Sample records for biomolecular structural determinations

  1. Synthesis and biosynthesis of {sup 13}C-, {sup 15}N-labeled deoxynucleosides useful for biomolecular structural determinations

    Energy Technology Data Exchange (ETDEWEB)

    Ashburn, D.A.; Garcia, K.; Hanners, J.L.; Silks, L.A. III; Unkefer, C.J. [Los Alamos National Laboratory, NM (United States)


    Currently, there is a great emphasis on elucidating the structure, function, and dynamics of DNA. Much of the research involved in this study uses nuclear magnetic resonance (NMR) spectroscopy. Effective use of NMR spectroscopy for DNA molecules with mw > 10,000 requires stable isotope enrichment. We present strategies for site-specific isotopic labeling of the purine bases adenosine and guanosine and the biosynthesis of (U-{sup 13}C, {sup 15}N) DNA from methylotropic bacteria. With commercially available 6-chloropurine, an effective two-step route leads to 2{prime}-deoxy-(amino-{sup 15}N)adenosine (dA). The resulting d(amino-{sup 15}N)A is used in a series of reactions to synthesize 2{prime}-deoxy-(2-{sup 13}C,1,amino-{sup 15}N{sub 2})guanosine or any combination thereof. An improved biosynthesis of labeled DNA has been accomplished using Methylobacterium extorquens AS1. Each liter of growth medium contains 4 g of methanol to yield 1 g of lyophilized cells. As much as 200 mg of RNA per liter of culture has been obtained. We are currently developing large-scale isolation protocols. General synthetic pathways to oligomeric DNA will be presented.

  2. From dynamics to structure and function of model biomolecular systems

    NARCIS (Netherlands)

    Fontaine-Vive-Curtaz, F.


    The purpose of this thesis was to extend recent works on structure and dynamics of hydrogen bonded crystals to model biomolecular systems and biological processes. The tools that we have used are neutron scattering (NS) and density functional theory (DFT) and force field (FF) based simulation method

  3. Computational and theoretical aspects of biomolecular structure and dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Garcia, A.E.; Berendzen, J.; Catasti, P., Chen, X. [and others


    This is the final report for a project that sought to evaluate and develop theoretical, and computational bases for designing, performing, and analyzing experimental studies in structural biology. Simulations of large biomolecular systems in solution, hydrophobic interactions, and quantum chemical calculations for large systems have been performed. We have developed a code that implements the Fast Multipole Algorithm (FMA) that scales linearly in the number of particles simulated in a large system. New methods have been developed for the analysis of multidimensional NMR data in order to obtain high resolution atomic structures. These methods have been applied to the study of DNA sequences in the human centromere, sequences linked to genetic diseases, and the dynamics and structure of myoglobin.

  4. Structure and Interactions of Isolated Biomolecular Building Blocks. (United States)

    de Vries, Mattanjah


    We investigate biomolecular building blocks and their clusters with each other and with water on a single molecular level. The motivation is the need to distinguish between intrinsic molecular properties and those that result from the biological environment. This is achieved by a combination of laser desorption and jet cooling, applied to aromatic amino acids, small peptides containing those, nucleobases and nucleosides. This approach is coupled with a number of laser spectroscopic techniques, including resonant multi-photon ionization, spectral hole burning and infra-red ion-dip spectroscopy. We will discuss examples illustrating how information can be obtained on spatial structure of individual biomolecules, including peptide conformations and details of DNA base-pairing.

  5. Computer programming and biomolecular structure studies: A step beyond internet bioinformatics. (United States)

    Likić, Vladimir A


    This article describes the experience of teaching structural bioinformatics to third year undergraduate students in a subject titled Biomolecular Structure and Bioinformatics. Students were introduced to computer programming and used this knowledge in a practical application as an alternative to the well established Internet bioinformatics approach that relies on access to the Internet and biological databases. This was an ambitious approach considering that the students mostly had a biological background. There were also time constraints of eight lectures in total and two accompanying practical sessions. The main challenge was that students had to be introduced to computer programming from a beginner level and in a short time provided with enough knowledge to independently solve a simple bioinformatics problem. This was accomplished with a problem directly relevant to the rest of the subject, concerned with the structure-function relationships and experimental techniques for the determination of macromolecular structure.

  6. Retroactivity in the Context of Modularly Structured Biomolecular Systems (United States)

    Pantoja-Hernández, Libertad; Martínez-García, Juan Carlos


    Synthetic biology has intensively promoted the technical implementation of modular strategies in the fabrication of biological devices. Modules are considered as networks of reactions. The behavior displayed by biomolecular systems results from the information processes carried out by the interconnection of the involved modules. However, in natural systems, module wiring is not a free-of-charge process; as a consequence of interconnection, a reactive phenomenon called retroactivity emerges. This phenomenon is characterized by signals that propagate from downstream modules (the modules that receive the incoming signals upon interconnection) to upstream ones (the modules that send the signals upon interconnection). Such retroactivity signals, depending of their strength, may change and sometimes even disrupt the behavior of modular biomolecular systems. Thus, analysis of retroactivity effects in natural biological and biosynthetic systems is crucial to achieve a deeper understanding of how this interconnection between functionally characterized modules takes place and how it impacts the overall behavior of the involved cell. By discussing the modules interconnection in natural and synthetic biomolecular systems, we propose that such systems should be considered as quasi-modular. PMID:26137457

  7. Computer Programming and Biomolecular Structure Studies: A Step beyond Internet Bioinformatics (United States)

    Likic, Vladimir A.


    This article describes the experience of teaching structural bioinformatics to third year undergraduate students in a subject titled "Biomolecular Structure and Bioinformatics." Students were introduced to computer programming and used this knowledge in a practical application as an alternative to the well established Internet bioinformatics…

  8. 核磁共振、X射线小角散射以及计算机模拟相结合构建生物大分子复合物的结构模型%Determining Structural Models of Biomolecular Complexes Integrating Nuclear Magnetic Resonance, Small-Angle X-ray Scattering and Computational Simulations

    Institute of Scientific and Technical Information of China (English)

    彭俊辉; 赵德彪; 文彬; 张志勇


    Structural biology has been paying more attention on biomolecular complexes over the past decades, since they are crucial for many biological processes. Among these techniques for structural determination, nuclear magnetic resonance (NMR) has its advantage when dealing with biomolecules with high flexibility in solution. Small-angle X-ray scattering (SAXS) is a very important complementary technique that provides information on global shape of biomolecules. For biomolecular complexes, it can be much easier to determine atomic structures of individual subunits through NMR. In addition, NMR can also provide other structural information, such as the interface and orientations between subunits, and long range distance and angular restraints. Therefore, to construct structural models of biomolecular complexes, it would be very appropriate to combine experimental restraints obtained through NMR and low-resolution shape information from SAXS by utilizing computational tools, which is the main topic of this review.%近年来,结构生物学研究越来越注重生物大分子复合物的解析,因为许多重要生物学过程都离不开复合物的参与.溶液核磁共振是目前重要的结构解析方法之一.X射线小角散射(SAXS)作为一种新的结构生物学实验手段,近年来发展迅速.SAXS 能提供生物大分子复合物的较低分辨率结构信息,而核磁共振能解析复合物中各个亚基的原子分辨率结构.此外,通过核磁共振还能得到亚基之间的界面、取向以及距离信息.因此近年来通过计算机模拟,整合核磁共振和 SAXS 不同分辨率的结构信息,可以用来搭建生物大分子复合物的结构模型.该综述重点介绍这方面的研究进展.

  9. Conformational thermodynamics guided structural reconstruction of biomolecular fragments. (United States)

    Sikdar, Samapan; Chakrabarti, J; Ghosh, Mahua


    Computational prediction of structure for macromolecular fragments is a formidable challenge. Here we show that the differences in conformational thermodynamics, computed using the equilibrium distribution of dihedral angles from molecular dynamics simulation, can identify the better model for the missing residues in the metal ion free (apo) skeletal muscle Troponin C (TnC). We use the model to understand Troponin I interaction with calcium (Ca(2+)) ion bound TnC. Our method to compare conformational thermodynamics between different models can be easily generalized to any macromolecule to understand the structure and function even if experimental structures are not resolved.

  10. Biomolecular Deuteration for Neutron Structural Biology and Dynamics. (United States)

    Haertlein, Michael; Moulin, Martine; Devos, Juliette M; Laux, Valerie; Dunne, Orla; Forsyth, V Trevor


    Neutron scattering studies provide important information in structural biology that is not accessible using other approaches. The uniqueness of the technique, and its complementarity with X-ray scattering, is greatest when full use is made of deuterium labeling. The ability to produce tailor-made deuterium-labeled biological macromolecules allows neutron studies involving solution scattering, crystallography, reflection, and dynamics to be optimized in a manner that has major impact on the scope, quality, and throughput of work in these areas. Deuteration facilities have now been developed at many neutron centres throughout the world; these are having a crucial effect on neutron studies in the life sciences and on biologically related studies in soft matter. This chapter describes methods that have been developed for the efficient production of deuterium-labeled samples for a wide range of neutron scattering applications. Examples are given that illustrate the use of these samples for each of the main techniques. Perspectives for biological deuterium labeling are discussed in relation to developments at current facilities and those that are planned in the future.

  11. Stable isotope applications in biomolecular structure and mechanisms. A meeting to bring together producers and users of stable-isotope-labeled compounds to assess current and future needs

    Energy Technology Data Exchange (ETDEWEB)

    Trewhella, J.; Cross, T.A.; Unkefer, C.J. [eds.


    Knowledge of biomolecular structure is a prerequisite for understanding biomolecular function, and stable isotopes play an increasingly important role in structure determination of biological molecules. The first Conference on Stable Isotope Applications in Biomolecular Structure and Mechanisms was held in Santa Fe, New Mexico, March 27--31, 1994. More than 120 participants from 8 countries and 44 institutions reviewed significant developments, discussed the most promising applications for stable isotopes, and addressed future needs and challenges. Participants focused on applications of stable isotopes for studies of the structure and function of proteins, peptides, RNA, and DNA. Recent advances in NMR techniques neutron scattering, EPR, and vibrational spectroscopy were highlighted in addition to the production and synthesis of labeled compounds. This volume includes invited speaker and poster presentations as well as a set of reports from discussion panels that focused on the needs of the scientific community and the potential roles of private industry, the National Stable Isotope Resource, and the National High Magnetic Field Laboratory in serving those needs. This is the leading abstract. Individual papers are processed separately for the database.

  12. iGNM 2.0: the Gaussian network model database for biomolecular structural dynamics. (United States)

    Li, Hongchun; Chang, Yuan-Yu; Yang, Lee-Wei; Bahar, Ivet


    Gaussian network model (GNM) is a simple yet powerful model for investigating the dynamics of proteins and their complexes. GNM analysis became a broadly used method for assessing the conformational dynamics of biomolecular structures with the development of a user-friendly interface and database, iGNM, in 2005. We present here an updated version, iGNM 2.0, which covers more than 95% of the structures currently available in the Protein Data Bank (PDB). Advanced search and visualization capabilities, both 2D and 3D, permit users to retrieve information on inter-residue and inter-domain cross-correlations, cooperative modes of motion, the location of hinge sites and energy localization spots. The ability of iGNM 2.0 to provide structural dynamics data on the large majority of PDB structures and, in particular, on their biological assemblies makes it a useful resource for establishing the bridge between structure, dynamics and function.

  13. Potential-of-mean-force description of ionic interactions and structural hydration in biomolecular systems

    Energy Technology Data Exchange (ETDEWEB)

    Hummer, G.; Garcia, A.E. [Los Alamos National Lab., NM (United States). Theoretical Biology and Biophysics Group; Soumpasis, D.M. [Max-Planck-Inst for Biophysical Chemistry, Goettingen (Germany). Biocomputation Group


    To understand the functioning of living organisms on a molecular level, it is crucial to dissect the intricate interplay of the immense number of biological molecules. Most of the biochemical processes in cells occur in a liquid environment formed mainly by water and ions. This solvent environment plays an important role in biological systems. The potential-of-mean-force (PMF) formalism attempts to describe quantitatively the interactions of the solvent with biological macromolecules on the basis of an approximate statistical-mechanical representation. At its current status of development, it deals with ionic effects on the biomolecular structure and with the structural hydration of biomolecules. The underlying idea of the PMF formalism is to identify the dominant sources of interactions and incorporate these interactions into the theoretical formalism using PMF`s (or particle correlation functions) extracted from bulk-liquid systems. In the following, the authors shall briefly outline the statistical-mechanical foundation of the PMF formalism and introduce the PMF expansion formalism, which is intimately linked to superposition approximations for higher-order particle correlation functions. The authors shall then sketch applications, which describe the effects of the ionic environment on nucleic-acid structure. Finally, the authors shall present the more recent extension of the PMF idea to describe quantitatively the structural hydration of biomolecules. Results for the interface of ice and water and for the hydration of deoxyribonucleic acid (DNA) will be discussed.

  14. Modeling Structural Dynamics of Biomolecular Complexes by Coarse-Grained Molecular Simulations. (United States)

    Takada, Shoji; Kanada, Ryo; Tan, Cheng; Terakawa, Tsuyoshi; Li, Wenfei; Kenzaki, Hiroo


    Due to hierarchic nature of biomolecular systems, their computational modeling calls for multiscale approaches, in which coarse-grained (CG) simulations are used to address long-time dynamics of large systems. Here, we review recent developments and applications of CG modeling methods, focusing on our methods primarily for proteins, DNA, and their complexes. These methods have been implemented in the CG biomolecular simulator, CafeMol. Our CG model has resolution such that ∼10 non-hydrogen atoms are grouped into one CG particle on average. For proteins, each amino acid is represented by one CG particle. For DNA, one nucleotide is simplified by three CG particles, representing sugar, phosphate, and base. The protein modeling is based on the idea that proteins have a globally funnel-like energy landscape, which is encoded in the structure-based potential energy function. We first describe two representative minimal models of proteins, called the elastic network model and the classic Go̅ model. We then present a more elaborate protein model, which extends the minimal model to incorporate sequence and context dependent local flexibility and nonlocal contacts. For DNA, we describe a model developed by de Pablo's group that was tuned to well reproduce sequence-dependent structural and thermodynamic experimental data for single- and double-stranded DNAs. Protein-DNA interactions are modeled either by the structure-based term for specific cases or by electrostatic and excluded volume terms for nonspecific cases. We also discuss the time scale mapping in CG molecular dynamics simulations. While the apparent single time step of our CGMD is about 10 times larger than that in the fully atomistic molecular dynamics for small-scale dynamics, large-scale motions can be further accelerated by two-orders of magnitude with the use of CG model and a low friction constant in Langevin dynamics. Next, we present four examples of applications. First, the classic Go̅ model was used to

  15. Computational methods to study the structure and dynamics of biomolecules and biomolecular processes from bioinformatics to molecular quantum mechanics

    CERN Document Server


    Since the second half of the 20th century machine computations have played a critical role in science and engineering. Computer-based techniques have become especially important in molecular biology, since they often represent the only viable way to gain insights into the behavior of a biological system as a whole. The complexity of biological systems, which usually needs to be analyzed on different time- and size-scales and with different levels of accuracy, requires the application of different approaches, ranging from comparative analysis of sequences and structural databases, to the analysis of networks of interdependence between cell components and processes, through coarse-grained modeling to atomically detailed simulations, and finally to molecular quantum mechanics. This book provides a comprehensive overview of modern computer-based techniques for computing the structure, properties and dynamics of biomolecules and biomolecular processes. The twenty-two chapters, written by scientists from all over t...

  16. Variational Methods for Biomolecular Modeling

    CERN Document Server

    Wei, Guo-Wei


    Structure, function and dynamics of many biomolecular systems can be characterized by the energetic variational principle and the corresponding systems of partial differential equations (PDEs). This principle allows us to focus on the identification of essential energetic components, the optimal parametrization of energies, and the efficient computational implementation of energy variation or minimization. Given the fact that complex biomolecular systems are structurally non-uniform and their interactions occur through contact interfaces, their free energies are associated with various interfaces as well, such as solute-solvent interface, molecular binding interface, lipid domain interface, and membrane surfaces. This fact motivates the inclusion of interface geometry, particular its curvatures, to the parametrization of free energies. Applications of such interface geometry based energetic variational principles are illustrated through three concrete topics: the multiscale modeling of biomolecular electrosta...

  17. Integrative NMR for biomolecular research. (United States)

    Lee, Woonghee; Cornilescu, Gabriel; Dashti, Hesam; Eghbalnia, Hamid R; Tonelli, Marco; Westler, William M; Butcher, Samuel E; Henzler-Wildman, Katherine A; Markley, John L


    NMR spectroscopy is a powerful technique for determining structural and functional features of biomolecules in physiological solution as well as for observing their intermolecular interactions in real-time. However, complex steps associated with its practice have made the approach daunting for non-specialists. We introduce an NMR platform that makes biomolecular NMR spectroscopy much more accessible by integrating tools, databases, web services, and video tutorials that can be launched by simple installation of NMRFAM software packages or using a cross-platform virtual machine that can be run on any standard laptop or desktop computer. The software package can be downloaded freely from the NMRFAM software download page ( ), and detailed instructions are available from the Integrative NMR Video Tutorial page ( ).

  18. Biomolecular EPR spectroscopy

    CERN Document Server

    Hagen, Wilfred Raymond


    Comprehensive, Up-to-Date Coverage of Spectroscopy Theory and its Applications to Biological SystemsAlthough a multitude of books have been published about spectroscopy, most of them only occasionally refer to biological systems and the specific problems of biomolecular EPR (bioEPR). Biomolecular EPR Spectroscopy provides a practical introduction to bioEPR and demonstrates how this remarkable tool allows researchers to delve into the structural, functional, and analytical analysis of paramagnetic molecules found in the biochemistry of all species on the planet. A Must-Have Reference in an Intrinsically Multidisciplinary FieldThis authoritative reference seamlessly covers all important bioEPR applications, including low-spin and high-spin metalloproteins, spin traps and spin lables, interaction between active sites, and redox systems. It is loaded with practical tricks as well as do's and don'ts that are based on the author's 30 years of experience in the field. The book also comes with an unprecedented set of...

