacterial protein toxins have long been known as the primary virulence factor(s) for a variety of pathogenic bacteria and are the most powerful human poisons.On the other hand,it has been well documented that urokinase-type plasminogen activator (uPA) and urokinase plasminogen activator receptor (uPAR),making up the uPA system,are overexpressed in a variety of human tumors and tumor cell lines.The expression of uPA system is highly correlated with tumor invasion and metastasis.To exploit these characteristics in the design of tumor cell-selective cytotoxins,two prominent bacterial protein toxins,i.e.,the diphtheria toxin and anthrax toxin are deliberately engineered through placing a sequence targeted specifically by the uPA system to form anticancer recombinant fusion proteins.These uPA system-targeted bacterial protein toxins are activated selectively on the surface of uPA systemexpressing tumor cells,thereby killing these cells.This article provides a review on the latest progress in the exploitation of these recombinant fusion proteins as potent tumoricidal agents.It is perceptible that the strategies for cancer therapy are being innovated by this novel therapeutic approach.

  11. Vector design Tour de Force: integrating combinatorial and rational approaches to derive novel adeno-associated virus variants.

    Science.gov (United States)

    Marsic, Damien; Govindasamy, Lakshmanan; Currlin, Seth; Markusic, David M; Tseng, Yu-Shan; Herzog, Roland W; Agbandje-McKenna, Mavis; Zolotukhin, Sergei

    2014-11-01

    Methodologies to improve existing adeno-associated virus (AAV) vectors for gene therapy include either rational approaches or directed evolution to derive capsid variants characterized by superior transduction efficiencies in targeted tissues. Here, we integrated both approaches in one unified design strategy of "virtual family shuffling" to derive a combinatorial capsid library whereby only variable regions on the surface of the capsid are modified. Individual sublibraries were first assembled in order to preselect compatible amino acid residues within restricted surface-exposed regions to minimize the generation of dead-end variants. Subsequently, the successful families were interbred to derive a combined library of ~8 × 10(5) complexity. Next-generation sequencing of the packaged viral DNA revealed capsid surface areas susceptible to directed evolution, thus providing guidance for future designs. We demonstrated the utility of the library by deriving an AAV2-based vector characterized by a 20-fold higher transduction efficiency in murine liver, now equivalent to that of AAV8.

  12. Rational drug design and synthesis of molecules targeting the angiotensin II type 1 and type 2 receptors.

    Science.gov (United States)

    Kellici, Tahsin F; Tzakos, Andreas G; Mavromoustakos, Thomas

    2015-03-02

    The angiotensin II (Ang II) type 1 and type 2 receptors (AT1R and AT2R) orchestrate an array of biological processes that regulate human health. Aberrant function of these receptors triggers pathophysiological responses that can ultimately lead to death. Therefore, it is important to design and synthesize compounds that affect beneficially these two receptors. Cardiovascular disease, which is attributed to the overactivation of the vasoactive peptide hormone Αng II, can now be treated with commercial AT1R antagonists. Herein, recent achievements in rational drug design and synthesis of molecules acting on the two AT receptors are reviewed. Quantitative structure activity relationships (QSAR) and molecular modeling on the two receptors aim to assist the search for new active compounds. As AT1R and AT2R are GPCRs and drug action is localized in the transmembrane region the role of membrane bilayers is exploited. The future perspectives in this field are outlined. Tremendous progress in the field is expected if the two receptors are crystallized, as this will assist the structure based screening of the chemical space and lead to new potent therapeutic agents in cardiovascular and other diseases.

  13. Structure-based approach to rationally design a chimeric protein for an effective vaccine against Group B Streptococcus infections

    Science.gov (United States)

    Nuccitelli, Annalisa; Cozzi, Roberta; Gourlay, Louise J.; Donnarumma, Danilo; Necchi, Francesca; Norais, Nathalie; Telford, John L.; Rappuoli, Rino; Bolognesi, Martino; Maione, Domenico; Grandi, Guido; Rinaudo, C. Daniela

    2011-01-01

    Structural vaccinology is an emerging strategy for the rational design of vaccine candidates. We successfully applied structural vaccinology to design a fully synthetic protein with multivalent protection activity. In Group B Streptococcus, cell-surface pili have aroused great interest because of their direct roles in virulence and importance as protective antigens. The backbone subunit of type 2a pilus (BP-2a) is present in six immunogenically different but structurally similar variants. We determined the 3D structure of one of the variants, and experimentally demonstrated that protective antibodies specifically recognize one of the four domains that comprise the protein. We therefore constructed a synthetic protein constituted by the protective domain of each one of the six variants and showed that the chimeric protein protects mice against the challenge with all of the type 2a pilus-carrying strains. This work demonstrates the power of structural vaccinology and will facilitate the development of an optimized, broadly protective pilus-based vaccine against Group B Streptococcus by combining the uniquely generated chimeric protein with protective pilin subunits from two other previously identified pilus types. In addition, this work describes a template procedure that can be followed to develop vaccines against other bacterial pathogens. PMID:21593422

  14. Rational design of efficient electrode–electrolyte interfaces for solid-state energy storage using ion soft landing

    Science.gov (United States)

    Prabhakaran, Venkateshkumar; Mehdi, B. Layla; Ditto, Jeffrey J.; Engelhard, Mark H.; Wang, Bingbing; Gunaratne, K. Don D.; Johnson, David C.; Browning, Nigel D.; Johnson, Grant E.; Laskin, Julia

    2016-01-01

    The rational design of improved electrode–electrolyte interfaces (EEI) for energy storage is critically dependent on a molecular-level understanding of ionic interactions and nanoscale phenomena. The presence of non-redox active species at EEI has been shown to strongly influence Faradaic efficiency and long-term operational stability during energy storage processes. Herein, we achieve substantially higher performance and long-term stability of EEI prepared with highly dispersed discrete redox-active cluster anions (50 ng of pure ∼0.75 nm size molybdenum polyoxometalate (POM) anions on 25 μg (∼0.2 wt%) carbon nanotube (CNT) electrodes) by complete elimination of strongly coordinating non-redox species through ion soft landing (SL). Electron microscopy provides atomically resolved images of a uniform distribution of individual POM species soft landed directly on complex technologically relevant CNT electrodes. In this context, SL is established as a versatile approach for the controlled design of novel surfaces for both fundamental and applied research in energy storage. PMID:27097686

  15. Semi-Rational Design of Geobacillus stearothermophilus L-Lactate Dehydrogenase to Access Various Chiral α-Hydroxy Acids.

    Science.gov (United States)

    Aslan, Aşkın Sevinç; Birmingham, William R; Karagüler, Nevin Gül; Turner, Nicholas J; Binay, Barış

    2016-06-01

    Chiral α-hydroxy acids (AHAs) are rapidly becoming important synthetic building blocks, in particular for the production of pharmaceuticals and other fine chemicals. Chiral compounds of a variety of functionalities are now often derived using enzymes, and L-lactate dehydrogenase from the thermophilic organism Geobacillus stearothermophilus (bsLDH) has the potential to be employed for the industrial synthesis of chiral α-hydroxy acids. Despite the thorough characterization of this enzyme, generation of variants with high activity on non-natural substrates has remained difficult and therefore limits the use of bsLDH in industry. Here, we present the engineering of bsLDH using semi-rational design as a method of focusing screening in a small and smart library for novel biocatalysts. In this study, six mutant libraries were designed in an effort to expand the substrate range of bsLDH. The eight variants identified as having enhanced activity toward the selected α-keto acids belonged to the same library, which targeted two positions simultaneously. These new variants now may be useful biocatalysts for chiral synthesis of α-hydroxy acids.

  16. Rational design of efficient electrode-electrolyte interfaces for solid-state energy storage using ion soft landing

    Science.gov (United States)

    Prabhakaran, Venkateshkumar; Mehdi, B. Layla; Ditto, Jeffrey J.; Engelhard, Mark H.; Wang, Bingbing; Gunaratne, K. Don D.; Johnson, David C.; Browning, Nigel D.; Johnson, Grant E.; Laskin, Julia

    2016-04-01

    The rational design of improved electrode-electrolyte interfaces (EEI) for energy storage is critically dependent on a molecular-level understanding of ionic interactions and nanoscale phenomena. The presence of non-redox active species at EEI has been shown to strongly influence Faradaic efficiency and long-term operational stability during energy storage processes. Herein, we achieve substantially higher performance and long-term stability of EEI prepared with highly dispersed discrete redox-active cluster anions (50 ng of pure ~0.75 nm size molybdenum polyoxometalate (POM) anions on 25 μg (~0.2 wt%) carbon nanotube (CNT) electrodes) by complete elimination of strongly coordinating non-redox species through ion soft landing (SL). Electron microscopy provides atomically resolved images of a uniform distribution of individual POM species soft landed directly on complex technologically relevant CNT electrodes. In this context, SL is established as a versatile approach for the controlled design of novel surfaces for both fundamental and applied research in energy storage.

  17. Rational design of biaryl pharmacophore inserted noscapine derivatives as potent tubulin binding anticancer agents

    Science.gov (United States)

    Santoshi, Seneha; Manchukonda, Naresh Kumar; Suri, Charu; Sharma, Manya; Sridhar, Balasubramanian; Joseph, Silja; Lopus, Manu; Kantevari, Srinivas; Baitharu, Iswar; Naik, Pradeep Kumar

    2015-03-01

    We have strategically designed a series of noscapine derivatives by inserting biaryl pharmacophore (a major structural constituent of many of the microtubule-targeting natural anticancer compounds) onto the scaffold structure of noscapine. Molecular interaction of these derivatives with α,β-tubulin heterodimer was investigated by molecular docking, molecular dynamics simulation, and binding free energy calculation. The predictive binding affinity indicates that the newly designed noscapinoids bind to tubulin with a greater affinity. The predictive binding free energy (ΔGbind, pred) of these derivatives (ranging from -5.568 to -5.970 kcal/mol) based on linear interaction energy (LIE) method with a surface generalized Born (SGB) continuum solvation model showed improved binding affinity with tubulin compared to the lead compound, natural α-noscapine (-5.505 kcal/mol). Guided by the computational findings, these new biaryl type α-noscapine congeners were synthesized from 9-bromo-α-noscapine using optimized Suzuki reaction conditions for further experimental evaluation. The derivatives showed improved inhibition of the proliferation of human breast cancer cells (MCF-7), human cervical cancer cells (HeLa) and human lung adenocarcinoma cells (A549), compared to natural noscapine. The cell cycle analysis in MCF-7 further revealed that these compounds alter the cell cycle profile and cause mitotic arrest at G2/M phase more strongly than noscapine. Tubulin binding assay revealed higher binding affinity to tubulin, as suggested by dissociation constant (Kd) of 126 ± 5.0 µM for 5a, 107 ± 5.0 µM for 5c, 70 ± 4.0 µM for 5d, and 68 ± 6.0 µM for 5e compared to noscapine (Kd of 152 ± 1.0 µM). In fact, the experimentally determined value of ΔGbind, expt (calculated from the Kd value) are consistent with the predicted value of ΔGbind, pred calculated based on LIE-SGB. Based on these results, one of the derivative 5e of this series was used for further toxicological

  18. Quantum Chemical-Based Protocol for the Rational Design of Covalent Inhibitors.

    Science.gov (United States)

    Schirmeister, Tanja; Kesselring, Jochen; Jung, Sascha; Schneider, Thomas H; Weickert, Anastasia; Becker, Johannes; Lee, Wook; Bamberger, Denise; Wich, Peter R; Distler, Ute; Tenzer, Stefan; Johé, Patrick; Hellmich, Ute A; Engels, Bernd

    2016-07-13

    We propose a structure-based protocol for the development of customized covalent inhibitors. Starting from a known inhibitor, in the first and second steps appropriate substituents of the warhead are selected on the basis of quantum mechanical (QM) computations and hybrid approaches combining QM with molecular mechanics (QM/MM). In the third step the recognition unit is optimized using docking approaches for the noncovalent complex. These predictions are finally verified by QM/MM or molecular dynamic simulations. The applicability of our approach is successfully demonstrated by the design of reversible covalent vinylsulfone-based inhibitors for rhodesain. The examples show that our approach is sufficiently accurate to identify compounds with the desired properties but also to exclude nonpromising ones.

  19. Biobased building blocks for the rational design of renewable block polymers.

    Science.gov (United States)

    Holmberg, Angela L; Reno, Kaleigh H; Wool, Richard P; Epps, Thomas H

    2014-10-14

    Block polymers (BPs) derived from biomass (biobased) are necessary components of a sustainable future that relies minimally on petroleum-based plastics for applications ranging from thermoplastic elastomers and pressure-sensitive adhesives to blend compatibilizers. To facilitate their adoption, renewable BPs must be affordable, durable, processable, versatile, and reasonably benign. Their desirability further depends on the relative sustainability of the renewable resources and the methods employed in the monomer and polymer syntheses. Various strategies allow these BPs' characteristics to be tuned and enhanced for commercial applications, and many of these techniques also can be applied to manipulate the wide-ranging mechanical and thermal properties of biobased and self-assembling block polymers. From feedstock to application, this review article highlights promising renewable BPs, plus their material and assembly properties, in support of de novo design strategies that could revolutionize material sustainability.

  20. Rational Design of Push-Pull Fluorene Dyes: Synthesis and Structure-Photophysics Relationship.

    Science.gov (United States)

    Shaya, Janah; Fontaine-Vive, Fabien; Michel, Benoît Y; Burger, Alain

    2016-07-18

    Our work surveyed experimental and theoretical investigations to construct highly emissive D-π-A (D=donor, A=acceptor) fluorenes. The synthetic routes were optimised to be concise and gram-scalable. The molecular design was first rationalised by varying the electron-withdrawing group from an aldehyde, ketotriazole or succinyl to methylenemalonitrile or benzothiadiazole. The electron-donating group was next varied from aliphatic or aromatic amines to saturated cyclic amines ranging from aziridine to azepane. Spectroscopic studies correlated with TD-DFT calculations provided the optimised structures. The selected push-pull dyes exhibited visible absorptions, significant brightness, important solvatofluorochromism, mega-Stokes shifts (>250 nm) and dramatic shifts in emission to the near-infrared. The current library includes the comprehensive characterization of 16 prospective dyes for fluorescence applications. Among them, several fluorene derivatives bearing different conjugation anchors were tested for coupling and demonstrated to preserve the photophysical responses once further bound.

  1. Rational design of temperature-sensitive alleles using computational structure prediction.

    Directory of Open Access Journals (Sweden)

    Christopher S Poultney

    Full Text Available Temperature-sensitive (ts mutations are mutations that exhibit a mutant phenotype at high or low temperatures and a wild-type phenotype at normal temperature. Temperature-sensitive mutants are valuable tools for geneticists, particularly in the study of essential genes. However, finding ts mutations typically relies on generating and screening many thousands of mutations, which is an expensive and labor-intensive process. Here we describe an in silico method that uses Rosetta and machine learning techniques to predict a highly accurate "top 5" list of ts mutations given the structure of a protein of interest. Rosetta is a protein structure prediction and design code, used here to model and score how proteins accommodate point mutations with side-chain and backbone movements. We show that integrating Rosetta relax-derived features with sequence-based features results in accurate temperature-sensitive mutation predictions.

  2. Enzyme molecular dynamics simulations in different solvents: Fundamental effects and a new paradigm for rational design

    Energy Technology Data Exchange (ETDEWEB)

    Ornstein, R.L. [Pacific Northwest National Lab., Richland, WA (United States)

    1997-12-31

    Developing enzymes that are functional in nonaqueous solutions may prove useful in the development of new strategies for environmental remediation and monitoring, as well as in developing `green` processes. To gain a fundamental understanding of the structural and dynamic consequences to an enzyme induced by such solvents, we compared simulation results for the well characterized protease enzyme subtilisin Carlsberg in different solvents, including water, carbon tetrachloride, and dimethyl sulfoxide. Serendipitously, we observed a small number of solvent-dependent `tight-binding` site between the enzyme and each solvent. Such solvent-dependent `tight-binding` site information may offer a new simulation paradigm for protein engineering and drug design. Examples will be offered for the cases of subtilisin and a glutathione S-transferase.

  3. Rational Design of Alpha-Helical Antimicrobial Peptides: Do's and Don'ts

    DEFF Research Database (Denmark)

    Uggerhøj, Lars Erik; Poulsen, Tanja Juul; Munk, Jens Kristian

    2015-01-01

    Antimicrobial peptides (AMPs) are promising candidates for battling multiresistant bacteria. Despite extensive research, structure–activity relationships of AMPs are not fully understood, and there is a lack of structural data relating to AMPs in lipids. Here we present the NMR structure of anoplin...... (GLLKRIKTLL-NH2) in a micellar environment. A vast library of substitutions was designed and tested for antimicrobial and hemolytic activity, as well as for changes in structure and lipid interactions. This showed that improvement of antimicrobial activity without concomitant introduction of strong hemolytic...... activity can be achieved through subtle increases in the hydrophobicity of the hydrophobic face or through subtle increases in the polarity of the hydrophilic face of the helix, or—most efficiently—a combination of both. A set of guidelines based on the results is given, for assistance in how to modify...

  4. Glutamic acid and its derivatives: candidates for rational design of anticancer drugs.

    Science.gov (United States)

    Ali, Imran; Wani, Waseem A; Haque, Ashanul; Saleem, Kishwar

    2013-05-01

    Throughout the history of human civilizations, cancer has been a major health problem. Its treatment has been interesting but challenging to scientists. Glutamic acid and its derivative glutamine are known to play interesting roles in cancer genesis, hence, it was realized that structurally variant glutamic acid derivatives may be designed and developed and, might be having antagonistic effects on cancer. The present article describes the state-of-art of glutamic acid and its derivatives as anticancer agents. Attempts have been made to explore the effectivity of drug-delivery systems based on glutamic acid for the delivery of anticancer drugs. Moreover, efforts have also been made to discuss the mechanism of action of glutamic acid derivatives as anticancer agents, clinical applications of glutamic acid derivatives, as well as recent developments and future perspectives of glutamic acid drug development have also been discussed.

  5. Rational design of a fibroblast growth factor 21-based clinical candidate, LY2405319.

    Directory of Open Access Journals (Sweden)

    Alexei Kharitonenkov

    Full Text Available Fibroblast growth factor 21 is a novel hormonal regulator with the potential to treat a broad variety of metabolic abnormalities, such as type 2 diabetes, obesity, hepatic steatosis, and cardiovascular disease. Human recombinant wild type FGF21 (FGF21 has been shown to ameliorate metabolic disorders in rodents and non-human primates. However, development of FGF21 as a drug is challenging and requires re-engineering of its amino acid sequence to improve protein expression and formulation stability. Here we report the design and characterization of a novel FGF21 variant, LY2405319. To enable the development of a potential drug product with a once-daily dosing profile, in a preserved, multi-use formulation, an additional disulfide bond was introduced in FGF21 through Leu118Cys and Ala134Cys mutations. FGF21 was further optimized by deleting the four N-terminal amino acids, His-Pro-Ile-Pro (HPIP, which was subject to proteolytic cleavage. In addition, to eliminate an O-linked glycosylation site in yeast a Ser167Ala mutation was introduced, thus allowing large-scale, homogenous protein production in Pichia pastoris. Altogether re-engineering of FGF21 led to significant improvements in its biopharmaceutical properties. The impact of these changes was assessed in a panel of in vitro and in vivo assays, which confirmed that biological properties of LY2405319 were essentially identical to FGF21. Specifically, subcutaneous administration of LY2405319 in ob/ob and diet-induced obese (DIO mice over 7-14 days resulted in a 25-50% lowering of plasma glucose coupled with a 10-30% reduction in body weight. Thus, LY2405319 exhibited all the biopharmaceutical and biological properties required for initiation of a clinical program designed to test the hypothesis that administration of exogenous FGF21 would result in effects on disease-related metabolic parameters in humans.

  6. Rational design of fluorescent membrane probes for apoptosis based on 3-hydroxyflavone

    Science.gov (United States)

    Darwich, Zeinab; Kucherak, Oleksandr A.; Kreder, Rémy; Richert, Ludovic; Vauchelles, Romain; Mély, Yves; Klymchenko, Andrey S.

    2013-06-01

    Environment-sensitive probes constitute powerful tools for monitoring changes in the physico-chemical properties of cell plasma membranes. Among these probes, 3-hydroxyflavone probes are of great interest due to their dual emission and ratiometric response. Here, three probes derived from the parent F2N12S were designed, characterized and applied to monitor the membrane changes occurring during apoptosis. These three probes were designed to orient the dye vertically in the membrane. They differ by the length of their alkyl chains (from 4 to 8 carbons), which were included to optimize their affinity to the lipid membranes. Among these three probes, the one with medium chain length (hexyl) showed the best affinity to model and cell membranes, while the one with the longest alkyl chains (octyl) did not efficiently stain the membranes, probably due to aggregation. The new probes were found to be more sensitive than F2N12S to both the lipid phase and surface charge in lipid vesicles and to loss of lipid order in cell plasma membranes after cholesterol extraction. The one with the shortest (butyl) chains was found to be the most sensitive to apoptosis, while the one with medium-length (hexyl) chains was the brightest. Interestingly, apoptosis induced by different agents led to similar spectroscopic effects to those produced by the loss of lipid order and change in the surface charge, confirming that apoptosis decreases the lipid order and increases the negative surface charge in the outer leaflet of cell membranes. In conclusion, these studies report the relationship between the probe structures and their sensitivity to lipid order, surface charge and apoptosis and propose new probes for membrane research.

  7. Rational polynomials

    Energy Technology Data Exchange (ETDEWEB)

    Blackett, S.A. [Univ. of Auckland (New Zealand). Dept of Engineering Science

    1996-02-01

    Numerical analysis is an important part of Engineering. Frequently relationships are not adequately understood, or too complicated to be represented by theoretical formulae. Instead, empirical approximations based on observed relationships can be used for simple fast and accurate evaluations. Historically, storage of data has been a large constraint on approximately methods. So the challenge is to find a sufficiently accurate representation of data which is valid over as large a range as possible while requiring the storage of only a few numerical values. Polynomials, popular as approximation functions because of their simplicity, can be used to represent simple data. Equation 1.1 shows a simple 3rd order polynomial approximation. However, just increasing the order and number of terms included in a polynomial approximation does not improve the overall result. Although the function may fit exactly to observed data, between these points it is likely that the approximation is increasingly less smooth and probably inadequate. An alternative to adding further terms to the approximation is to make the approximation rational. Equation 1.2 shows a rational polynomial, 3rd order in the numerator and denominator. A rational polynomial approximation allows poles and this can greatly enhance an approximation. In Sections 2 and 3 two different methods for fitting rational polynomials to a given data set are detailed. In Section 4, consideration is given to different rational polynomials used on adjacent regions. Section 5 shows the performance of the rational polynomial algorithms. Conclusions are presented in Section 6.

  8. Electromagnetic modelling and rational design of GLAD thin films for optical applications

    Science.gov (United States)

    Leontyev, Viktor A.

    This thesis presents a theoretical study of columnar films, fabricated by glancing angle deposition (GLAD), as photonic bandgap structures and metamaterials with predictable dielectric and magnetic response. Glancing angle deposition (GLAD) employs extremely oblique vapour incidence and computerized substrate motion to produce nanocolumns with a variety of shapes. Columns grow in random or periodic arrays and may be periodic in one, two, or three dimensions. The films' optical properties were studied using finite-difference time-domain and finite-difference frequency-domain methods, as well as effective medium theories, with support from experimental research. A large part of the thesis is devoted to column arrays with subwavelength intercolumnar distance and periodically modulated column shape. Among them, s-shaped columns were designed as polarizers for linearly polarized light. Simulations have shown a competitive effect from two structural anisotropy sources, causing a band gap suppression for one of two linear polarizations, and high polarizing ability. Simulations were compared to the measurements with a very good agreement in spectral response. Subwavelength column arrays were further explored as anisotropic interference mirrors with omnidirectional reflection bands. Index graded vertical post films were designed, having up to four times wider reflection bands than in the isotropic analogs. Band gap properties of 3D periodic GLAD columns were studied on the example of square-spiral photonic crystals. A significant influence of column cross-section was shown, that currently prevents fabrication of square spirals with a 3D band gap in the visible range. Inverted square-spiral films have better performance, which is further improved by material redistribution along the spiral. Lastly, this work studies the effective dielectric response of porous columnar films with metal particles. Characteristic matrix formalism was combined with finite-difference modelling to

  9. Rational design of multifunctional micelles against doxorubicin-sensitive and doxorubicin-resistant MCF-7 human breast cancer cells

    Science.gov (United States)

    Hong, Wei; Shi, Hong; Qiao, Mingxi; Gao, Xiang; Yang, Jie; Tian, Chunlian; Zhang, Dexian; Niu, Shengli; Liu, Mingchun

    2017-01-01

    Even though a tremendous number of multifunctional nanocarriers have been developed to tackle heterogeneous cancer cells, little attention has been paid to elucidate how to rationally design a multifunctional nanocarrier. In this study, three individual functions (active targeting, stimuli-triggered release and endo-lysosomal escape) were evaluated in doxorubicin (DOX)-sensitive MCF-7 cells and DOX-resistant MCF-7/ADR cells by constructing four kinds of micelles with active-targeting (AT-M), passive targeting, pH-triggered release (pHT-M) and endo-lysosomal escape (endoE-M) function, respectively. AT-M demonstrated the strongest cytotoxicity against MCF-7 cells and the highest cellular uptake of DOX due to the folate-mediated endocytosis. However, AT-M failed to exhibit the best efficacy against MCF-7/ADR cells, while endoE-M exhibited the strongest cytotoxicity against MCF-7/ADR cells and the highest cellular uptake of DOX due to the lowest elimination of DOX from the cells. This was attributed to the carrier-facilitated endo-lysosomal escape of DOX, which avoided exocytosis by lysosome secretion, resulting in an effective accumulation of DOX in the cytoplasm. The enhanced elimination of DOX from the MCF-7/ADR cells also accounted for the remarkable decrease in cytotoxicity against the cells of AT-M. Three micelles were further evaluated with MCF-7 cells and MCF-7/ADR-resistant cells xenografted mice model. In accordance with the in vitro results, AT-M and endoE-M demonstrated the strongest inhibition on the MCF-7 and MCF-7/ADR xenografted tumor, respectively. Active targeting and active targeting in combination with endo-lysosomal escape have been demonstrated to be the primary function for a nanocarrier against doxorubicin-sensitive and doxorubicin-resistant MCF-7 cells, respectively. These results indicate that the rational design of multifunctional nanocarriers for cancer therapy needs to consider the heterogeneous cancer cells and the primary function needs

  10. High-throughput identification and rational design of synergistic small-molecule pairs for combating and bypassing antibiotic resistance.

    Science.gov (United States)

    Wambaugh, Morgan A; Shakya, Viplendra P S; Lewis, Adam J; Mulvey, Matthew A; Brown, Jessica C S

    2017-06-01

    Antibiotic-resistant infections kill approximately 23,000 people and cost $20,000,000,000 each year in the United States alone despite the widespread use of small-molecule antimicrobial combination therapy. Antibiotic combinations typically have an additive effect: the efficacy of the combination matches the sum of the efficacies of each antibiotic when used alone. Small molecules can also act synergistically when the efficacy of the combination is greater than the additive efficacy. However, synergistic combinations are rare and have been historically difficult to identify. High-throughput identification of synergistic pairs is limited by the scale of potential combinations: a modest collection of 1,000 small molecules involves 1 million pairwise combinations. Here, we describe a high-throughput method for rapid identification of synergistic small-molecule pairs, the overlap2 method (O2M). O2M extracts patterns from chemical-genetic datasets, which are created when a collection of mutants is grown in the presence of hundreds of different small molecules, producing a precise set of phenotypes induced by each small molecule across the mutant set. The identification of mutants that show the same phenotype when treated with known synergistic molecules allows us to pinpoint additional molecule combinations that also act synergistically. As a proof of concept, we focus on combinations with the antibiotics trimethoprim and sulfamethizole, which had been standard treatment against urinary tract infections until widespread resistance decreased efficacy. Using O2M, we screened a library of 2,000 small molecules and identified several that synergize with the antibiotic trimethoprim and/or sulfamethizole. The most potent of these synergistic interactions is with the antiviral drug azidothymidine (AZT). We then demonstrate that understanding the molecular mechanism underlying small-molecule synergistic interactions allows the rational design of additional combinations that

  11. Rational design of dendrimer/lipid nanoassemblies in drug delivery for cancer chemotherapy

    Science.gov (United States)

    Sun, Qihang

    Nanocarriers can minimize the side effects and improve therapeutic efficacy of anticancer drugs. Although some success has been achieved via active or passive drug delivery to tumor cells, the known nanocarriers are far from satisfying therapeutic efficacy expectations. This is because they usually fail in one of the four crucial requirements, that is, to retain drug in blood circulation but release it reliably in tumor cells and to be stealthy in transport in circulation and tumor tissue but sticky upon arrival at the tumor cell. Therefore, the goal of this work is to fabricate nanoassemblies of dendrimers and lipids to address all these challenges. Particularly, nanoassemblies designed and prepared in this work are illustrated to improve the tumor tissue penetration. Examples of dendrimers synthesized in this work are water-insoluble, pH-dependent water-insoluble and water-soluble biodegradable polyester dendrimers. These dendrimers are shown to be encapsulated by commonly used fusogenic and long-circulating lipids to form reliable nanoassemblies. The dendrimer/lipid nanocarriers are used to demonstrate a cascade drug delivery. They are expected to be stable in circulation, due to their appropriately large size, but to release the drug-loaded dendrimers in tumor tissue. The released dendrimers carrying drugs are much smaller and hence expected to have a much deeper penetration throughout the tumor tissue.

  12. Rational design of berberine-based FtsZ inhibitors with broad-spectrum antibacterial activity.

    Directory of Open Access Journals (Sweden)

    Ning Sun

    Full Text Available Inhibition of the functional activity of Filamenting temperature-sensitive mutant Z (FtsZ protein, an essential and highly conserved bacterial cytokinesis protein, is a promising approach for the development of a new class of antibacterial agents. Berberine, a benzylisoquinoline alkaloid widely used in traditional Chinese and native American medicines for its antimicrobial properties, has been recently reported to inhibit FtsZ. Using a combination of in silico structure-based design and in vitro biological assays, 9-phenoxyalkyl berberine derivatives were identified as potent FtsZ inhibitors. Compared to the parent compound berberine, the derivatives showed a significant enhancement of antibacterial activity against clinically relevant bacteria, and an improved potency against the GTPase activity and polymerization of FtsZ. The most potent compound 2 strongly inhibited the proliferation of Gram-positive bacteria, including methicillin-resistant S. aureus and vancomycin-resistant E. faecium, with MIC values between 2 and 4 µg/mL, and was active against the Gram-negative E. coli and K. pneumoniae, with MIC values of 32 and 64 µg/mL respectively. The compound perturbed the formation of cytokinetic Z-ring in E. coli. Also, the compound interfered with in vitro polymerization of S. aureus FtsZ. Taken together, the chemical modification of berberine with 9-phenoxyalkyl substituent groups greatly improved the antibacterial activity via targeting FtsZ.

  13. G3 Assisted Rational Design of Chemical Sensor Array Using Carbonitrile Neutral Receptors

    Directory of Open Access Journals (Sweden)

    Yatimah Alias

    2013-10-01

    Full Text Available Combined computational and experimental strategies for the systematic design of chemical sensor arrays using carbonitrile neutral receptors are presented. Binding energies of acetonitrile, n-pentylcarbonitrile and malononitrile with Ca(II, Mg(II, Be(II and H+ have been investigated with the B3LYP, G3, CBS-QB3, G4 and MQZVP methods, showing a general trend H+ > Be(II > Mg(II > Ca(II. Hydrogen bonding, donor-acceptor and cation-lone pair electron simple models were employed in evaluating the performance of computational methods. Mg(II is bound to acetonitrile in water by 12.5 kcal/mol, and in the gas phase the receptor is more strongly bound by 33.3 kcal/mol to Mg(II compared to Ca(II. Interaction of bound cations with carbonitrile reduces the energies of the MOs involved in the proposed σ-p conjugated network. The planar malononitrile-Be(II complex possibly involves a π-network with a cationic methylene carbon. Fabricated potentiometric chemical sensors show distinct signal patterns that can be exploited in sensor array applications.

  14. A rational design for the selective detection of dopamine using conducting polymers.

    Science.gov (United States)

    Fabregat, Georgina; Casanovas, Jordi; Redondo, Edurne; Armelin, Elaine; Alemán, Carlos

    2014-05-07

    Poly(N-methylpyrrole) (PNMPy), poly(N-cyanoethylpyrrole) (PNCPy) and poly(3,4-ethylenedioxythiophene) (PEDOT) films have been prepared using both single and two polymerization steps for the selective determination of low concentrations of dopamine, ascorbic acid and uric acid in tertiary mixtures. Analysis of the sensitivity and resolution parameters derived from the electrochemical response of such films indicates that PEDOT is the most appropriate for the unambiguous detection of the three species. Indeed, the performance of PEDOT is practically independent of the presence of both gold nanoparticles at the surface of the film and interphases inside the film, even though these two factors are known to improve the electroactivity of conducting polymers. Quantum mechanical calculations on model complexes have been used to examine the intermolecular interaction involved in complexes formed by PEDOT chains and oxidized dopamine, ascorbic acid and uric acid. Results show that such complexes are mainly stabilized by C-HO interactions rather than by conventional hydrogen bonds. In order to improve the sensitivity of PEDOT through the formation of specific hydrogen bonds, a derivative bearing a hydroxymethyl group attached to the dioxane ring of each repeat unit has been designed. Poly(hydroxymethyl-3,4-ethylenedioxythiophene) (PHMeDOT) has been prepared and characterized by FTIR, UV-vis spectroscopy, cyclic voltammetry, scanning electron microscopy and atomic force microscopy. Finally, the performance of PHMeDOT and PEDOT for the selective detection of the species mentioned above has been compared.

  15. Rationally designed porous polystyrene encapsulated zirconium phosphate nanocomposite for highly efficient fluoride uptake in waters

    Science.gov (United States)

    Zhang, Qingrui; Du, Qing; Jiao, Tifeng; Zhang, Zhaoxiang; Wang, Sufeng; Sun, Qina; Gao, Faming

    2013-01-01

    Fluoride pollution in waters has engulfed worldwide regions and an excess of fluoride intake always causes skeletal fluorosis. Herein, a novel hybrid nanomaterial ZrP-MPN was fabricated for fluoride retention by encapsulating nano-ZrP onto macroporous polystyrene materials modified with quaternary ammonium groups. The as-obtained materials exhibited favorable removal of fluoride ions from aqueous solution in presence of common anions (SO42−/NO3−/Cl−) at high contents. Moreover outstanding sorption properties were also detected by involving series of commercial adsorbents (AA/magnetite/GFH/manganese sands) as references. Such satisfactory performances might be ascribed to the structural design of nanocomposite. (1) the CH2N+(CH3)3Cl groups enhances sorption diffusion and preconcentration in sorbent phase theoretically based on Donnan membrane principle; (2) the embedded ZrP nanoparticles also devotes to the efficient adsorption capacities due to its size-dependent specific properties. Additionally, the exhausted ZrP-MPN could be regenerated readily by alkaline solution. Thus, ZrP-MPN was a promising material for fluoride retention in waters. PMID:23989688

  16. pH sensitive silica nanotubes as rationally designed vehicles for NSAIDs delivery.

    Science.gov (United States)

    Sousa, Célia T; Nunes, Cláudia; Proença, Mariana P; Leitão, Diana C; Lima, José L F C; Reis, Salette; Araújo, João P; Lúcio, Marlene

    2012-06-01

    A novel pH-sensitive drug delivery system based on functionalized silica nanotubes was developed for the incorporation of non-steroidal anti-inflammatory drugs (NSAIDs), aimed at a tailored drug release in acidic conditions characteristic of inflamed tissues. Silica nanotubes (SNTs) were synthesized by a nanoporous alumina template assisted sol-gel method. Inner surfaces were physically and chemically modified to improve both the functionalization and subsequent incorporation of the drug. Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), energy dispersive spectroscopy (EDS) and transmission electron microscopy (TEM) were used to characterize the designed nanocarriers and their functionalization. To achieve the highest degree of functionalization, three types of aminosilanes were tested and calcination conditions were optimized. APTES was shown to be the most effective aminosilane regarding the functionalization of the SNTs' inner surface and an adequate calcination temperature (220°C) was found to attain mechanical stability without compromising functionalization efficiency. Finally, the incorporation of naproxen into the nanotubes was accessed by fluorescence measurements and drug release studies were performed, revealing that the electrostatic linkage ensures effective release of the drug in the acidic pH typical of inflamed cells, while maintaining the SNT-drug conjugates stable at the typical bloodstream pH.

  17. Rational Design of Potent Antagonists to the Human Growth Hormone Receptor

    Science.gov (United States)

    Fuh, Germaine; Cunningham, Brian C.; Fukunaga, Rikiro; Nagata, Shigekazu; Goeddel, David V.; Wells, James A.

    1992-06-01

    A hybrid receptor was constructed that contained the extracellular binding domain of the human growth hormone (hGH) receptor linked to the transmembrane and intracellular domains of the murine granulocyte colony-stimulating factor receptor. Addition of hGH to a myeloid leukemia cell line (FDC-P1) that expressed the hybrid receptor caused proliferation of these cells. The mechanism for signal transduction of the hybrid receptor required dimerization because monoclonal antibodies to the hGH receptor were agonists whereas their monovalent fragments were not. Receptor dimerization occurs sequentially-a receptor binds to site 1 on hGH, and then a second receptor molecule binds to site 2 on hGH. On the basis of this sequential mechanism, which may occur in many other cytokine receptors, inactive hGH analogs were designed that were potent antagonists to hGH-induced cell proliferation. Such antagonists could be useful for treating clinical conditions of hGH excess, such as acromegaly.

  18. Switching the Regioselectivity of a Cyclohexanone Monooxygenase toward (+)-trans-Dihydrocarvone by Rational Protein Design.

    Science.gov (United States)

    Balke, Kathleen; Schmidt, Sandy; Genz, Maika; Bornscheuer, Uwe T

    2016-01-15

    The regioselectivity of the Baeyer-Villiger monooxygenase-catalyzed oxidation is governed mostly by electronic effects leading to the migration of the higher substituted residue. However, in some cases, substrate binding occurs in a way that the less substituted residue lies in an antiperiplanar orientation to the peroxy bond in the Criegee intermediate yielding in the formation of the "abnormal" lactone product. We are the first to demonstrate a complete switch in the regioselectivity of the BVMO from Arthrobacter sp. (CHMOArthro) as exemplified for (+)-trans-dihydrocarvone by redesigning the active site of the enzyme. In the designed triple mutant, the substrate binds in an inverted orientation leading to a ratio of 99:1 in favor of the normal lactone instead of exclusive formation of the abnormal lactone in case of the wild type enzyme. In order to validate our computational study, the beneficial mutations were successfully transferred to the CHMO from Acinetobacter sp. (CHMOAcineto), again yielding in a complete switch of regioselectivity.

  19. A rational approach towards the design of chitosan-based nanoparticles obtained by ionotropic gelation.

    Science.gov (United States)

    Kleine-Brueggeney, H; Zorzi, G K; Fecker, T; El Gueddari, N E; Moerschbacher, B M; Goycoolea, F M

    2015-11-01

    Chitosan is a linear aminopolysaccharide that has been widely used for the formation of chitosan-based nanoparticles by ionic gelation with sodium tripolyphosphate (TPP). Often, the experimental design used to obtain these systems does not take into consideration important variables, such as the degree of acetylation (DA) and the molecular weight (Mw) of chitosan. In this work, we studied the formation of chitosan-TPP nanoparticles with chitosan samples of varying DA and Mw (DA0 ∼ 0-47% and Mw ∼ 2.5-282 kDa). We addressed the influence the degree of space occupancy and the degree of crosslinking on the physical properties of chitosan-TPP nanoparticles. Nanoparticles that comprised chitosan of DA ∼ 0-21.7% behaved differently than those made of chitosan of DA ∼ 34.7-47%. We attributed these differences to the polymer conformation and chain flexibility of the distinct chitosans in solution. Moreover, chitosan of high Mw were found to have a stronger preference for incorporating into the formed nanoparticles than do low-Mw ones, as determined by SEC-HPLC. These results open new perspectives to understand the formation of chitosan nanoparticles by the ionic gelation technique.

  20. New mimetic peptides inhibitors of Αβ aggregation. Molecular guidance for rational drug design.

    Science.gov (United States)

    Barrera Guisasola, Exequiel E; Andujar, Sebastián A; Hubin, Ellen; Broersen, Kerensa; Kraan, Ivonne M; Méndez, Luciana; Delpiccolo, Carina M L; Masman, Marcelo F; Rodríguez, Ana M; Enriz, Ricardo D

    2015-05-01

    A new series of mimetic peptides possessing a significant Aβ aggregation modulating effect was reported here. These compounds were obtained based on a molecular modelling study which allowed us to perform a structural-based virtual selection. Monitoring Aβ aggregation by thioflavin T fluorescence and transmission electron microscopy revealed that fibril formation was significantly decreased upon prolonged incubation in presence of the active compounds. Dot blot analysis suggested a decrease of soluble oligomers strongly associated with cognitive decline in Alzheimer's disease. For the molecular dynamics simulations, we used an Aβ42 pentameric model where the compounds were docked using a blind docking technique. To analyze the dynamic behaviour of the complexes, extensive molecular dynamics simulations were carried out in explicit water. We also measured parameters or descriptors that allowed us to quantify the effect of these compounds as potential inhibitors of Aβ aggregation. Thus, significant alterations in the structure of our Aβ42 protofibril model were identified. Among others we observed the destruction of the regular helical twist, the loss of a stabilizing salt bridge and the loss of a stabilizing hydrophobic interaction in the β1 region. Our results may be helpful in the structural identification and understanding of the minimum structural requirements for these molecules and might provide a guide in the design of new aggregation modulating ligands.

  1. Rationally designed porous polystyrene encapsulated zirconium phosphate nanocomposite for highly efficient fluoride uptake in waters

    Science.gov (United States)

    Zhang, Qingrui; Du, Qing; Jiao, Tifeng; Zhang, Zhaoxiang; Wang, Sufeng; Sun, Qina; Gao, Faming

    2013-08-01

    Fluoride pollution in waters has engulfed worldwide regions and an excess of fluoride intake always causes skeletal fluorosis. Herein, a novel hybrid nanomaterial ZrP-MPN was fabricated for fluoride retention by encapsulating nano-ZrP onto macroporous polystyrene materials modified with quaternary ammonium groups. The as-obtained materials exhibited favorable removal of fluoride ions from aqueous solution in presence of common anions (SO42-/NO3-/Cl-) at high contents. Moreover outstanding sorption properties were also detected by involving series of commercial adsorbents (AA/magnetite/GFH/manganese sands) as references. Such satisfactory performances might be ascribed to the structural design of nanocomposite. (1) the CH2N+(CH3)3Cl groups enhances sorption diffusion and preconcentration in sorbent phase theoretically based on Donnan membrane principle; (2) the embedded ZrP nanoparticles also devotes to the efficient adsorption capacities due to its size-dependent specific properties. Additionally, the exhausted ZrP-MPN could be regenerated readily by alkaline solution. Thus, ZrP-MPN was a promising material for fluoride retention in waters.

  2. Rational design and validation of a Tip60 histone acetyltransferase inhibitor

    Science.gov (United States)

    Gao, Chunxia; Bourke, Emer; Scobie, Martin; Famme, Melina Arcos; Koolmeister, Tobias; Helleday, Thomas; Eriksson, Leif A.; Lowndes, Noel F.; Brown, James A. L.

    2014-06-01

    Histone acetylation is required for many aspects of gene regulation, genome maintenance and metabolism and dysfunctional acetylation is implicated in numerous diseases, including cancer. Acetylation is regulated by histone acetyltransferases (HATs) and histone deacetylases and currently, few general HAT inhibitors have been described. We identified the HAT Tip60 as an excellent candidate for targeted drug development, as Tip60 is a key mediator of the DNA damage response and transcriptional co-activator. Our modeling of Tip60 indicated that the active binding pocket possesses opposite charges at each end, with the positive charges attributed to two specific side chains. We used structure based drug design to develop a novel Tip60 inhibitor, TH1834, to fit this specific pocket. We demonstrate that TH1834 significantly inhibits Tip60 activity in vitro and treating cells with TH1834 results in apoptosis and increased unrepaired DNA damage (following ionizing radiation treatment) in breast cancer but not control cell lines. Furthermore, TH1834 did not affect the activity of related HAT MOF, as indicated by H4K16Ac, demonstrating specificity. The modeling and validation of the small molecule inhibitor TH1834 represents a first step towards developing additional specific, targeted inhibitors of Tip60 that may lead to further improvements in the treatment of breast cancer.

  3. Improvements in Rational Design Strategies of Inulin Derivative Polycation for siRNA Delivery.

    Science.gov (United States)

    Sardo, Carla; Craparo, Emanuela Fabiola; Porsio, Barbara; Giammona, Gaetano; Cavallaro, Gennara

    2016-07-11

    The advances of short interfering RNA (siRNA)-mediated therapy provide a powerful option for the treatment of many diseases, including cancer, by silencing the expression of targeted genes involved in the progression of the pathology. On this regard, a new pH-responsive polycation derived from inulin, Inulin-g-imidazole-g-diethylenetriamine (INU-IMI-DETA), was designed and employed to produce INU-IMI-DETA/siRNA "Inulin COmplex Nanoaggregates" (ICONs). The experimental results showed that INU-IMI-DETA exhibited strong cationic characteristics and high solubility in the pH range 3-5 and self-aggregation triggered by pH increase and physiological salt concentration. INU-IMI-DETA showed as well a high buffering capacity in the endosomal pH range of 7.4-5.1. In the concentration range between 25 and 1000 μg/mL INU-IMI-DETA had no cytotoxic effect on breast cancer cells (MCF-7) and no lytic effect on human red blood cells. ICONs were prepared by two-step procedure involving complexation and precipitation into DPBS buffer (pH 7.4) to produce siRNA-loaded nanoaggregates with minimized surface charge and suitable size for parenteral administration. Bafilomycin A1 inhibited transfection on MCF-7 cells, indicating that the protonation of the imidazole groups in the endolysosome pathway favors the escape of the system from endolysosomal compartment, increasing the amount of siRNA that can reach the cytoplasm.

  4. Towards a Rational Design of Zeolite-Polymer Composite Nanofibers for Efficient Adsorption of Creatinine

    Directory of Open Access Journals (Sweden)

    Ryo Takai

    2016-01-01

    Full Text Available This report describes the compositional and structural design strategy of a zeolite-polymer composite nanofiber mesh for the efficient removal of uremic toxins towards blood purification application. The nanofiber is fabricated by electrospinning composite solution of biocompatible poly(ethylene-co-vinyl alcohol (EVOH and zeolite particles which are capable of selectively adsorbing uremic toxins such as creatinine. By controlling electrospinning conditions carefully, the incorporated zeolites in EVOH were found to correspond closely to the feed ratios. Elemental mapping images of Si show that zeolites were uniformly blended within the fibers. The fabricated composite fibers successfully adsorbed creatinine from solution and the adsorption capacity reached a maximum at 12 h. The crystallinity of the nanofiber was also controlled by varying the composition of ethylene content in EVOH. Less crystallinity resulted in higher creatinine adsorption capacity due to the barrier property of EVOH. Cytotoxicity assay demonstrated that the composite fibers showed less toxicity than free zeolite particles which killed more than 95% of cells. The proposed composite fibers, therefore, have the potential to be utilized as a new approach to removing creatinine selectively from the bloodstream.

  5. Rational design of redox mediators for advanced Li-O2 batteries

    Science.gov (United States)

    Lim, Hee-Dae; Lee, Byungju; Zheng, Yongping; Hong, Jihyun; Kim, Jinsoo; Gwon, Hyeokjo; Ko, Youngmin; Lee, Minah; Cho, Kyeongjae; Kang, Kisuk

    2016-06-01

    The discovery of effective catalysts is an important step towards achieving Li-O2 batteries with long cycle life and high round-trip efficiency. Soluble-type catalysts or redox mediators (RMs) possess great advantages over conventional solid catalysts, generally exhibiting much higher efficiency. Here, we select a series of organic RM candidates as a model system to identify the key descriptor in determining the catalytic activities and stabilities in Li-O2 cells. It is revealed that the level of ionization energies, readily available parameters from a database of the molecules, can serve such a role when comparing with the formation energy of Li2O2 and the highest occupied molecular orbital energy of the electrolyte. It is demonstrated that they are critical in reducing the overpotential and improving the stability of Li-O2 cells, respectively. Accordingly, we propose a general principle for designing feasible catalysts and report a RM, dimethylphenazine, with a remarkably low overpotential and high stability.