  19. Proteopedia: Exciting Advances in the 3D Encyclopedia of Biomolecular Structure (United States)

    Prilusky, Jaime; Hodis, Eran; Sussman, Joel L.

    Proteopedia is a collaborative, 3D web-encyclopedia of protein, nucleic acid and other structures. Proteopedia ( ) presents 3D biomolecule structures in a broadly accessible manner to a diverse scientific audience through easy-to-use molecular visualization tools integrated into a wiki environment that anyone with a user account can edit. We describe recent advances in the web resource in the areas of content and software. In terms of content, we describe a large growth in user-added content as well as improvements in automatically-generated content for all PDB entry pages in the resource. In terms of software, we describe new features ranging from the capability to create pages hidden from public view to the capability to export pages for offline viewing. New software features also include an improved file-handling system and availability of biological assemblies of protein structures alongside their asymmetric units.

  20. [Advances in biomolecular machine: methane monooxygenases]. (United States)

    Lu, Jixue; Wang, Shizhen; Fang, Baishan


    Methane monooxygenases (MMO), regarded as "an amazing biomolecular machine", catalyze the oxidation of methane to methanol under aerobic conditions. MMO catalyze the oxidation of methane elaborately, which is a novel way to catalyze methane to methanol. Furthermore, MMO can inspire the biomolecular machine design. In this review, we introduced MMO including structure, gene and catalytic mechanism. The history and the taxonomy of MMO were also introduced.

  1. A guide to the visual analysis and communication of biomolecular structural data. (United States)

    Johnson, Graham T; Hertig, Samuel


    Biologists regularly face an increasingly difficult task - to effectively communicate bigger and more complex structural data using an ever-expanding suite of visualization tools. Whether presenting results to peers or educating an outreach audience, a scientist can achieve maximal impact with minimal production time by systematically identifying an audience's needs, planning solutions from a variety of visual communication techniques and then applying the most appropriate software tools. A guide to available resources that range from software tools to professional illustrators can help researchers to generate better figures and presentations tailored to any audience's needs, and enable artistically inclined scientists to create captivating outreach imagery.

  2. Stability of Complex Biomolecular Structures: Vander Waals, Hydrogen Bond Cooperativity, and Nuclear Quantum Effects

    CERN Document Server

    Rossi, Mariana; Michaelides, Angelos


    Biomolecules are complex systems stabilized by a delicate balance of weak interactions, making it important to assess all energetic contributions in an accurate manner. However, it is a priori unclear which contributions make more of an impact. Here, we examine stacked polyglutamine (polyQ) strands, a peptide repeat often found in amyloid aggregates. We investigate the role of hydrogen bond (HB) cooperativity, van der Waals (vdW) dispersion interactions, and quantum contributions to free energies, including anharmonicities through density functional theory and ab initio path integral simulations. Of these various factors, we find that the largest impact on structural stabilization comes from vdW interactions. HB cooperativity is the second largest contribution as the size of the stacked chain grows. Competing nuclear quantum effects make the net quantum contribution small but very sensitive to anharmonicities, vdW, and the number of HBs. Our results suggest that a reliable treatment of these systems can only ...

  3. H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations. (United States)

    Anandakrishnan, Ramu; Aguilar, Boris; Onufriev, Alexey V


    The accuracy of atomistic biomolecular modeling and simulation studies depend on the accuracy of the input structures. Preparing these structures for an atomistic modeling task, such as molecular dynamics (MD) simulation, can involve the use of a variety of different tools for: correcting errors, adding missing atoms, filling valences with hydrogens, predicting pK values for titratable amino acids, assigning predefined partial charges and radii to all atoms, and generating force field parameter/topology files for MD. Identifying, installing and effectively using the appropriate tools for each of these tasks can be difficult for novice and time-consuming for experienced users. H++ ( is a free open-source web server that automates the above key steps in the preparation of biomolecular structures for molecular modeling and simulations. H++ also performs extensive error and consistency checking, providing error/warning messages together with the suggested corrections. In addition to numerous minor improvements, the latest version of H++ includes several new capabilities and options: fix erroneous (flipped) side chain conformations for HIS, GLN and ASN, include a ligand in the input structure, process nucleic acid structures and generate a solvent box with specified number of common ions for explicit solvent MD.

  4. Physics at the biomolecular interface fundamentals for molecular targeted therapy

    CERN Document Server

    Fernández, Ariel


    This book focuses primarily on the role of interfacial forces in understanding biological phenomena at the molecular scale. By providing a suitable statistical mechanical apparatus to handle the biomolecular interface, the book becomes uniquely positioned to address core problems in molecular biophysics. It highlights the importance of interfacial tension in delineating a solution to the protein folding problem, in unravelling the physico-chemical basis of enzyme catalysis and protein associations, and in rationally designing molecular targeted therapies. Thus grounded in fundamental science, the book develops a powerful technological platform for drug discovery, while it is set to inspire scientists at any level in their careers determined to address the major challenges in molecular biophysics. The acknowledgment of how exquisitely the structure and dynamics of proteins and their aqueous environment are related attests to the overdue recognition that biomolecular phenomena cannot be effectively understood w...

  5. Programming in biomolecular computation

    DEFF Research Database (Denmark)

    Hartmann, Lars Røeboe; Jones, Neil; Simonsen, Jakob Grue


    Our goal is to provide a top-down approach to biomolecular computation. In spite of widespread discussion about connections between biology and computation, one question seems notable by its absence: Where are the programs? We identify a number of common features in programming that seem conspicu...

  6. What determines family structure?


    Blau, David M.; van der Klaauw, Wilbert


    We estimate the effects of policy and labor market variables on the fertility, union formation and dissolution, type of union (cohabiting versus married), and partner choices of the NLSY79 cohort of women. These demographic behaviors interact to determine the family structure experienced by the children of these women: living with the biological mother and the married or cohabiting biological father, a married or cohabiting step father, or no man. We find that the average wage rates available...

  7. Dipolar recoupling NMR of biomolecular self-assemblies : determining inter- and intrastrand distances in fibrilized Alzheimer's {betta}-amyloid peptide.

    Energy Technology Data Exchange (ETDEWEB)

    Gregory, D. M.; Senzinger, T. L. S.; Burkoth, T. S.; Miller-Auer, H.; Lynn, D. G.; Meredith, S. C.; Botto, R. E.; Chemistry; Univ. of Chicago


    data, taken together, refine the DRAWS method, and demonstrate its precision and utility in obtaining high resolution structural data in complex biomolecular aggregates such as A{beta}.

  8. A statistical mechanical description of biomolecular hydration

    Energy Technology Data Exchange (ETDEWEB)



    We present an efficient and accurate theoretical description of the structural hydration of biological macromolecules. The hydration of molecules of almost arbitrary size (tRNA, antibody-antigen complexes, photosynthetic reaction centre) can be studied in solution and in the crystal environment. The biomolecular structure obtained from x-ray crystallography, NMR, or modeling is required as input information. The structural arrangement of water molecules near a biomolecular surface is represented by the local water density analogous to the corresponding electron density in an x-ray diffraction experiment. The water-density distribution is approximated in terms of two- and three-particle correlation functions of solute atoms with water using a potentials-of-mean-force expansion.

  9. Programming in biomolecular computation

    DEFF Research Database (Denmark)

    Hartmann, Lars Røeboe; Jones, Neil; Simonsen, Jakob Grue


    executable, but are also compilable and interpretable. It is universal: all computable functions can be computed (in natural ways and without arcane encodings of data and algorithm); it is also uniform: new “hardware” is not needed to solve new problems; and (last but not least) it is Turing complete......Our goal is to provide a top-down approach to biomolecular computation. In spite of widespread discussion about connections between biology and computation, one question seems notable by its absence: Where are the programs? We introduce a model of computation that is evidently programmable......, by programs reminiscent of low-level computer machine code; and at the same time biologically plausible: its functioning is defined by a single and relatively small set of chemical-like reaction rules. Further properties: the model is stored-program: programs are the same as data, so programs are not only...

  10. Programming in Biomolecular Computation

    DEFF Research Database (Denmark)

    Hartmann, Lars; Jones, Neil; Simonsen, Jakob Grue


    Our goal is to provide a top-down approach to biomolecular computation. In spite of widespread discussion about connections between biology and computation, one question seems notable by its absence: Where are the programs? We introduce a model of computation that is evidently programmable......, by programs reminiscent of low-level computer machine code; and at the same time biologically plausible: its functioning is defined by a single and relatively small set of chemical-like reaction rules. Further properties: the model is stored-program: programs are the same as data, so programs are not only...... in a strong sense: a universal algorithm exists, that is able to execute any program, and is not asymptotically inefficient. A prototype model has been implemented (for now in silico on a conventional computer). This work opens new perspectives on just how computation may be specified at the biological level....

  11. Charge transport through biomolecular wires in a solvent: bridging molecular dynamics and model Hamiltonian approaches. (United States)

    Gutiérrez, R; Caetano, R A; Woiczikowski, B P; Kubar, T; Elstner, M; Cuniberti, G


    We present a hybrid method based on a combination of classical molecular dynamics simulations, quantum-chemical calculations, and a model Hamiltonian approach to describe charge transport through biomolecular wires with variable lengths in presence of a solvent. The core of our approach consists in a mapping of the biomolecular electronic structure, as obtained from density-functional based tight-binding calculations of molecular structures along molecular dynamics trajectories, onto a low-dimensional model Hamiltonian including the coupling to a dissipative bosonic environment. The latter encodes fluctuation effects arising from the solvent and from the molecular conformational dynamics. We apply this approach to the case of pG-pC and pA-pT DNA oligomers as paradigmatic cases and show that the DNA conformational fluctuations are essential in determining and supporting charge transport.

  12. Biomolecular electrostatics and solvation: a computational perspective. (United States)

    Ren, Pengyu; Chun, Jaehun; Thomas, Dennis G; Schnieders, Michael J; Marucho, Marcelo; Zhang, Jiajing; Baker, Nathan A


    An understanding of molecular interactions is essential for insight into biological systems at the molecular scale. Among the various components of molecular interactions, electrostatics are of special importance because of their long-range nature and their influence on polar or charged molecules, including water, aqueous ions, proteins, nucleic acids, carbohydrates, and membrane lipids. In particular, robust models of electrostatic interactions are essential for understanding the solvation properties of biomolecules and the effects of solvation upon biomolecular folding, binding, enzyme catalysis, and dynamics. Electrostatics, therefore, are of central importance to understanding biomolecular structure and modeling interactions within and among biological molecules. This review discusses the solvation of biomolecules with a computational biophysics view toward describing the phenomenon. While our main focus lies on the computational aspect of the models, we provide an overview of the basic elements of biomolecular solvation (e.g. solvent structure, polarization, ion binding, and non-polar behavior) in order to provide a background to understand the different types of solvation models.

  13. Quantitative characterization of biomolecular assemblies and interactions using atomic force microscopy. (United States)

    Yang, Yong; Wang, Hong; Erie, Dorothy A


    Atomic force microscopy (AFM) has been applied in many biological investigations in the past 15 years. This review focuses on the application of AFM for quantitatively characterizing the structural and thermodynamic properties of protein-protein and protein-nucleic acid complexes. AFM can be used to determine the stoichiometries and association constants of multiprotein assemblies and to quantify changes in conformations of proteins and protein-nucleic acid complexes. In addition, AFM in solution permits the observation of the dynamic properties of biomolecular complexes and the measurement of intermolecular forces between biomolecules. Recent advances in cryogenic AFM, AFM on two-dimensional crystals, carbon nanotube probes, solution imaging, high-speed AFM, and manipulation capabilities enhance these applications by improving AFM resolution and the dynamic and operative capabilities of the AFM. These developments make AFM a powerful tool for investigating the biomolecular assemblies and interactions that govern gene regulation.

  14. Grid computing and biomolecular simulation. (United States)

    Woods, Christopher J; Ng, Muan Hong; Johnston, Steven; Murdock, Stuart E; Wu, Bing; Tai, Kaihsu; Fangohr, Hans; Jeffreys, Paul; Cox, Simon; Frey, Jeremy G; Sansom, Mark S P; Essex, Jonathan W


    Biomolecular computer simulations are now widely used not only in an academic setting to understand the fundamental role of molecular dynamics on biological function, but also in the industrial context to assist in drug design. In this paper, two applications of Grid computing to this area will be outlined. The first, involving the coupling of distributed computing resources to dedicated Beowulf clusters, is targeted at simulating protein conformational change using the Replica Exchange methodology. In the second, the rationale and design of a database of biomolecular simulation trajectories is described. Both applications illustrate the increasingly important role modern computational methods are playing in the life sciences.

  15. The HADDOCK web server for data-driven biomolecular docking

    NARCIS (Netherlands)

    de Vries, S.J.; van Dijk, M.; Bonvin, A.M.J.J.


    Computational docking is the prediction or modeling of the three-dimensional structure of a biomolecular complex, starting from the structures of the individual molecules in their free, unbound form. HADDOC K is a popular docking program that takes a datadriven approach to docking, with support for

  16. Azurin for Biomolecular Electronics: a Reliability Study (United States)

    Bramanti, Alessandro; Pompa, Pier Paolo; Maruccio, Giuseppe; Calabi, Franco; Arima, Valentina; Cingolani, Roberto; Corni, Stefano; Di Felice, Rosa; De Rienzo, Francesca; Rinaldi, Ross


    The metalloprotein azurin, used in biomolecular electronics, is investigated with respect to its resilience to high electric fields and ambient conditions, which are crucial reliability issues. Concerning the effect of electric fields, two models of different complexity agree indicating an unexpectedly high robustness. Experiments in device-like conditions confirm that no structural modifications occur, according to fluorescence spectra, even after a 40-min exposure to tens of MV/m. Ageing is then investigated experimentally, at ambient conditions and without field, over several days. Only a small conformational rearrangement is observed in the first tens of hours, followed by an equilibrium state.

  17. Nanoarchitectonics of biomolecular assemblies for functional applications (United States)

    Avinash, M. B.; Govindaraju, T.


    The stringent processes of natural selection and evolution have enabled extraordinary structure-function properties of biomolecules. Specifically, the archetypal designs of biomolecules, such as amino acids, nucleobases, carbohydrates and lipids amongst others, encode unparalleled information, selectivity and specificity. The integration of biomolecules either with functional molecules or with an embodied functionality ensures an eclectic approach for novel and advanced nanotechnological applications ranging from electronics to biomedicine, besides bright prospects in systems chemistry and synthetic biology. Given this intriguing scenario, our feature article intends to shed light on the emerging field of functional biomolecular engineering.

  18. Structural determination of argon trimer

    Directory of Open Access Journals (Sweden)

    Xiguo Xie


    Full Text Available Rare gas clusters are model systems to investigate structural properties at finite size. However, their structures are difficult to be determined with available experimental techniques because of the strong coupling between the vibration and the rotation. Here we experimentally investigated multiple ionization and fragmentation dynamics of argon trimer by ultrashort intense laser fields and reconstructed their structures with Coulomb explosion technique. The measured structure distribution was compared with our finite-temperature ab initio calculations and the discrepancy was discussed. The present study provides a guidance for the development of theoretical methods for exploring the geometric structure of rare gas clusters.

  19. The biomolecular corona of nanoparticles in circulating biological media (United States)

    Pozzi, D.; Caracciolo, G.; Digiacomo, L.; Colapicchioni, V.; Palchetti, S.; Capriotti, A. L.; Cavaliere, C.; Zenezini Chiozzi, R.; Puglisi, A.; Laganà, A.


    When nanoparticles come into contact with biological media, they are covered by a biomolecular `corona', which confers a new identity to the particles. In all the studies reported so far nanoparticles are incubated with isolated plasma or serum that are used as a model for protein adsorption. Anyway, bodily fluids are dynamic in nature so the question arises on whether the incubation protocol, i.e. dynamic vs. static incubation, could affect the composition and structure of the biomolecular corona. Here we let multicomponent liposomes interact with fetal bovine serum (FBS) both statically and dynamically, i.e. in contact with circulating FBS (~40 cm s-1). The structure and composition of the liposome-protein corona, as determined by dynamic light scattering, electrophoretic light scattering and liquid chromatography tandem mass spectrometry, were found to be dependent on the incubation protocol. Specifically, following dynamic exposure to FBS, multicomponent liposomes were less enriched in complement proteins and appreciably more enriched in apolipoproteins and acute phase proteins (e.g. alpha-1-antitrypsin and inter-alpha-trypsin inhibitor heavy chain H3) that are involved in relevant interactions between nanoparticles and living systems. Supported by our results, we speculate that efficient predictive modeling of nanoparticle behavior in vivo will require accurate knowledge of nanoparticle-specific protein fingerprints in circulating biological media.When nanoparticles come into contact with biological media, they are covered by a biomolecular `corona', which confers a new identity to the particles. In all the studies reported so far nanoparticles are incubated with isolated plasma or serum that are used as a model for protein adsorption. Anyway, bodily fluids are dynamic in nature so the question arises on whether the incubation protocol, i.e. dynamic vs. static incubation, could affect the composition and structure of the biomolecular corona. Here we let

  20. Determinants and Polynomial Root Structure (United States)

    De Pillis, L. G.


    A little known property of determinants is developed in a manner accessible to beginning undergraduates in linear algebra. Using the language of matrix theory, a classical result by Sylvester that describes when two polynomials have a common root is recaptured. Among results concerning the structure of polynomial roots, polynomials with pairs of…

  1. Biomolecular rods and tubes in nanotechnology (United States)

    Bittner, Alexander M.


    Biomolecules are vitally important elements in nanoscale science and also in future nanotechnology. Their shape and their chemical and physical functionality can give them a big advantage over inorganic and organic substances. While this becomes most obvious in proteins and peptides, with their complicated, but easily controlled chemistry, other biomolecular substances such as DNA, lipids and carbohydrates can also be important. In this review, the emphasis is on one-dimensional molecules and on molecules that self-assemble into linear structures, and on their potential applications. An important aspect is that biomolecules can act as templates, i.e. their shape and chemical properties can be employed to arrange inorganic substances such as metals or metal compounds on the nanometre scale. In particular, rod- and tube-like nanostructures can show physical properties that are different from those of the bulk material, and thus these structures are likely to be a basis for new technology.

  2. Differential geometry-based solvation and electrolyte transport models for biomolecular modeling: a review


    Wei, Guo Wei; Baker, Nathan A.


    This chapter reviews the differential geometry-based solvation and electrolyte transport for biomolecular solvation that have been developed over the past decade. A key component of these methods is the differential geometry of surfaces theory, as applied to the solvent-solute boundary. In these approaches, the solvent-solute boundary is determined by a variational principle that determines the major physical observables of interest, for example, biomolecular surface area, enclosed volume, el...

  3. Nonequilibrium phase transitions in biomolecular signal transduction (United States)

    Smith, Eric; Krishnamurthy, Supriya; Fontana, Walter; Krakauer, David


    We study a mechanism for reliable switching in biomolecular signal-transduction cascades. Steady bistable states are created by system-size cooperative effects in populations of proteins, in spite of the fact that the phosphorylation-state transitions of any molecule, by means of which the switch is implemented, are highly stochastic. The emergence of switching is a nonequilibrium phase transition in an energetically driven, dissipative system described by a master equation. We use operator and functional integral methods from reaction-diffusion theory to solve for the phase structure, noise spectrum, and escape trajectories and first-passage times of a class of minimal models of switches, showing how all critical properties for switch behavior can be computed within a unified framework.

  4. Structure determination of enterovirus 71

    Energy Technology Data Exchange (ETDEWEB)

    Plevka, Pavel; Perera, Rushika; Cardosa, Jane; Kuhn, Richard J.; Rossmann, Michael G. (Purdue); (Sentinext)


    Enterovirus 71 is a picornavirus that causes hand, foot and mouth disease but may induce fatal neurological illness in infants and young children. Enterovirus 71 crystallized in a body-centered orthorhombic space group with two particles in general orientations in the crystallographic asymmetric unit. Determination of the particle orientations required that the locked rotation function excluded the twofold symmetry axes from the set of icosahedral symmetry operators. This avoided the occurrence of misleading high rotation-function values produced by the alignment of icosahedral and crystallographic twofold axes. Once the orientations and positions of the particles had been established, the structure was solved by molecular replacement and phase extension.


    Institute of Scientific and Technical Information of China (English)


    @@ Structural genomics and proteomics were born from the understanding that functions of a protein are dictated by its 3D structure and dynamics. To understand protein functions on a genomic scale, we must know protein structures on a genomic scale. High resolution NMR can be used for this purpose. Traditional multidimensional NMR structure determination protocols become ineffective for structural genomics since to obtain a structure of a small protein of 15kD requires many months of painstaking spectral analysis and modeling. Recent advances in magnet and probe technology and in experimental methods have expanded the range of proteins amenable to structure determination and make the large scale structure determination possible. These advances are (1) effective expression systems for protein production, (2) introduction of cryoprobe, (3) structure determination with the use of the minimal amount of structural restraints obtained from the chemical shifts, residual dipolar couplings, NOEs, and computer modeling. In this talk,Iwill briefly outline these developments and related works done in our NMR lab.

  6. Interacting with the biomolecular solvent accessible surface via a haptic feedback device

    Directory of Open Access Journals (Sweden)

    Hayward Steven


    Full Text Available Abstract Background From the 1950s computer based renderings of molecules have been produced to aid researchers in their understanding of biomolecular structure and function. A major consideration for any molecular graphics software is the ability to visualise the three dimensional structure of the molecule. Traditionally, this was accomplished via stereoscopic pairs of images and later realised with three dimensional display technologies. Using a haptic feedback device in combination with molecular graphics has the potential to enhance three dimensional visualisation. Although haptic feedback devices have been used to feel the interaction forces during molecular docking they have not been used explicitly as an aid to visualisation. Results A haptic rendering application for biomolecular visualisation has been developed that allows the user to gain three-dimensional awareness of the shape of a biomolecule. By using a water molecule as the probe, modelled as an oxygen atom having hard-sphere interactions with the biomolecule, the process of exploration has the further benefit of being able to determine regions on the molecular surface that are accessible to the solvent. This gives insight into how awkward it is for a water molecule to gain access to or escape from channels and cavities, indicating possible entropic bottlenecks. In the case of liver alcohol dehydrogenase bound to the inhibitor SAD, it was found that there is a channel just wide enough for a single water molecule to pass through. Placing the probe coincident with crystallographic water molecules suggests that they are sometimes located within small pockets that provide a sterically stable environment irrespective of hydrogen bonding considerations. Conclusion By using the software, named HaptiMol ISAS (available from, one can explore the accessible surface of biomolecules using a three-dimensional input device to gain insights into the shape and water

  7. Global Langevin model of multidimensional biomolecular dynamics (United States)

    Schaudinnus, Norbert; Lickert, Benjamin; Biswas, Mithun; Stock, Gerhard


    Molecular dynamics simulations of biomolecular processes are often discussed in terms of diffusive motion on a low-dimensional free energy landscape F ( 𝒙 ) . To provide a theoretical basis for this interpretation, one may invoke the system-bath ansatz á la Zwanzig. That is, by assuming a time scale separation between the slow motion along the system coordinate x and the fast fluctuations of the bath, a memory-free Langevin equation can be derived that describes the system's motion on the free energy landscape F ( 𝒙 ) , which is damped by a friction field and driven by a stochastic force that is related to the friction via the fluctuation-dissipation theorem. While the theoretical formulation of Zwanzig typically assumes a highly idealized form of the bath Hamiltonian and the system-bath coupling, one would like to extend the approach to realistic data-based biomolecular systems. Here a practical method is proposed to construct an analytically defined global model of structural dynamics. Given a molecular dynamics simulation and adequate collective coordinates, the approach employs an "empirical valence bond"-type model which is suitable to represent multidimensional free energy landscapes as well as an approximate description of the friction field. Adopting alanine dipeptide and a three-dimensional model of heptaalanine as simple examples, the resulting Langevin model is shown to reproduce the results of the underlying all-atom simulations. Because the Langevin equation can also be shown to satisfy the underlying assumptions of the theory (such as a delta-correlated Gaussian-distributed noise), the global model provides a correct, albeit empirical, realization of Zwanzig's formulation. As an application, the model can be used to investigate the dependence of the system on parameter changes and to predict the effect of site-selective mutations on the dynamics.

  8. Combination of biomolecular and stable isotope techniques to determine the origin of organic matter used by bacterial communities: application to sediment

    NARCIS (Netherlands)

    Creach, V.; Lucas, F.; Deleu, C.; Bertru, G.; Mariotti, A.


    Natural isotopic composition is a good tool to trace organic matter in ecosystems. Recent studies used a combination of molecular and stable isotope techniques to determine the origin of the organic carbon used by bacteria in the water column. In our study, we show that this procedure can be used fo

  9. Quantum dynamics of bio-molecular systems in noisy environments


    Huelga S.F.; Plenio M.B.


    We discuss three different aspects of the quantum dynamics of bio-molecular systems and more generally complex networks in the presence of strongly coupled environments. Firstly, we make a case for the systematic study of fundamental structural elements underlying the quantum dynamics of these systems, identify such elements and explore the resulting interplay of quantum dynamics and environmental decoherence. Secondly, we critically examine some existing approaches to the numerical descripti...

  10. Structural determinants of glomerular permeability. (United States)

    Deen, W M; Lazzara, M J; Myers, B D


    Recent progress in relating the functional properties of the glomerular capillary wall to its unique structure is reviewed. The fenestrated endothelium, glomerular basement membrane (GBM), and epithelial filtration slits form a series arrangement in which the flow diverges as it enters the GBM from the fenestrae and converges again at the filtration slits. A hydrodynamic model that combines morphometric findings with water flow data in isolated GBM has predicted overall hydraulic permeabilities that are consistent with measurements in vivo. The resistance of the GBM to water flow, which accounts for roughly half that of the capillary wall, is strongly dependent on the extent to which the GBM surfaces are blocked by cells. The spatial frequency of filtration slits is predicted to be a very important determinant of the overall hydraulic permeability, in keeping with observations in several glomerular diseases in humans. Whereas the hydraulic resistances of the cell layers and GBM are additive, the overall sieving coefficient for a macromolecule (its concentration in Bowman's space divided by that in plasma) is the product of the sieving coefficients for the individual layers. Models for macromolecule filtration reveal that the individual sieving coefficients are influenced by one another and by the filtrate velocity, requiring great care in extrapolating in vitro observations to the living animal. The size selectivity of the glomerular capillary has been shown to be determined largely by the cellular layers, rather than the GBM. Controversial findings concerning glomerular charge selectivity are reviewed, and it is concluded that there is good evidence for a role of charge in restricting the transmural movement of albumin. Also discussed is an effect of albumin that has received little attention, namely, its tendency to increase the sieving coefficients of test macromolecules via steric interactions. Among the unresolved issues are the specific contributions of the

  11. Biomolecular papain thin films grown by matrix assisted and conventional pulsed laser deposition: A comparative study (United States)

    György, E.; Pérez del Pino, A.; Sauthier, G.; Figueras, A.


    Biomolecular papain thin films were grown both by matrix assisted pulsed laser evaporation (MAPLE) and conventional pulsed laser deposition (PLD) techniques with the aid of an UV KrF∗ (λ =248 nm, τFWHM≅20 ns) excimer laser source. For the MAPLE experiments the targets submitted to laser radiation consisted on frozen composites obtained by dissolving the biomaterial powder in distilled water at 10 wt % concentration. Conventional pressed biomaterial powder targets were used in the PLD experiments. The surface morphology of the obtained thin films was studied by atomic force microscopy and their structure and composition were investigated by Fourier transform infrared spectroscopy. The possible physical mechanisms implied in the ablation processes of the two techniques, under comparable experimental conditions were identified. The results showed that the growth mode, surface morphology as well as structure of the deposited biomaterial thin films are determined both by the incident laser fluence value as well as target preparation procedure.

  12. Structure determination of enterovirus 71


    Plevka, Pavel; Perera, Rushika; Cardosa, Jane; Kuhn, Richard J.; Rossmann, Michael G


    Determination of the orientation of the enterovirus 71 virions in the crystal required the calculation of a locked rotation function that included only icosahedral threefold and fivefold symmetry axes. Otherwise, misleading high rotation-function values were produced by accidental alignment of icosahedral and crystallographic twofold axes.


    NARCIS (Netherlands)



    The structure of tin zirconium trisulfide is of the NH4CdCl3 type with double columns of edge-sharing Zr octahedra. These columns are linked together by Sn atoms. Sn is coordinated to three S atoms at 2 x 2.619 (2) and 2.765 (2) angstrom; a fourth S atom is at 3.065 (2) angstrom. The zirconium coord

  14. Determinants of Glycosaminoglycan (GAG Structure

    Directory of Open Access Journals (Sweden)

    Kristian Prydz


    Full Text Available Proteoglycans (PGs are glycosylated proteins of biological importance at cell surfaces, in the extracellular matrix, and in the circulation. PGs are produced and modified by glycosaminoglycan (GAG chains in the secretory pathway of animal cells. The most common GAG attachment site is a serine residue followed by a glycine (-ser-gly-, from which a linker tetrasaccharide extends and may continue as a heparan sulfate, a heparin, a chondroitin sulfate, or a dermatan sulfate GAG chain. Which type of GAG chain becomes attached to the linker tetrasaccharide is influenced by the structure of the protein core, modifications occurring to the linker tetrasaccharide itself, and the biochemical environment of the Golgi apparatus, where GAG polymerization and modification by sulfation and epimerization take place. The same cell type may produce different GAG chains that vary, depending on the extent of epimerization and sulfation. However, it is not known to what extent these differences are caused by compartmental segregation of protein cores en route through the secretory pathway or by differential recruitment of modifying enzymes during synthesis of different PGs. The topic of this review is how different aspects of protein structure, cellular biochemistry, and compartmentalization may influence GAG synthesis.

  15. Structural determinants of hospital closure. (United States)

    Longo, D R; Chase, G A


    In a retrospective case-control study, structural characteristics of hospitals that closed during the years 1976-1980 were contrasted with three comparison groups: hospitals that were acquired in a merger; hospitals that joined a multihospital system; and hospitals that remained autonomously opened, to investigate these characteristics as predictors of closure. Characteristics investigated included environmental, structural, and process variables. The independent variables were measured 5 years prior to outcome. Findings indicate that closed hospitals resemble hospitals acquired in a merger ("failure"), and likewise autonomous hospitals resemble hospitals that join a multihospital system ("success"). The most important predictors of hospital failure were the physician-to-population ratio, the East North Central and West North Central census regions, the level of diversification, low occupancy rate, location in a standard metropolitan statistical area, the chief executive officer's lack of affiliation in the American College of Hospital Administrators, profit status, bed size of less than 50, and presence in a state with a rate-setting agency. Surprisingly, this study shows the bed-to-population ratio to be unrelated to closure. In addition, the findings strongly support the open-system perspective, which, unlike the closed-system perspective, is concerned with the vulnerability of the organization to the uncontrollable and often unpredictable influences of the environment.

  16. Conducting polymer based biomolecular electronic devices

    Indian Academy of Sciences (India)

    B D Malhotra; Rahul Singhal


    Biomolecular electronics is rapidly evolving from physics, chemistry, biology, electronics and information technology. Organic materials such as proteins, pigments and conducting polymers have been considered as alternatives for carrying out the functions that are presently being performed by semiconductor silicon. Conducting polymers such as polypyrroles, polythiophenes and polyanilines have been projected for applications for a wide range of biomolecular electronic devices such as optical, electronic, drug-delivery, memory and biosensing devices. Our group has been actively working towards the application of conducting polymers to Schottky diodes, metal–insulator–semiconductor (MIS) devices and biosensors for the past 10 years. This paper is a review of some of the results obtained at our laboratory in the area of conducting polymer biomolecular electronics.

  17. The determinants of Dutch capital structure choice

    NARCIS (Netherlands)

    Chen, Linda H.; Jiang, George J.


    This paper uses the structural equation modeling (SEM) technique to empirically test the determinants of capital structure choice for Dutch firms. We include major factors identified by capital structure theories and construct proxies for these factors with consideration of specific institutional se

  18. Origin of organic molecules and biomolecular homochirality. (United States)

    Podlech, J


    Theories about the origin of biomolecular homochirality, which seems to be a prerequisite for the creation of life, are discussed. First, possible terrestrial and extraterrestrial sources of organic molecules are outlined. Then, mechanisms for the formation of enantiomerically enriched compounds and for the amplification of their chirality are described.

  19. Thermodynamic properties of water solvating biomolecular surfaces (United States)

    Heyden, Matthias

    Changes in the potential energy and entropy of water molecules hydrating biomolecular interfaces play a significant role for biomolecular solubility and association. Free energy perturbation and thermodynamic integration methods allow calculations of free energy differences between two states from simulations. However, these methods are computationally demanding and do not provide insights into individual thermodynamic contributions, i.e. changes in the solvent energy or entropy. Here, we employ methods to spatially resolve distributions of hydration water thermodynamic properties in the vicinity of biomolecular surfaces. This allows direct insights into thermodynamic signatures of the hydration of hydrophobic and hydrophilic solvent accessible sites of proteins and small molecules and comparisons to ideal model surfaces. We correlate dynamic properties of hydration water molecules, i.e. translational and rotational mobility, to their thermodynamics. The latter can be used as a guide to extract thermodynamic information from experimental measurements of site-resolved water dynamics. Further, we study energy-entropy compensations of water at different hydration sites of biomolecular surfaces. This work is supported by the Cluster of Excellence RESOLV (EXC 1069) funded by the Deutsche Forschungsgemeinschaft.

  20. Biomolecular Modification of Inorganic Crystal Growth

    Energy Technology Data Exchange (ETDEWEB)

    De Yoreo, J J


    The fascinating shapes and hierarchical designs of biomineralized structures are an inspiration to materials scientists because of the potential they suggest for biomolecular control over materials synthesis. Conversely, the failure to prevent or limit tissue mineralization in the vascular, skeletal, and urinary systems is a common source of disease. Understanding the mechanisms by which organisms direct or limit crystallization has long been a central challenge to the biomineralization community. One prevailing view is that mineral-associated macromolecules are responsible for either inhibiting crystallization or initiating and stabilizing non-equilibrium crystal polymorphs and morphologies through interactions between anionic moieties and cations in solution or at mineralizing surfaces. In particular, biomolecules that present carboxyl groups to the growing crystal have been implicated as primary modulators of growth. Here we review the results from a combination of in situ atomic force microscopy (AFM) and molecular modeling (MM) studies to investigate the effect of specific interactions between carboxylate-rich biomolecules and atomic steps on crystal surfaces during the growth of carbonates, oxalates and phosphates of calcium. Specifically, we how the growth kinetics and morphology depend on the concentration of additives that include citrate, simple amino acids, synthetic Asp-rich polypeptides, and naturally occurring Asp-rich proteins found in both functional and pathological mineral tissues. The results reveal a consistent picture of shape modification in which stereochemical matching of modifiers to specific atomic steps drives shape modification. Inhibition and other changes in growth kinetics are shown to be due to a range of mechanisms that depend on chemistry and molecular size. Some effects are well described by classic crystal growth theories, but others, such as step acceleration due to peptide charge and hydrophylicity, were previously unrealized

  1. Simultaneous determination of protein structure and dynamics

    DEFF Research Database (Denmark)

    Lindorff-Larsen, Kresten; Best, Robert B.; DePristo, M. A.


    We present a protocol for the experimental determination of ensembles of protein conformations that represent simultaneously the native structure and its associated dynamics. The procedure combines the strengths of nuclear magnetic resonance spectroscopy-for obtaining experimental information at ...