  6. Rationally designed coiled-coil DNA looping peptides control DNA topology.

    Science.gov (United States)

    Gowetski, Daniel B; Kodis, Erin J; Kahn, Jason D

    2013-09-01

    Artificial DNA looping peptides were engineered to study the roles of protein and DNA flexibility in controlling the geometry and stability of protein-mediated DNA loops. These LZD (leucine zipper dual-binding) peptides were derived by fusing a second, C-terminal, DNA-binding region onto the GCN4 bZip peptide. Two variants with different coiled-coil lengths were designed to control the relative orientations of DNA bound at each end. Electrophoretic mobility shift assays verified formation of a sandwich complex containing two DNAs and one peptide. Ring closure experiments demonstrated that looping requires a DNA-binding site separation of 310 bp, much longer than the length needed for natural loops. Systematic variation of binding site separation over a series of 10 constructs that cyclize to form 862-bp minicircles yielded positive and negative topoisomers because of two possible writhed geometries. Periodic variation in topoisomer abundance could be modeled using canonical DNA persistence length and torsional modulus values. The results confirm that the LZD peptides are stiffer than natural DNA looping proteins, and they suggest that formation of short DNA loops requires protein flexibility, not unusual DNA bendability. Small, stable, tunable looping peptides may be useful as synthetic transcriptional regulators or components of protein-DNA nanostructures.

  7. Towards a rational spacer design for bivalent inhibition of estrogen receptor

    Science.gov (United States)

    Bujotzek, Alexander; Shan, Min; Haag, Rainer; Weber, Marcus

    2011-03-01

    Estrogen receptors are known drug targets that have been linked to several kinds of cancer. The structure of the estrogen receptor ligand binding domain is available and reveals a homodimeric layout. In order to improve the binding affinity of known estrogen receptor inhibitors, bivalent compounds have been developed that consist of two individual ligands linked by flexible tethers serving as spacers. So far, binding affinities of the bivalent compounds do not surpass their monovalent counterparts. In this article, we focus our attention on the molecular spacers that are used to connect the individual ligands to form bivalent compounds, and describe their thermodynamic contribution during the ligand binding process. We use computational methods to predict structural and entropic parameters of different spacer structures. We find that flexible spacers introduce a number of effects that may interfere with ligand binding and possibly can be connected to the low binding affinities that have been reported in binding assays. Based on these findings, we try to provide guidelines for the design of novel molecular spacers.

  8. Rational design of human DNA ligase inhibitors that target cellular DNA replication and repair.

    Science.gov (United States)

    Chen, Xi; Zhong, Shijun; Zhu, Xiao; Dziegielewska, Barbara; Ellenberger, Tom; Wilson, Gerald M; MacKerell, Alexander D; Tomkinson, Alan E

    2008-05-01

    Based on the crystal structure of human DNA ligase I complexed with nicked DNA, computer-aided drug design was used to identify compounds in a database of 1.5 million commercially available low molecular weight chemicals that were predicted to bind to a DNA-binding pocket within the DNA-binding domain of DNA ligase I, thereby inhibiting DNA joining. Ten of 192 candidates specifically inhibited purified human DNA ligase I. Notably, a subset of these compounds was also active against the other human DNA ligases. Three compounds that differed in their specificity for the three human DNA ligases were analyzed further. L82 inhibited DNA ligase I, L67 inhibited DNA ligases I and III, and L189 inhibited DNA ligases I, III, and IV in DNA joining assays with purified proteins and in cell extract assays of DNA replication, base excision repair, and nonhomologous end-joining. L67 and L189 are simple competitive inhibitors with respect to nicked DNA, whereas L82 is an uncompetitive inhibitor that stabilized complex formation between DNA ligase I and nicked DNA. In cell culture assays, L82 was cytostatic whereas L67 and L189 were cytotoxic. Concordant with their ability to inhibit DNA repair in vitro, subtoxic concentrations of L67 and L189 significantly increased the cytotoxicity of DNA-damaging agents. Interestingly, the ligase inhibitors specifically sensitized cancer cells to DNA damage. Thus, these novel human DNA ligase inhibitors will not only provide insights into the cellular function of these enzymes but also serve as lead compounds for the development of anticancer agents.

  9. Rational design of an auxin antagonist of the SCF(TIR1) auxin receptor complex.

    Science.gov (United States)

    Hayashi, Ken-ichiro; Neve, Joshua; Hirose, Masakazu; Kuboki, Atsuhito; Shimada, Yukihisa; Kepinski, Stefan; Nozaki, Hiroshi

    2012-03-16

    The plant hormone auxin is a master regulator of plant growth and development. By regulating rates of cell division and elongation and triggering specific patterning events, indole 3-acetic acid (IAA) regulates almost every aspect of plant development. The perception of auxin involves the formation of a ternary complex consisting of an F-box protein of the TIR1/AFB family of auxin receptors, the auxin molecule, and a member the Aux/IAA family of co-repressor proteins. In this study, we identified a potent auxin antagonist, α-(phenylethyl-2-oxo)-IAA, as a lead compound for TIR1/AFB receptors by in silico virtual screening. This molecule was used as the basis for the development of a more potent TIR1 antagonist, auxinole (α-[2,4-dimethylphenylethyl-2-oxo]-IAA), using a structure-based drug design approach. Auxinole binds TIR1 to block the formation of the TIR1-IAA-Aux/IAA complex and so inhibits auxin-responsive gene expression. Molecular docking analysis indicates that the phenyl ring in auxinole would strongly interact with Phe82 of TIR1, a residue that is crucial for Aux/IAA recognition. Consistent with this predicted mode of action, auxinole competitively inhibits various auxin responses in planta. Additionally, auxinole blocks auxin responses of the moss Physcomitrella patens, suggesting activity over a broad range of species. Our works not only substantiates the utility of chemical tools for plant biology but also demonstrates a new class of small molecule inhibitor of protein-protein interactions common to mechanisms of perception of other plant hormones, such as jasmonate, gibberellin, and abscisic acid.

  10. Rational Design, Structural and Thermodynamic Characterization of a Hyperstable Variant of the Villin Headpiece Helical Subdomain

    Energy Technology Data Exchange (ETDEWEB)

    Bi,Y.; Cho, J.; Kim, E.; Shan, B.; Schindelin, H.; Raleigh, D.

    2007-01-01

    A hyperstable variant of the small independently folded helical subdomain (HP36) derived from the F-actin binding villin headpiece was designed by targeting surface electrostatic interactions and helical propensity. A double mutant N68A, K70M was significantly more stable than wild type. The T{sub m} of wild type in aqueous buffer is 73.0 {sup o}C, whereas the double mutant did not display a complete unfolding transition. The double mutant could not be completely unfolded even by 10 M urea. In 3 M urea, the T{sub m} of wild type is 54.8 {sup o}C while that of the N68AK70M double mutant is 73.9 {sup o}C. Amide H/{sup 2}H exchange studies show that the pattern of exchange is very similar for wild type and the double mutant. The structures of a K70M single mutant and the double mutant were determined by X-ray crystallography and are identical to that of the wild type. Analytical ultracentrifugation demonstrates that the proteins are monomeric. The hyperstable mutant described here is expected to be useful for folding studies of HP36 because studies of the wild type domain have sometimes been limited by its marginal stability. The results provide direct evidence that naturally occurring miniature protein domains have not been evolutionarily optimized for global stability. The stabilizing effect of this double mutant could not be predicted by sequence analysis because K70 is conserved in the larger intact headpiece for functional reasons.

  11. Rational design of organic semiconductors for texture control and self-patterning on halogenated surfaces

    KAUST Repository

    Ward, Jeremy W.

    2014-05-15

    Understanding the interactions at interfaces between the materials constituting consecutive layers within organic thin-film transistors (OTFTs) is vital for optimizing charge injection and transport, tuning thin-film microstructure, and designing new materials. Here, the influence of the interactions at the interface between a halogenated organic semiconductor (OSC) thin film and a halogenated self-assembled monolayer on the formation of the crystalline texture directly affecting the performance of OTFTs is explored. By correlating the results from microbeam grazing incidence wide angle X-ray scattering (μGIWAXS) measurements of structure and texture with OTFT characteristics, two or more interaction paths between the terminating atoms of the semiconductor and the halogenated surface are found to be vital to templating a highly ordered morphology in the first layer. These interactions are effective when the separating distance is lower than 2.5 dw, where dw represents the van der Waals distance. The ability to modulate charge carrier transport by several orders of magnitude by promoting "edge-on" versus "face-on" molecular orientation and crystallographic textures in OSCs is demonstrated. It is found that the "edge-on" self-assembly of molecules forms uniform, (001) lamellar-textured crystallites which promote high charge carrier mobility, and that charge transport suffers as the fraction of the "face-on" oriented crystallites increases. The role of interfacial halogenation in mediating texture formation and the self-patterning of organic semiconductor films, as well as the resulting effects on charge transport in organic thin-film transistors, are explored. The presence of two or more anchoring sites between a halogenated semiconductor and a halogenated self-assembled monolayer, closer than about twice the corresponding van der Waals distance, alter the microstructure and improve electrical properties. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Rational design and characterization of D-Phe-Pro-D-Arg-derived direct thrombin inhibitors.

    Directory of Open Access Journals (Sweden)

    Ana C Figueiredo

    Full Text Available The tremendous social and economic impact of thrombotic disorders, together with the considerable risks associated to the currently available therapies, prompt for the development of more efficient and safer anticoagulants. Novel peptide-based thrombin inhibitors were identified using in silico structure-based design and further validated in vitro. The best candidate compounds contained both L- and D-amino acids, with the general sequence D-Phe(P3-Pro(P2-D-Arg(P1-P1'-CONH₂. The P1' position was scanned with L- and D-isomers of natural or unnatural amino acids, covering the major chemical classes. The most potent non-covalent and proteolysis-resistant inhibitors contain small hydrophobic or polar amino acids (Gly, Ala, Ser, Cys, Thr at the P1' position. The lead tetrapeptide, D-Phe-Pro-D-Arg-D-Thr-CONH₂, competitively inhibits α-thrombin's cleavage of the S2238 chromogenic substrate with a K(i of 0.92 µM. In order to understand the molecular details of their inhibitory action, the three-dimensional structure of three peptides (with P1' L-isoleucine (fPrI, L-cysteine (fPrC or D-threonine (fPrt in complex with human α-thrombin were determined by X-ray crystallography. All the inhibitors bind in a substrate-like orientation to the active site of the enzyme. The contacts established between the D-Arg residue in position P1 and thrombin are similar to those observed for the L-isomer in other substrates and inhibitors. However, fPrC and fPrt disrupt the active site His57-Ser195 hydrogen bond, while the combination of a P1 D-Arg and a bulkier P1' residue in fPrI induce an unfavorable geometry for the nucleophilic attack of the scissile bond by the catalytic serine. The experimental models explain the observed relative potency of the inhibitors, as well as their stability to proteolysis. Moreover, the newly identified direct thrombin inhibitors provide a novel pharmacophore platform for developing antithrombotic agents by exploring the

  13. Rational Design of Analyte Channels of the Green Fluorescent Protein for Biosensor Applications

    Directory of Open Access Journals (Sweden)

    Natta Tansila, Tanawut Tantimongcolwat, Chartchalerm Isarankura-Na-Ayudhya, Chanin Nantasenamat, Virapong Prachayasittikul

    2007-01-01

    Full Text Available A novel solvent-exposed analyte channel, generated by F165G substitution, on the surface of green fluorescent protein (designated His6GFPuv/F165G was successfully discovered by the aid of molecular modeling software (PyMOL in conjunction with site-directed mutagenesis. Regarding the high predictive performance of PyMOL, two pore-containing mutants namely His6GFPuv/H148G and His6GFPuv/H148G/F165G were also revealed. The pore sizes of F165G, H148G, and the double mutant H148G/F165G were in the order of 4, 4.5 and 5.5 Å, respectively. These mutants were subjected to further investigation on the effect of small analytes (e.g. metal ions and hydrogen peroxide as elucidated by fluorescence quenching experiments. Results revealed that the F165G mutant exhibited the highest metal sensitivity at physiological pH. Meanwhile, the other 2 mutants lacking histidine at position 148 had lower sensitivity against Zn2+ and Cu2+ than those of the template protein (His6GFPuv. Hence, a significant role of this histidine residue in mediating metal transfer toward the GFP chromophore was proposed and evidently demonstrated by testing in acidic condition. Results revealed that at pH 6.5 the order of metal sensitivity was found to be inverted whereby the H148G/F165G became the most sensitive mutant. The dissociation constants (Kd to metal ions were in the order of 4.88×10-6 M, 16.67×10-6 M, 25×10-6 M, and 33.33×10-6 M for His6GFPuv/F165G, His6GFPuv, His6GFPuv/H148G/F165G and His6GFPuv/H148G, respectively. Sensitivity against hydrogen peroxide was in the order of H148G/F165G > H148G > F165G indicating the crucial role of pore diameters. However, it should be mentioned that H148G substitution caused a markedly decrease in pH- and thermo-stability. Taken together, our findings rendered the novel pore of GFP as formed by F165G substitution to be a high impact channel without adversely affecting the intrinsic fluorescent properties. This opens up a great potential of

  14. The dementia and disability project in Thai elderly: rational, design, methodology and early results

    Directory of Open Access Journals (Sweden)

    Senanarong Vorapun

    2013-01-01

    .5% of 1964 subjects were free of chronic diseases. Treatment gap (indicating those who have untreated or inadequate treatment of diabetes mellitus and hypertension in Thai elders in this study was 37% and 55.5% respectively. 62.6% of Thai elders have ApoE3E3 allele. Prevalence of positive ApoE4 gene in this study is 22.85%. 38.6% of Thai elders who had MRI brain study have moderate to severe white matter lesions. Conclusion The large and comprehensive set of measurements in DDP allows a wide-ranging explanation of the functional and clinical features to be investigated in relation to white matter lesions or cortical atrophy of the brain in Thai elderly population. An almost 2 year follow up was made available to those with MCI and dementia and some of the cognitively normal elderly. The longitudinal design will provide great understanding of the possible contributors to disability in the elderly and to the progression of cognitive decline in Thai elders.

  15. Rational Design of ZnO:H/ZnO Bilayer Structure for High-Performance Thin-Film Transistors.

    Science.gov (United States)

    Abliz, Ablat; Huang, Chun-Wei; Wang, Jingli; Xu, Lei; Liao, Lei; Xiao, Xiangheng; Wu, Wen-Wei; Fan, Zhiyong; Jiang, Changzhong; Li, Jinchai; Guo, Shishang; Liu, Chuansheng; Guo, Tailiang

    2016-03-01

    The intriguing properties of zinc oxide-based semiconductors are being extensively studied as they are attractive alternatives to current silicon-based semiconductors for applications in transparent and flexible electronics. Although they have promising properties, significant improvements on performance and electrical reliability of ZnO-based thin film transistors (TFTs) should be achieved before they can be applied widely in practical applications. This work demonstrates a rational and elegant design of TFT, composed of poly crystalline ZnO:H/ZnO bilayer structure without using other metal elements for doping. The field-effect mobility and gate bias stability of the bilayer structured devices have been improved. In this device structure, the hydrogenated ultrathin ZnO:H active layer (∼3 nm) could provide suitable carrier concentration and decrease the interface trap density, while thick pure-ZnO layer could control channel conductance. Based on this novel structure, a high field-effect mobility of 42.6 cm(2) V(-1) s(-1), a high on/off current ratio of 10(8) and a small subthreshold swing of 0.13 V dec(-1) have been achieved. Additionally, the bias stress stability of the bilayer structured devices is enhanced compared to the simple single channel layer ZnO device. These results suggest that the bilayer ZnO:H/ZnO TFTs have a great potential for low-cost thin-film electronics.

  16. Rational design of glycerol dehydratase: Swapping the genes encoding the subunits of glycerol dehydratase to improve enzymatic properties

    Institute of Scientific and Technical Information of China (English)

    QI Xianghui; SUN Liang; LUO Zhaofei; WU Jiequn; MENG Xiaolei; TANG Yue; WEI Yutuo; HUANG Ribo

    2006-01-01

    1,3-propanediol (1,3-PD) is an important material for chemical industry, and there has been always much interest in the production of 1,3-PD using all possible routes. The genes encoding glycerol dehydratase (GDHt) from Citrobacter freundii,Klebsiella pneumoniae and metagenome were cloned and expressed in E. coli. All glycerol dehydratases but the one from metagenome could be detected to show enzyme activities. In order to improve the enzymatic properties of GDHts, the genes encoding α and β-γ subunits were cloned, and the enzyme characteristics were evolved by rational design based on their 3D structures which were constructed by homology modeling. Six heteroenzymes were obtained by swapping the α subunit genes of these three different-source-derived GDHts. The pH,thermal stability and Vmax of some heteroenzymes were dramatically improved by 2-5 times compared with the wild one (GDHtKP). The GDHt cloned from metagenome, originally proved to be with no enzyme activity, was converted into active enzyme by swapping its subunits with other different GDHts. In addition, the effect of subtle 3D structural changes on the properties of the enzyme was also observed.

  17. Rational Design of Molecular Hole-Transporting Materials for Perovskite Solar Cells: Direct versus Inverted Device Configurations.

    Science.gov (United States)

    Grisorio, Roberto; Iacobellis, Rosabianca; Listorti, Andrea; De Marco, Luisa; Cipolla, Maria Pia; Manca, Michele; Rizzo, Aurora; Abate, Antonio; Gigli, Giuseppe; Suranna, Gian Paolo

    2017-07-26

    Due to a still limited understanding of the reasons making 2,2',7,7'-tetrakis(N,N-di-p-methoxyphenylamine)-9,9'-spirobifluorene (Spiro-OMeTAD) the state-of-the-art hole-transporting material (HTM) for emerging photovoltaic applications, the molecular tailoring of organic components for perovskite solar cells (PSCs) lacks in solid design criteria. Charge delocalization in radical cationic states can undoubtedly be considered as one of the essential prerequisites for an HTM, but this aspect has been investigated to a relatively minor extent. In marked contrast with the 3-D structure of Spiro-OMeTAD, truxene-based HTMs Trux1 and Trux2 have been employed for the first time in PSCs fabricated with a direct (n-i-p) or inverted (p-i-n) architecture, exhibiting a peculiar behavior with respect to the referential HTM. Notwithstanding the efficient hole extraction from the perovskite layer exhibited by Trux1 and Trux2 in direct configuration devices, their photovoltaic performances were detrimentally affected by their poor hole transport. Conversely, an outstanding improvement of the photovoltaic performances in dopant-free inverted configuration devices compared to Spiro-OMeTAD was recorded, ascribable to the use of thinner HTM layers. The rationalization of the photovoltaic performances exhibited by different configuration devices discussed in this paper can provide new and unexpected prospects for engineering the interface between the active layer of perovskite-based solar cells and the hole transporters.

  18. Rational design of sulfonated A3 adenosine receptor-selective nucleosides as pharmacological tools to study chronic neuropathic pain.

    Science.gov (United States)

    Paoletta, Silvia; Tosh, Dilip K; Finley, Amanda; Gizewski, Elizabeth T; Moss, Steven M; Gao, Zhan-Guo; Auchampach, John A; Salvemini, Daniela; Jacobson, Kenneth A

    2013-07-25

    (N)-Methanocarba(bicyclo[3.1.0]hexane)adenosine derivatives were probed for sites of charged sulfonate substitution, which precludes diffusion across biological membranes, e.g., blood-brain barrier. Molecular modeling predicted that sulfonate groups on C2-phenylethynyl substituents would provide high affinity at both mouse (m) and human (h) A3 adenosine receptors (ARs), while a N(6)-p-sulfophenylethyl substituent would determine higher hA3AR vs mA3AR affinity. These modeling predictions, based on steric fitting of the binding cavity and crucial interactions with key residues, were confirmed by binding/efficacy studies of synthesized sulfonates. N(6)-3-Chlorobenzyl-2-(3-sulfophenylethynyl) derivative 7 (MRS5841) bound selectively to h/m A3ARs (Ki(hA3AR) = 1.9 nM) as agonist, while corresponding p-sulfo isomer 6 (MRS5701) displayed mixed A1/A3AR agonism. Both nucleosides administered ip reduced mouse chronic neuropathic pain that was ascribed to either A3AR or A1/A3AR using A3AR genetic deletion. Thus, rational design methods based on A3AR homology models successfully predicted sites for sulfonate incorporation, for delineating adenosine's CNS vs peripheral actions.

  19. The operation of enzymatic fuel cell fabricated with rationally designed poly(caprolactone-g-ethylene glycol) copolymers.

    Science.gov (United States)

    Korkut, Seyda; Kilic, Muhammet Samet; Sanal, Timur; Hazer, Baki

    2017-07-01

    This study describes construction of an enzymatic fuel cell comprised of poly(caprolactone-g-ethylene glycol) coated novel glucose oxidase anode and laccase cathode. Rationally designed poly(caprolactone-g-ethylene glycol) containing various poly(ethylene glycol) percentages ranging between 2.67 and 15.04% were synthesized chemically and tested separately for operation of the fuel cell system to achieve the best energy generation. The maximum power density was found to be 80.55μWcm(-2) at 0.91V (vs. Ag/AgCl) in pH5, 100mM citrate buffer (20°C) by the addition of 30mM of glucose from the electrodes coated with 11.34% poly(ethylene glycol) containing polymer with a quantity of 600μg. High poly(ethylene glycol) percentages with more numbers of long poly(ethylene glycol) brushes lead to the creation of a complexity in the polymer morphology and steric hindrance effect for electron transport. The graft copolymer was easily used for the fuel cell system owing to its biocompatible and microporous film morphology. The grafted polymer was able to facilitate enzymatic glucose oxidation and oxygen reduction while simultaneously producing high catalytic electrical currents. Copyright © 2017 Elsevier B.V. All rights reserved.

  20. Ni And Co Segregations On Selective Surface Facets And Rational Design Of Layered Lithium Transition-metal Oxide Cathodes

    Energy Technology Data Exchange (ETDEWEB)

    Yan, Pengfei; Zheng, Jianming; Zheng, Jiaxin; Wang, Zhiguo; Teng, Gaofeng; Kuppan, Saravanan; Xiao, Jie; Chen, Guoying; Pan, Feng; Zhang, Jiguang; Wang, Chong M.

    2016-05-05

    The chemical processes occurring on the surface of cathode materials during battery cycling play a crucial role in determining battery’s performance. However, our understanding on such surface chemistry is far from clear due to the complexity of redox chemistry during battery charge/discharge. In this work, through intensive aberration corrected STEM investigation on eight layered oxide cathode materials, we report two important findings on the pristine oxides. First, Ni and Co show strong plane selectivity when building up their respective surface segregation layers (SSL). Specifically, Ni-SSL is exclusively developed on (200)m facet in Li-Mn-rich oxides (monoclinic C2/m symmetry) and (012)h facet in Mn-Ni equally rich oxides (hexagonal R-3m symmetry), while Co-SSL has a strong preference to (20-2)m plane with minimal Co-SSL also developed on some other planes in LMR cathodes. Structurally, Ni-SSLs tend to form spinel-like lattice while Co-SSLs are in a rock-salt-like structure. Secondly, by increasing Ni concentration in these layered oxides, Ni and Co SSLs can be suppressed and even eliminated. Our findings indicate that Ni and Co SSLs are tunable through controlling particle morphology and oxide composition, which opens up a new way for future rational design and synthesis of cathode materials.

  1. Structure-Based Rational Design to Enhance the Solubility and Thermostability of a Bacterial Laccase Lac15

    Science.gov (United States)

    Fang, Zemin; Zhou, Peng; Chang, Fei; Yin, Qiang; Fang, Wei; Yuan, Jing; Zhang, Xuecheng; Xiao, Yazhong

    2014-01-01

    Bacterial laccases are ideal alternatives of fungal laccases for specific industrial applications due to specific characteristics such as alkalescence dependence and high chloride tolerance. However, some bacterial laccases presented as inclusion bodies when expressing in Escherichia coli and showed thermal instability. In this study, rational design was employed to enhance the solubility and the thermostablity of the bacterial laccase Lac15-His6 based on the crystal structure obtained previously. After deletion of His-tag and residues323–332, the obtained Lac15D was completely expressed in soluble form even at a higher temperature of 28°C, compared to only 50% of Lac15-His6 expressed solubly at 16°C. It showed a two-time higher activity at temperatures lower than 35°C and a half-life increasing from 72 min to 150 min at 45°C. When used in chromogenic reactions, Lac15D showed constant activity toward dye precursors and their combinations under alkaline conditions, demonstrating its application potential in hair coloring biotechnology. PMID:25036001

  2. Rational design and construction of temporary steel tower bases; Karitetto kiso sekkei seko no gorika ni tsuite

    Energy Technology Data Exchange (ETDEWEB)

    Ikemoto, M. [Kansai Electric Power Co. Inc., Osaka (Japan)

    2000-01-10

    Current design and construction of temporary steel tower bases are equivalent to those for permanent facilities, and removal of the whole base concrete requires a great deal of labor and cost. The newly developed rational liner plate type base uses no concrete, and uses liner plates in place of adhesive and frictional parts of previous base floor plates. The workability of back-filling using sandbags is very excellent. Use of improved soil material as back-filling mortar of liner plates shows a favorable separability. The whole base is reusable because of no damage of each component member. Unlike concrete bases, the liner plate base produces no waste materials due to removal. The steel-base anchor type base can reduce both excavating and back-filling soil by using earth anchors, and reduce excavating soil as much as possible by allotting lifting force to each earth anchor. Reduction of both excavating and back-filling soil makes the removing work of bases simple. Cost reduction of 30-40% was attained by each newly developed base as compared with costs of conventional bases. (NEDO)

  3. Coronavirus non-structural protein 1 is a major pathogenicity factor: implications for the rational design of coronavirus vaccines.

    Directory of Open Access Journals (Sweden)

    Roland Züst

    2007-08-01

    Full Text Available Attenuated viral vaccines can be generated by targeting essential pathogenicity factors. We report here the rational design of an attenuated recombinant coronavirus vaccine based on a deletion in the coding sequence of the non-structural protein 1 (nsp1. In cell culture, nsp1 of mouse hepatitis virus (MHV, like its SARS-coronavirus homolog, strongly reduced cellular gene expression. The effect of nsp1 on MHV replication in vitro and in vivo was analyzed using a recombinant MHV encoding a deletion in the nsp1-coding sequence. The recombinant MHV nsp1 mutant grew normally in tissue culture, but was severely attenuated in vivo. Replication and spread of the nsp1 mutant virus was restored almost to wild-type levels in type I interferon (IFN receptor-deficient mice, indicating that nsp1 interferes efficiently with the type I IFN system. Importantly, replication of nsp1 mutant virus in professional antigen-presenting cells such as conventional dendritic cells and macrophages, and induction of type I IFN in plasmacytoid dendritic cells, was not impaired. Furthermore, even low doses of nsp1 mutant MHV elicited potent cytotoxic T cell responses and protected mice against homologous and heterologous virus challenge. Taken together, the presented attenuation strategy provides a paradigm for the development of highly efficient coronavirus vaccines.

  4. Rational design of a monomeric and photostable far-red fluorescent protein for fluorescence imaging in vivo.

    Science.gov (United States)

    Yu, Dan; Dong, Zhiqiang; Gustafson, William Clay; Ruiz-González, Rubén; Signor, Luca; Marzocca, Fanny; Borel, Franck; Klassen, Matthew P; Makhijani, Kalpana; Royant, Antoine; Jan, Yuh-Nung; Weiss, William A; Guo, Su; Shu, Xiaokun

    2016-02-01

    Fluorescent proteins (FPs) are powerful tools for cell and molecular biology. Here based on structural analysis, a blue-shifted mutant of a recently engineered monomeric infrared fluorescent protein (mIFP) has been rationally designed. This variant, named iBlueberry, bears a single mutation that shifts both excitation and emission spectra by approximately 40 nm. Furthermore, iBlueberry is four times more photostable than mIFP, rendering it more advantageous for imaging protein dynamics. By tagging iBlueberry to centrin, it has been demonstrated that the fusion protein labels the centrosome in the developing zebrafish embryo. Together with GFP-labeled nucleus and tdTomato-labeled plasma membrane, time-lapse imaging to visualize the dynamics of centrosomes in radial glia neural progenitors in the intact zebrafish brain has been demonstrated. It is further shown that iBlueberry can be used together with mIFP in two-color protein labeling in living cells and in two-color tumor labeling in mice.

  5. Combined data preprocessing and multivariate statistical analysis characterizes fed-batch culture of mouse hybridoma cells for rational medium design.

    Science.gov (United States)

    Selvarasu, Suresh; Kim, Do Yun; Karimi, Iftekhar A; Lee, Dong-Yup

    2010-10-01

    We present an integrated framework for characterizing fed-batch cultures of mouse hybridoma cells producing monoclonal antibody (mAb). This framework systematically combines data preprocessing, elemental balancing and statistical analysis technique. Initially, specific rates of cell growth, glucose/amino acid consumptions and mAb/metabolite productions were calculated via curve fitting using logistic equations, with subsequent elemental balancing of the preprocessed data indicating the presence of experimental measurement errors. Multivariate statistical analysis was then employed to understand physiological characteristics of the cellular system. The results from principal component analysis (PCA) revealed three major clusters of amino acids with similar trends in their consumption profiles: (i) arginine, threonine and serine, (ii) glycine, tyrosine, phenylalanine, methionine, histidine and asparagine, and (iii) lysine, valine and isoleucine. Further analysis using partial least square (PLS) regression identified key amino acids which were positively or negatively correlated with the cell growth, mAb production and the generation of lactate and ammonia. Based on these results, the optimal concentrations of key amino acids in the feed medium can be inferred, potentially leading to an increase in cell viability and productivity, as well as a decrease in toxic waste production. The study demonstrated how the current methodological framework using multivariate statistical analysis techniques can serve as a potential tool for deriving rational medium design strategies. Copyright © 2010 Elsevier B.V. All rights reserved.

  6. Structure-based rational design to enhance the solubility and thermostability of a bacterial laccase Lac15.

    Directory of Open Access Journals (Sweden)

    Zemin Fang

    Full Text Available Bacterial laccases are ideal alternatives of fungal laccases for specific industrial applications due to specific characteristics such as alkalescence dependence and high chloride tolerance. However, some bacterial laccases presented as inclusion bodies when expressing in Escherichia coli and showed thermal instability. In this study, rational design was employed to enhance the solubility and the thermostablity of the bacterial laccase Lac15-His6 based on the crystal structure obtained previously. After deletion of His-tag and residues323-332, the obtained Lac15D was completely expressed in soluble form even at a higher temperature of 28°C, compared to only 50% of Lac15-His6 expressed solubly at 16°C. It showed a two-time higher activity at temperatures lower than 35°C and a half-life increasing from 72 min to 150 min at 45°C. When used in chromogenic reactions, Lac15D showed constant activity toward dye precursors and their combinations under alkaline conditions, demonstrating its application potential in hair coloring biotechnology.

  7. Hydrogen initiative: An integrated approach toward rational nanocatalyst design for hydrogen production. Technical Report-Year 1

    Energy Technology Data Exchange (ETDEWEB)

    Vlachos, Dionisios G. [Univ. of Delaware, Newark, DE (United States); Buttrey, Douglas J. [Univ. of Delaware, Newark, DE (United States); Lauterbach, Jochen A. [Univ. of Delaware, Newark, DE (United States)

    2007-03-29

    The overall objective of this grant is to develop a rational framework for the discovery of low cost, robust, and active nano-catalysts that will enable efficient hydrogen production. Our approach will be the first demonstration of integrated multiscale model, nano-catalyst synthesis, and nanoscale characterization assisted high throughput experimentation (HTE). We will initially demonstrate our approach with ammonia decomposition on noble metal catalysts. Our research focuses on many elements of the Hydrogen Initiative in the Focus Area of “Design of Catalysts at the Nanoscale’. It combines high-throughput screening methods with various nanostructure synthesis protocols, advanced measurements, novel in situ and ex situ characterization techniques, and multiscale theory, modeling and simulation. This project directly addresses several of the long-term goals of the DOE/BES program. In particular, new nanoscale catalytic materials will be synthesized, characterized and modeled for the production of hydrogen from ammonia and a computational framework will be developed for efficient extraction of information from experimental data and for rational design of catalysts whose impact goes well beyond the proposed hydrogen production project. In the first year of the grant, we have carried out HTE screening using a 16 parallel microreactor coupled with an FTIR analysis system. We screened nearly twenty single metals and several bimetallic catalysts as a function of temperature, catalyst loading, inlet composition, and temperature (order of 400 experiments). We have found that Ru is the best single metal catalyst and no better catalysts were found among the library of bimetallics we have created so far. Furthermore, we have investigated promoting effects (i.e., K, Cs, and Ba) of the Ru catalyst. We have found that K is the dominant promoter of increased Ru activity. Response surface experimental design has led to substantial improvements of the Ru catalyst with promotion

  8. Rational design of cyclic peptide modulators of the transcriptional coactivator CBP: a new class of p53 inhibitors.

    Science.gov (United States)

    Gerona-Navarro, Guillermo; Yoel-Rodríguez; Mujtaba, Shiraz; Frasca, Antonio; Patel, Jigneshkumar; Zeng, Lei; Plotnikov, Alexander N; Osman, Roman; Zhou, Ming-Ming

    2011-02-23

    The CREB binding protein (CBP) is a human transcriptional coactivator consisting of several conserved functional modules, which interacts with distinct transcription factors including nuclear receptors, CREB, and STAT proteins. Despite the importance of CBP in transcriptional regulation, many questions regarding the role of its particular domains in CBP functions remain unanswered. Therefore, developing small molecules capable of selectively modulating a single domain of CBP is of invaluable aid at unraveling its prominent activities. Here we report the design, synthesis, and biological evaluation of conformationally restricted peptides as novel modulators for the acetyl-lysine binding bromodomain (BRD) of CBP. Utilizing a target structure-guided and computer-aided rational design approach, we developed a series of cyclic peptides with affinity for CBP BRD significantly greater than those of its biological ligands, including lysine-acetylated histones and tumor suppressor p53. The best cyclopeptide of the series exhibited a K(d) of 8.0 μM, representing a 24-fold improvement in affinity over that of the linear lysine 382-acetylated p53 peptide. This lead peptide is highly selective for CBP BRD over BRDs from other transcriptional proteins. Cell-based functional assays carried out in colorectal carcinoma HCT116 cells further demonstrated the efficacy of this compound to modulate p53 stability and function in response to DNA damage. Our results strongly argue that these CBP modulators can effectively inhibit p53 transcriptional activity by blocking p53K382ac binding to CBP BRD and promoting p53 instability by changes of its post-translational modification states, a different mechanism than that of the p53 inhibitors reported to date.

  9. Rational Molecular Design of Potent PLK1 PBD Domain-binding Phosphopeptides Using Preferential Amino Acid Building Blocks.

    Science.gov (United States)

    Mao, Xin-Li; Wang, Kui-Feng; Zhu, Feng; Pan, Zhao-Hu; Wu, Guo-Min; Zhu, Hong-Yuan

    2016-08-01

    Polo-like kinase 1 (PLK1) is an important regulator in diverse aspects of the cell cycle and proliferation. The protein has a highly conserved polo-box domain (PBD) present in C-terminal noncatalytic region, which exhibits a relatively broad sequence specificity in recognizing and binding phosphorylated substrates to control substrate phosphorylation by the kinase. In order to elucidate the structural basis, thermodynamic property, and biological implication underlying PBD-substrate recognition and association, a systematic amino acid preference profile of phosphopeptide interaction with PLK1 PBD domain was established via virtual mutagenesis analysis and mutation energy calculation, from which the contribution of different amino acids at each residue position of two reference phosphopeptides to domain-peptide binding was characterized comprehensively and quantitatively. With the profile, we are able to determine the favorable, neutral, and unfavorable amino acid types for each position of PBD-binding phosphopeptides, and we also explored the molecular origin of the broad sequence specificity in PBD-substrate recognition. To practice computational findings, the profile was further employed to guide rational design of potent PBD binders; three 6-mer phosphopeptides (i.e., IQSpSPC, LQSpTPF, and LNSpTPT) were successfully developed, which can efficiently target PBD domain with high affinity (Kd = 5.7 ± 1.1, 0.75 ± 0.18, and 7.2 ± 2.6 μm, resp.) as measured by a fluorescence anisotropy assay. The complex structure of PLK1 PBD domain with a newly designed, potent phosphopeptide LQSpTPF as well as diverse noncovalent chemical forces, such as H-bonds and hydrophobic interactions at the complex interface, were examined in detail to reveal the molecular mechanism of high affinity and stability of the complex system.

  10. Determination of rational design parameters of a multi-stage solar water desalination still using transient mathematical modelling

    Energy Technology Data Exchange (ETDEWEB)

    Shatat, M.I.M.; Mahkamov, K. [School of Engineering, Durham University, South Road, Durham, DH1 3LE (United Kingdom)

    2010-01-15

    The paper describes the experimental investigations of the performance of a multi-stage water desalination still connected to a heat pipe evacuated tube solar collector with aperture area of 1.7 m{sup 2}. The multi-stage solar still water desalination system was designed to recover latent heat from evaporation and condensation processes in four stages. The variation in the solar radiation during a typical mid-summer day in the Middle East region was simulated on the test rig using an array of 110 halogen floodlights covering the area of the collector. The results of tests demonstrate that the system produces about 9 kg of fresh water per day and has a solar collector efficiency of about 68%. However, the overall efficiency of the laboratory test rig at this stage of the investigations was found to be at the level of 33% due to excessive heat losses in the system. The analysis of the distilled water showed that its quality was within the World Health Organization guidelines. The still's operation was numerically simulated by employing a mathematical model based on a system of ordinary energy and mass conservation differential equations written for each stage of the still. A computer program was developed for transient simulations of the evaporation and condensation processes inside the multi-stage still. Experimental results obtained and theoretical predictions were found to be in good agreement. The results on the determination of rational design dimensions and number of stages of the still for a given aperture of the solar collector are also presented in this work. (author)

  11. Rational Design, Synthesis and Pharmacological Evaluation of the (2R)- and (2S)-Stereoisomers of 3-(2-Carboxypyrrolidinyl)-2-methyl Acetic Acid as Ligands for the Ionotropic Glutamate Receptors

    DEFF Research Database (Denmark)

    Rasmussen, Julie; Storgaard, Morten; Pickering, Darryl S;

    2011-01-01

    In this paper we describe the rational design, synthesis and pharmacological evaluation of two new stereoisomeric (S)-glutamate (Glu) analogues. The rational design was based on hybrid structures of the natural product kainic acid, a synthetic analogue CPAA and the high-affinity Glu analogue SYM...

  12. 连续梁墩柱合理设计的影响因素分析%Factor Analysis of Continuous Beam Pier Columns Rational Design

    Institute of Scientific and Technical Information of China (English)

    张帅; 肖锋文; 赵杰丽

    2012-01-01

    随着连续梁桥的广泛应用,连续梁桥墩柱的合理设计值得深入研究.从影响连续梁桥墩柱设计的主要因素出发,深入分析各影响因素的重要性,为连续梁桥墩柱合理设计提供参考.%With the wide application of the continuous beam bridge, the rational design of continuous beam pier column worthy of further study. In this article, starting from the main factors affecting the continuous beam bridge pier column design. In-depth analysis of the importance of each factor in order to give reference for the rational design of continuous beam bridge pier column.

  13. Diethylstilbestrol-scaffold-based pregnane X receptor modulators.

    Science.gov (United States)

    Hodnik, Žiga; Tomašič, Tihomir; Smodiš, Domen; D'Amore, Claudio; Mašič, Lucija Peterlin; Fiorucci, Stefano; Kikelj, Danijel

    2015-10-20

    Due to its function as a regulator of drug-metabolizing enzymes and transporters, pregnane X receptor (PXR) represents an important factor involved in drug metabolism. In this work, we describe the discovery of diethylstilbestrol-based PXR modulators, which were designed from marine sulfated steroids with PXR agonistic activity, solomonsterols A and B, and our recently reported bazedoxifene scaffold-derived PXR antagonists. The methylated diethylstilbestrol derivative 1 displayed potent PXR agonistic activity with an EC50 value of 10.5 μM, whereas compounds 3, 4 and 6 (IC50 for 6 = 27.4 μM) and diethylstilbestrol (2) itself (IC50 = 14.6 μM) exhibited PXR antagonistic effects in HepG2 cells. The PXR modulatory effects of the synthesized diethylstilbestrol derivatives were further confirmed by the induction of PXR-regulated CYP3A4 expression with compound 1, as well as by the inhibition of the rifaximin-promoted up-regulation of CYP3A4 expression with 2 and its derivative 6.

  14. Rational Teaching.

    Science.gov (United States)

    Macmillan, C. J. B.

    1985-01-01

    The recognition of teaching as a special relationship among individuals is currently being overlooked in much contemporary educational research and policymaking. The author examines the philosophy of rationality in teaching and relates it to the educational vision presented in George Orwell's novel, "Nineteen Eighty-Four." (CB)

  15. Confucian Rationalism

    Science.gov (United States)

    Lam, Chi-Ming

    2014-01-01

    Nowadays, there is still a widely held view that the Chinese and Western modes of thought are quite distinct from each other. In particular, the Chinese mode of thought derived from Confucianism is considered as comparatively less rational than the Western one. In this article, I first argue that although the analogical mode of argumentation,…

  16. Uniform Ni/SiO2@Au magnetic hollow microspheres: rational design and excellent catalytic performance in 4-nitrophenol reduction

    Science.gov (United States)

    Zhang, Shenghuan; Gai, Shili; He, Fei; Dai, Yunlu; Gao, Peng; Li, Lei; Chen, Yujin; Yang, Piaoping

    2014-05-01

    A unique and rational design was presented to fabricate Ni/SiO2@Au magnetic hollow microspheres (MHMs) with interesting structures and well-dispersed metal nanoparticles. Hierarchical nickel silicate hollow microspheres were synthesized using silica colloidal spheres as a chemical template. Then, Ni/SiO2 MHMs with well-dispersed Ni nanoparticles were prepared via an in situ reduction approach. Ni/SiO2@Au MHMs were finally obtained by immobilizing uniform Au nanoparticles onto Ni/SiO2 support through a low-temperature chemical reduction process. It was found that Ni/SiO2@Au MHMs inherit the shape and uniformity of the original silica scaffold, and Ni NPs and Au NPs, which were less than 5 nm in size, were well dispersed on the mesoporous silica shell with narrow size distribution. Both Ni/SiO2 and Ni/SiO2@Au MHMs showed excellent catalytic activity in the 4-nitrophenol reduction reaction. Importantly, introduction of a small amount of Au NPs onto Ni/SiO2 MHMs markedly improved the catalytic activity. In particular, Ni/SiO2@Au MHMs showed high conversion even after re-use for several cycles with magnetic separation. The unique structure, high catalytic performance, and ease of separation make Ni/SiO2@Au MHMs highly promising candidates for diverse applications.A unique and rational design was presented to fabricate Ni/SiO2@Au magnetic hollow microspheres (MHMs) with interesting structures and well-dispersed metal nanoparticles. Hierarchical nickel silicate hollow microspheres were synthesized using silica colloidal spheres as a chemical template. Then, Ni/SiO2 MHMs with well-dispersed Ni nanoparticles were prepared via an in situ reduction approach. Ni/SiO2@Au MHMs were finally obtained by immobilizing uniform Au nanoparticles onto Ni/SiO2 support through a low-temperature chemical reduction process. It was found that Ni/SiO2@Au MHMs inherit the shape and uniformity of the original silica scaffold, and Ni NPs and Au NPs, which were less than 5 nm in size, were well

  17. TOPICAL REVIEW: Rational design of new materials for spintronics: Co2FeZ (Z=Al, Ga, Si, Ge

    Directory of Open Access Journals (Sweden)

    Benjamin Balke et al

    2008-01-01

    Full Text Available Spintronic is a multidisciplinary field and a new research area. New materials must be found for satisfying the different types of demands. The search for stable half-metallic ferromagnets and ferromagnetic semiconductors with Curie temperatures higher than room temperature is still a challenge for solid state scientists. A general understanding of how structures are related to properties is a necessary prerequisite for material design. Computational simulations are an important tool for a rational design of new materials. The new developments in this new field are reported from the point of view of material scientists. The development of magnetic Heusler compounds specifically designed as material for spintronic applications has made tremendous progress in the very recent past. Heusler compounds can be made as half-metals, showing a high spin polarization of the conduction electrons of up to 100% in magnetic tunnel junctions. High Curie temperatures were found in Co2-based Heusler compounds with values up to 1120 K in Co2FeSi. The latest results at the time of writing are a tunnelling magnet resistance (TMR device made from the Co2FeAl0.5Si0.5 Heusler compound and working at room temperature with a (TMR effect higher than 200%. Good interfaces and a well-ordered compound are the precondition to realize the predicted half-metallic properties. The series Co2FeAl1- xSix is found to exhibit half-metallic ferromagnetism over a broad range, and it is shown that electron doping stabilizes the gap in the minority states for x=0.5. This might be a reason for the exceptional temperature behaviour of Co2FeAl0.5Si0.5 TMR devices. Using x-ray diffraction (XRD, it was shown conclusively that Co2FeAl crystallizes in the B2 structure whereas Co2FeSi crystallizes in the L21 structure. For the compounds Co2FeGa or Co2FeGe, with Curie temperatures expected higher than 1000 K, the standard XRD technique using laboratory sources cannot be used to easily distinguish

  18. Computational molecular modeling and structural rationalization for the design of a drug-loaded PLLA/PVA biopolymeric membrane

    Energy Technology Data Exchange (ETDEWEB)

    Sibeko, B; Pillay, V; Choonara, Y E; Khan, R A; Danckwerts, M P [Department of Pharmacy and Pharmacology, University of the Witwatersrand, 7 York Road, Parktown, 2193 Johannesburg (South Africa); Modi, G [Division of Neurosciences, Department of Neurology, University of the Witwatersrand, Johannesburg (South Africa); Iyuke, S E [School of Chemical and Metallurgical Engineering, University of the Witwatersrand, Johannesburg (South Africa); Naidoo, D, E-mail: viness.pillay@wits.ac.z [Division of Neurosciences, Department of Neurosurgery, University of the Witwatersrand, Johannesburg (South Africa)

    2009-02-15

    The purpose of this study was to design, characterize and assess the influence of triethanolamine (TEA) on the physicomechanical properties and release of methotrexate (MTX) from a composite biopolymeric membrane. Conjugated poly(L-lactic acid) (PLLA) and poly(vinyl alcohol) (PVA) membranes were prepared by immersion precipitation with and without the addition of TEA. Drug entrapment efficiency (DEE) and release studies were performed in phosphate buffered saline (pH 7.4, 37 deg. C). Scanning electron microscopy elucidated the membrane surface morphology. Computational and structural molecular modeling rationalized the potential mechanisms of membrane formation and MTX release. Bi-axial force-distance (F-D) extensibility profiles were generated to determine the membrane toughness, elasticity and fracturability. Membranes were significantly toughened by the addition of TEA as a discrete rubbery phase within the co-polymer matrix. MTX-TEA-PLLA-PVA membranes were tougher (F = 89 N) and more extensible (D = 8.79 mm) compared to MTX-PLLA-PVA (F = 35 N, D = 3.7 mm) membranes as a greater force of extension and fracture distance were required (N = 10). DEE values were relatively high (>80%, N = 5) for both formulations. Photomicrographs revealed distinct crystalline layered morphologies with macro-pores. MTX was released by tri-phasic kinetics with a lower fractional release of MTX from MTX-TEA-PLLA-PVA membranes compared to MTX-PLLA-PVA. TEA provided a synergistic approach to improving the membrane physicomechanical properties and modulation of MTX release. The composite biopolymeric membrane may therefore be suitable for the novel delivery of MTX in the treatment of chronic primary central nervous system lymphoma.