  2. Direct atomic structure determination by the inspection of structural phase. (United States)

    Nakashima, Philip N H; Moodie, Alexander F; Etheridge, Joanne


    A century has passed since Bragg solved the first atomic structure using diffraction. As with this first structure, all atomic structures to date have been deduced from the measurement of many diffracted intensities using iterative and statistical methods. We show that centrosymmetric atomic structures can be determined without the need to measure or even record a diffracted intensity. Instead, atomic structures can be determined directly and quickly from the observation of crystallographic phases in electron diffraction patterns. Furthermore, only a few phases are required to achieve high resolution. This represents a paradigm shift in structure determination methods, which we demonstrate with the moderately complex α-Al2O3. We show that the observation of just nine phases enables the location of all atoms with a resolution of better than 0.1 Å. This level of certainty previously required the measurement of thousands of diffracted intensities.

  3. Global analysis of time-resolved fluorescence microspectroscopy and applications in biomolecular studies

    NARCIS (Netherlands)

    Laptenok, S.


    Understanding the properties of biomolecular networks is of central importance in life sciences. Optical microscopy has been very useful to determine the sub-cellular localisation of proteins but it cannot reveal whether proteins interact with one another. Micro-spectroscopic techniques (combining m

  4. Protein Structure Determination Using Chemical Shifts

    DEFF Research Database (Denmark)

    Christensen, Anders Steen

    In this thesis, a protein structure determination using chemical shifts is presented. The method is implemented in the open source PHAISTOS protein simulation framework. The method combines sampling from a generative model with a coarse-grained force field and an energy function that includes...... chemical shifts. The method is benchmarked on folding simulations of five small proteins. In four cases the resulting structures are in excellent agreement with experimental data, the fifth case fail likely due to inaccuracies in the energy function. For the Chymotrypsin Inhibitor protein, a structure...... is determined using only chemical shifts recorded and assigned through automated processes. The CARMSD to the experimental X-ray for this structure is 1.1. Å. Additionally, the method is combined with very sparse NOE-restraints and evolutionary distance restraints and tested on several protein structures >100...

  5. Simple approach for ranking structure determining residues

    Directory of Open Access Journals (Sweden)

    Oscar D. Luna-Martínez


    Full Text Available Mutating residues has been a common task in order to study structural properties of the protein of interest. Here, we propose and validate a simple method that allows the identification of structural determinants; i.e., residues essential for preservation of the stability of global structure, regardless of the protein topology. This method evaluates all of the residues in a 3D structure of a given globular protein by ranking them according to their connectivity and movement restrictions without topology constraints. Our results matched up with sequence-based predictors that look up for intrinsically disordered segments, suggesting that protein disorder can also be described with the proposed methodology.

  6. Simple approach for ranking structure determining residues. (United States)

    Luna-Martínez, Oscar D; Vidal-Limón, Abraham; Villalba-Velázquez, Miryam I; Sánchez-Alcalá, Rosalba; Garduño-Juárez, Ramón; Uversky, Vladimir N; Becerril, Baltazar


    Mutating residues has been a common task in order to study structural properties of the protein of interest. Here, we propose and validate a simple method that allows the identification of structural determinants; i.e., residues essential for preservation of the stability of global structure, regardless of the protein topology. This method evaluates all of the residues in a 3D structure of a given globular protein by ranking them according to their connectivity and movement restrictions without topology constraints. Our results matched up with sequence-based predictors that look up for intrinsically disordered segments, suggesting that protein disorder can also be described with the proposed methodology.

  7. Application of Nanodiamonds in Biomolecular Mass Spectrometry

    Directory of Open Access Journals (Sweden)

    Ping Cheng


    Full Text Available The combination of nanodiamond (ND with biomolecular mass spectrometry (MS makes rapid, sensitive detection of biopolymers from complex biosamples feasible. Due to its chemical inertness, optical transparency and biocompatibility, the advantage of NDs in MS study is unique. Furthermore, functionalization on the surfaces of NDs expands their application in the fields of proteomics and genomics for specific requirements greatly. This review presents methods of MS analysis based on solid phase extraction and elution on NDs and different application examples including peptide, protein, DNA, glycan and others. Owing to the quick development of nanotechnology, surface chemistry, new MS methods and the intense interest in proteomics and genomics, a huge increase of their applications in biomolecular MS analysis in the near future can be predicted.

  8. Improvements in continuum modeling for biomolecular systems

    CERN Document Server

    Qiao, Yu


    Modeling of biomolecular systems plays an essential role in understanding biological processes, such as ionic flow across channels, protein modification or interaction, and cell signaling. The continuum model described by the Poisson-Boltzmann (PB)/Poisson-Nernst-Planck (PNP) equations has made great contributions towards simulation of these processes. However, the model has shortcomings in its commonly used form and cannot capture (or cannot accurately capture) some important physical properties of biological systems. Considerable efforts have been made to improve the continuum model to account for discrete particle interactions and to make progress in numerical methods to provide accurate and efficient simulation. This review will summarize recent main improvements in continuum modeling for biomolecular systems, with focus on the size-modified models, the coupling of the classical density functional theory and PNP equations, the coupling of polar and nonpolar interactions, and numerical progress.

  9. MPBEC, a Matlab Program for Biomolecular Electrostatic Calculations. (United States)

    Vergara-Perez, Sandra; Marucho, Marcelo


    One of the most used and efficient approaches to compute electrostatic properties of biological systems is to numerically solve the Poisson-Boltzmann (PB) equation. There are several software packages available that solve the PB equation for molecules in aqueous electrolyte solutions. Most of these software packages are useful for scientists with specialized training and expertise in computational biophysics. However, the user is usually required to manually take several important choices, depending on the complexity of the biological system, to successfully obtain the numerical solution of the PB equation. This may become an obstacle for researchers, experimentalists, even students with no special training in computational methodologies. Aiming to overcome this limitation, in this article we present MPBEC, a free, cross-platform, open-source software that provides non-experts in the field an easy and efficient way to perform biomolecular electrostatic calculations on single processor computers. MPBEC is a Matlab script based on the Adaptative Poisson Boltzmann Solver, one of the most popular approaches used to solve the PB equation. MPBEC does not require any user programming, text editing or extensive statistical skills, and comes with detailed user-guide documentation. As a unique feature, MPBEC includes a useful graphical user interface (GUI) application which helps and guides users to configure and setup the optimal parameters and approximations to successfully perform the required biomolecular electrostatic calculations. The GUI also incorporates visualization tools to facilitate users pre- and post- analysis of structural and electrical properties of biomolecules.

  10. MPBEC, a Matlab Program for Biomolecular Electrostatic Calculations (United States)

    Vergara-Perez, Sandra; Marucho, Marcelo


    One of the most used and efficient approaches to compute electrostatic properties of biological systems is to numerically solve the Poisson-Boltzmann (PB) equation. There are several software packages available that solve the PB equation for molecules in aqueous electrolyte solutions. Most of these software packages are useful for scientists with specialized training and expertise in computational biophysics. However, the user is usually required to manually take several important choices, depending on the complexity of the biological system, to successfully obtain the numerical solution of the PB equation. This may become an obstacle for researchers, experimentalists, even students with no special training in computational methodologies. Aiming to overcome this limitation, in this article we present MPBEC, a free, cross-platform, open-source software that provides non-experts in the field an easy and efficient way to perform biomolecular electrostatic calculations on single processor computers. MPBEC is a Matlab script based on the Adaptative Poisson-Boltzmann Solver, one of the most popular approaches used to solve the PB equation. MPBEC does not require any user programming, text editing or extensive statistical skills, and comes with detailed user-guide documentation. As a unique feature, MPBEC includes a useful graphical user interface (GUI) application which helps and guides users to configure and setup the optimal parameters and approximations to successfully perform the required biomolecular electrostatic calculations. The GUI also incorporates visualization tools to facilitate users pre- and post-analysis of structural and electrical properties of biomolecules.

  11. Capital Structure Determinants and Governance Structure Variety in Franchising

    NARCIS (Netherlands)

    T. Jiang (Tao)


    textabstractThis thesis investigates two questions: the determinants of capital structure in franchising and its subsequent impact on the franchise financing decisions; and the efficient governance structure choice in franchising. We posit that firms franchise in order to benefit from the reduced fr

  12. Application of Nanodiamonds in Biomolecular Mass Spectrometry


    Ping Cheng; Xianglei Kong


    The combination of nanodiamond (ND) with biomolecular mass spectrometry (MS) makes rapid, sensitive detection of biopolymers from complex biosamples feasible. Due to its chemical inertness, optical transparency and biocompatibility, the advantage of NDs in MS study is unique. Furthermore, functionalization on the surfaces of NDs expands their application in the fields of proteomics and genomics for specific requirements greatly. This review presents methods of MS analysis based on solid phase...

  13. Advances on surface structural determination by LEED. (United States)

    Soares, Edmar A; de Castilho, Caio M C; de Carvalho, Vagner E


    In the last 40 years, low energy electron diffraction (LEED) has proved to be the most reliable quantitative technique for surface structural determination. In this review, recent developments related to the theory that gives support to LEED structural determination are discussed under a critical analysis of the main theoretical approximation-the muffin-tin calculation. The search methodologies aimed at identifying the best matches between theoretical and experimental intensity versus voltage curves are also considered, with the most recent procedures being reviewed in detail.

  14. Advances on surface structural determination by LEED

    Energy Technology Data Exchange (ETDEWEB)

    Soares, Edmar A; De Carvalho, Vagner E [Departamento de Fisica, ICEX, Universidade Federal de Minas Gerais, 31270-090, Belo Horizonte, MG (Brazil); De Castilho, Caio M C, E-mail: [Grupo de Fisica de SuperfIcies e Materiais, Instituto de Fisica and Instituto Nacional de Ciencia e Tecnologia em Energia e Ambiente (CIENAM)INCT-E and A, Universidade Federal da Bahia, Campus Universitario da Federacao, 40170-115, Salvador, BA (Brazil)


    In the last 40 years, low energy electron diffraction (LEED) has proved to be the most reliable quantitative technique for surface structural determination. In this review, recent developments related to the theory that gives support to LEED structural determination are discussed under a critical analysis of the main theoretical approximation-the muffin-tin calculation. The search methodologies aimed at identifying the best matches between theoretical and experimental intensity versus voltage curves are also considered, with the most recent procedures being reviewed in detail. (topical review)

  15. Representing Personal Determinants in Causal Structures. (United States)

    Bandura, Albert


    Responds to Staddon's critique of the author's earlier article and addresses issues raised by Staddon's (1984) alternative models of causality. The author argues that it is not the formalizability of causal processes that is the issue but whether cognitive determinants of behavior are reducible to past stimulus inputs in causal structures.…

  16. Crystal structure of meteoritic schreibersites: determination of absolute structure (United States)

    Skála, Roman; Císařová, Ivana

    Minerals of the schreibersite nickelphosphide series (Fe,Ni)3P crystallize in the non-centrosymmetric space group Ibar 4. As a consequence, they can possess two different spatial arrangements of the constituting atoms within the unit cell, related by the inversion symmetry operation. Here, we present the crystal structure refinements from single crystal X-ray diffraction data for schreibersite grains from iron meteorites Acuña, Carlton, Hex River Mts. (three different crystals), Odessa (two different crystals), Sikhote Alin, and Toluca aiming for the determination of the absolute structure of the examined crystals. The crystals studied cover the composition range from 58 mol% to 80 mol% Fe3P end-member. Unit-cell parameter a and volume of the unit cell V, as well as certain topological structural parameters tightly correlate with Fe3P content. Unit-cell parameter c, on the other hand, does not show such strong correlation. Eight of the nine crystal structure refinements allowed unambiguous absolute structure assignment. The single crystal extracted from Toluca is, however, of poor quality and consequently the structure refinement did not provide as good results as the rest of the materials. Also, this crystal has only weak inversion distinguishing power to provide unequivocal absolute structure determination. Six of the eight unambiguous absolute structure determinations indicated inverted atomic arrangement compared to that reported in earlier structure refinements (here called standard). Only two grains, one taken from Odessa iron and the other from the Hex River Mts. meteorite, reveal the dominance of standard crystal structure setting.

  17. Systematic evaluation of bundled SPC water for biomolecular simulations. (United States)

    Gopal, Srinivasa M; Kuhn, Alexander B; Schäfer, Lars V


    In bundled SPC water models, the relative motion of groups of four water molecules is restrained by distance-dependent potentials. Bundled SPC models have been used in hybrid all-atom/coarse-grained (AA/CG) multiscale simulations, since they enable to couple atomistic SPC water with supra-molecular CG water models that effectively represent more than a single water molecule. In the present work, we systematically validated and critically tested bundled SPC water models as solvent for biomolecular simulations. To that aim, we investigated both thermodynamic and structural properties of various biomolecular systems through molecular dynamics (MD) simulations. Potentials of mean force of dimerization of pairs of amino acid side chains as well as hydration free energies of single side chains obtained with bundled SPC and standard (unrestrained) SPC water agree closely with each other and with experimental data. Decomposition of the hydration free energies into enthalpic and entropic contributions reveals that in bundled SPC, this favorable agreement of the free energies is due to a larger degree of error compensation between hydration enthalpy and entropy. The Ramachandran maps of Ala3, Ala5, and Ala7 peptides are similar in bundled and unrestrained SPC, whereas for the (GS)2 peptide, bundled water leads to a slight overpopulation of extended conformations. Analysis of the end-to-end distance autocorrelation times of the Ala5 and (GS)2 peptides shows that sampling in more viscous bundled SPC water is about two times slower. Pronounced differences between the water models were found for the structure of a coiled-coil dimer, which is instable in bundled SPC but not in standard SPC. In addition, the hydration of the active site of the serine protease α-chymotrypsin depends on the water model. Bundled SPC leads to an increased hydration of the active site region, more hydrogen bonds between water and catalytic triad residues, and a significantly slower exchange of water

  18. Barcoded microchips for biomolecular assays. (United States)

    Zhang, Yi; Sun, Jiashu; Zou, Yu; Chen, Wenwen; Zhang, Wei; Xi, Jianzhong Jeff; Jiang, Xingyu


    Multiplexed assay of analytes is of great importance for clinical diagnostics and other analytical applications. Barcode-based bioassays with the ability to encode and decode may realize this goal in a straightforward and consistent manner. We present here a microfluidic barcoded chip containing several sets of microchannels with different widths, imitating the commonly used barcode. A single barcoded microchip can carry out tens of individual protein/nucleic acid assays (encode) and immediately yield all assay results by a portable barcode reader or a smartphone (decode). The applicability of a barcoded microchip is demonstrated by human immunodeficiency virus (HIV) immunoassays for simultaneous detection of three targets (anti-gp41 antibody, anti-gp120 antibody, and anti-gp36 antibody) from six human serum samples. We can also determine seven pathogen-specific oligonucleotides by a single chip containing both positive and negative controls.

  19. Insights into cancer severity from biomolecular interaction mechanisms (United States)

    Raimondi, Francesco; Singh, Gurdeep; Betts, Matthew J.; Apic, Gordana; Vukotic, Ranka; Andreone, Pietro; Stein, Lincoln; Russell, Robert B.


    To attain a deeper understanding of diseases like cancer, it is critical to couple genetics with biomolecular mechanisms. High-throughput sequencing has identified thousands of somatic mutations across dozens of cancers, and there is a pressing need to identify the few that are pathologically relevant. Here we use protein structure and interaction data to interrogate nonsynonymous somatic cancer mutations, identifying a set of 213 molecular interfaces (protein-protein, -small molecule or –nucleic acid) most often perturbed in cancer, highlighting several potentially novel cancer genes. Over half of these interfaces involve protein-small-molecule interactions highlighting their overall importance in cancer. We found distinct differences in the predominance of perturbed interfaces between cancers and histological subtypes and presence or absence of certain interfaces appears to correlate with cancer severity. PMID:27698488

  20. Orientation of biomolecular assemblies in a microfluidic jet

    Energy Technology Data Exchange (ETDEWEB)

    Priebe, M; Kalbfleisch, S; Tolkiehn, M; Salditt, T [Institut fuer Roentgenphysik, Universitaet Goettingen, Goettingen (Germany); Koester, S [Courant Research Centre Nano-Spectroscopy and X-Ray Imaging, Universitaet Goettingen, Goettingen (Germany); Abel, B [Institut fuer Physikalische Chemie, Universitaet Goettingen, Goettingen (Germany); Davies, R J, E-mail: tsalditt@gwdg.d [ID13, ESRF, Grenoble (France)


    We have investigated multilamellar lipid assemblies in a microfluidic jet, operating at high shear rates of the order of 10{sup 7} s{sup -1}. Compared to classical Couette cells or rheometers, the shear rate was increased by at least 2-3 orders of magnitude, and the sample volume was scaled down correspondingly. At the same time, the jet is characterized by high extensional stress due to elongational flow. A focused synchrotron x-ray beam was used to measure the structure and orientation of the lipid assemblies in the jet. The diffraction patterns indicate conventional multilamellar phases, aligned with the membrane normals oriented along the velocity gradient of the jet. The results indicate that the setup may be well suited for coherent diffractive imaging of oriented biomolecular assemblies and macromolecules at the future x-ray free electron laser (XFEL) sources.

  1. Quantum dynamics of bio-molecular systems in noisy environments

    CERN Document Server

    Plenio, M B


    We discuss three different aspects of the quantum dynamics of bio-molecular systems and more generally complex networks in the presence of strongly coupled environments. Firstly, we make a case for the systematic study of fundamental structural elements underlying the quantum dynamics of these systems, identify such elements and explore the resulting interplay of quantum dynamics and environmental decoherence. Secondly, we critically examine some existing approaches to the numerical description of system-environment interaction in the non-perturbative regime and present a promising new method that can overcome some limitations of existing methods. Thirdly, we present an approach towards deciding and quantifying the non-classicality of the action of the environment and the observed system-dynamics. We stress the relevance of these tools for strengthening the interplay between theoretical and experimental research in this field.

  2. Hybrid organic semiconductor lasers for bio-molecular sensing. (United States)

    Haughey, Anne-Marie; Foucher, Caroline; Guilhabert, Benoit; Kanibolotsky, Alexander L; Skabara, Peter J; Burley, Glenn; Dawson, Martin D; Laurand, Nicolas


    Bio-functionalised luminescent organic semiconductors are attractive for biophotonics because they can act as efficient laser materials while simultaneously interacting with molecules. In this paper, we present and discuss a laser biosensor platform that utilises a gain layer made of such an organic semiconductor material. The simple structure of the sensor and its operation principle are described. Nanolayer detection is shown experimentally and analysed theoretically in order to assess the potential and the limits of the biosensor. The advantage conferred by the organic semiconductor is explained, and comparisons to laser sensors using alternative dye-doped materials are made. Specific biomolecular sensing is demonstrated, and routes to functionalisation with nucleic acid probes, and future developments opened up by this achievement, are highlighted. Finally, attractive formats for sensing applications are mentioned, as well as colloidal quantum dots, which in the future could be used in conjunction with organic semiconductors.

  3. Determinants of the detrital arthropod community structure

    DEFF Research Database (Denmark)

    Lessard, J.P.; Sackett, Tara E.; Reynolds, William N.;


    Understanding the factors that shape community structure, and whether those factors vary geographically, has a long history in ecology. Because the abiotic environment often varies in predictable ways along elevational gradients, montane systems are ideal to study geographic variation in the dete......Understanding the factors that shape community structure, and whether those factors vary geographically, has a long history in ecology. Because the abiotic environment often varies in predictable ways along elevational gradients, montane systems are ideal to study geographic variation...... in the determinants of community structure. In this study, we first examined the relative importance of environmental gradients, microclimate, and food resources in driving spatial variation in the structure of detrital communities in forests of the southeastern USA. Then, in order to assess whether the determinants...... for the effect of climatic variation along the elevational gradient, food resource addition and microclimate alteration influenced the richness and abundance of some taxa. However, the effect of food resource addition and microclimate alteration on the richness and abundance of arthropods did not vary...

  4. Nanotube-Based Chemical and Biomolecular Sensors

    Institute of Scientific and Technical Information of China (English)

    J.Koh; B.Kim; S.Hong; H.Lim; H.C.Choi


    We present a brief review about recent results regarding carbon nanotube (CNT)-based chemical and biomolecular sensors. For the fabrication of CNT-based sensors, devices containing CNT channels between two metal electrodes are first fabricated usually via chemical vapor deposition (CVD) process or "surface programmed assembly" method. Then, the CNT surfaces are often functionalized to enhance the selectivity of the sensors. Using this process, highly-sensitive CNT-based sensors can be fabricated for the selective detection of various chemical and biological molecules such as hydrogen, ammonia, carbon monoxide, chlorine gas, DNA, glucose, alcohol, and proteins.

  5. Scalable Molecular Dynamics for Large Biomolecular Systems

    Directory of Open Access Journals (Sweden)

    Robert K. Brunner


    Full Text Available We present an optimized parallelization scheme for molecular dynamics simulations of large biomolecular systems, implemented in the production-quality molecular dynamics program NAMD. With an object-based hybrid force and spatial decomposition scheme, and an aggressive measurement-based predictive load balancing framework, we have attained speeds and speedups that are much higher than any reported in literature so far. The paper first summarizes the broad methodology we are pursuing, and the basic parallelization scheme we used. It then describes the optimizations that were instrumental in increasing performance, and presents performance results on benchmark simulations.

  6. Micro and Nanotechnologies Enhanced Biomolecular Sensing

    Directory of Open Access Journals (Sweden)

    Tza-Huei Wang


    Full Text Available This editorial summarizes some of the recent advances of micro and nanotechnology-based tools and devices for biomolecular detection. These include the incorporation of nanomaterials into a sensor surface or directly interfacing with molecular probes to enhance target detection via more rapid and sensitive responses, and the use of self-assembled organic/inorganic nanocomposites that inhibit exceptional spectroscopic properties to enable facile homogenous assays with efficient binding kinetics. Discussions also include some insight into microfluidic principles behind the development of an integrated sample preparation and biosensor platform toward a miniaturized and fully functional system for point of care applications.

  7. Fundamentos biomoleculares de la diabetes mellitus



    La diabetes mellitus es una enfermedad endocrina con importantes implicaciones a nivel sistémico, como: angiopatía, neuropatía, retinopatía y nefropatía, entre otras. Estas  complicaciones tienen su origen en eventos biomoleculares desencadenados por la hiperglicemia.  La presente revisión de tema trata sobre la estructura y síntesis de la insulina en las células β del páncreas; los eventos moleculares y bioquímicos que activan su secreción como respuesta a una alta concentración de glucosa e...

  8. Biomolecular Aspects of Mercury Transformations (United States)

    Johs, A.; Shi, L.; Miller, S. M.; Summers, A. O.; Liang, L.


    Bacteria participate significantly in mercury transformation in natural and industrial environments. Previous studies have shown that bacterial mercury resistance is mediated by the mer operon, typically located on transposons or plasmids. It encodes specific genes that facilitate uptake of mercury species, cleavage of organomercurials, and reduction of Hg(II) to Hg(0). Expression of mer operon genes is regulated by MerR, a metal-responsive regulator protein on the level of transcription. In vitro studies have shown that MerR forms a non-transcribing pre-initiation complex with RNA polymerase and the promoter DNA. Binding of Hg(II) induces conformational changes in MerR and other components of the complex resulting in the transcription of mer operon genes. As part of ongoing investigations on allosteric conformational changes induced by Hg(II) in dimeric MerR, and the implications on the binding of RNA polymerase to the promoter of the mer operon, we applied small angle scattering to study the regulatory mechanism of MerR in the presence and absence of Hg(II). Our results show that in the presence of Hg(II) the MerR dimer undergoes a significant reorientation from a compact state to a conformation revealing two distinct domains. Bacterial reduction of Hg(II) can also occur at concentrations too low to induce mer operon functions. Dissimilatory metal reducing bacteria, such as Shewanella and Geobacter are able to reduce Hg(II) in the presence of mineral oxides. This process has been linked to the activity of outer membrane multiheme cytochromes. We isolated and purified a decaheme outer membrane cytochrome OmcA from Shewanella oneidensis MR-1 and characterized its envelope shape in solution by small angle x-ray scattering. Structural features were identified and compared to homology models. These results show that OmcA is an elongated macromolecule consisting of separate modules, which may be connected by flexible linkers.

  9. Out-of-equilibrium biomolecular interactions monitored by picosecond fluorescence in microfluidic droplets. (United States)

    Maillot, Sacha; Carvalho, Alain; Vola, Jean-Pierre; Boudier, Christian; Mély, Yves; Haacke, Stefan; Léonard, Jérémie


    We developed a new experimental approach combining Time-Resolved Fluorescence (TRF) spectroscopy and Droplet Microfluidics (DμF) to investigate the relaxation dynamics of structurally heterogeneous biomolecular systems. Here DμF was used to produce with minimal material consumption an out-of-equilibrium, fluorescently labeled biomolecular complex by rapid mixing within the droplets. TRF detection was implemented with a streak camera to monitor the time evolution of the structural heterogeneity of the complex along its relaxation towards equilibrium while it propagates inside the microfluidic channel. The approach was validated by investigating the fluorescence decay kinetics of a model interacting system of bovine serum albumin and Patent Blue V. Fluorescence decay kinetics are acquired with very good signal-to-noise ratio and allow for global, multicomponent fluorescence decay analysis, evidencing heterogeneous structural relaxation over several 100 ms.

  10. Energy dissipation in biomolecular machines

    Energy Technology Data Exchange (ETDEWEB)

    Lervik, Anders


    The operation of a molecular pump, the calcium pump of sarcoplasmic reticulum is studied using mesoscopic non-equilibrium thermodynamics and molecular dynamics. The mesoscopic non-equilibrium thermodynamic description of the pump is compared to the description obtained in the framework of Hill for kinetic enzyme cycles. By comparing these two descriptions at isothermal conditions, they are found to be equivalent. This supports the validity of the mesoscopic approach. An extension of the mesoscopic non-equilibrium framework to also include a heat flux and the corresponding temperature difference is proposed. This can be used to model phenomena such as non-shivering thermogenesis, a process which lack a theoretical description in the kinetic cycle picture. Further, the heat transfer in the calcium pump is studied using molecular dynamics. This is done in order to obtain phenomenological parameters that can be used for the modeling of thermogenesis. A non-stationary non-equilibrium molecular dynamics approach is developed, which may be used to study heat transfer between a small object and the surrounding solvent. This methodology is applied to the calcium pump solvated in water. It is found that the thermal conductivity of the protein is low (0.2 W K-1 m-1) compared to water (0.6 WK-1 m-1). This means that the protein may sustain a large temperature gradient across its structure. The simulations also show that the protein-water surface is important for the heat transfer. The time scale for vibrational energy relaxation is found to be of order 10/100 ps which strengthens the local equilibrium assumption of mesoscopic non-equilibrium thermodynamics. Mesoscopic non-equilibrium thermodynamics is also applied to calculate the thermodynamic efficiency of the calcium pump embedded in lipid bilayers of varying length and from different tissues. This is done in order to show the applicability of mesoscopic non-equilibrium thermodynamics to interpret experimental data. The

  11. Improvements in continuum modeling for biomolecular systems (United States)

    Yu, Qiao; Ben-Zhuo, Lu


    Modeling of biomolecular systems plays an essential role in understanding biological processes, such as ionic flow across channels, protein modification or interaction, and cell signaling. The continuum model described by the Poisson- Boltzmann (PB)/Poisson-Nernst-Planck (PNP) equations has made great contributions towards simulation of these processes. However, the model has shortcomings in its commonly used form and cannot capture (or cannot accurately capture) some important physical properties of the biological systems. Considerable efforts have been made to improve the continuum model to account for discrete particle interactions and to make progress in numerical methods to provide accurate and efficient simulations. This review will summarize recent main improvements in continuum modeling for biomolecular systems, with focus on the size-modified models, the coupling of the classical density functional theory and the PNP equations, the coupling of polar and nonpolar interactions, and numerical progress. Project supported by the National Natural Science Foundation of China (Grant No. 91230106) and the Chinese Academy of Sciences Program for Cross & Cooperative Team of the Science & Technology Innovation.

  12. Smartphones for cell and biomolecular detection. (United States)

    Liu, Xiyuan; Lin, Tung-Yi; Lillehoj, Peter B


    Recent advances in biomedical science and technology have played a significant role in the development of new sensors and assays for cell and biomolecular detection. Generally, these efforts are aimed at reducing the complexity and costs associated with diagnostic testing so that it can be performed outside of a laboratory or hospital setting, requiring minimal equipment and user involvement. In particular, point-of-care (POC) testing offers immense potential for many important applications including medical diagnosis, environmental monitoring, food safety, and biosecurity. When coupled with smartphones, POC systems can offer portability, ease of use and enhanced functionality while maintaining performance. This review article focuses on recent advancements and developments in smartphone-based POC systems within the last 6 years with an emphasis on cell and biomolecular detection. These devices typically comprise multiple components, such as detectors, sample processors, disposable chips, batteries, and software, which are integrated with a commercial smartphone. One of the most important aspects of developing these systems is the integration of these components onto a compact and lightweight platform that requires minimal power. Researchers have demonstrated several promising approaches employing various detection schemes and device configurations, and it is expected that further developments in biosensors, battery technology and miniaturized electronics will enable smartphone-based POC technologies to become more mainstream tools in the scientific and biomedical communities.

  13. Assembly of single wall carbon nanotube-metal nanohybrids using biomolecular components (United States)

    Kim, Sang Nyon; Slocik, Joseph M.; Naik, Rajesh R.


    Biomaterials such as nucleic acids and proteins can be exploited to create higher order structures. The biomolecular components such as DNA and peptides have been used to assemble nanoparticles with high fidelity. Here, we use DNA and peptides, and their preferential interaction with inorganic and carbon nanomaterials to form homogeneous hybrids. The enhanced binding of Pt ions to both DNA and peptide functionalized nanoparticles mediates the assembly of carbon nanotubes functionalized with DNA with peptide coated gold nanoparticles.

  14. Stochastic Simulation of Biomolecular Reaction Networks Using the Biomolecular Network Simulator Software (United States)


    investigate the simulation of a biomolecular reaction network with BNS, a simple model of a generic self-assembling catalytic ligation reaction in a...Amino Acid Pools Nucleotide Triphosphate Pools Nucleotide Monophosphate Pools Ligation Reaction 1551 517 7 RESULTS Simulation of exemplar...and reaction r8 is the catalytic ligation reaction . In figures 5(B) through 5(F), both the time-averaged event rate for a single simulation run

  15. Biomolecular Markers in Cancer of the Tongue

    Directory of Open Access Journals (Sweden)

    Daris Ferrari


    Full Text Available The incidence of tongue cancer is increasing worldwide, and its aggressiveness remains high regardless of treatment. Genetic changes and the expression of abnormal proteins have been frequently reported in the case of head and neck cancers, but the little information that has been published concerning tongue tumours is often contradictory. This review will concentrate on the immunohistochemical expression of biomolecular markers and their relationships with clinical behaviour and prognosis. Most of these proteins are associated with nodal stage, tumour progression and metastases, but there is still controversy concerning their impact on disease-free and overall survival, and treatment response. More extensive clinical studies are needed to identify the patterns of molecular alterations and the most reliable predictors in order to develop tailored anti-tumour strategies based on the targeting of hypoxia markers, vascular and lymphangiogenic factors, epidermal growth factor receptors, intracytoplasmatic signalling and apoptosis.

  16. Biomolecular computing systems: principles, progress and potential. (United States)

    Benenson, Yaakov


    The task of information processing, or computation, can be performed by natural and man-made 'devices'. Man-made computers are made from silicon chips, whereas natural 'computers', such as the brain, use cells and molecules. Computation also occurs on a much smaller scale in regulatory and signalling pathways in individual cells and even within single biomolecules. Indeed, much of what we recognize as life results from the remarkable capacity of biological building blocks to compute in highly sophisticated ways. Rational design and engineering of biological computing systems can greatly enhance our ability to study and to control biological systems. Potential applications include tissue engineering and regeneration and medical treatments. This Review introduces key concepts and discusses recent progress that has been made in biomolecular computing.

  17. Fundamentos biomoleculares de la diabetes mellitus

    Directory of Open Access Journals (Sweden)

    Katiana Mendoza


    Full Text Available La diabetes mellitus es una enfermedad endocrina con importantes implicaciones a nivel sistémico, como: angiopatía, neuropatía, retinopatía y nefropatía, entre otras. Estas  complicaciones tienen su origen en eventos biomoleculares desencadenados por la hiperglicemia.  La presente revisión de tema trata sobre la estructura y síntesis de la insulina en las células β del páncreas; los eventos moleculares y bioquímicos que activan su secreción como respuesta a una alta concentración de glucosa en sangre; la cascada de señalización generada por la unión de la insulina a su receptor sobre células diana; y las alteraciones metabólicas que los diferentes tipos de diabetes mellitus producen.

  18. Structure determination by X-ray crystallography

    CERN Document Server

    Ladd, M F C


    Crystallography may be described as the science of the structure of materi­ als, using this word in its widest sense, and its ramifications are apparent over a broad front of current scientific endeavor. It is not surprising, therefore, to find that most universities offer some aspects of crystallography in their undergraduate courses in the physical sciences. It is the principal aim of this book to present an introduction to structure determination by X-ray crystal­ lography that is appropriate mainly to both final-year undergraduate studies in crystallography, chemistry, and chemical physics, and introductory post­ graduate work in this area of crystallography. We believe that the book will be of interest in other disciplines, such as physics, metallurgy, biochemistry, and geology, where crystallography has an important part to play. In the space of one book, it is not possible either to cover all aspects of crystallography or to treat all the subject matter completely rigorously. In particular, certain ...

  19. Crystal structure determination of Jatrorrhizine chloride

    Institute of Scientific and Technical Information of China (English)

    LEI XianRong; YANG JianHua; LIN Xiang; DAI Qin; CHENG Qiang; GUO LingHong; LI Hui


    Optimum resolution data of powder X-ray diffraction (PXRD) for Jatrorrhizine (Jat) were collected by an X' Pert Pro MPD diffractometer with an X'celerator detector under the stepwise scanning condition as 8.255 ms and 0.00836°per step,2θrange of 50°-80° and total scanning period of 8-10 min. Indexing of the crystal system and a search of the space group from the powder X-ray diffraction data were conducted by the computational crystallography method. The pilot crystal models of Jat were globally optimized with Monte Carlo method and then refined with the Rietveld method. In parallel with PXRD test,single crystals of Jat were cultured in an aqueous solution by a slow-decreasing temperature method,then its crystal structure was determined by single crystal X-ray diffraction (SCXRD). Both crystal structures from PXRD and SCXRD are identical. The results show that the crystal structure of Jat belongs to a monoclinic system and the space group P21/c. The parameters of cell dimensions from PXRD are a=7.69(A),b= 12.55(A),c=20.89(A),β=106.53°,Z=4,and V=1933.4(A)3,meanwhile the parameters from SCXRD are a=7.72(A),b=12.61(A),c=20.99(A),β=106.38°,Z=4,and V=1961.3(A)3.