  19. Rational design of an AKR1C3-resistant analog of PR-104 for enzyme-prodrug therapy.

    Science.gov (United States)

    Mowday, Alexandra M; Ashoorzadeh, Amir; Williams, Elsie M; Copp, Janine N; Silva, Shevan; Bull, Matthew R; Abbattista, Maria R; Anderson, Robert F; Flanagan, Jack U; Guise, Christopher P; Ackerley, David F; Smaill, Jeff B; Patterson, Adam V

    2016-09-15

    The clinical stage anti-cancer agent PR-104 has potential utility as a cytotoxic prodrug for exogenous bacterial nitroreductases expressed from replicating vector platforms. However substrate selectivity is compromised due to metabolism by the human one- and two-electron oxidoreductases cytochrome P450 oxidoreductase (POR) and aldo-keto reductase 1C3 (AKR1C3). Using rational drug design we developed a novel mono-nitro analog of PR-104A that is essentially free of this off-target activity in vitro and in vivo. Unlike PR-104A, there was no biologically relevant cytotoxicity in cells engineered to express AKR1C3 or POR, under aerobic or anoxic conditions, respectively. We screened this inert prodrug analog, SN34507, against a type I bacterial nitroreductase library and identified E. coli NfsA as an efficient bioactivator using a DNA damage response assay and recombinant enzyme kinetics. Expression of E. coli NfsA in human colorectal cancer cells led to selective cytotoxicity to SN34507 that was associated with cell cycle arrest and generated a robust 'bystander effect' at tissue-like cell densities when only 3% of cells were NfsA positive. Anti-tumor activity of SN35539, the phosphate pre-prodrug of SN34507, was established in 'mixed' tumors harboring a minority of NfsA-positive cells and demonstrated marked tumor control following heterogeneous suicide gene expression. These experiments demonstrate that off-target metabolism of PR-104 can be avoided and identify the suicide gene/prodrug partnership of E. coli NfsA/SN35539 as a promising combination for development in armed vectors.

  20. Site-Directed Mutagenesis of a Hyperthermophilic Endoglucanase Cel12B from Thermotoga maritima Based on Rational Design.

    Directory of Open Access Journals (Sweden)

    Jinfeng Zhang

    Full Text Available To meet the demand for the application of high activity and thermostable cellulases in the production of new-generation bioethanol from nongrain-cellulose sources, a hyperthermostable β-1,4-endoglucase Cel12B from Thermotoga maritima was selected for further modification by gene site-directed mutagenesis method in the present study, based on homology modeling and rational design. As a result, two recombinant enzymes showed significant improvement in enzyme activity by 77% and 87%, respectively, higher than the parental enzyme TmCel12B. Furthermore, the two mutants could retain 80% and 90.5% of their initial activity after incubation at 80°C for 8 h, while only 45% for 5 h to TmCel12B. The Km and Vmax of the two recombinant enzymes were 1.97±0.05 mM, 4.23±0.15 μmol·mg(-1·min(-1 of TmCel12B-E225H-K207G-D37V, and 2.97±0.12 mM, 3.15±0.21 μmol·mg(-1·min(-1 of TmCel12B-E225H-K207G, respectively, when using CMC-Na as the substrate. The roles of the mutation sites were also analyzed and evaluated in terms of electron density, hydrophobicity of the modeled protein structures. The recombinant enzymes may be used in the hydrolysis of cellulose at higher temperature in the future. It was concluded that the gene mutagenesis approach of a certain active residues may effectively improve the performance of cellulases for the industrial applications and contribute to the study the thermostable mechanism of thermophilic enzymes.

  1. Site-Directed Mutagenesis of a Hyperthermophilic Endoglucanase Cel12B from Thermotoga maritima Based on Rational Design

    Science.gov (United States)

    Zhang, Jinfeng; Shi, Hao; Xu, Linyu; Zhu, Xiaoyan; Li, Xiangqian

    2015-01-01

    To meet the demand for the application of high activity and thermostable cellulases in the production of new-generation bioethanol from nongrain-cellulose sources, a hyperthermostable β-1,4-endoglucase Cel12B from Thermotoga maritima was selected for further modification by gene site-directed mutagenesis method in the present study, based on homology modeling and rational design. As a result, two recombinant enzymes showed significant improvement in enzyme activity by 77% and 87%, respectively, higher than the parental enzyme TmCel12B. Furthermore, the two mutants could retain 80% and 90.5% of their initial activity after incubation at 80°C for 8 h, while only 45% for 5 h to TmCel12B. The Km and Vmax of the two recombinant enzymes were 1.97±0.05 mM, 4.23±0.15 μmol·mg-1·min-1 of TmCel12B-E225H-K207G-D37V, and 2.97±0.12 mM, 3.15±0.21 μmol·mg-1·min-1 of TmCel12B-E225H-K207G, respectively, when using CMC-Na as the substrate. The roles of the mutation sites were also analyzed and evaluated in terms of electron density, hydrophobicity of the modeled protein structures. The recombinant enzymes may be used in the hydrolysis of cellulose at higher temperature in the future. It was concluded that the gene mutagenesis approach of a certain active residues may effectively improve the performance of cellulases for the industrial applications and contribute to the study the thermostable mechanism of thermophilic enzymes. PMID:26218520

  2. Combination of POMs and deliberately designed macrocations: a rational approach for synthesis of POM-pillared metal-organic framework.

    Science.gov (United States)

    Lan, Ya-Qian; Li, Shun-Li; Shao, Kui-Zhan; Wang, Xin-Long; Hao, Xiang-Rong; Su, Zhong-Min

    2009-02-14

    Two POM-pillared 3D porous compounds, [Cu(I)Cu(II)(Cu(II)fcz)(2)(H(2)O)(5)(PMo(VI)(10)Mo(V)(2)O(40))].6H(2)O () and [Cu(I)(2)(Cu(II)fcz)(2)(H(2)O)(2)(PMo(VI)(8)V(V)(3)V(IV)(3)O(42))].6H(2)O () (Hfcz = fluconazole, (1-(2,4-difluorophenyl)-1,1-bis[(1H-1,2,4-triazol-1-yl)methyl]benzyl alcohol) have been constructed based on different polyanions, (Cufcz)(2)(2+) macrocations and copper cations by the hydrothermal method. The (Cufcz)(2)(2+) macrocations link Cu cations to generate a 2D wavelike cationic sheet. Then the POM anions act as pillars to the cationic sheet to form different POM-pillared 3D frameworks. In compound 2 , the polyanion exhibits a rare coordination mode and acts as a penta-dentate ligand, which acts as to pillars to the cationic sheet to form an unprecedented 3D (3,4,5,6)-connected open framework with (3.6.7)(3(2).6.7(3))(3(3).4.6(2).7(3).8)(3(4).4(2).6(2).7(6).8)(3(2).6(2).7(6).8(4).10) topology. In compound , polyanions covalently link cationic sheets to extend to an unusual 3D (3,4,6)-connected framework with the (5(2).6)(5(2).6(2).7.9)(5(4).6(4).7(4).9(3)) topology. To the best of our knowledge, it is the first time that POM-pillared 3D metal-organic frameworks have been realized by combining POMs with deliberately designed macrocations and transition-metal ions, using a rational approach for synthesis of POM-based open metal-organic frameworks. In addition, the electrochemical behaviors of compounds 1 and 2 have been investigated.

  3. A New Rational-based Optimal Design Strategy of Ship Structure Based on Multi-level Analysis and Super-element Modeling Method

    Institute of Scientific and Technical Information of China (English)

    Li Sun; Deyu Wang

    2011-01-01

    A new multi-level analysis method of introducing the super-element modeling method,derived from the multi-level analysis method first proposed by O.F.Hughes,has been proposed in this paper to solve the problem of high time cost in adopting a rational-based optimal design method for ship structural design.Furthermore,the method was verified by its effective application in optimization of the mid-ship section of a container ship.A full 3-D FEM model of a ship,suffering static and quasi-static loads,was used as the analyzing object for evaluating the structural performance of the mid-ship module,including static strength and buckling performance.Research results reveal that this new method could substantially reduce the computational cost of the rational-based optimization problem without decreasing its accuracy,which increases the feasibility and economic efficiency of using a rational-based optimal design method in ship structural design.

  4. Rational Design and Characterization of the Novel, Broad and Potent Bispecific HIV-1 Neutralizing Antibody iMabm36

    Science.gov (United States)

    Sun, Ming; Pace, Craig S.; Yao, Xin; Yu, Faye; Padte, Neal N.; Huang, Yaoxing; Seaman, Michael S.; Li, Qihan; Ho, David D.

    2014-01-01

    While broadly neutralizing monoclonal antibodies (bNAbs) have always been considered potential therapeutic options for the prophylactic and treatment of HIV infection, their lack of breadth against all HIV variants has been one of the limiting factors. To provide sufficient neutralization breadth and potency against diverse viruses, including neutralization escape variants, strategies to combine different bNAbs have been explored recently. We rationally designed and engineered a novel bispecific HIV-1 neutralizing antibody (bibNAb), iMabm36, for high potency and breadth against HIV. iMabm36 is composed of the anti-CD4 Ab ibalizumab (iMab) linked to two copies of the single-domain Ab m36 which targets a highly conserved CD4-induced epitope. iMabm36 neutralizes a majority of a large, multi-clade panel of pseudoviruses (96%, n=118) at an IC50 concentration of less than 10 μg/mL, with 83% neutralized at an IC50 concentration of less than 0.1μg/ml. In addition, iMabm36 neutralizes six replication-competent transmitted-founder viruses to 100% inhibition at a concentration of less than 0.1μg/ml in a PBMC-based neutralizing assay. Mechanistically, improved antiviral activity of iMabm36 is dependent on both CD4 binding activity of iMab component and CD4i binding activity of the m36 component. After characterizing viral resistance to iMabm36 neutralization was due to mutations residing in the bridging sheet of gp120, an optimized m36 variant was engineered that, when fused to iMab, improved antiviral activity significantly. Together inter-dependency of this dual mechanism of action enables iMabm36 to potently inhibit HIV-1 entry. These results demonstrate that mechanistic-based design of bibNAbs could generate potential preventive and therapeutic candidates for HIV/AIDS. PMID:24853313

  5. 化纤行业中异形喷丝板的合理设计%Rational design about profiled spinneret in chemical fibre industry

    Institute of Scientific and Technical Information of China (English)

    李沈阳

    2014-01-01

    文章对异形喷丝板的性能特点等方面进行了分析,通过分析比较,提出了异形喷丝板新的合理化设计方法及理念。%Based on the analysis and comparison of performance characteristics of profiled spinneret,the new rational design methods and ideas of profiled spinneret are put forward in this paper.

  6. Rational valuations

    Directory of Open Access Journals (Sweden)

    Georg Spielthenner

    2007-01-01

    Full Text Available Valuations are ubiquitous. We may be for or against genetically modified food; we find some politicians irresponsible; we prefer Beethoven to rock ‘n’ roll or vice versa; some enjoy bird-watching while others find it boring; and we may think that we have to tighten up on green-house gas emissions. Valuing is pervasive and often we are not even aware that we are valuing. However, many of ourvaluations are ill grounded and rationally defective. They are frequently based on misinformation, sloppy thinking, prejudice, and are biased in many ways as psychological research shows. For this reason there is widespread agreement among phi-losophers that we need an account of substantive valuational rationality, both for the theory of practical reasoning and for ethics as well. My main objectin this paper is to outline such an account and to present a principle that allows a non-technical rational criticism of valuations

  7. Bounded Rationality

    Directory of Open Access Journals (Sweden)

    Ballester Pla, Coralio

    2012-03-01

    Full Text Available The observation of the actual behavior by economic decision makers in the lab and in the field justifies that bounded rationality has been a generally accepted assumption in many socio-economic models. The goal of this paper is to illustrate the difficulties involved in providing a correct definition of what a rational (or irrational agent is. In this paper we describe two frameworks that employ different approaches for analyzing bounded rationality. The first is a spatial segregation set-up that encompasses two optimization methodologies: backward induction and forward induction. The main result is that, even under the same state of knowledge, rational and non-rational agents may match their actions. The second framework elaborates on the relationship between irrationality and informational restrictions. We use the beauty contest (Nagel, 1995 as a device to explain this relationship.

    La observación del comportamiento de los agentes económicos tanto en el laboratorio como en la vida real justifica que la racionalidad acotada sea un supuesto aceptado en numerosos modelos socio-económicos. El objetivo de este artículo es ilustrar las dificultades que conlleva una correcta definición de qué es un agente racional (irracional. En este artículo se describen dos marcos que emplean diferentes metodologías para analizar la racionalidad acotada. El primero es un modelo de segregación espacial donde se contrastan dos metodologías de optimización: inducción hacia atrás y hacia adelante. El resultado principal es que, incluso con el mismo nivel de conocimiento, tanto agentes racionales como irracionales podrían coincidir en sus acciones. El segundo marco trabaja sobre la relación entre irracionalidad y restricción de información. Se utiliza el juego llamado “beauty contest” (Nagel 1995 como mecanismo para explicar dicha relación.

  8. Why Does the Molecular Structure of Broadly Neutralizing Monoclonal Antibodies Isolated from Individuals Infected with HIV-1 not Inform the Rational Design of an HIV-1 Vaccine?

    Directory of Open Access Journals (Sweden)

    Marc H V Van Regenmortel

    2015-05-01

    Full Text Available It is commonly assumed that neutralizing Mabs that bind to the HIV-1 Env glycoprotein are more specific reagents than anti-HIV-1 polyclonal antisera and that knowledge of the structure of these Mabs facilitates the rational design of effective HIV-1 vaccine immunogens. However, after more than ten years of unsuccessful experimentation using the structure-based reverse vaccinology approach, it is now evident that it is not possible to infer from the structure of neutralizing Mabs which HIV immunogens induced their formation nor which vaccine immunogens will elicit similar Abs in an immunized host. The use of Mabs for developing an HIV-1 vaccine was counterproductive because it overlooked the fact that the apparent specificity of a Mab very much depends on the selection procedure used to obtain it and also did not take into account that an antibody is never monospecific for a single epitope but is always polyspecific for many epitopes. When the rationale of the proponents of the unsuccessful rational design strategy is analyzed, it appears that investigators who claim they are designing a vaccine immunogen are only improving the binding reactivity of a single epitope-paratope pair and are not actually designing an immunogen able to generate protective antibodies. The task of a designer consists in imagining what type of immunogen is likely to elicit a protective immune response but in the absence of knowledge regarding which features of the immune system are responsible for producing a functional neutralizing activity in antibodies, it is not feasible to intentionally optimize a potential immunogen candidate in order to obtain the desired outcome. The only available option is actually to test possible solutions by trial-and-error experiments until the preset goal is perhaps attained. Rational design and empirical approaches in HIV vaccine research should thus not be opposed as alternative options since empirical testing is an integral part of a so

  9. 现代建筑设计中的感性思想与理性思维%Perceptual Thinking and Rational Thinking in Design of Modern Architecture

    Institute of Scientific and Technical Information of China (English)

    王秀; 周茜

    2014-01-01

    The perceptual thinking and rational thinking is a unity of contradictory and mutual support in the architectural design. The author carried out an analysis and examples of pr- oof in this perceptual thinking and rational thinking in the architectural design and discussed that how an excelent arc- hitect to correctly handle the dialectical relationship between perceptual experience and rational thinking in the process of the creation of architectural works.%建筑设计中的感性思想与理性思维是一对互相矛盾而又互相依托的统一体。本文以建筑设计中的感性思想与理性思维的分析与实例举证,探讨了优秀的建筑师在创作建筑作品过程中,怎样正确处理感性体验与理性思想的辩证关系。

  10. Rational decisions

    CERN Document Server

    Binmore, Ken

    2008-01-01

    It is widely held that Bayesian decision theory is the final word on how a rational person should make decisions. However, Leonard Savage--the inventor of Bayesian decision theory--argued that it would be ridiculous to use his theory outside the kind of small world in which it is always possible to ""look before you leap."" If taken seriously, this view makes Bayesian decision theory inappropriate for the large worlds of scientific discovery and macroeconomic enterprise. When is it correct to use Bayesian decision theory--and when does it need to be modified? Using a minimum of mathematics,

  11. Incorporation of a single His residue by rational design enables thiol-ester hydrolysis by human glutathione transferase A1-1

    OpenAIRE

    Hederos, Sofia; Broo, Kerstin S.; Jakobsson, Emma; Kleywegt, Gerard J.; Mannervik, Bengt; Baltzer, Lars

    2004-01-01

    A strategy for rational enzyme design is reported and illustrated by the engineering of a protein catalyst for thiol-ester hydrolysis. Five mutants of human glutathione (GSH; γ-Glu-Cys-Gly) transferase A1-1 were designed in the search for a catalyst and to provide a set of proteins from which the reaction mechanism could be elucidated. The single mutant A216H catalyzed the hydrolysis of the S-benzoyl ester of GSH under turnover conditions with a kcat/KM of 156 M–1·min–1, and a catalytic profi...

  12. Rationalization: A Bibliography.

    Science.gov (United States)

    Pedrini, D. T.; Pedrini, Bonnie C.

    Rationalization was studied by Sigmund Freud and was specifically labeled by Ernest Jones. Rationalization ought to be differentiated from rational, rationality, logical analysis, etc. On the one hand, rationalization is considered a defense mechanism, on the other hand, rationality is not. Haan has done much work with self-report inventories and…

  13. Rationally Designed Graphene-Nanotube 3D Architectures with a Seamless Nodal Junction for Efficient Energy Conversion and Storage

    Science.gov (United States)

    2015-09-04

    have indicated that 3D carbon architectures, particularly a 3D pillared structure, consisting of parallel graphene layers supported by vertically...building blocks. A few groups have tried to prepare multilayered 3D graphene- CNT pillared structures (3–7). However, most of the reported prepa- ration... copper wire under 1000°C with meth- ane as the carbon source and used as the counter electrode while the CNT fiber was obtained by dry spinning from

  14. Rational inattention or rational overreaction?

    DEFF Research Database (Denmark)

    Browning, Martin; Hansen, Lars Gårn; Smed, Sinne

    We investigate differences in how consumers of fish react to health information in the mass media. We specify a dynamic empirical model that allows for heterogeneity in all basic parameters of consumer behavior as well as in how consumers react to information. We estimate the model using a unique...... houshold panel tracking consumption, prices, news stories and media habits over 24 quarters. We fi nd that the consumers most likely to be ’rationally ignorant’ of health effects react more dramatically to health news than the consumers who most likely are well informed....

  15. Rational inattention or rational overreaction?

    DEFF Research Database (Denmark)

    Browning, Martin; Hansen, Lars Gårn; Smed, Sinne

    We investigate differences in how consumers of fish react to health information in the mass media. We specify a dynamic empirical model that allows for heterogeneity in all basic parameters of consumer behavior as well as in how consumers react to information. We estimate the model using a unique...... houshold panel tracking consumption, prices, news stories and media habits over 24 quarters. We fi nd that the consumers most likely to be ’rationally ignorant’ of health effects react more dramatically to health news than the consumers who most likely are well informed....

  16. Rational Design of Human Metapneumovirus Live Attenuated Vaccine Candidates by Inhibiting Viral mRNA Cap Methyltransferase

    Science.gov (United States)

    Zhang, Yu; Wei, Yongwei; Zhang, Xiaodong; Cai, Hui; Niewiesk, Stefan

    2014-01-01

    ABSTRACT The paramyxoviruses human respiratory syncytial virus (hRSV), human metapneumovirus (hMPV), and human parainfluenza virus type 3 (hPIV3) are responsible for the majority of pediatric respiratory diseases and inflict significant economic loss, health care costs, and emotional burdens. Despite major efforts, there are no vaccines available for these viruses. The conserved region VI (CR VI) of the large (L) polymerase proteins of paramyxoviruses catalyzes methyltransferase (MTase) activities that typically methylate viral mRNAs at positions guanine N-7 (G-N-7) and ribose 2′-O. In this study, we generated a panel of recombinant hMPVs carrying mutations in the S-adenosylmethionine (SAM) binding site in CR VI of L protein. These recombinant viruses were specifically defective in ribose 2′-O methylation but not G-N-7 methylation and were genetically stable and highly attenuated in cell culture and viral replication in the upper and lower respiratory tracts of cotton rats. Importantly, vaccination of cotton rats with these recombinant hMPVs (rhMPVs) with defective MTases triggered a high level of neutralizing antibody, and the rats were completely protected from challenge with wild-type rhMPV. Collectively, our results indicate that (i) amino acid residues in the SAM binding site in the hMPV L protein are essential for 2′-O methylation and (ii) inhibition of mRNA cap MTase can serve as a novel target to rationally design live attenuated vaccines for hMPV and perhaps other paramyxoviruses, such as hRSV and hPIV3. IMPORTANCE Human paramyxoviruses, including hRSV, hMPV, and hPIV3, cause the majority of acute upper and lower respiratory tract infections in humans, particularly in infants, children, the elderly, and immunocompromised individuals. Currently, there is no licensed vaccine available. A formalin-inactivated vaccine is not suitable for these viruses because it causes enhanced lung damage upon reinfection with the same virus. A live attenuated vaccine

  17. A multiphysics/multiscale 2D numerical simulation of scaffold-based cartilage regeneration under interstitial perfusion in a bioreactor.

    Science.gov (United States)

    Sacco, Riccardo; Causin, Paola; Zunino, Paolo; Raimondi, Manuela T

    2011-07-01

    In vitro tissue engineering is investigated as a potential source of functional tissue constructs for cartilage repair, as well as a model system for controlled studies of cartilage development and function. Among the different kinds of devices for the cultivation of 3D cartilage cell colonies, we consider here polymeric scaffold-based perfusion bioreactors, where an interstitial fluid supplies nutrients and oxygen to the growing biomass. At the same time, the fluid-induced shear acts as a physiologically relevant stimulus for the metabolic activity of cells, provided that the shear stress level is appropriately tuned. In this complex environment, mathematical and computational modeling can help in the optimal design of the bioreactor configuration. In this perspective, we propose a computational model for the simulation of the biomass growth, under given inlet and geometrical conditions, where nutrient concentration, fluid dynamic field and cell growth are consistently coupled. The biomass growth model is calibrated with respect to the shear stress dependence on experimental data using a simplified short-time analysis in which the nutrient concentration and the fluid-induced shear stress are assumed constant in time and uniform in space. Volume averaging techniques are used to derive effective parameters that allow to upscale the microscopic structural properties to the macroscopic level. The biomass growth predictions obtained in this way are significant for long times of culture.

  18. Novel Scaffold FingerPrint (SFP): applications in scaffold hopping and scaffold-based selection of diverse compounds.

    Science.gov (United States)

    Rabal, Obdulia; Amr, Fares Ibrahim; Oyarzabal, Julen

    2015-01-26

    A novel 2D Scaffold FingerPrint (SFP) for mining ring fragments is presented. The rings are described not only by their topology, shape, and pharmacophoric features (hydrogen-bond acceptors and donors, their relative locations, sp3 carbons, and chirality) but also by the position and nature of their growing vectors because they play a critical role from the drug discovery perspective. SFP can be used (i) to identify alternative chemotypes to a reference ring either in a visual mode or by running quantitative similarity searches and (ii) in chemotype-based diversity selections. Two retrospective case studies focused on melanin concentrating hormone 1-receptor antagonists (MCH-R1) and phosphodiesterase-5 inhibitors (PDE5) demonstrate the capability of this method for identifying novel structurally different and synthetically accessible chemotypes. Good enrichment factor (155 and 219) and recall values (46% and 73%) are found within the first 100 ranked hits (0.3% of screened database). Our 2D SFP descriptor outperforms well-validated current gold-standard 2D fingerprints (ECFP_6) and 3D approaches based on shape and electrostatic similarity. Scaffold-based selection of diverse compounds has a critical impact on corporate library design and compound acquisitions; thus, a novel strategy is introduced that uses diverse scaffold selections using this SFP descriptor combined with R-group selection at the different substitution sites. Both approaches are available as part of an interactive web-based application that requires minimal input and no computational knowledge by medicinal chemists.

  19. Discovery of a New Class of Ionotropic Glutamate Receptor Antagonists by the Rational Design of (2S,3R)-3-(3-Carboxyphenyl)-pyrrolidine-2-carboxylic Acid

    DEFF Research Database (Denmark)

    Larsen, Ann Møller; Venskutonyte, Raminta; Valadés, Elena Antón;

    2011-01-01

    -5. In this article, we present the discovery of (2S,3R)-3-(3-carboxyphenyl)-pyrrolidine-2-carboxylic acid (1) based on a rational design process. Target compound 1 was synthesized by a stereoselective strategy in 10 steps from commercially available starting materials. Binding affinities of 1 at native ionotropic......The kainic acid (KA) receptors belong to the class of glutamate (Glu) receptors in the brain and constitute a promising target for the treatment of neurological and/ or psychiatric diseases such as schizophrenia, major depression, and epilepsy. Five KA subtypes have been identified and named GluK1...