  20. Investigation of the Human Disease Osteogenesis Imperfecta: A Research-Based Introduction to Concepts and Skills in Biomolecular Analysis (United States)

    Mate, Karen; Sim, Alistair; Weidenhofer, Judith; Milward, Liz; Scott, Judith


    A blended approach encompassing problem-based learning (PBL) and structured inquiry was used in this laboratory exercise based on the congenital disease Osteogenesis imperfecta (OI), to introduce commonly used techniques in biomolecular analysis within a clinical context. During a series of PBL sessions students were presented with several…

  1. Changes in biomolecular profile in a single nucleolus during cell fixation. (United States)

    Kuzmin, Andrey N; Pliss, Artem; Prasad, Paras N


    Fixation of biological sample is an essential technique applied in order to "freeze" in time the intracellular molecular content. However, fixation induces changes of the cellular molecular structure, which mask physiological distribution of biomolecules and bias interpretation of results. Accurate, sensitive, and comprehensive characterization of changes in biomolecular composition, occurring during fixation, is crucial for proper analysis of experimental data. Here we apply biomolecular component analysis for Raman spectra measured in the same nucleoli of HeLa cells before and after fixation by either formaldehyde solution or by chilled ethanol. It is found that fixation in formaldehyde does not strongly affect the Raman spectra of nucleolar biomolecular components, but may significantly decrease the nucleolar RNA concentration. At the same time, ethanol fixation leads to a proportional increase (up to 40%) in concentrations of nucleolar proteins and RNA, most likely due to cell shrinkage occurring in the presence of coagulant fixative. Ethanol fixation also triggers changes in composition of nucleolar proteome, as indicated by an overall reduction of the α-helical structure of proteins and increase in the concentration of proteins containing the β-sheet conformation. We conclude that cross-linking fixation is a more appropriate protocol for mapping of proteins in situ. At the same time, ethanol fixation is preferential for studies of RNA-containing macromolecules. We supplemented our quantitative Raman spectroscopic measurements with mapping of the protein and lipid macromolecular groups in live and fixed cells using coherent anti-Stokes Raman scattering nonlinear optical imaging.

  2. Nanogap biosensors for electrical and label-free detection of biomolecular interactions

    Energy Technology Data Exchange (ETDEWEB)

    Kyu Kim, Sang; Cho, Hyunmin; Park, Hye-Jung; Kwon, Dohyoung; Min Lee, Jeong; Hyun Chung, Bong, E-mail: [BioNanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, PO Box 115, Yuseong, Daejeon 305-600 (Korea, Republic of)


    We demonstrate nanogap biosensors for electrical and label-free detection of biomolecular interactions. Parallel fabrication of nanometer distance gaps has been achieved using a silicon anisotropic wet etching technique on a silicon-on-insulator (SOI) wafer with a finely controllable silicon device layer. Since silicon anisotropic wet etching resulted in a trapezoid-shaped structure whose end became narrower during the etching, the nanogap structure was simply fabricated on the device layer of a SOI wafer. The nanogap devices were individually addressable and a gap size of less than 60 nm was obtained. We demonstrate that the nanogap biosensors can electrically detect biomolecular interactions such as biotin/streptavidin and antigen/antibody pairs. The nanogap devices show a current increase when the proteins are bound to the surface. The current increases proportionally depending upon the concentrations of the molecules in the range of 100 fg ml{sup -1}-100 ng ml{sup -1} at 1 V bias. It is expected that the nanogap developed here could be a highly sensitive biosensor platform for label-free detection of biomolecular interactions.

  3. Biomolecular interactions in HCV nucleocapsid-like particles as revealed by vibrational spectroscopy (United States)

    Rodríguez-Casado, Arantxa; Molina, Marina; Carmona, Pedro


    Hepatitis C virus (HCV) occurs in the form of 55-65 nm spherical particles, but the structure of the virion remains to be clarified. Structural studies of HCV have been hampered by the lack of an appropriate cell culture system. However, structural analyses of HCV components can provide an essential framework for understanding of the molecular mechanism of virion assembly. This article reviews the potential of vibrational spectroscopy aimed at the knowledge of HCV structural biology, particularly regarding biomolecular interactions in nucleocapsid-like particles obtained in vitro.

  4. A starting point for fluorescence-based single-molecule measurements in biomolecular research. (United States)

    Gust, Alexander; Zander, Adrian; Gietl, Andreas; Holzmeister, Phil; Schulz, Sarah; Lalkens, Birka; Tinnefeld, Philip; Grohmann, Dina


    Single-molecule fluorescence techniques are ideally suited to provide information about the structure-function-dynamics relationship of a biomolecule as static and dynamic heterogeneity can be easily detected. However, what type of single-molecule fluorescence technique is suited for which kind of biological question and what are the obstacles on the way to a successful single-molecule microscopy experiment? In this review, we provide practical insights into fluorescence-based single-molecule experiments aiming for scientists who wish to take their experiments to the single-molecule level. We especially focus on fluorescence resonance energy transfer (FRET) experiments as these are a widely employed tool for the investigation of biomolecular mechanisms. We will guide the reader through the most critical steps that determine the success and quality of diffusion-based confocal and immobilization-based total internal reflection fluorescence microscopy. We discuss the specific chemical and photophysical requirements that make fluorescent dyes suitable for single-molecule fluorescence experiments. Most importantly, we review recently emerged photoprotection systems as well as passivation and immobilization strategies that enable the observation of fluorescently labeled molecules under biocompatible conditions. Moreover, we discuss how the optical single-molecule toolkit has been extended in recent years to capture the physiological complexity of a cell making it even more relevant for biological research.

  5. A Starting Point for Fluorescence-Based Single-Molecule Measurements in Biomolecular Research

    Directory of Open Access Journals (Sweden)

    Alexander Gust


    Full Text Available Single-molecule fluorescence techniques are ideally suited to provide information about the structure-function-dynamics relationship of a biomolecule as static and dynamic heterogeneity can be easily detected. However, what type of single-molecule fluorescence technique is suited for which kind of biological question and what are the obstacles on the way to a successful single-molecule microscopy experiment? In this review, we provide practical insights into fluorescence-based single-molecule experiments aiming for scientists who wish to take their experiments to the single-molecule level. We especially focus on fluorescence resonance energy transfer (FRET experiments as these are a widely employed tool for the investigation of biomolecular mechanisms. We will guide the reader through the most critical steps that determine the success and quality of diffusion-based confocal and immobilization-based total internal reflection fluorescence microscopy. We discuss the specific chemical and photophysical requirements that make fluorescent dyes suitable for single-molecule fluorescence experiments. Most importantly, we review recently emerged photoprotection systems as well as passivation and immobilization strategies that enable the observation of fluorescently labeled molecules under biocompatible conditions. Moreover, we discuss how the optical single-molecule toolkit has been extended in recent years to capture the physiological complexity of a cell making it even more relevant for biological research.

  6. Enthalpy-entropy compensation in biomolecular halogen bonds measured in DNA junctions. (United States)

    Carter, Megan; Voth, Andrea Regier; Scholfield, Matthew R; Rummel, Brittany; Sowers, Lawrence C; Ho, P Shing


    Interest in noncovalent interactions involving halogens, particularly halogen bonds (X-bonds), has grown dramatically in the past decade, propelled by the use of X-bonding in molecular engineering and drug design. However, it is clear that a complete analysis of the structure-energy relationship must be established in biological systems to fully exploit X-bonds for biomolecular engineering. We present here the first comprehensive experimental study to correlate geometries with their stabilizing potentials for fluorine (F), chlorine (Cl), bromine (Br), or iodine (I) X-bonds in a biological context. For these studies, we determine the single-crystal structures of DNA Holliday junctions containing halogenated uracil bases that compete X-bonds against classic hydrogen bonds (H-bonds), estimate the enthalpic energies of the competing interactions in the crystal system through crystallographic titrations, and compare the enthalpic and entropic energies of bromine and iodine X-bonds in solution by differential scanning calorimetry. The culmination of these studies demonstrates that enthalpic stabilization of X-bonds increases with increasing polarizability from F to Cl to Br to I, which is consistent with the σ-hole theory of X-bonding. Furthermore, an increase in the X-bonding potential is seen to direct the interaction toward a more ideal geometry. However, the entropic contributions to the total free energies must also be considered to determine how each halogen potentially contributes to the overall stability of the interaction. We find that bromine has the optimal balance between enthalpic and entropic energy components, resulting in the lowest free energy for X-bonding in this DNA system. The X-bond formed by iodine is more enthalpically stable, but this comes with an entropic cost, which we attribute to crowding effects. Thus, the overall free energy of an X-bonding interaction balances the stabilizing electrostatic effects of the σ-hole against the competing

  7. Accelerated search for biomolecular network models to interpret high-throughput experimental data

    Directory of Open Access Journals (Sweden)

    Sokhansanj Bahrad A


    Full Text Available Abstract Background The functions of human cells are carried out by biomolecular networks, which include proteins, genes, and regulatory sites within DNA that encode and control protein expression. Models of biomolecular network structure and dynamics can be inferred from high-throughput measurements of gene and protein expression. We build on our previously developed fuzzy logic method for bridging quantitative and qualitative biological data to address the challenges of noisy, low resolution high-throughput measurements, i.e., from gene expression microarrays. We employ an evolutionary search algorithm to accelerate the search for hypothetical fuzzy biomolecular network models consistent with a biological data set. We also develop a method to estimate the probability of a potential network model fitting a set of data by chance. The resulting metric provides an estimate of both model quality and dataset quality, identifying data that are too noisy to identify meaningful correlations between the measured variables. Results Optimal parameters for the evolutionary search were identified based on artificial data, and the algorithm showed scalable and consistent performance for as many as 150 variables. The method was tested on previously published human cell cycle gene expression microarray data sets. The evolutionary search method was found to converge to the results of exhaustive search. The randomized evolutionary search was able to converge on a set of similar best-fitting network models on different training data sets after 30 generations running 30 models per generation. Consistent results were found regardless of which of the published data sets were used to train or verify the quantitative predictions of the best-fitting models for cell cycle gene dynamics. Conclusion Our results demonstrate the capability of scalable evolutionary search for fuzzy network models to address the problem of inferring models based on complex, noisy biomolecular

  8. Utilizing plasma physics to create biomolecular movies

    Energy Technology Data Exchange (ETDEWEB)

    Hau-Riege, S [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)


    In spring of 2000, the LCLS Scientific Advisory Committee selected the top scientific experiments for LCLS. One of the proposed flagship experiments is atomic-resolution three-dimensional structure determination of isolated biolgical macromolecules and particles, with the ultimate goal of obtaining molecular (snapshot) movies. The key enabling insight was that radiation damage may be overcome by using x-ray pulses that are shorter than the time it takes for damage to manifest itself.

  9. Stochastic Simulation of Biomolecular Networks in Dynamic Environments.

    Directory of Open Access Journals (Sweden)

    Margaritis Voliotis


    Full Text Available Simulation of biomolecular networks is now indispensable for studying biological systems, from small reaction networks to large ensembles of cells. Here we present a novel approach for stochastic simulation of networks embedded in the dynamic environment of the cell and its surroundings. We thus sample trajectories of the stochastic process described by the chemical master equation with time-varying propensities. A comparative analysis shows that existing approaches can either fail dramatically, or else can impose impractical computational burdens due to numerical integration of reaction propensities, especially when cell ensembles are studied. Here we introduce the Extrande method which, given a simulated time course of dynamic network inputs, provides a conditionally exact and several orders-of-magnitude faster simulation solution. The new approach makes it feasible to demonstrate-using decision-making by a large population of quorum sensing bacteria-that robustness to fluctuations from upstream signaling places strong constraints on the design of networks determining cell fate. Our approach has the potential to significantly advance both understanding of molecular systems biology and design of synthetic circuits.

  10. The fidelity of dynamic signaling by noisy biomolecular networks.

    Directory of Open Access Journals (Sweden)

    Clive G Bowsher

    Full Text Available Cells live in changing, dynamic environments. To understand cellular decision-making, we must therefore understand how fluctuating inputs are processed by noisy biomolecular networks. Here we present a general methodology for analyzing the fidelity with which different statistics of a fluctuating input are represented, or encoded, in the output of a signaling system over time. We identify two orthogonal sources of error that corrupt perfect representation of the signal: dynamical error, which occurs when the network responds on average to other features of the input trajectory as well as to the signal of interest, and mechanistic error, which occurs because biochemical reactions comprising the signaling mechanism are stochastic. Trade-offs between these two errors can determine the system's fidelity. By developing mathematical approaches to derive dynamics conditional on input trajectories we can show, for example, that increased biochemical noise (mechanistic error can improve fidelity and that both negative and positive feedback degrade fidelity, for standard models of genetic autoregulation. For a group of cells, the fidelity of the collective output exceeds that of an individual cell and negative feedback then typically becomes beneficial. We can also predict the dynamic signal for which a given system has highest fidelity and, conversely, how to modify the network design to maximize fidelity for a given dynamic signal. Our approach is general, has applications to both systems and synthetic biology, and will help underpin studies of cellular behavior in natural, dynamic environments.


    Institute of Scientific and Technical Information of China (English)

    WANG De-ming; GAI Bing-zheng


    For calculating the stiffness function of a structure, the differential equation of the vibration of the structure was divided into the differential equation on the original stiffness function that was known, and Fredholm integral equation of the first kind on the undetermined stiffness function that was unknown. And the stable solutions of the integral equation, when the smooth factor was equal to zero, was solved by the extrapolation with p smooth factors. So the stiffness function of the structure is obtained. Applied examples show that the method is feasible and effective.

  12. Determining crystal structures through crowdsourcing and coursework (United States)

    Horowitz, Scott; Koepnick, Brian; Martin, Raoul; Tymieniecki, Agnes; Winburn, Amanda A.; Cooper, Seth; Flatten, Jeff; Rogawski, David S.; Koropatkin, Nicole M.; Hailu, Tsinatkeab T.; Jain, Neha; Koldewey, Philipp; Ahlstrom, Logan S.; Chapman, Matthew R.; Sikkema, Andrew P.; Skiba, Meredith A.; Maloney, Finn P.; Beinlich, Felix R. M.; Caglar, Ahmet; Coral, Alan; Jensen, Alice Elizabeth; Lubow, Allen; Boitano, Amanda; Lisle, Amy Elizabeth; Maxwell, Andrew T.; Failer, Barb; Kaszubowski, Bartosz; Hrytsiv, Bohdan; Vincenzo, Brancaccio; de Melo Cruz, Breno Renan; McManus, Brian Joseph; Kestemont, Bruno; Vardeman, Carl; Comisky, Casey; Neilson, Catherine; Landers, Catherine R.; Ince, Christopher; Buske, Daniel Jon; Totonjian, Daniel; Copeland, David Marshall; Murray, David; Jagieła, Dawid; Janz, Dietmar; Wheeler, Douglas C.; Cali, Elie; Croze, Emmanuel; Rezae, Farah; Martin, Floyd Orville; Beecher, Gil; de Jong, Guido Alexander; Ykman, Guy; Feldmann, Harald; Chan, Hugo Paul Perez; Kovanecz, Istvan; Vasilchenko, Ivan; Connellan, James C.; Borman, Jami Lynne; Norrgard, Jane; Kanfer, Jebbie; Canfield, Jeffrey M.; Slone, Jesse David; Oh, Jimmy; Mitchell, Joanne; Bishop, John; Kroeger, John Douglas; Schinkler, Jonas; McLaughlin, Joseph; Brownlee, June M.; Bell, Justin; Fellbaum, Karl Willem; Harper, Kathleen; Abbey, Kirk J.; Isaksson, Lennart E.; Wei, Linda; Cummins, Lisa N.; Miller, Lori Anne; Bain, Lyn; Carpenter, Lynn; Desnouck, Maarten; Sharma, Manasa G.; Belcastro, Marcus; Szew, Martin; Szew, Martin; Britton, Matthew; Gaebel, Matthias; Power, Max; Cassidy, Michael; Pfützenreuter, Michael; Minett, Michele; Wesselingh, Michiel; Yi, Minjune; Cameron, Neil Haydn Tormey; Bolibruch, Nicholas I.; Benevides, Noah; Kathleen Kerr, Norah; Barlow, Nova; Crevits, Nykole Krystyne; Dunn, Paul; Silveira Belo Nascimento Roque, Paulo Sergio; Riber, Peter; Pikkanen, Petri; Shehzad, Raafay; Viosca, Randy; James Fraser, Robert; Leduc, Robert; Madala, Roman; Shnider, Scott; de Boisblanc, Sharon; Butkovich, Slava; Bliven, Spencer; Hettler, Stephen; Telehany, Stephen; Schwegmann, Steven A.; Parkes, Steven; Kleinfelter, Susan C.; Michael Holst, Sven; van der Laan, T. J. A.; Bausewein, Thomas; Simon, Vera; Pulley, Warwick; Hull, William; Kim, Annes Yukyung; Lawton, Alexis; Ruesch, Amanda; Sundar, Anjali; Lawrence, Anna-Lisa; Afrin, Antara; Maheshwer, Bhargavi; Turfe, Bilal; Huebner, Christian; Killeen, Courtney Elizabeth; Antebi-Lerrman, Dalia; Luan, Danny; Wolfe, Derek; Pham, Duc; Michewicz, Elaina; Hull, Elizabeth; Pardington, Emily; Galal, Galal Osama; Sun, Grace; Chen, Grace; Anderson, Halie E.; Chang, Jane; Hewlett, Jeffrey Thomas; Sterbenz, Jennifer; Lim, Jiho; Morof, Joshua; Lee, Junho; Inn, Juyoung Samuel; Hahm, Kaitlin; Roth, Kaitlin; Nair, Karun; Markin, Katherine; Schramm, Katie; Toni Eid, Kevin; Gam, Kristina; Murphy, Lisha; Yuan, Lucy; Kana, Lulia; Daboul, Lynn; Shammas, Mario Karam; Chason, Max; Sinan, Moaz; Andrew Tooley, Nicholas; Korakavi, Nisha; Comer, Patrick; Magur, Pragya; Savliwala, Quresh; Davison, Reid Michael; Sankaran, Roshun Rajiv; Lewe, Sam; Tamkus, Saule; Chen, Shirley; Harvey, Sho; Hwang, Sin Ye; Vatsia, Sohrab; Withrow, Stefan; Luther, Tahra K.; Manett, Taylor; Johnson, Thomas James; Ryan Brash, Timothy; Kuhlman, Wyatt; Park, Yeonjung; Popović, Zoran; Baker, David; Khatib, Firas; Bardwell, James C. A.