  20. Current status of rational design of pro-drugs targeting the intestinal di/tri-peptide transporter hPEPT1 (SLC15A1)

    DEFF Research Database (Denmark)

    Saaby, Lasse; Nielsen, Carsten Uhd; Steffansen, Bente;

    2013-01-01

    The intestinal di/tri-peptide transporter hPEPT1 has broad substrate specificity, accommodating uptake of the majority of investigated di- and tripeptides, as well as of a number of drug compounds. This transport system has a high capacity and it has been hypothesized that hPEPT1-mediated uptake ...... in the field, the present review aims at giving a brief overview of structure-activity relationships for hPEPT1, and to provide a critical evaluation of whether hPEPT1-targeted prodrugs can be rationally designed....

  1. A rationally designed dual role anode material for lithium-ion and sodium-ion batteries: case study of eco-friendly Fe3O4.

    Science.gov (United States)

    Hariharan, Srirama; Saravanan, Kuppan; Ramar, Vishwanathan; Balaya, Palani

    2013-02-28

    Identifying dual role electrode materials capable of storing both lithium and sodium are thought to be highly relevant, as these materials could find potential applications simultaneously in lithium and sodium ion batteries. In this regard, the concept of dual alkali storage is demonstrated in Fe(3)O(4) anode material undergoing conversion reaction. To enable improved storage, a rational active material and electrode design is proposed. Accordingly, the following features were simultaneously incorporated into the design: (i) an optimal particle size, (ii) a conducting matrix, (iii) adequately large active material surface area and (iv) strong electrode material-current collector integrity. Electrodes incorporating this rational design exhibit excellent high rate performance and impressive cyclability during lithium storage. For instance, Fe(3)O(4) electrodes deliver a charge capacity of 950 mAh g(-1) at 1.2 C (~2.6 times higher than graphite and 5.4 times higher than Li(4)Ti(5)O(12)). Further, these electrodes show no signs of capacity fade even up to 1100 cycles. Impressively, the cells could also be charged-discharged to 65% of their theoretical capacity in just 5 min or 12 C (11.11 A g(-1)). The rate performance and cyclability of lithium storage achieved here are amongst the highest reported values in the literature for the conversion reaction in Fe(3)O(4). Besides lithium storage, the dual role of this anode is shown by demonstrating its sodium storage ability by conversion reaction for the first time.

  2. Rational kinematics

    CERN Document Server

    Angeles, Jorge

    1988-01-01

    A rational study of kinematics is a treatment of the subject based on invariants, i.e., quantities that remain essentially unchanged under a change of observer. An observer is understood to be a reference frame supplied with a clock (Truesdell 1966). This study will therefore include an introduction to invariants. The language of these is tensor analysis and multilinear algebra, both of which share many isomorphic relations, These subjects are treated in full detail in Ericksen (1960) and Bowen and Wang (1976), and hence will not be included here. Only a short account of notation and definitions will be presented. Moreover, definitions and basic concepts pertaining to the kinematics of rigid bodies will be also included. Although the kinematics of rigid bodies can be regarded as a particular case of the kinematics of continua, the former deserves attention on its own merits for several reasons. One of these is that it describes locally the motions undergone by continua. Another reason is that a whole area of ...

  3. PCB抗干扰设计中的合理分层%The Rational Delamination in Anti-interference Design of PCB

    Institute of Scientific and Technical Information of China (English)

    孙露

    2012-01-01

    The design of PCB delamination makes a big difference to the system of anti-interference ability. PCB design must be abided by the rule and conforms to the demand of anti-interference. This paper focuses on the rational delamination in PCB design, considers and fulfills the requirements of anti-interference.%PCB分层的设计对系统抗干扰能力影响很大。在进行PCB设计时,必须遵守PCB设计的一般原则,并应符合抗干扰设计的要求。本文重点讨论在PCB设计过程中合理分层,充分考虑并满足抗干扰性需求。

  4. Theoretical Studies in Heterogenous Catalysis: Towards a Rational Design of Novel Catalysts for Hydrodesulfurization and Hydrogen Production

    Energy Technology Data Exchange (ETDEWEB)

    Rodriguez,J.A.; Liu, P.

    2008-10-01

    potential to become the next generation of industrial HDS catalysts. Then, systematic studies concerned with the hydrogen-evolution reaction (HER) on extended surfaces, organometallic complexes and enzymes are presented. Finally, the reasons for the high catalytic activity of Au-CeO{sub 2} and Cu-CeO{sub 2} in the production of hydrogen through the water-gas shift reaction (CO + H{sub 2}O {yields} H{sub 2} + CO{sub 2}) are analyzed. It is shown that theoretical methods are very valuable tools for helping in the rational design of heterogeneous catalysts.

  5. 基于3D打印的钛合金-生物陶瓷复合结构人工骨支架设计%Design of Ti Alloy-biological Ceramics Composite Structure Artificial Bone Scaffold Based on 3D Printing

    Institute of Scientific and Technical Information of China (English)

    2016-01-01

    为了研究钛合金网架的置入对所设计的钛合金-生物陶瓷复合结构人工骨支架的影响,利用Ansys软件建立了钛合金网架、生物陶瓷支架及复合结构人工骨支架,分析了复合结构的力学性能,以及钛合金网架的横梁和立柱的直径及受力面积对支架力学性能的影响.结果表明:钛合金网架结构的置入有助于提高复合结构支架的力学性能,增加钛合金立柱的列数与直径有助于提高生物陶瓷支架的力学性能.%In order to study the influence of Ti alloy grid on the Ti alloy-biological ceramics composite structure artificial bone scaffold which was designed ,the Ansys software was used to build the structure model of Ti alloy grid,biological ceramics scaffold and composite structure artificial bone scaffold. The mechanical properties of composite structure scaffold and the influence of the diameter of the beam and column and the forced area on the mechanical properties of biological ceramics structure in composite structure were analyzed. The result show that Ti alloy grid structure enhanced the mechanical properties of the biological ceramics scaffold ,and increase the column numbers and diameter could help to improve the mechanical properties of the biological ceramics scaffold.

  6. Rational design of anatase TiO2 architecture with hierarchical nanotubes and hollow microspheres for high-performance dye-sensitized solar cells

    Science.gov (United States)

    Gu, Jiuwang; Khan, Javid; Chai, Zhisheng; Yuan, Yufei; Yu, Xiang; Liu, Pengyi; Wu, Mingmei; Mai, Wenjie

    2016-01-01

    Large surface area, sufficient light-harvesting and superior electron transport property are the major factors for an ideal photoanode of dye-sensitized solar cells (DSSCs), which requires rational design of the nanoarchitectures and smart integration of state-of-the-art technologies. In this work, a 3D anatase TiO2 architecture consisting of vertically aligned 1D hierarchical TiO2 nanotubes (NTs) with ultra-dense branches (HTNTs, bottom layer) and 0D hollow TiO2 microspheres with rough surface (HTS, top layer) is first successfully constructed on transparent conductive fluorine-doped tin oxide glass through a series of facile processes. When used as photoanodes, the DSSCs achieve a very large short-current density of 19.46 mA cm-2 and a high overall power conversion efficiency of 8.38%. The remarkable photovoltaic performance is predominantly ascribed to the enhanced charge transport capacity of the NTs (function as the electron highway), the large surface area of the branches (act as the electron branch lines), the pronounced light harvesting efficiency of the HTS (serve as the light scattering centers), and the engineered intimate interfaces between all of them (minimize the recombination effect). Our work demonstrates a possibility of fabricating superior photoanodes for high-performance DSSCs by rational design of nanoarchitectures and smart integration of multi-functional components.

  7. Structure-based rational design of a Toll-like receptor 4 (TLR4 decoy receptor with high binding affinity for a target protein.

    Directory of Open Access Journals (Sweden)

    Jieun Han

    Full Text Available Repeat proteins are increasingly attracting much attention as alternative scaffolds to immunoglobulin antibodies due to their unique structural features. Nonetheless, engineering interaction interface and understanding molecular basis for affinity maturation of repeat proteins still remain a challenge. Here, we present a structure-based rational design of a repeat protein with high binding affinity for a target protein. As a model repeat protein, a Toll-like receptor4 (TLR4 decoy receptor composed of leucine-rich repeat (LRR modules was used, and its interaction interface was rationally engineered to increase the binding affinity for myeloid differentiation protein 2 (MD2. Based on the complex crystal structure of the decoy receptor with MD2, we first designed single amino acid substitutions in the decoy receptor, and obtained three variants showing a binding affinity (K(D one-order of magnitude higher than the wild-type decoy receptor. The interacting modes and contributions of individual residues were elucidated by analyzing the crystal structures of the single variants. To further increase the binding affinity, single positive mutations were combined, and two double mutants were shown to have about 3000- and 565-fold higher binding affinities than the wild-type decoy receptor. Molecular dynamics simulations and energetic analysis indicate that an additive effect by two mutations occurring at nearby modules was the major contributor to the remarkable increase in the binding affinities.

  8. Enhanced Thermostability of Lipoxygenase from Anabaena sp. PCC 7120 by Site-Directed Mutagenesis Based on Computer-Aided Rational Design.

    Science.gov (United States)

    Diao, Hanwen; Zhang, Chong; Wang, Shuicheng; Lu, Fengxia; Lu, Zhaoxin

    2016-04-01

    Lipoxygenase from Anabaena sp. PCC 7120 (Ana-LOX) was thermally unstable. So, improving the thermostability of the enzyme was quite essential. The target site of Ana-LOX selected for site-directed mutagenesis was based on computer-aided rational design. The thermostability and specific activity of Ana-LOX were improved with replacing valine with alanine at the target site 421 and the site 40. Compared to the wild-type enzyme which has a half-life (T 1/2) of inactivation of 3.8 min at 50 °C, the T 1/2 of mutant enzymes with V421A and V40A substitution increased to 4.4 and 7.0 min, respectively. The double mutant V421A/V40A showed a synergistic effect with a T 1/2 value of 8.3 min, resulting in a 1.18-fold improvement compared to the original Ana-LOX. V421A, V40A, and V421A/V40A also obtained 4.83, 41.58, and 80.07 % increase in specific activity, respectively. This study provides useful theoretical reference for enzyme molecular modification and computer-aided rational design.

  9. Rational design of liposomal drug delivery systems, a review: Combined experimental and computational studies of lipid membranes, liposomes and their PEGylation.

    Science.gov (United States)

    Bunker, Alex; Magarkar, Aniket; Viitala, Tapani

    2016-10-01

    Combined experimental and computational studies of lipid membranes and liposomes, with the aim to attain mechanistic understanding, result in a synergy that makes possible the rational design of liposomal drug delivery system (LDS) based therapies. The LDS is the leading form of nanoscale drug delivery platform, an avenue in drug research, known as "nanomedicine", that holds the promise to transcend the current paradigm of drug development that has led to diminishing returns. Unfortunately this field of research has, so far, been far more successful in generating publications than new drug therapies. This partly results from the trial and error based methodologies used. We discuss experimental techniques capable of obtaining mechanistic insight into LDS structure and behavior. Insight obtained purely experimentally is, however, limited; computational modeling using molecular dynamics simulation can provide insight not otherwise available. We review computational research, that makes use of the multiscale modeling paradigm, simulating the phospholipid membrane with all atom resolution and the entire liposome with coarse grained models. We discuss in greater detail the computational modeling of liposome PEGylation. Overall, we wish to convey the power that lies in the combined use of experimental and computational methodologies; we hope to provide a roadmap for the rational design of LDS based therapies. Computational modeling is able to provide mechanistic insight that explains the context of experimental results and can also take the lead and inspire new directions for experimental research into LDS development. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.

  10. Material Specific Rational Design of A1B2C3O7 High-Tc Superconductors without Copper [A, B, C = Cations

    Science.gov (United States)

    Isikaku-Ironkwe, O'paul; Schaffer, Michael J.

    Soon after the discovery of YBa2Cu3O7 with Tc = 93K, a similar structured system with Ag replacing Cu was discovered with a Tc = 50K. Also, the discovery of Ba0 . 6 K0 . 4 BiO3 with Tc = 30K indicated that Cu was not indispensable for high temperature superconductivity (HTSC). Latter, the discoveries of the Pnictide and Chalcogenide high-Tc superconductors confirmed those earlier experimental indications. Using our recently developed Material Specific Characterization Dataset (MSCD) model for analysis and design of superconductors, we have computed many designs that satisfy the MSCD characteristics of YBa2Cu3O7 as a design model. Our design recognizes the valence state characteristics that make YBa2Cu3O6 a semiconductor, while YBa2Cu3O7is a superconductor. Here we present ten material specific rational design examples of potential A1B2C3O7 HTSCs without Cu, using the YBa2Cu3O7 design model. This MSCD design model opens the possibility for search and discovery of high-Tc oxide superconductor systems without copper.

  11. A study of the active site of influenza virus sialidase: an approach to the rational design of novel anti-influenza drugs.

    Science.gov (United States)

    von Itzstein, M; Dyason, J C; Oliver, S W; White, H F; Wu, W Y; Kok, G B; Pegg, M S

    1996-01-19

    The development of sialidase inhibitor-based potential anti-influenza drugs using rational drug design techniques has been of recent interest. The present study details as investigation of the active site of influenza virus sialidase by using the program GRID in an attempt to design more potent inhibitors in the hope they will eventually lead to anti-influenza drugs. A number of different probes (amino, carboxy, hydroxy, methyl, etc) have been used in an effort to determine the functional groups most likely to improve the binding of the starting template 2-deoxy-2,3-didehydro-N-acetylneuraminic acid (Neu5Ac2en). The data have correctly predicted the binding regions for the carboxylate, acetamido (NH and methyl), and glycerol (OH) groups of N-acetylneuraminic acid. Moreover, the data suggest that the addition of certain functionalities (amino group) at the C-4 position should enhance the overall binding.

  12. A Rationally Designed Nitrogen-Rich Metal-Organic Framework and Its Exceptionally High CO2 and H2 Uptake Capability

    Science.gov (United States)

    Wang, Xiao-Jun; Li, Pei-Zhou; Chen, Yifei; Zhang, Quan; Zhang, Huacheng; Chan, Xiu Xiang; Ganguly, Rakesh; Li, Yongxin; Jiang, Jianwen; Zhao, Yanli

    2013-01-01

    On the way towards a sustainable low-carbon future, the design and construction of chemical or physical adsorbents for CO2 capture and clean energy storage are vital technology. The incorporation of accessible nitrogen-donor sites into the pore walls of porous adsorbents can dramatically affect the CO2 uptake capacity and selectivity on account of the dipole-quadrupole interactions between the polarizable CO2 molecule and the accessible nitrogen site. In the present work, a nitrogen-rich rth-type metal-organic framework (MOF) was constructed based on rational design and careful synthesis. The MOF presents exceptionally high uptake capacity not only for CO2 but also for H2, which is attributed to favorable interactions between the gas molecules and the nitrogen-rich triazole units of the MOF proved by both experimental measurements and theoretical molecular simulations.

  13. Rational design and metabolic analysis of Escherichia coli for effective production of L-tryptophan at high concentration.

    Science.gov (United States)

    Chen, Lin; Zeng, An-Ping

    2017-01-01

    L-tryptophan (L-trp) is a biosynthetic precursor of various bioactive components with pharmaceutical interest. The development of an efficient L-trp production strain using targeted molecular engineering approaches is challenging due to the requirement of several precursors and the complex regulations of the pathways involved. In this study, we present a rationally engineered and genetically stable L-trp overproducing Escherichia coli strain. The streamlined strain E. coli S028 is able to efficiently produce 34-40 g/L of L-trp with a yield of 0.15 g L-trp/g glucose and a productivity of 0.60 g/L/h in fed-batch fermentations. The titer and productivity of L-trp achieved are over twice as much as those reported so far for rationally developed L-trp producers. In addition, for the first time, both intracellular and extracellular concentrations of L-trp and the key metabolites in a L-trp hyperproducer strain were measured with an automated fast-sampling unit which is connected to a well-controlled bioreactor. The time series metabolic analysis gives valuable information about the regulation of L-trp synthesis in a highly productive strain and reveals targets for further improvement. Among others, it was found that L-trp and the byproduct glutamate (L-glu) accumulated to an extremely high level in the cell initially whereas the intracellular concentrations of glutamine (L-gln) stayed at a relatively low level throughout the fermentation. The metabolic analysis suggests that (a) the engineered serine biosynthesis pathway was able to effectively synthesize the substrate serine (intracellular concentration > 8 mM) for L-trp production, while (b) the substrate L-gln with an intracellular concentration of 0.8-1.2 mM seems to limit the biosynthesis of L-trp, even though L-glu was overproduced intra- and extracellularly. Thus, an increased availability of glutamine synthetase which catalyzes L-glu conversion to L-gln and an overexpression of the L-trp exporter gene

  14. Design and Applications of Biodegradable Polyester Tissue Scaffolds Based on Endogenous Monomers Found in Human Metabolism

    Directory of Open Access Journals (Sweden)

    Devin G. Barrett

    2009-10-01

    Full Text Available Synthetic polyesters have deeply impacted various biomedical and engineering fields, such as tissue scaffolding and therapeutic delivery. Currently, many applications involving polyesters are being explored with polymers derived from monomers that are endogenous to the human metabolism. Examples of these monomers include glycerol, xylitol, sorbitol, and lactic, sebacic, citric, succinic, α-ketoglutaric, and fumaric acids. In terms of mechanical versatility, crystallinity, hydrophobicity, and biocompatibility, polyesters synthesized partially or completely from these monomers can display a wide range of properties. The flexibility in these macromolecular properties allows for materials to be tailored according to the needs of a particular application. Along with the presence of natural monomers that allows for a high probability of biocompatibility, there is also an added benefit that this class of polyesters is more environmentally friendly than many other materials used in biomedical engineering. While the selection of monomers may be limited by nature, these polymers have produced or have the potential to produce an enormous number of successes in vitro and in vivo.

  15. Rational design of genetically stable, live-attenuated poliovirus vaccines of all three serotypes: relevance to poliomyelitis eradication.

    Science.gov (United States)

    Macadam, Andrew J; Ferguson, Geraldine; Stone, David M; Meredith, Janet; Knowlson, Sarah; Auda, Ghazi; Almond, Jeffrey W; Minor, Philip D

    2006-09-01

    The global eradication of poliomyelitis caused by wild-type virus is likely to be completed within the next few years, despite immense logistic and political difficulties, and may ultimately be followed by the cessation of vaccination. However, the existing live-attenuated vaccines have the potential to revert to virulence, causing occasional disease, and viruses can be shed by immunocompromised individuals for prolonged periods of time. Moreover, several outbreaks of poliomyelitis have been shown to be caused by viruses derived from the Sabin vaccine strains. The appearance of such strains depends on the prevailing circumstances but poses a severe obstacle to strategies for stopping vaccination. Vaccine strains that are incapable of reversion at a measurable rate would provide a possible solution. Here, we describe the constructions of strains of type 3 poliovirus that are stabilized by the introduction of four mutations in the 5' noncoding region compared to the present vaccine. The strains are genetically and phenotypically stable under conditions where the present vaccine loses the attenuating mutation in the 5' noncoding region completely. Type 1 and type 2 strains in which the entire 5' noncoding regions of Sabin 1 and Sabin 2 were replaced exactly with that of one of the type 3 strains were also constructed. The genetic stability of 5' noncoding regions of these viruses matched that of the type 3 strains, but significant phenotypic reversion occurred, illustrating the potential limitations of a rational approach to the genetic stabilization of live RNA virus vaccines.

  16. Rationally re-designed mutation of NAD-independent l-lactate dehydrogenase: high optical resolution of racemic mandelic acid by the engineered Escherichia coli

    Directory of Open Access Journals (Sweden)

    Jiang Tianyi

    2012-11-01

    Full Text Available Abstract Background NAD-independent l-lactate dehydrogenase (l-iLDH from Pseudomonas stutzeri SDM can potentially be used for the kinetic resolution of small aliphatic 2-hydroxycarboxylic acids. However, this enzyme showed rather low activity towards aromatic 2-hydroxycarboxylic acids. Results Val-108 of l-iLDH was changed to Ala by rationally site-directed mutagenesis. The l-iLDH mutant exhibited much higher activity than wide-type l-iLDH towards l-mandelate, an aromatic 2-hydroxycarboxylic acid. Using the engineered Escherichia coli expressing the mutant l-iLDH as a biocatalyst, 40 g·L-1 of dl-mandelic acid was converted to 20.1 g·L-1 of d-mandelic acid (enantiomeric purity higher than 99.5% and 19.3 g·L-1 of benzoylformic acid. Conclusions A new biocatalyst with high catalytic efficiency toward an unnatural substrate was constructed by rationally re-design mutagenesis. Two building block intermediates (optically pure d-mandelic acid and benzoylformic acid were efficiently produced by the one-pot biotransformation system.

  17. Rational Design of Disulfide Bonds Increases Thermostability of a Mesophilic 1,3-1,4-β-Glucanase from Bacillus terquilensis

    Science.gov (United States)

    Xu, Xin; Li, Qi

    2016-01-01

    1,3–1,4-β-glucanase is an important biocatalyst in brewing industry and animal feed industry, while its low thermostability often reduces its application performance. In this study, the thermostability of a mesophilic β-glucanase from Bacillus terquilensis was enhanced by rational design and engineering of disulfide bonds in the protein structure. Protein spatial configuration was analyzed to pre-exclude the residues pairs which negatively conflicted with the protein structure and ensure the contact of catalytic center. The changes in protein overall and local flexibility among the wild-type enzyme and the designated mutants were predicted to select the potential disulfide bonds for enhancement of thermostability. Two residue pairs (N31C-T187C and P102C-N125C) were chosen as engineering targets and both of them were proved to significantly enhance the protein thermostability. After combinational mutagenesis, the double mutant N31C-T187C/P102C-N125C showed a 48.3% increase in half-life value at 60°C and a 4.1°C rise in melting temperature (Tm) compared to wild-type enzyme. The catalytic property of N31C-T187C/P102C-N125C mutant was similar to that of wild-type enzyme. Interestingly, the optimal pH of double mutant was shifted from pH6.5 to pH6.0, which could also increase its industrial application. By comparison with mutants with single-Cys substitutions, the introduction of disulfide bonds and the induced new hydrogen bonds were proved to result in both local and overall rigidification and should be responsible for the improved thermostability. Therefore, the introduction of disulfide bonds for thermostability improvement could be rationally and highly-effectively designed by combination with spatial configuration analysis and molecular dynamics simulation. PMID:27100881

  18. Rational design of carboxyl groups perpendicularly attached to a graphene sheet: a platform for enhanced biosensing applications.

    Science.gov (United States)

    Bonanni, Alessandra; Chua, Chun Kiang; Pumera, Martin

    2014-01-01

    Graphene oxide (GO)-based materials offer great potential for biofunctionalization with applications ranging from biosensing to drug delivery. Such biofunctionalization utilizes specific functional groups, typically a carboxyl moiety, as anchoring points for biomolecule. However, due to the fact that the exact chemical structure of GO is still largely unknown and poorly defined (it was postulated to consist of various oxygen-containing groups, such as epoxy, hydroxyl, carboxyl, carbonyl, and peroxy in varying ratios), it is challenging to fabricate highly biofunctionalized GO surfaces. The predominant anchoring sites (i.e., carboxyl groups) are mainly present as terminal groups on the edges of GO sheets and thus account for only a fraction of the oxygen-containing groups on GO. Herein, we suggest a direct solution to the long-standing problem of limited abundance of carboxyl groups on GO; GO was first reduced to graphene and consequently modified with only carboxyl groups grafted perpendicularly to its surface by a rational synthesis using free-radical addition of isobutyronitrile with subsequent hydrolysis. Such grafted graphene oxide can contain a high amount of carboxyl groups for consequent biofunctionalization, at which the extent of grafting is limited only by the number of carbon atoms in the graphene plane; in contrast, the abundance of carboxyl groups on "classical" GO is limited by the amount of terminal carbon atoms. Such a graphene platform embedded with perpendicularly grafted carboxyl groups was characterized in detail by X-ray photoelectron spectroscopy, cyclic voltammetry, and electrochemical impedance spectroscopy, and its application was exemplified with single-nucleotide polymorphism detection. It was found that the removal of oxygen functionalities after the chemical reduction enhanced the electron-transfer rate of the graphene. More importantly, the introduction of carboxyl groups promoted a more efficient immobilization of DNA probes on the

  19. THE APPLICATION OF ASC-ANALYSIS TO DETERMINE RATIONAL DESIGN FEATURES AND PARAMETERS OF THE MODES RELATIVE TO THE SCREW DRUMS FOR MIXING ANIMAL FEED

    Directory of Open Access Journals (Sweden)

    Marchenko A. Y.

    2016-06-01

    Full Text Available The authors have developed and manufactured a large number of different designs of relative helical drums for mixing animal feed. We have conducted 749 field experiments with the drums of the 10 different designs with different parameters modes of operation. In all experiments, we measured the quality of the feed mixture. However, directly based on empirical data, rational choice of design features and parameters of the operation modes of the reels is not possible. For this, you must first develop a model reflecting these empirical data. The construction of meaningful analytical models of different types of drums is a difficult and demanding scientific task, the complexity of which is due to the large variety and complexity of forms of drums and their mode of usage, a large number of diverse physical factors affecting the processes in the drum. As a consequence, the development of analytical models associated with a large number of simplifying assumptions that reduce their versatility and reliability. Therefore, it is important to search of a mathematical method and software tools provide a quick and simple for the user to identify and influence the design of the drum and the parameters of the operating modes on the quality of the feed mixture directly on the basis of empirical (experimental data. The work proposes a solution to this problem with the use of a new universal innovative method of artificial intelligence: automated system-cognitive analysis (ASC-analysis and its programmatic Toolkit – universal cognitive analytical system called "Eidos". In the system of "Eidos" we have implemented a software interface that provides direct input into the system large amounts of empirical data from Excel file. Created on their basis in the system of "Eidos" system-cognitive model allows the visual form to reflect the effect of the structure of the drum and the parameters of the operating modes on the quality of the resulting feed mixture and to

  20. Rational design of micro-RNA-like bifunctional siRNAs targeting HIV and the HIV coreceptor CCR5.

    Science.gov (United States)

    Ehsani, Ali; Saetrom, Pål; Zhang, Jane; Alluin, Jessica; Li, Haitang; Snøve, Ola; Aagaard, Lars; Rossi, John J

    2010-04-01

    Small-interfering RNAs (siRNAs) and micro-RNAs (miRNAs) are distinguished by their modes of action. SiRNAs serve as guides for sequence-specific cleavage of complementary mRNAs and the targets can be in coding or noncoding regions of the target transcripts. MiRNAs inhibit translation via partially complementary base-pairing to 3' untranslated regions (UTRs) and are generally ineffective when targeting coding regions of a transcript. In this study, we deliberately designed siRNAs that simultaneously direct cleavage and translational suppression of HIV RNAs, or cleavage of the mRNA encoding the HIV coreceptor CCR5 and suppression of translation of HIV. These bifunctional siRNAs trigger inhibition of HIV infection and replication in cell culture. The design principles have wide applications throughout the genome, as about 90% of genes harbor sites that make the design of bifunctional siRNAs possible.

  1. Towards Rational Designing of Efficient Sensitizers Based on Thiophene and Infrared Dyes for Dye-Sensitized Solar Cells

    Directory of Open Access Journals (Sweden)

    Ahmad Irfan

    2014-01-01

    Full Text Available Geometries, electronic properties, and absorption spectra of the dyes which are a combination of thiophene based dye (THPD and IR dyes (covering IR region; TIRBD1-TIRBD3 were performed using density functional theory (DFT and time dependent density functional theory (TD-DFT, respectively. Different electron donating groups, electron withdrawing groups, and IR dyes have been substituted on THPD to enhance the efficiency. The bond lengths of new designed dyes are almost the same. The lowest unoccupied molecular orbital energies of designed dyes are above the conduction band of TiO2 and the highest occupied molecular orbital energies are below the redox couple revealing that TIRBD1-TIRBD3 would be better sensitizers for dye-sensitized solar cells. The broad spectra and low energy gap also showed that designed materials would be efficient sensitizers.

  2. Computational medicinal chemistry for rational drug design: Identification of novel chemical structures with potential anti-tuberculosis activity.

    Science.gov (United States)

    Koseki, Yuji; Aoki, Shunsuke

    2014-01-01

    Tuberculosis (TB) is caused by the bacterium Mycobacterium tuberculosis and is a common infectious disease with high mortality and morbidity. The increasing prevalence of drug-resistant strains of TB presents a major public health problem. Due to the lack of effective drugs to treat these drug-resistant strains, the discovery or development of novel anti-TB drugs is important. Computer-aided drug design has become an established strategy for the identification of novel active chemicals through a combination of several drug design tools. In this review, we summarise the current chemotherapy for TB, describe attractive target proteins for the development of antibiotics against TB, and detail several computational drug design strategies that may contribute to the further identification of active chemicals for the treatment of not only TB but also other diseases.

  3. Rational design, synthesis and antitubercular evaluation of novel 2-(trifluoromethyl)phenothiazine-[1,2,3]triazole hybrids.

    Science.gov (United States)

    Addla, Dinesh; Jallapally, Anvesh; Gurram, Divya; Yogeeswari, Perumal; Sriram, Dharmarajan; Kantevari, Srinivas

    2014-01-01

    Molecular hybridization is an emerging structural modification tool to design molecules with better pharmacophoric properties. A series of novel 2-(trifluoromethyl)phenothiazine-1,2,3-triazoles 5a-v designed by hybridizing two antitubercular drugs trifluoperazine and I-A09 in a single molecular architecture, were synthesized in very good yields using click chemistry. Among the all '22' compounds screened for in vitro antimycobacterial activity against Mycobacterium tuberculosis H37Rv (Mtb), three analogs 5c, 5l and 5o were found to be most potent (MIC: 6.25μg/mL) antitubercular agents with good selectivity index.

  4. Rational design and synthesis of new quorum-sensing inhibitors derived from acylated homoserine lactones and natural products from garlic

    DEFF Research Database (Denmark)

    Persson, T.; Rasmussen, Thomas Bovbjerg; Skindersoe, M.

    2005-01-01

    with similarity both to sulfides 10a-s and to bioactive structures from garlic. Design and biological screening of all compounds presented in this work targeted inhibition of quorum-sensing comprising competitive inhibition of transcriptional regulators LuxR and LasR. The design was based on critical interactions...... within the binding-site and structural motifs in molecular components isolated from garlic, 7 and 8, shown to be quorum-sensing inhibitors but not antibiotics. A potent quorum-sensing inhibitor N-(heptylsulfanylacetyl)-L-homoserine lactone (10c) was identified. Together with data collected for the other...

  5. Structural similarity between binding sites in influenza sialidase and isocitrate dehydrogenase: implications for an alternative approach to rational drug design.

    OpenAIRE

    Poirrette, A. R.; Artymiuk, P. J.; Grindley, H. M.; Rice, D.W.; Willett, P.

    1994-01-01

    Using searching techniques based on algorithms derived from graph theory, we have established a similarity between a 3-dimensional cluster of side chains implicated in drug binding in influenza sialidase and side chains involved in isocitrate binding in Escherichia coli isocitrate dehydrogenase. The possible implications of the use of such comparative methods in drug design are discussed.

  6. Rational Design of High-Number dsDNA Fragments Based on Thermodynamics for the Construction of Full-Length Genes in a Single Reaction.

    Science.gov (United States)

    Birla, Bhagyashree S; Chou, Hui-Hsien

    2015-01-01

    Gene synthesis is frequently used in modern molecular biology research either to create novel genes or to obtain natural genes when the synthesis approach is more flexible and reliable than cloning. DNA chemical synthesis has limits on both its length and yield, thus full-length genes have to be hierarchically constructed from synthesized DNA fragments. Gibson Assembly and its derivatives are the simplest methods to assemble multiple double-stranded DNA fragments. Currently, up to 12 dsDNA fragments can be assembled at once with Gibson Assembly according to its vendor. In practice, the number of dsDNA fragments that can be assembled in a single reaction are much lower. We have developed a rational design method for gene construction that allows high-number dsDNA fragments to be assembled into full-length genes in a single reaction. Using this new design method and a modified version of the Gibson Assembly protocol, we have assembled 3 different genes from up to 45 dsDNA fragments at once. Our design method uses the thermodynamic analysis software Picky that identifies all unique junctions in a gene where consecutive DNA fragments are specifically made to connect to each other. Our novel method is generally applicable to most gene sequences, and can improve both the efficiency and cost of gene assembly.

  7. Rational Design of High-Number dsDNA Fragments Based on Thermodynamics for the Construction of Full-Length Genes in a Single Reaction.

    Directory of Open Access Journals (Sweden)

    Bhagyashree S Birla

    Full Text Available Gene synthesis is frequently used in modern molecular biology research either to create novel genes or to obtain natural genes when the synthesis approach is more flexible and reliable than cloning. DNA chemical synthesis has limits on both its length and yield, thus full-length genes have to be hierarchically constructed from synthesized DNA fragments. Gibson Assembly and its derivatives are the simplest methods to assemble multiple double-stranded DNA fragments. Currently, up to 12 dsDNA fragments can be assembled at once with Gibson Assembly according to its vendor. In practice, the number of dsDNA fragments that can be assembled in a single reaction are much lower. We have developed a rational design method for gene construction that allows high-number dsDNA fragments to be assembled into full-length genes in a single reaction. Using this new design method and a modified version of the Gibson Assembly protocol, we have assembled 3 different genes from up to 45 dsDNA fragments at once. Our design method uses the thermodynamic analysis software Picky that identifies all unique junctions in a gene where consecutive DNA fragments are specifically made to connect to each other. Our novel method is generally applicable to most gene sequences, and can improve both the efficiency and cost of gene assembly.

  8. Rational Design of High-Number dsDNA Fragments Based on Thermodynamics for the Construction of Full-Length Genes in a Single Reaction

    Science.gov (United States)

    Birla, Bhagyashree S.; Chou, Hui-Hsien

    2015-01-01

    Gene synthesis is frequently used in modern molecular biology research either to create novel genes or to obtain natural genes when the synthesis approach is more flexible and reliable than cloning. DNA chemical synthesis has limits on both its length and yield, thus full-length genes have to be hierarchically constructed from synthesized DNA fragments. Gibson Assembly and its derivatives are the simplest methods to assemble multiple double-stranded DNA fragments. Currently, up to 12 dsDNA fragments can be assembled at once with Gibson Assembly according to its vendor. In practice, the number of dsDNA fragments that can be assembled in a single reaction are much lower. We have developed a rational design method for gene construction that allows high-number dsDNA fragments to be assembled into full-length genes in a single reaction. Using this new design method and a modified version of the Gibson Assembly protocol, we have assembled 3 different genes from up to 45 dsDNA fragments at once. Our design method uses the thermodynamic analysis software Picky that identifies all unique junctions in a gene where consecutive DNA fragments are specifically made to connect to each other. Our novel method is generally applicable to most gene sequences, and can improve both the efficiency and cost of gene assembly. PMID:26716828

  9. 理性主义设计思想的形成与发展%The Development of the Rationalism Design Conception

    Institute of Scientific and Technical Information of China (English)

    韩俊

    2009-01-01

    20世纪初,理性主义设计思想萌芽于德意志工业同盟,形成于20世纪20年代的德国包豪斯,二战前在欧洲各国迅速发展,二战后广泛影响欧美各国,成为现代设计重要的设计思想,直至60年代兴起的波普设计思潮使其遭到颠覆.%At the beginning of the 20th century,the design conception of rationalism turned up from the manufactory industry in Germany,and then completed its theorization in the Bauhaus school in Germany during the 1920s.It got its fast development in the countries of Europe before World War 2,and exerted a great impact on European and American countries after world War 2.It was one of the most important idea of design at that time.Until 1960,with the advent of the design style of Pop,it was gradually replaced.

  10. Rationally Designed Vaccines Targeting the V2 Region of HIV-1 gp120 Induce a Focused, Cross-Clade-Reactive, Biologically Functional Antibody Response.

    Science.gov (United States)

    Zolla-Pazner, Susan; Powell, Rebecca; Yahyaei, Sara; Williams, Constance; Jiang, Xunqing; Li, Wei; Lu, Shan; Wang, Shixia; Upadhyay, Chitra; Hioe, Catarina E; Totrov, Max; Kong, Xiangpeng

    2016-12-15

    Strong antibody (Ab) responses against V1V2 epitopes of the human immunodeficiency virus type 1 (HIV-1) gp120 envelope (Env) correlated with reduced infection rates in studies of HIV, simian-human immunodeficiency virus (SHIV), and simian immunodeficiency virus (SIV). In order to focus the Ab response on V1V2, we used six V1V2 sequences and nine scaffold proteins to construct immunogens which were tested using various immunization regimens for their ability to induce cross-reactive and biologically active V2 Abs in rabbits. A prime/boost immunization strategy was employed using gp120 DNA and various V1V2-scaffold proteins. The rabbit polyclonal Ab responses (i) were successfully focused on the V1V2 region, with weak or only transient responses to other Env epitopes, (ii) displayed broad cross-reactive binding activity with gp120s and the V1V2 regions of diverse strains from clades B, C, and E, (iii) included V2 Abs with specificities similar to those found in HIV-infected individuals, and (iv) remained detectable ≥1 year after the last boosting dose. Importantly, sera from rabbits receiving V1V2-scaffold immunogens displayed Ab-dependent cellular phagocytosis whereas sera from rabbits receiving only gp120 did not. The results represent the first fully successful example of reverse vaccinology in the HIV vaccine field with rationally designed epitope scaffold immunogens inducing Abs that recapitulate the epitope specificity and biologic activity of the human monoclonal Abs from which the immunogens were designed. Moreover, this is the first immunogenicity study using epitope-targeting, rationally designed vaccine constructs that induced an Fc-mediated activity associated with protection from infection with HIV, SIV, and SHIV. Novel immunogens were designed to focus the antibody response of rabbits on the V1V2 epitopes of HIV-1 gp120 since such antibodies were associated with reduced infection rates of HIV, SIV, and SHIV. The vaccine-induced antibodies were broadly

  11. Ferroelectric polymer scaffolds based on a copolymer of tetrafluoroethylene with vinylidene fluoride: fabrication and properties.

    Science.gov (United States)

    Bolbasov, E N; Anissimov, Y G; Pustovoytov, A V; Khlusov, I A; Zaitsev, A A; Zaitsev, K V; Lapin, I N; Tverdokhlebov, S I

    2014-07-01

    A solution blow spinning technique is a method developed recently for making nonwoven webs of micro- and nanofibres. The principal advantage of this method compared to a more traditional electrospinning process is its significantly higher production rate. In this work, the solution blow spinning method was further developed to produce nonwoven polymeric scaffolds based on a copolymer of tetrafluoroethylene with vinylidene fluoride solution in acetone. A crucial feature of the proposed method is that high-voltage equipment is not required, which further improves the method's economics. Scanning electron microscopy analysis of the samples demonstrated that the surface morphology of the nonwoven materials is dependent on the polymer concentration in the spinning solution. It was concluded that an optimum morphology of the nonwoven scaffolds for medical applications is achieved by using a 5% solution of the copolymer. It was established that the scaffolds produced from the 5% solution have a fractal structure and anisotropic mechanical properties. X-ray diffraction, infrared spectroscopy, Raman spectroscopy and differential scanning calorimetry demonstrated that the fabricated nonwoven materials have crystal structures that exhibit ferroelectric properties. Gas chromatography has shown that the amount of acetone in the nonwoven material does not exceed the maximum allowable concentration of 0.5%. In vitro analysis, using the culture of motile cells, confirmed that the nonwoven material is non-toxic and does not alter the morpho-functional status of stem cells for short-term cultivation, and therefore can potentially be used in medical applications.

  12. Rational design of protein stability: effect of (2S,4R-4-fluoroproline on the stability and folding pathway of ubiquitin.

    Directory of Open Access Journals (Sweden)

    Maria D Crespo

    Full Text Available BACKGROUND: Many strategies have been employed to increase the conformational stability of proteins. The use of 4-substituted proline analogs capable to induce pre-organization in target proteins is an attractive tool to deliver an additional conformational stability without perturbing the overall protein structure. Both, peptides and proteins containing 4-fluorinated proline derivatives can be stabilized by forcing the pyrrolidine ring in its favored puckering conformation. The fluorinated pyrrolidine rings of proline can preferably stabilize either a C(γ-exo or a C(γ-endo ring pucker in dependence of proline chirality (4R/4S in a complex protein structure. To examine whether this rational strategy can be generally used for protein stabilization, we have chosen human ubiquitin as a model protein which contains three proline residues displaying C(γ-exo puckering. METHODOLOGY/PRINCIPAL FINDINGS: While (2S,4R-4-fluoroproline ((4R-FPro containing ubiquitinin can be expressed in related auxotrophic Escherichia coli strain, all attempts to incorporate (2S,4S-4-fluoroproline ((4S-FPro failed. Our results indicate that (4R-FPro is favoring the C(γ-exo conformation present in the wild type structure and stabilizes the protein structure due to a pre-organization effect. This was confirmed by thermal and guanidinium chloride-induced denaturation profile analyses, where we observed an increase in stability of -4.71 kJ·mol(-1 in the case of (4R-FPro containing ubiquitin ((4R-FPro-ub compared to wild type ubiquitin (wt-ub. Expectedly, activity assays revealed that (4R-FPro-ub retained the full biological activity compared to wt-ub. CONCLUSIONS/SIGNIFICANCE: The results fully confirm the general applicability of incorporating fluoroproline derivatives for improving protein stability. In general, a rational design strategy that enforces the natural occurring proline puckering conformation can be used to stabilize the desired target protein.

  13. Rational Design of Coumarin Derivatives as CK2 Inhibitors by Improving the Interaction with the Hinge Region.

    Science.gov (United States)

    Zhang, Na; Chen, Wen-Juan; Zhou, Yue; Zhao, Hongtao; Zhong, Ru-Gang

    2016-01-01

    Design of novel coumarin derivatives as CK2 inhibitors were attempted by targeting the interaction with the hinge region. A set of substituents capable of forming a hydrogen bond or halogen bond with the hinge region were screened in silico, and trifluoromethyl emerges as a promising motif by forming favorable electrostatic interaction and a presumable halogen bond with the hinge region. As proof of concept, three trifluoromethyl derivatives of coumarin were synthesized and tested in vitro. The results indicated that replacement of methyl by trifluoromethyl leads to a modest 5-fold improvement in potency, with the most active compound being 0.4 µM. The newly designed compounds were further screened on one lung cancer cell line A549, showing low micromolar anti-proliferative activity.

  14. Rational Design of a GFP-Based Fluorogenic Caspase Reporter for Imaging Apoptosis In Vivo.

    Science.gov (United States)

    To, Tsz-Leung; Schepis, Antonino; Ruiz-González, Rubén; Zhang, Qiang; Yu, Dan; Dong, Zhiqiang; Coughlin, Shaun R; Shu, Xiaokun

    2016-07-21

    Fluorescence resonance energy transfer-based executioner caspase reporters using GFP are important tools for imaging apoptosis. While these reporters are useful for imaging apoptosis in cultured cells, their in vivo application has been handicapped by poor signal to noise. Here, we report the design and characterization of a GFP-based fluorogenic protease reporter, dubbed ZipGFP. ZipGFP-based TEV protease reporter increased fluorescence 10-fold after activation by protease. A ZipGFP-based executioner caspase reporter visualized apoptosis in live zebrafish embryos with spatiotemporal resolution. Thus, the ZipGFP-based caspase reporter may be useful for monitoring apoptosis during animal development and for designing reporters of proteases beyond the executioner caspases.

  15. Rational design of vaccine targets and strategies for HIV: a crossroad of statistical physics, biology, and medicine

    Science.gov (United States)

    Chakraborty, Arup K.; Barton, John P.

    2017-03-01

    Vaccination has saved more lives than any other medical procedure. Pathogens have now evolved that have not succumbed to vaccination using the empirical paradigms pioneered by Pasteur and Jenner. Vaccine design strategies that are based on a mechanistic understanding of the pertinent immunology and virology are required to confront and eliminate these scourges. In this perspective, we describe just a few examples of work aimed to achieve this goal by bringing together approaches from statistical physics with biology and clinical research.

  16. Rational Design of a Chalcogenopyrylium-Based Surface-Enhanced Resonance Raman Scattering-Nanoprobe with Attomolar Sensitivity

    Science.gov (United States)

    Wall, Matthew A.; Huang, Ruimin; Detty, Michael R.; Kircher, Moritz F.

    2015-01-01

    High sensitivity and specificity are two desirable features in biomedical imaging. Raman imaging has surfaced as a promising optical modality that offers both. Here, we report the design and synthesis of a group of near infrared absorbing 2-thienyl-substituted chalcogenopyrylium dyes tailored to have high affinity for gold. When adsorbed onto gold nanoparticles, these dyes produce biocompatible SERRS-nanoprobes with attomolar limits of detection amenable to ultrasensitive in vivo multiplexed tumor and disease marker detection. PMID:25800697

  17. Rational design of a chalcogenopyrylium-based surface-enhanced resonance Raman scattering nanoprobe with attomolar sensitivity

    Science.gov (United States)

    Harmsen, Stefan; Bedics, Matthew A.; Wall, Matthew A.; Huang, Ruimin; Detty, Michael R.; Kircher, Moritz F.

    2015-03-01

    High sensitivity and specificity are two desirable features in biomedical imaging. Raman imaging has surfaced as a promising optical modality that offers both. Here we report the design and synthesis of a group of near-infrared absorbing 2-thienyl-substituted chalcogenopyrylium dyes tailored to have high affinity for gold. When adsorbed onto gold nanoparticles, these dyes produce biocompatible SERRS nanoprobes with attomolar limits of detection amenable to ultrasensitive in vivo multiplexed tumour and disease marker detection.

  18. Structure-based in-silico rational design of a selective peptide inhibitor for thymidine monophosphate kinase of mycobacterium tuberculosis.

    Science.gov (United States)

    Kumar, Manoj; Sharma, Sujata; Srinivasan, Alagiri; Singh, Tej P; Kaur, Punit

    2011-05-01

    Tuberculosis still remains one of the most deadly infectious diseases. The emergence of drug resistant strains has fuelled the quest for novel drugs and drug targets for its successful treatment. Thymidine monophosphate kinase (TMPK) lies at the point where the salvage and de novo synthetic pathways meet in nucleotide synthesis. TMPK in M.tb has emerged as an attractive drug target since blocking it will affect both the pathways involved in the thymidine triphosphate synthesis. Moreover, the unique differences at the active site of TMPK enzyme in M.tb and humans can be exploited for the development of ideal drug candidates. Based on a detailed evaluation of known inhibitors and available three-dimensional structures of TMPK, several peptidic inhibitors were designed. In silico docking and selectivity analysis of these inhibitors with TMPK from M.tb and human was carried out to examine their differential binding at the active site. The designed tripeptide, Trp-Pro-Asp, was found to be most selective for M.tb. The ADMET analysis of this peptide indicated that it is likely to be a drug candidate. The tripeptide so designed is a suitable lead molecule for the development of novel TMPK inhibitors as anti-tubercular drugs.

  19. 使用Rational Rose进行基于J2EE体系结构的面向对象程序设计%Object Orient Program Design Base On J2EE Architecture Using Rational Rose

    Institute of Scientific and Technical Information of China (English)

    贾文珏; 赵明; 唐文凤; 张锋; 王法英

    2002-01-01

    本文首先介绍了基于UML的可视化建模工具--Ratonal Rose及J2EE体系结构,然后结合项目经验介绍使用Rational Rose和MVC设计模式进行基于J2EE体系结构的面向对象程序设计.

  20. From Molecular to Macroscopic via the Rational Design of a Self-Assembled 3D DNA Crystal

    Energy Technology Data Exchange (ETDEWEB)

    Zheng, J.; Birktoft, J; Yi, C; Tong, W; Ruojie, S; Constantinou, P; Ginell, S; Chenge, M; Seeman, N

    2009-01-01

    We live in a macroscopic three-dimensional (3D) world, but our best description of the structure of matter is at the atomic and molecular scale. Understanding the relationship between the two scales requires a bridge from the molecular world to the macroscopic world. Connecting these two domains with atomic precision is a central goal of the natural sciences, but it requires high spatial control of the 3D structure of matter1. The simplest practical route to producing precisely designed 3D macroscopic objects is to form a crystalline arrangement by self-assembly, because such a periodic array has only conceptually simple requirements: a motif that has a robust 3D structure, dominant affinity interactions between parts of the motif when it self-associates, and predictable structures for these affinity interactions. Fulfilling these three criteria to produce a 3D periodic system is not easy, but should readily be achieved with well-structured branched DNA motifs tailed by sticky ends2. Complementary sticky ends associate with each other preferentially and assume the well-known B-DNA structure when they do so3; the helically repeating nature of DNA facilitates the construction of a periodic array. It is essential that the directions of propagation associated with the sticky ends do not share the same plane, but extend to form a 3D arrangement of matter. Here we report the crystal structure at 4?Angstroms resolution of a designed, self-assembled, 3D crystal based on the DNA tensegrity triangle4. The data demonstrate clearly that it is possible to design and self-assemble a well-ordered macromolecular 3D crystalline lattice with precise control.