    We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit players achieved the most accurate structure. Analysing the target protein of the competition, YPL067C, uncovered a new family of histidine triad proteins apparently involved in the prevention of amyloid toxicity. From this study, we conclude that crystallographers can utilize crowdsourcing to interpret electron density information and to produce structure solutions of the highest quality.

  13. Combining vibrational biomolecular spectroscopy with chemometric techniques for the study of response and sensitivity of molecular structures/functional groups mainly related to lipid biopolymer to various processing applications. (United States)

    Yu, Gloria Qingyu; Yu, Peiqiang


    The objectives of this project were to (1) combine vibrational spectroscopy with chemometric multivariate techniques to determine the effect of processing applications on molecular structural changes of lipid biopolymer that mainly related to functional groups in green- and yellow-type Crop Development Centre (CDC) pea varieties [CDC strike (green-type) vs. CDC meadow (yellow-type)] that occurred during various processing applications; (2) relatively quantify the effect of processing applications on the antisymmetric CH3 ("CH3as") and CH2 ("CH2as") (ca. 2960 and 2923 cm(-1), respectively), symmetric CH3 ("CH3s") and CH2 ("CH2s") (ca. 2873 and 2954 cm(-1), respectively) functional groups and carbonyl C=O ester (ca. 1745 cm(-1)) spectral intensities as well as their ratios of antisymmetric CH3 to antisymmetric CH2 (ratio of CH3as to CH2as), ratios of symmetric CH3 to symmetric CH2 (ratio of CH3s to CH2s), and ratios of carbonyl C=O ester peak area to total CH peak area (ratio of C=O ester to CH); and (3) illustrate non-invasive techniques to detect the sensitivity of individual molecular functional group to the various processing applications in the recently developed different types of pea varieties. The hypothesis of this research was that processing applications modified the molecular structure profiles in the processed products as opposed to original unprocessed pea seeds. The results showed that the different processing methods had different impacts on lipid molecular functional groups. Different lipid functional groups had different sensitivity to various heat processing applications. These changes were detected by advanced molecular spectroscopy with chemometric techniques which may be highly related to lipid utilization and availability. The multivariate molecular spectral analyses, cluster analysis, and principal component analysis of original spectra (without spectral parameterization) are unable to fully distinguish the structural differences in the

  14. Determining crystal structures through crowdsourcing and coursework



    We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit pla...


    Directory of Open Access Journals (Sweden)

    Pejman Kamkarian


    Full Text Available This paper explores a strategy for determining public space safety. Due to varied purposes and locations, each public space has architecture as well as facilities. A generalized analysis of capacities for public spaces is essential. The method we propose is to examine a public space with a given architecture. We used Bayesian Belief Network to determine the level of safety and identify points of weakness in public spaces.



    Pejman Kamkarian; Henry Hexmoor


    This paper explores a strategy for determining public space safety. Due to varied purposes and locations, each public space has architecture as well as facilities. A generalized analysis of capacities for public spaces is essential. The method we propose is to examine a public space with a given architecture. We used Bayesian Belief Network to determine the level of safety and identify points of weakness in public spaces.

  17. Structure determination by X-ray crystallography

    CERN Document Server

    Ladd, M F C


    X-ray crystallography provides us with the most accurate picture we can get of atomic and molecular structures in crystals. It provides a hard bedrock of structural results in chemistry and in mineralogy. In biology, where the structures are not fully crystalline, it can still provide valuable results and, indeed, the impact here has been revolutionary. It is still an immense field for young workers, and no doubt will provide yet more striking develop­ ments of a major character. It does, however, require a wide range of intellectual application, and a considerable ability in many fields. This book will provide much help. It is a very straightforward and thorough guide to every aspect of the subject. The authors are experienced both as research workers themselves and as teachers of standing, and this is shown in their clarity of exposition. There are plenty of iliustrations and worked examples to aid the student to obtain a real grasp of the subject.

  18. Determination of hair structure and shape. (United States)

    Schlake, Thomas


    The hair follicle attracted significant attention as a model for the investigation of diverse biological problems. Whereas its morphology and the structure of the hair shaft are known in detail, the molecular biology of this miniorgan is significantly less characterised. Many efforts focussed on the development of the hair follicle and its stem cell reservoir; by contrast, the follicular product, the hair, which is interesting not only in terms of cosmetics was neglected. This review highlights our current knowledge of the control of hair structure and shape with emphasis on mouse hair follicle biology and discusses continuing problems.

  19. Electron Diffraction Determination of Nanoscale Structures

    Energy Technology Data Exchange (ETDEWEB)

    Parks, Joel H


    Dominant research results on adsorption on gold clusters are reviewed, including adsorption of H{sub 2}O and O{sub 2} on gold cluster cations and anions, kinetics of CO adsorption to middle sized gold cluster cations, adsorption of CO on Au{sub n}{sup +} with induced changes in structure, and H{sub 2}O enhancement of CO adsorption.

  20. A mechanical Turing machine: blueprint for a biomolecular computer. (United States)

    Shapiro, Ehud


    We describe a working mechanical device that embodies the theoretical computing machine of Alan Turing, and as such is a universal programmable computer. The device operates on three-dimensional building blocks by applying mechanical analogues of polymer elongation, cleavage and ligation, movement along a polymer, and control by molecular recognition unleashing allosteric conformational changes. Logically, the device is not more complicated than biomolecular machines of the living cell, and all its operations are part of the standard repertoire of these machines; hence, a biomolecular embodiment of the device is not infeasible. If implemented, such a biomolecular device may operate in vivo, interacting with its biochemical environment in a program-controlled manner. In particular, it may 'compute' synthetic biopolymers and release them into its environment in response to input from the environment, a capability that may have broad pharmaceutical and biological applications.

  1. Determination of micro structural corrosion by BN

    Energy Technology Data Exchange (ETDEWEB)

    Zergoug, M.; Kamel, G.; Benchaala, A. [Laboratoire d' Electronique et d' Electrotechnique, Centre de soudage et de controle, Route de Dely Ibrahim, B.P:64, Cheraga (Algeria)


    The quality control of industrial components requires adaptation and the development of new material characterization and particular non destructive testing techniques. To characterize steel, it would be useful to know its chemical composition, physic-chemical constitution, metallurgical state (annealed, hammered) and other parameters (superficial and chemical processing, etc.). The testing method using Barkhausen noise (B.N.) is a particular method, which can be applied on ferromagnetic materials. It is a magnetic non destructive evaluation (NDE) method and can provide very important information about the material microstructure. The work here presented documents the ability to determine the metallurgical state of steel submitted to the corrosive attack by electrochemical process. The samples are characterized by Barkhausen noise as non destructive methods and are compared with methods as metallography, micro hardness measurement, and toughness determination. (authors)

  2. The Determination and Development of Sectoral Structure



    The development over time of sectors in terms of value added and employment has common characteristics in all economies. We develop a simple Ricardian multi-sector general equilibrium model that allows for (i) non-unitary income elasticities, (ii) different paces of technological progress per sector, and (iii) endogenously determined technological progress per sector. A model with these ingredients allows us to replicate the sectoral developments that are found empirically, and which are show...

  3. Structural determinants of MALT1 protease activity. (United States)

    Wiesmann, Christian; Leder, Lukas; Blank, Jutta; Bernardi, Anna; Melkko, Samu; Decock, Arnaud; D'Arcy, Allan; Villard, Frederic; Erbel, Paulus; Hughes, Nicola; Freuler, Felix; Nikolay, Rainer; Alves, Juliano; Bornancin, Frederic; Renatus, Martin


    The formation of the CBM (CARD11-BCL10-MALT1) complex is pivotal for antigen-receptor-mediated activation of the transcription factor NF-κB. Signaling is dependent on MALT1 (mucosa-associated lymphoid tissue lymphoma translocation protein 1), which not only acts as a scaffolding protein but also possesses proteolytic activity mediated by its caspase-like domain. It remained unclear how the CBM activates MALT1. Here, we provide biochemical and structural evidence that MALT1 activation is dependent on its dimerization and show that mutations at the dimer interface abrogate activity in cells. The unliganded protease presents itself in a dimeric yet inactive state and undergoes substantial conformational changes upon substrate binding. These structural changes also affect the conformation of the C-terminal Ig-like domain, a domain that is required for MALT1 activity. Binding to the active site is coupled to a relative movement of caspase and Ig-like domains. MALT1 binding partners thus may have the potential of tuning MALT1 protease activity without binding directly to the caspase domain.

  4. How structure determines correlations in neuronal networks.

    Directory of Open Access Journals (Sweden)

    Volker Pernice


    Full Text Available Networks are becoming a ubiquitous metaphor for the understanding of complex biological systems, spanning the range between molecular signalling pathways, neural networks in the brain, and interacting species in a food web. In many models, we face an intricate interplay between the topology of the network and the dynamics of the system, which is generally very hard to disentangle. A dynamical feature that has been subject of intense research in various fields are correlations between the noisy activity of nodes in a network. We consider a class of systems, where discrete signals are sent along the links of the network. Such systems are of particular relevance in neuroscience, because they provide models for networks of neurons that use action potentials for communication. We study correlations in dynamic networks with arbitrary topology, assuming linear pulse coupling. With our novel approach, we are able to understand in detail how specific structural motifs affect pairwise correlations. Based on a power series decomposition of the covariance matrix, we describe the conditions under which very indirect interactions will have a pronounced effect on correlations and population dynamics. In random networks, we find that indirect interactions may lead to a broad distribution of activation levels with low average but highly variable correlations. This phenomenon is even more pronounced in networks with distance dependent connectivity. In contrast, networks with highly connected hubs or patchy connections often exhibit strong average correlations. Our results are particularly relevant in view of new experimental techniques that enable the parallel recording of spiking activity from a large number of neurons, an appropriate interpretation of which is hampered by the currently limited understanding of structure-dynamics relations in complex networks.

  5. Determining building interior structures using compressive sensing (United States)

    Lagunas, Eva; Amin, Moeness G.; Ahmad, Fauzia; Nájar, Montse


    We consider imaging of the building interior structures using compressive sensing (CS) with applications to through-the-wall imaging and urban sensing. We consider a monostatic synthetic aperture radar imaging system employing stepped frequency waveform. The proposed approach exploits prior information of building construction practices to form an appropriate sparse representation of the building interior layout. We devise a dictionary of possible wall locations, which is consistent with the fact that interior walls are typically parallel or perpendicular to the front wall. The dictionary accounts for the dominant normal angle reflections from exterior and interior walls for the monostatic imaging system. CS is applied to a reduced set of observations to recover the true positions of the walls. Additional information about interior walls can be obtained using a dictionary of possible corner reflectors, which is the response of the junction of two walls. Supporting results based on simulation and laboratory experiments are provided. It is shown that the proposed sparsifying basis outperforms the conventional through-the-wall CS model, the wavelet sparsifying basis, and the block sparse model for building interior layout detection.

  6. Structural Determinants of Sleeping Beauty Transposase Activity. (United States)

    Abrusán, György; Yant, Stephen R; Szilágyi, András; Marsh, Joseph A; Mátés, Lajos; Izsvák, Zsuzsanna; Barabás, Orsolya; Ivics, Zoltán


    Transposases are important tools in genome engineering, and there is considerable interest in engineering more efficient ones. Here, we seek to understand the factors determining their activity using the Sleeping Beauty transposase. Recent work suggests that protein coevolutionary information can be used to classify groups of physically connected, coevolving residues into elements called "sectors", which have proven useful for understanding the folding, allosteric interactions, and enzymatic activity of proteins. Using extensive mutagenesis data, protein modeling and analysis of folding energies, we show that (i) The Sleeping Beauty transposase contains two sectors, which span across conserved domains, and are enriched in DNA-binding residues, indicating that the DNA binding and endonuclease functions of the transposase coevolve; (ii) Sector residues are highly sensitive to mutations, and most mutations of these residues strongly reduce transposition rate; (iii) Mutations with a strong effect on free energy of folding in the DDE domain of the transposase significantly reduce transposition rate. (iv) Mutations that influence DNA and protein-protein interactions generally reduce transposition rate, although most hyperactive mutants are also located on the protein surface, including residues with protein-protein interactions. This suggests that hyperactivity results from the modification of protein interactions, rather than the stabilization of protein fold.

  7. Determination of atomic cluster structure with cluster fusion algorithm

    DEFF Research Database (Denmark)

    Obolensky, Oleg I.; Solov'yov, Ilia; Solov'yov, Andrey V.


    We report an efficient scheme of global optimization, called cluster fusion algorithm, which has proved its reliability and high efficiency in determination of the structure of various atomic clusters.......We report an efficient scheme of global optimization, called cluster fusion algorithm, which has proved its reliability and high efficiency in determination of the structure of various atomic clusters....

  8. Syntheses and Structure Determinations of Calcium Thiolates. (United States)

    Chadwick, Scott; Englich, Ulrich; Noll, Bruce; Ruhlandt-Senge, Karin


    The exploration of synthetic methodologies toward heavy alkaline-earth chalcogenolates resulted in the preparation and structural characterization of a family of calcium thiolates, including [Ca(SC(6)F(5))(2)(py)(4)], 1 (py = pyridine), the separated ion-triple [Ca(18-crown-6)(NH(3))(3))][SMes](2).2THF, 2 (Mes = 2,4,6-tBu(3)C(6)H(2)), and the contact triple [Ca(18-crown-6)(SMes)(2)].THF, 3. Compound 1 was prepared by treating [Ca(N(SiMe(3))(2))(2)](2) with 4 equiv of HSC(6)F(5) under addition of pyridine. The thiolates 2 and 3 were synthesized by treatment of calcium metal dissolved in dry, liquid NH(3) under addition of 2 equiv of HSMes and crown ether or, alternatively, by the reduction of MesSSMes with calcium metal in dry, liquid ammonia. We also report two reaction products isolated during attempted calcium thiolate syntheses: [CaBr(4)(THF)(2)(&mgr;(2)-Li)(2)(THF)(4)], 4, isolated as the product of a salt elimination reaction between CaBr(2) and 2 equiv of [Li(THF)(n)()S-2,4,6-(i)()Pr(3)C(6)H(2)](m)(). [(NH(4))(py)(SC(6)F(5))], 5, was obtained as the sole product in the reaction of metallic calcium with HSC(6)F(5) in liquid ammonia under addition of pyridine. All compounds were characterized by single-crystal X-ray crystallography in addition to IR and NMR spectroscopy.

  9. Determination of Ice Characteristics for Marine Hydroengineering Structures

    Energy Technology Data Exchange (ETDEWEB)

    Kantarzhi, I. G., E-mail: [Moscow State University of Civil Engineering (MSGU) (Russian Federation); Maderich, V. S., E-mail:; Koshebutskii, V. I., E-mail: [Ukrainian Center of Environmental and Water Projects (UTsÉVP) (Ukraine)


    Problems and potential approaches to determining ice characteristics for sea hydroengineering structures design are considered. A system for numerical modeling of ice dynamics is presented. The system may be used to define ice characteristics on approaches to structures with due regard for local hydrometeorological conditions and ice loads on structures. System application examples are presented for determining computational scenarios for ice loads at structures of the Pevek floating nuclear power plant (FNPP), as well as for the breakwater pier under reconstruction in Vanino. A scenario approach is used to determined ice loads.

  10. Transient response characteristics in a biomolecular integral controller. (United States)

    Sen, Shaunak


    The cellular behaviour of perfect adaptation is achieved through the use of an integral control element in the underlying biomolecular circuit. It is generally unclear how integral action affects the important aspect of transient response in these biomolecular systems, especially in light of the fact that it typically deteriorates the transient response in engineering contexts. To address this issue, the authors investigated the transient response in a computational model of a simple biomolecular integral control system involved in bacterial signalling. They find that the transient response can actually speed up as the integral gain parameter increases. On further analysis, they find that the underlying dynamics are composed of slow and fast modes and the speed-up of the transient response is because of the speed-up of the slow-mode dynamics. Finally, they note how an increase in the integral gain parameter also leads to a decrease in the amplitude of the transient response, consistent with the overall improvement in the transient response. These results should be useful in understanding the overall effect of integral action on system dynamics, particularly for biomolecular systems.

  11. Exposing biomolecular properties one molecule at a time

    NARCIS (Netherlands)

    Elmalk, Abdalmohsen


    The work described in this thesis was aimed at the study of the functional properties of (isolated and purified) biomolecular systems at the single-molecule level. Two prerequisites are essential for successfully achieving this goal. First of all, single biomolecules should be observable, which mean

  12. Biomolecular recognition mechanisms studied by NMR spectroscopy and MD simulations

    NARCIS (Netherlands)

    Hsu, Shang-Te Danny


    This thesis describes the use of solution Nuclear Magnetic Resonance (NMR) spectroscopy and Molecular Dynamics (MD) simulations to study the mechanism of biomolecular recognition with two model systems: i) lipid II-binding lantibiotics (lanthionine-containing antibiotics) and ii) the human immunodef

  13. Bases biomoleculares do fotoenvelhecimento Molecular basis of photoaging

    Directory of Open Access Journals (Sweden)

    Suelen Montagner


    Full Text Available Com o aumento da expectativa de vida, o estudo do processo de envelhecimento orgânico tem sido estimulado. O envelhecimento da pele, órgão que espelha os sinais do tempo, é processo de deterioração progressiva, tempo-dependente, e pode ser intensificado pela exposição solar, então designado fotoenvelhecimento. O dano das radiações sobre diversas estruturas celulares e cutâneas leva a alterações morfológicas nesses componentes, fruto de modificações biomoleculares. Muitas pesquisas são desenvolvidas com o intuito de combater ou minimizar os efeitos do fotoenvelhecimento, porém a principal estratégia nesse sentido continua sendo a prevenção, só conseguida pelo progressivo desvendar dos mecanismos fisiopatogênicos envolvidos nesse processo.As a result of the increase in life expectancy, the study of the organic process of aging has been stimulated. Skin ageing, which reflects the signs of time, is a time-dependent process of progressive deterioration that can be intensified by sun exposure, which is known as photoaging. The damage of radiation on various cell structures and on the skin results in molecular and morphological changes to these components. Many research studies are performed to try to minimize the effects of photoaging; however, the main strategy to manage it is still prevention, which will only be achieved once we learn about the mechanisms involved in the process.