  1. Rational Design of Micro-RNA-like Bifunctional siRNAs Targeting HIV and the HIV Coreceptor CCR5

    OpenAIRE

    2010-01-01

    Small-interfering RNAs (siRNAs) and micro-RNAs (miRNAs) are distinguished by their modes of action. SiRNAs serve as guides for sequence-specific cleavage of complementary mRNAs and the targets can be in coding or noncoding regions of the target transcripts. MiRNAs inhibit translation via partially complementary base-pairing to 3′ untranslated regions (UTRs) and are generally ineffective when targeting coding regions of a transcript. In this study, we deliberately designed siRNAs that simultan...

  2. Guest-responsive structural adaptation of a rationally-designed molecular tweezer based on Tröger’s base

    Indian Academy of Sciences (India)

    Ishita Neogi; Alankriti Bajpai; Jarugu Narasimha Moorthy

    2014-09-01

    We have designed and synthesized a modified Tröger’s base TB in which the sterically-rigidified aryl rings that protrude into its groove were envisaged to preclude self-inclusion. From a limited preliminary experimentation, TB has been found to exhibit guest inclusion. The X-ray determined structures of the crystals of guest-free TB and its inclusion compounds with acetonitrile and -dichlorobenzene reveal remarkable adaptability of the TB core to undergo subtle structural changes in response to the guest that is included. The structural analyses demonstrate the fact that TB behaves like a molecular tweezer.

  3. Molecular basis of differential selectivity of cyclobutyl-substituted imidazole inhibitors against CDKs: insights for rational drug design.

    Directory of Open Access Journals (Sweden)

    Soumya Lipsa Rath

    Full Text Available Cyclin-dependent kinases (CDKs belong to the CMGC subfamily of protein kinases and play crucial roles in eukaryotic cell division cycle. At least seven different CDKs have been reported to be implicated in the cell cycle regulation in vertebrates. These CDKs are highly homologous and contain a conserved catalytic core. This makes the design of inhibitors specific for a particular CDK difficult. There is, however, growing need for CDK5 specific inhibitors to treat various neurodegenerative diseases. Recently, cis-substituted cyclobutyl-4-aminoimidazole inhibitors have been identified as potent CDK5 inhibitors that gave up to 30-fold selectivity over CDK2. Available IC50 values also indicate a higher potency of this class of inhibitors over commercially available drugs, such as roscovitine. To understand the molecular basis of higher potency and selectivity of these inhibitors, here, we present molecular dynamics simulation results of CDK5/p25 and CDK2/CyclinE complexed with a series of cyclobutyl-substituted imidazole inhibitors and roscovitine. The atomic details of the stereospecificity and selectivity of these inhibitors are obtained from energetics and binding characteristics to the CDK binding pocket. The study not only complements the experimental findings, but also provides a wealth of detailed information that could help the structure-based drug designing processes.

  4. A rational design for improving the trypsin resistance of aflatoxin-detoxifizyme (ADTZ) based on molecular structure evaluation.

    Science.gov (United States)

    Qiu, Yuxin; Wu, Xiyang; Xie, Chunfang; Hu, Yadong; Liu, Daling; Ma, Yi; Yao, Dongsheng

    2016-05-01

    The resistance of feed enzymes against proteases is crucial in livestock farming. In this study, the trypsin resistance of aflatoxin-detoxifizyme (ADTZ) is improved. ADTZ possesses 72 lys/arg residue sites, 45 of which are scattered on the outermost layers of the molecule (RSA≧25%). These 45 lys/arg sites could be target sites for trypsin hydrolysis. By considering shape-matching (including physical and secondary bond interactions) and the "induced fit-effect", we hypothesized that some of these lys/arg sites are vulnerable to trypsin. A protein-protein docking simulation method was used to avoid the massive computational requirements and to address the intricacy of selecting candidate sites, as candidate site selection is affected by space displacement. Optimal mutants (K244Q/K213C/K270T and R356E/K357T/R623C) were predicted by computational design with protein folding energy analysis and molecular dynamics simulations. A trypsin digestion assay was performed, and the mutants displayed much higher stability against trypsin hydrolysis compared to the native enzyme. Moreover, temperature- and pH-activity profiles revealed that the designed mutations did not affect the catalytic activity of the enzyme.

  5. Transport and collision dynamics in periodic asymmetric obstacle arrays: Rational design of microfluidic rare-cell immunocapture devices

    Science.gov (United States)

    Gleghorn, Jason P.; Smith, James P.; Kirby, Brian J.

    2013-09-01

    Microfluidic obstacle arrays have been used in numerous applications, and their ability to sort particles or capture rare cells from complex samples has broad and impactful applications in biology and medicine. We have investigated the transport and collision dynamics of particles in periodic obstacle arrays to guide the design of convective, rather than diffusive, transport-based immunocapture microdevices. Ballistic and full computational fluid dynamics simulations are used to understand the collision modes that evolve in cylindrical obstacle arrays with various geometries. We identify previously unrecognized collision mode structures and differential size-based collision frequencies that emerge from these arrays. Previous descriptions of transverse displacements that assume unidirectional flow in these obstacle arrays cannot capture mode transitions properly as these descriptions fail to capture the dependence of the mode transitions on column spacing and the attendant change in the flow field. Using these analytical and computational simulations, we elucidate design parameters that induce high collision rates for all particles larger than a threshold size or selectively increase collision frequencies for a narrow range of particle sizes within a polydisperse population. Furthermore, we investigate how the particle Péclet number affects collision dynamics and mode transitions and demonstrate that experimental observations from various obstacle array geometries are well described by our computational model.

  6. When inhibitors do not inhibit: critical evaluation of rational drug design targeting chorismate mutase from Mycobacterium tuberculosis.

    Science.gov (United States)

    Munack, Steffi; Leroux, Vincent; Roderer, Kathrin; Ökvist, Mats; van Eerde, André; Gundersen, Lise-Lotte; Krengel, Ute; Kast, Peter

    2012-11-01

    Tuberculosis (TB) is a devastating disease that claims millions of lives every year. Hindered access or non-compliance to medication, especially in developing countries, led to drug resistance, further aggravating the situation. With current standard therapies in use for over 50 years and only few new candidates in clinical trials, there is an urgent call for new TB drugs. A powerful tool for the development of new medication is structure-guided design, combined with virtual screening or docking studies. Here, we report the results of a drug-design project, which we based on a publication that claimed the structure-guided discovery of several promising and highly active inhibitors targeting the secreted chorismate mutase (*MtCM) from Mycobacterium tuberculosis. We set out to further improve on these compounds and synthesized a series of new derivatives. Thorough evaluation of these molecules in enzymatic assays revealed, to our dismay, that neither the claimed lead compounds, nor any of the synthesized derivatives, show any inhibitory effects against *MtCM.

  7. Rational Design of Ruthenium Complexes Containing 2,6-Bis(benzimidazolyl)pyridine Derivatives with Radiosensitization Activity by Enhancing p53 Activation.

    Science.gov (United States)

    Deng, Zhiqin; Yu, Lianling; Cao, Wenqiang; Zheng, Wenjie; Chen, Tianfeng

    2015-06-01

    The rational design of metal-based complexes is an effective strategy for the discovery of potent sensitizers for use in cancer radiotherapy. In this study, we synthesized three ruthenium complexes containing bis-benzimidazole derivatives: Ru(bbp)Cl3 (1), [Ru(bbp)2 ]Cl2 (2 a) (in which bbp=2,6-bis(benzimidazol-1-yl)pyridine), and [Ru(bbp)2]Cl2 (2 b) (where bbp=2,6-bis-(6-nitrobenzimidazol-2-yl)pyridine). We evaluated their radiosensitization capacities in vitro and mechanisms of action. Complex 2 b was found to be particularly effective in sensitizing human melanoma A375 cells toward radiation, with a sensitivity enhancement ratio of 2.4. Along with this potency, complex 2 b exhibited a high degree of selectivity between human cancer and normal cells. Mechanistic studies revealed that 2 b promotes radiation-induced accumulation of intracellular reactive oxygen species (ROS) by reacting with cellular glutathione (GSH) and then causing DNA stand breaks. The subsequent DNA damage induces phosphorylation of p53 (p-p53) and upregulates the expression levels of p21, which inhibits the expression of cyclin-B, leading to G2M arrest. Moreover, p-p53 activates caspases-3 and -8, triggers cleavage of poly(ADP-ribose) polymerase (PARP), finally resulting in apoptosis. Taken together, the results of this study provide a strategy for the design of ruthenium-based radiosensitizers for use in cancer therapy.

  8. Synthesis and extraction studies with a rationally designed diamide ligand selective to actinide(iv) pertinent to the plutonium uranium redox extraction process.

    Science.gov (United States)

    Sharma, Shikha; Panja, Surajit; Bhattacharyya, Arunasis; Dhami, Prem S; Gandhi, Preetam M; Ghosh, Sunil K

    2016-05-04

    A new class of conformationally constrained oxa-bridged tricyclo-dicarboxamide (OTDA) ligand was rationally designed for the selective extraction of tetravalent actinides pertinent to the Plutonium Uranium Redox EXtraction (PUREX) process. Two of the designed diamide ligands were synthesized and extraction studies were performed for Pu(iv) from HNO3 medium. The mechanism of extraction was investigated by studying various parameters such as feed HNO3, NaNO3 and OTDA concentrations. The nature of the extracted species was found to be [Pu(NO3)4(OTDA)]. One of the OTDA ligands was elaborately tested and showed the selective extraction of Pu(iv) and Np(iv) over other actinide species, viz., U(vi), Np(v), Am(iii), lanthanides and fission products contained in a nuclear waste from the PUREX process. DFT calculations predicted the charge density on each of the coordinating 'O' atoms of OTDA supporting its high Pu(iv) selectivity over other ions studied and also provided the energy optimized structure of OTDA and its Pu(iv) complex.

  9. Rational design of a cytotoxic dinuclear Cu2 complex that binds by molecular recognition at two neighboring phosphates of the DNA backbone.

    Science.gov (United States)

    Jany, Thomas; Moreth, Alexander; Gruschka, Claudia; Sischka, Andy; Spiering, Andre; Dieding, Mareike; Wang, Ying; Samo, Susan Haji; Stammler, Anja; Bögge, Hartmut; Fischer von Mollard, Gabriele; Anselmetti, Dario; Glaser, Thorsten

    2015-03-16

    The mechanism of the cytotoxic function of cisplatin and related anticancer drugs is based on their binding to the nucleobases of DNA. The development of new classes of anticancer drugs requires establishing other binding modes. Therefore, we performed a rational design for complexes that target two neighboring phosphates of the DNA backbone by molecular recognition resulting in a family of dinuclear complexes based on 2,7-disubstituted 1,8-naphthalenediol. This rigid backbone preorganizes the two metal ions for molecular recognition at the distance of two neighboring phosphates in DNA of 6-7 Å. Additionally, bulky chelating pendant arms in the 2,7-position impede nucleobase complexation by steric hindrance. We successfully synthesized the Cu(II)2 complex of the designed family of dinuclear complexes and studied its binding to dsDNA by independent ensemble and single-molecule methods like gel electrophoresis, precipitation, and titration experiments followed by UV-vis spectroscopy, atomic force microscopy (AFM), as well as optical tweezers (OT) and magnetic tweezers (MT) DNA stretching. The observed irreversible binding of our dinuclear Cu(II)2 complex to dsDNA leads to a blocking of DNA synthesis as studied by polymerase chain reactions and cytotoxicity for human cancer cells.

  10. Optimizing the lattice design of a diffraction-limited storage ring with a rational combination of particle swarm and genetic algorithms

    Science.gov (United States)

    Jiao, Yi; Xu, Gang

    2017-02-01

    In the lattice design of a diffraction-limited storage ring (DLSR) consisting of compact multi-bend achromats (MBAs), it is challenging to simultaneously achieve an ultralow emittance and a satisfactory nonlinear performance, due to extremely large nonlinearities and limited tuning ranges of the element parameters. Nevertheless, in this paper we show that the potential of a DLSR design can be explored with a successive and iterative implementation of the multi-objective particle swarm optimization (MOPSO) and multi-objective genetic algorithm (MOGA). For the High Energy Photon Source, a planned kilometer-scale DLSR, optimizations indicate that it is feasible to attain a natural emittance of about 50 pm·rad, and simultaneously realize a sufficient ring acceptance for on-axis longitudinal injection, by using a hybrid MBA lattice. In particular, this study demonstrates that a rational combination of the MOPSO and MOGA is more effective than either of them alone, in approaching the true global optima of an explorative multi-objective problem with many optimizing variables and local optima. Supported by NSFC (11475202, 11405187) and Youth Innovation Promotion Association CAS (2015009)

  11. Optimizing the lattice design for a diffraction-limited storage ring with a rational combination of particle swarm and genetic algorithms

    CERN Document Server

    Jiao, Y

    2016-01-01

    In the design of a diffraction-limited storage ring (DLSR) consisting of compact multi-bend achromats (MBAs), it is challenging to simultaneously achieve an ultralow emittance and a satisfactory nonlinear performance, due to extremely large nonlinearities and limited tuning ranges of the element parameters. Nevertheless, taking the High Energy Photon Source (HEPS) as an example, we demonstrate that the potential of a DLSR design can be explored with a successive and iterative implementation of the particle swarm optimization (PSO) and multi-objective genetic algorithm (MOGA). It turns out that with a hybrid MBA lattice, it is feasible for the HEPS to attain a natural emittance of about 50 pm.rad, and meanwhile, realize a sufficient ring acceptance for beam accumulation with an on-axis longitudinal injection scheme. Particularly, this study indicates that a rational combination of the PSO and MOGA is more effective than either of them alone in approaching the true global optima, for an explorative multi-object...

  12. Rational design for cooperative recognition of specific nucleobases using β-cyclodextrin-modified DNAs and fluorescent ligands on DNA and RNA scaffolds.

    Science.gov (United States)

    Futamura, Akika; Uemura, Asuka; Imoto, Takeshi; Kitamura, Yusuke; Matsuura, Hirotaka; Wang, Chun-Xia; Ichihashi, Toshiki; Sato, Yusuke; Teramae, Norio; Nishizawa, Seiichi; Ihara, Toshihiro

    2013-08-05

    We propose a binary fluorimetric method for DNA and RNA analysis by the combined use of two probes rationally designed to work cooperatively. One probe is an oligonucleotide (ODN) conjugate bearing a β-cyclodextrin (β-CyD). The other probe is a small reporter ligand, which comprises linked molecules of a nucleobase-specific heterocycle and an environment-sensitive fluorophore. The heterocycle of the reporter ligand recognizes a single nucleobase displayed in a gap on the target labeled with the conjugate and, at the same time, the fluorophore moiety forms a luminous inclusion complex with nearby β-CyD. Three reporter ligands, MNDS (naphthyridine-dansyl linked ligand), MNDB (naphthyridine-DBD), and DPDB (pyridine-DBD), were used for DNA and RNA probing with 3'-end or 5'-end modified β-CyD-ODN conjugates. For the DNA target, the β-CyD tethered to the 3'-end of the ODN facing into the gap interacted with the fluorophore sticking out into the major groove of the gap site (MNDS and DPDB). Meanwhile the β-CyD on the 5'-end of the ODN interacted with the fluorophore in the minor groove (MNDB and DPDB). The results obtained by this study could be a guideline for the design of binary DNA/RNA probe systems based on controlling the proximity of functional molecules.

  13. Rational design of 5-phenyl-3-isoxazolecarboxylic acid ethyl esters as growth inhibitors of Mycobacterium tuberculosis. a potent and selective series for further drug development.

    Science.gov (United States)

    Lilienkampf, Annamaria; Pieroni, Marco; Wan, Baojie; Wang, Yuehong; Franzblau, Scott G; Kozikowski, Alan P

    2010-01-28

    New antituberculosis (anti-TB) drugs are urgently needed to shorten the 6-12 month treatment regimen and especially to battle drug-resistant Mycobacterium tuberculosis (Mtb) strains. In this study, we have continued our efforts to develop isoxazole-based anti-TB compounds by applying rational drug design approach. The biological activity and the structure-activity relationships (SAR) for a designed series of 5-phenyl-3-isoxazolecarboxylic acid ethyl ester derived anti-TB compounds were investigated. Several compounds were found to exhibit nanomolar activity against the replicating bacteria (R-TB) and low micromolar activity against the nonreplicating bacteria (NRP-TB). The series showed excellent selectivity toward Mtb, and in general, no cytotoxicity was observed in Vero cells (IC(50) > 128 muM). Notably, selected compounds also retained their activity against isoniazid (INH), rifampin (RMP), and streptomycin (SM) resistant Mtb strains. Hence, benzyloxy, benzylamino, and phenoxy derivatives of 5-phenyl-3-isoxazolecarboxylic acid ethyl esters represent a highly potent, selective, and versatile series of anti-TB compounds and as such present attractive lead compounds for further TB drug development.

  14. Toward rational design of amines for CO2 capture: Substituent effect on kinetic process for the reaction of monoethanolamine with CO2.

    Science.gov (United States)

    Xie, Hongbin; Wang, Pan; He, Ning; Yang, Xianhai; Chen, Jingwen

    2015-11-01

    Amines have been considered as promising candidates for post-combustion CO2 capture. A mechanistic understanding for the chemical processes involved in the capture and release of CO2 is important for the rational design of amines. In this study, the structural effects of amines on the kinetic competition among three typical products (carbamates, carbamic acids and bicarbonate) from amines+CO2 were investigated, in contrast to previous thermodynamic studies to tune the reaction of amines with CO2 based on desirable reaction enthalpy and reaction stoichiometry. We used a quantum chemical method to calculate the activation energies (Ea) for the reactions of a range of substituted monoethanolamines with CO2 covering three pathways to the three products. The results indicate that the formation of carbamates is the most favorable, among the three considered products. In addition, we found that the Ea values for all pathways linearly correlate with pKa of amines, and more importantly, the kinetic competition between carbamate and bicarbonate absorption pathways varies with pKa of the amines, i.e. stronger basicity results in less difference in Ea. These results highlight the importance of the consideration of kinetic competition among different reaction pathways in amine design.

  15. A de novo NADPH generation pathway for improving lysine production of Corynebacterium glutamicum by rational design of the coenzyme specificity of glyceraldehyde 3-phosphate dehydrogenase.

    Science.gov (United States)

    Bommareddy, Rajesh Reddy; Chen, Zhen; Rappert, Sugima; Zeng, An-Ping

    2014-09-01

    Engineering the cofactor availability is a common strategy of metabolic engineering to improve the production of many industrially important compounds. In this work, a de novo NADPH generation pathway is proposed by altering the coenzyme specificity of a native NAD-dependent glyceraldehyde 3-phosphate dehydrogenase (GAPDH) to NADP, which consequently has the potential to produce additional NADPH in the glycolytic pathway. Specifically, the coenzyme specificity of GAPDH of Corynebacterium glutamicum is systematically manipulated by rational protein design and the effect of the manipulation for cellular metabolism and lysine production is evaluated. By a combinatorial modification of four key residues within the coenzyme binding sites, different GAPDH mutants with varied coenzyme specificity were constructed. While increasing the catalytic efficiency of GAPDH towards NADP enhanced lysine production in all of the tested mutants, the most significant improvement of lysine production (~60%) was achieved with the mutant showing similar preference towards both NAD and NADP. Metabolic flux analysis with (13)C isotope studies confirmed that there was no significant change of flux towards the pentose phosphate pathway and the increased lysine yield was mainly attributed to the NADPH generated by the mutated GAPDH. The present study highlights the importance of protein engineering as a key strategy in de novo pathway design and overproduction of desired products.

  16. Binding of small molecules at interface of protein-protein complex - A newer approach to rational drug design.

    Science.gov (United States)

    Gurung, A B; Bhattacharjee, A; Ajmal Ali, M; Al-Hemaid, F; Lee, Joongku

    2017-02-01

    Protein-protein interaction is a vital process which drives many important physiological processes in the cell and has also been implicated in several diseases. Though the protein-protein interaction network is quite complex but understanding its interacting partners using both in silico as well as molecular biology techniques can provide better insights for targeting such interactions. Targeting protein-protein interaction with small molecules is a challenging task because of druggability issues. Nevertheless, several studies on the kinetics as well as thermodynamic properties of protein-protein interactions have immensely contributed toward better understanding of the affinity of these complexes. But, more recent studies on hot spots and interface residues have opened up new avenues in the drug discovery process. This approach has been used in the design of hot spot based modulators targeting protein-protein interaction with the objective of normalizing such interactions.

  17. Rational design and chromatographic evaluation of histamine imprinted polymers optimised for solid-phase extraction of wine samples.

    Science.gov (United States)

    Basozabal, Itsaso; Gomez-Caballero, Alberto; Diaz-Diaz, Goretti; Guerreiro, António; Gilby, Stuart; Goicolea, M Aranzazu; Barrio, Ramón J

    2013-09-20

    This article reports on the computational design, development and application of a molecularly imprinted polymer (MIP) with specific affinity towards histamine. Computational modelling was used to screen a monomer library in order to select the monomers able to form the strongest complex with the target analyte. These were subsequently used for MIP synthesis by radical polymerisation initiated by UV. MIPs were then evaluated by liquid chromatography and solid phase extraction (SPE) and best MIP behaviour was observed when itaconic acid was used as functional monomer. Finally, after optimisation of the polymer composition, MIPs were used as adsorbents for SPE and clean-up of histamine in wine samples. The proposed histamine extraction method with the MIP-SPE cartridge was found to be reproducible (wine extracts. The described methodology is simple and fast and is suitable for the selective histamine extraction and its subsequent quantification by HPLC-DAD from complex matrices such as wine samples.

  18. Highly fluorinated comb-shaped copolymers as proton exchange membranes (PEMs): improving PEM properties through rational design

    Energy Technology Data Exchange (ETDEWEB)

    Norsten, T.B.; Guiver, M.D.; Murphy, J.; Ding, J. [Institute for Chemical Process and Environmental Technology, National Research Council of Canada, 1200 Montreal Road, Ottawa, ON K1A 0R6 (Canada); Astill, T.; Holdcroft, S. [Institute for Fuel Cell Innovation, National Research Council, 3250 East Mall, Vancouver, BC V6T 1W5 (Canada); Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6 (Canada); Navessin, T. [Institute for Fuel Cell Innovation, National Research Council, 3250 East Mall, Vancouver, BC V6T 1W5 (Canada); Frankamp, B.L.; Rotello, V.M. [Department of Chemistry, University of Massachusetts, Amherst, MA 01003 (United States)

    2006-09-18

    A new class of comb-shaped polymers for use as a proton conducting membrane is presented. The polymer is designed to combine the beneficial physical, chemical, and structural attributes of fluorinated Nafion-like materials with higher-temperature, polyaromatic-based polymer backbones. The comb-shaped polymer unites a rigid, polyaromatic, hydrophobic backbone with lengthy hydrophilic polymer side chains; this combination affords direct control over the polymer nanostructure within the membrane and results in distinct microphase separation between the opposing domains. The microphase separation serves to compartmentalize water into the hydrophilic polymer side chain domains, resulting in effective membrane water management and excellent proton conductivities. (Abstract Copyright [2006], Wiley Periodicals, Inc.)

  19. Synthesis and Evaluation of a Rationally Designed Click-Based Library for G-Quadruplex Selective DNA Photocleavage

    Directory of Open Access Journals (Sweden)

    Dominic McBrayer

    2015-09-01

    Full Text Available DNA containing repeating G-rich sequences can adopt higher-order structures known as G-quadruplexes (G4. These structures are believed to form within telomeres and the promoter regions of some genes, particularly in a number of proto-oncogenes, where they may play a role in regulating transcription. Alternatively, G4 DNA may act as a barrier to replication. To investigate these potential biological roles, probes that combine highly selective G4 DNA targeting with photocleavage activity can allow temporal detection of G4 DNA, providing opportunities to obtain novel insights about the biological roles of G4 DNA. We have designed, synthesized, and screened a small library of potential selective G-quadruplex DNA photocleavage agents incorporating the G-quadruplex targeting moiety of 360A with known photocleavage groups linked via “click” chemistry.