  14. Bridging Nano- and Microtribology in Mechanical and Biomolecular Layers (United States)

    Tomala, Agnieszka; Göçerler, Hakan; Gebeshuber, Ille C.

    The physical and chemical composition of surfaces determine various important properties of solids such as corrosion rates, adhesive properties, frictional properties, catalytic activity, wettability, contact potential and - finally and most importantly - failure mechanisms. Very thin, weak layers (of man-made and biological origin) on much harder substrates that reduce friction are the focus of the micro- and nanotribological investigations presented in this chapter.Biomolecular layers fulfil various functions in organs of the human body. Examples comprise the skin that provides a protective physical barrier between the body and the environment, preventing unwanted inward and outward passage of water and electrolytes, reducing penetration by destructive chemicals, arresting the penetration of microorganisms and external antigens and absorbing radiation from the sun, or the epithelium of the cornea that blocks the passage of foreign material, such as dust, water and bacteria, into the eye and that contributes to the lubrication layer that ensures smooth movement of the eyelids over the eyeballs.Monomolecular thin films, additive-derived reaction layers and hard coatings are widely used to tailor tribological properties of surfaces. Nanotribological investigations on these substrates can reveal novel properties regarding the orientation of chemisorbed additive layers, development of rubbing films with time and the relation of frictional properties to surface characteristics in diamond coatings.Depending on the questions to be answered with the tribological research, various micro- and nanotribological measurement methods are applied, including scanning probe microscopy (AFM, FFM), scanning electron microscopy, microtribometer investigations, angle-resolved photoelectron spectroscopy and optical microscopy. Thoughts on the feasibility of a unified approach to energy-dissipating systems and how it might be reached (touching upon new ways of scientific publishing

  15. Ab initio structure determination via powder X-ray diffraction

    Indian Academy of Sciences (India)

    Digamber G Porob; T N Guru Row


    Structure determination by powder X-ray diffraction data has gone through a recent surge since it has become important to get to the structural information of materials which do not yield good quality single crystals. Although the method of structure completion when once the starting model is provided is facile through the Rietveld refinement technique, the structure solution ab initio os still not push-button technology. In this article a survey of the recent development in this area is provided with an illustration of the structure determination of -NaBi3V2O10.

  16. The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes. (United States)

    van Zundert, G C P; Rodrigues, J P G L M; Trellet, M; Schmitz, C; Kastritis, P L; Karaca, E; Melquiond, A S J; van Dijk, M; de Vries, S J; Bonvin, A M J J


    The prediction of the quaternary structure of biomolecular macromolecules is of paramount importance for fundamental understanding of cellular processes and drug design. In the era of integrative structural biology, one way of increasing the accuracy of modeling methods used to predict the structure of biomolecular complexes is to include as much experimental or predictive information as possible in the process. This has been at the core of our information-driven docking approach HADDOCK. We present here the updated version 2.2 of the HADDOCK portal, which offers new features such as support for mixed molecule types, additional experimental restraints and improved protocols, all of this in a user-friendly interface. With well over 6000 registered users and 108,000 jobs served, an increasing fraction of which on grid resources, we hope that this timely upgrade will help the community to solve important biological questions and further advance the field. The HADDOCK2.2 Web server is freely accessible to non-profit users at

  17. Determination of Hydrogen Bond Structure in Water versus Aprotic Environments To Test the Relationship Between Length and Stability

    Energy Technology Data Exchange (ETDEWEB)

    Sigala, Paul A.; Ruben, Eliza A.; Liu, Corey W.; Piccoli, Paula M. B.; Hohenstein, Edward G.; Martinez, Todd J.; Schultz, Arthur J.; Herschiag, Daniel


    Hydrogen bonds profoundly influence the architecture and activity of biological macromolecules. Deep appreciation of hydrogen bond contributions to biomolecular function thus requires a detailed understanding of hydrogen bond structure and energetics and the relationship between these properties. Hydrogen bond formation energies (Delta G(f)) are enormously more favorable in aprotic solvents than in water, and two classes of contributing factors have been proposed to explain this energetic difference, focusing respectively on the isolated and hydrogen-bonded species: (I) water stabilizes the dissociated donor and acceptor groups much better than aprotic solvents, thereby reducing the driving force for hydrogen bond formation; and (II) water lengthens hydrogen bonds compared to aprotic environments, thereby decreasing the potential energy within the hydrogen bond. Each model has been proposed to provide a dominant contribution to Delta G(f), but incisive tests that distinguish the importance of these contributions are lacking. Here we directly test the structural basis of model II. Neutron crystallography, NMR spectroscopy, and quantum mechanical calculations demonstrate that O-H center dot center dot center dot O hydrogen bonds in crystals, chloroform, acetone, and water have nearly identical lengths and very similar potential energy surfaces despite Delta G(f) differences >8 kcal/mol across these solvents. These results rule out a substantial contribution from solvent-dependent differences in hydrogen bond structure and potential energy after association (model II) and thus support the conclusion that differences in hydrogen bond Delta G(f) are predominantly determined by solvent interactions with the dissociated groups (model I). These findings advance our understanding of universal hydrogen-bonding interactions and have important implications for biology and engineering.

  18. Target selection and determination of function in structural genomics. (United States)

    Watson, James D; Todd, Annabel E; Bray, James; Laskowski, Roman A; Edwards, Aled; Joachimiak, Andrzej; Orengo, Christine A; Thornton, Janet M


    The first crucial step in any structural genomics project is the selection and prioritization of target proteins for structure determination. There may be a number of selection criteria to be satisfied, including that the proteins have novel folds, that they be representatives of large families for which no structure is known, and so on. The better the selection at this stage, the greater is the value of the structures obtained at the end of the experimental process. This value can be further enhanced once the protein structures have been solved if the functions of the given proteins can also be determined. Here we describe the methods used at either end of the experimental process: firstly, sensitive sequence comparison techniques for selecting a high-quality list of target proteins, and secondly the various computational methods that can be applied to the eventual 3D structures to determine the most likely biochemical function of the proteins in question.

  19. DockScreen: A Database of In Silico Biomolecular Interactions to Support Computational Toxicology

    Directory of Open Access Journals (Sweden)

    Michael-Rock Goldsmith


    Full Text Available We have developed DockScreen, a database of in silico biomolecular interactions designed to enable rational molecular toxicological insight within a computational toxicology framework. This database is composed of chemical/target (receptor and enzyme binding scores calculated by molecular docking of more than 1000 chemicals into 150 protein targets and contains nearly 135 thousand unique ligand/target binding scores. Obtaining this dataset was achieved using eHiTS (Simbiosys Inc., a fragment-based molecular docking approach with an exhaustive search algorithm, on a heterogeneous distributed high-performance computing framework. The chemical landscape covered in DockScreen comprises selected environmental and therapeutic chemicals. The target landscape covered in DockScreen was selected based on the availability of high-quality crystal structures that covered the assay space of phase I ToxCast in vitro assays. This in silico data provides continuous information that establishes a means for quantitatively comparing, on a structural biophysical basis, a chemical’s profile of biomolecular interactions. The combined minimum-score chemical/target matrix is provided.

  20. Cryo-EM Structure Determination Using Segmented Helical Image Reconstruction. (United States)

    Fromm, S A; Sachse, C


    Treating helices as single-particle-like segments followed by helical image reconstruction has become the method of choice for high-resolution structure determination of well-ordered helical viruses as well as flexible filaments. In this review, we will illustrate how the combination of latest hardware developments with optimized image processing routines have led to a series of near-atomic resolution structures of helical assemblies. Originally, the treatment of helices as a sequence of segments followed by Fourier-Bessel reconstruction revealed the potential to determine near-atomic resolution structures from helical specimens. In the meantime, real-space image processing of helices in a stack of single particles was developed and enabled the structure determination of specimens that resisted classical Fourier helical reconstruction and also facilitated high-resolution structure determination. Despite the progress in real-space analysis, the combination of Fourier and real-space processing is still commonly used to better estimate the symmetry parameters as the imposition of the correct helical symmetry is essential for high-resolution structure determination. Recent hardware advancement by the introduction of direct electron detectors has significantly enhanced the image quality and together with improved image processing procedures has made segmented helical reconstruction a very productive cryo-EM structure determination method.

  1. Crystallization and Structure Determination of Superantigens and Immune Receptor Complexes. (United States)

    Rödström, Karin E J; Lindkvist-Petersson, Karin


    Structure determination of superantigens and the complexes they form with immune receptors have over the years provided insight in their modes of action. This technique requires growing large and highly ordered crystals of the superantigen or receptor-superantigen complex, followed by exposure to X-ray radiation and data collection. Here, we describe methods for crystallizing superantigens and superantigen-receptor complexes using the vapor diffusion technique, how the crystals may be optimized, and lastly data collection and structure determination.

  2. NMRFAM-SDF: a protein structure determination framework

    Energy Technology Data Exchange (ETDEWEB)

    Dashti, Hesam; Lee, Woonghee; Tonelli, Marco; Cornilescu, Claudia C.; Cornilescu, Gabriel; Assadi-Porter, Fariba M.; Westler, William M.; Eghbalnia, Hamid R.; Markley, John L., E-mail: [University of Wisconsin-Madison, National Magnetic Resonance Facility at Madison, Biochemistry Department (United States)


    The computationally demanding nature of automated NMR structure determination necessitates a delicate balancing of factors that include the time complexity of data collection, the computational complexity of chemical shift assignments, and selection of proper optimization steps. During the past two decades the computational and algorithmic aspects of several discrete steps of the process have been addressed. Although no single comprehensive solution has emerged, the incorporation of a validation protocol has gained recognition as a necessary step for a robust automated approach. The need for validation becomes even more pronounced in cases of proteins with higher structural complexity, where potentially larger errors generated at each step can propagate and accumulate in the process of structure calculation, thereby significantly degrading the efficacy of any software framework. This paper introduces a complete framework for protein structure determination with NMR—from data acquisition to the structure determination. The aim is twofold: to simplify the structure determination process for non-NMR experts whenever feasible, while maintaining flexibility by providing a set of modules that validate each step, and to enable the assessment of error propagations. This framework, called NMRFAM-SDF (NMRFAM-Structure Determination Framework), and its various components are available for download from the NMRFAM website ( )

  3. China Takes the Lead in the Structural Determination of Lumbrokinase

    Institute of Scientific and Technical Information of China (English)


    @@ After five years of arduous work, CAS scientists re cently succeeded in determining the structure of lumbrokinase (earthworm fibrinolytic enzyme),shedding light on the understanding of this drug at the molecular level and laying a foundation for drug design based on its structure.

  4. Labor Market Structure and Salary Determination among Professional Basketball Players. (United States)

    Wallace, Michael


    The author investigates the labor market structure and determinants of salaries for professional basketball players. An expanded version of the resource perspective is used. A three-tiered model of labor market segmentation is revealed for professional basketball players, but other variables also are important in salary determination. (Author/CH)

  5. The Determinants of Capital Structure: Some Evidence from Banks


    Heider, Florian; Gropp, Reint


    This paper documents that standard cross-sectional determinants of firm leverage also apply to the capital structure of large banks in the United States and Europe. We find a remarkable consistency in sign, significance and economic magnitude. Like non-financial firms, banks appear to have stable capital structures at levels that are specific to each individual bank. The results suggest that capital requirements may only be of second-order importance for banks’ capital structures and confirm ...

  6. Integral membrane protein structure determination using pseudocontact shifts

    Energy Technology Data Exchange (ETDEWEB)

    Crick, Duncan J.; Wang, Jue X. [University of Cambridge, Department of Biochemistry (United Kingdom); Graham, Bim; Swarbrick, James D. [Monash University, Monash Institute of Pharmaceutical Sciences (Australia); Mott, Helen R.; Nietlispach, Daniel, E-mail: [University of Cambridge, Department of Biochemistry (United Kingdom)


    Obtaining enough experimental restraints can be a limiting factor in the NMR structure determination of larger proteins. This is particularly the case for large assemblies such as membrane proteins that have been solubilized in a membrane-mimicking environment. Whilst in such cases extensive deuteration strategies are regularly utilised with the aim to improve the spectral quality, these schemes often limit the number of NOEs obtainable, making complementary strategies highly beneficial for successful structure elucidation. Recently, lanthanide-induced pseudocontact shifts (PCSs) have been established as a structural tool for globular proteins. Here, we demonstrate that a PCS-based approach can be successfully applied for the structure determination of integral membrane proteins. Using the 7TM α-helical microbial receptor pSRII, we show that PCS-derived restraints from lanthanide binding tags attached to four different positions of the protein facilitate the backbone structure determination when combined with a limited set of NOEs. In contrast, the same set of NOEs fails to determine the correct 3D fold. The latter situation is frequently encountered in polytopical α-helical membrane proteins and a PCS approach is thus suitable even for this particularly challenging class of membrane proteins. The ease of measuring PCSs makes this an attractive route for structure determination of large membrane proteins in general.

  7. Characterization of a nanoscale S-layer protein based template for biomolecular patterning. (United States)

    Wong, Wing Sze; Yung, Pun To


    Well organized template for biomolecular conjugation is the foundation for biosensing. Most of the current devices are fabricated using lithographic patterning processes and self-assembly monolayer (SAM) methods. However, the research toward developing a sub-10 nm patterned, self-regenerated template on various types of substrates is limited, mainly due to the limited functional groups of the building material. Bacterial surface layer proteins (S-layer proteins) can self-assemble into ordered lattice with regular pore sizes of 2-8 nm on different material supports and interfaces. The ordered structure can regenerate after extreme variations of solvent conditions. In this work, we developed a nanoscale biomolecular template based on S-layer proteins on gold surface for fabrication of sensing layer in biosensors. S-layer proteins were isolated from Bacillus cereus, Lysinibacillus sphaericus and Geobacillus stearothermophilus. Protein concentrations were measured by Bradford assay. The protein purities were verified by SDS-PAGE, showing molecular weights ranging from 97-135 kDa. The hydrophilicity of the substrate surface was measured after surface treatments of protein recrystallization. Atomic force microscopic (AFM) measurement was performed on substrate surface, indicating a successful immobilization of a monolayer of S-layer protein with 8-9 nm height on gold surface. The template can be applied on various material supports and acts as a self-regenerated sensing layer of biosensors in the future.

  8. Structural determination of intact proteins using mass spectrometry (United States)

    Kruppa, Gary; Schoeniger, Joseph S.; Young, Malin M.


    The present invention relates to novel methods of determining the sequence and structure of proteins. Specifically, the present invention allows for the analysis of intact proteins within a mass spectrometer. Therefore, preparatory separations need not be performed prior to introducing a protein sample into the mass spectrometer. Also disclosed herein are new instrumental developments for enhancing the signal from the desired modified proteins, methods for producing controlled protein fragments in the mass spectrometer, eliminating complex microseparations, and protein preparatory chemical steps necessary for cross-linking based protein structure determination.Additionally, the preferred method of the present invention involves the determination of protein structures utilizing a top-down analysis of protein structures to search for covalent modifications. In the preferred method, intact proteins are ionized and fragmented within the mass spectrometer.

  9. Application of Frontal Affinity Chromatography to Study the Biomolecular Interactions with Trypsin. (United States)

    Hu, YuanYuan; Qian, Junqing; Guo, Hui; Jiang, ShengLan; Zhang, Zheng


    Trypsin is a serine protease that has been proposed as a potential therapeutic target for metabolic disorders and malignancy diseases, thus the identification of biomolecular interactions of compounds to trypsin could be of great therapeutic importance. In this study, trypsin was immobilized on a monolithic silica capillary column via sol-gel. The binding properties of four small molecules (daidzin, genistin, matrine and oxymatrine) to trypsin were examined using the trypsin affinity columns by frontal analysis. The results indicate that the matrine (dissociation constant, Kd = 7.904 μM) has stronger interaction with trypsin than the oxymatrine (Kd = 8.204 μM), whereas daidzin and genistin were nearly have no affinity with trypsin. The results demonstrated that the frontal affinity chromatography can be used for the direct determination of protein-protease inhibitor binding interactions and have several significant advantages, including easy fabricating, reproducible, minimal technological requirements and potential to become a reliable alternative for quantitative studies of biomolecular interactions.

  10. Biomolecular recognition and detection using gold-based nanoprobes (United States)

    Crew, Elizabeth

    The ability to control the biomolecular interactions is important for developing bioanalytical probes used in biomolecule and biomarker detections. This work aims at a fundamental understanding of the interactions and reactivities involving DNA, miRNA, and amino acids using gold-based nanoparticles as nanoprobes, which has implications for developing new strategies for the early detection of diseases, such as cancer, and controlled delivery of drugs. Surface modifications of the nanoprobes with DNA, miRNA, and amino acids and the nanoprobe directed biomolecular reactivities, such as complementary-strand binding, enzymatic cutting and amino acid interactions, have been investigated. Among various analytical techniques employed for the analysis of the biomolecule-nanoprobe interactions, surface enhanced Raman scattering spectroscopy (SERS) has been demonstrated to provide a powerful tool for real time monitoring of the DNA assembly and enzymatic cutting processes in solutions. This demonstration harnesses the "hot-spot" characteristic tuned by the interparticle biomolecular-regulated interactions and distances. The assembly of gold nanoparticles has also been exploited as sensing thin films on chemiresistor arrays for the detection of volatile organic compounds, including biomarker molecules associated with diabetes. Important findings of the nanoprobes in delivering miRNA to cells, detecting DNA hybridization kinetics, discerning chiral recognition with enantiomeric cysteines, and sensing biomarker molecules with the nanostructured thin films will be discussed, along with their implications to enhancing sensitivity, selectivity and limits of detection.

  11. Solution influence on biomolecular equilibria - Nucleic acid base associations (United States)

    Pohorille, A.; Pratt, L. R.; Burt, S. K.; Macelroy, R. D.


    Various attempts to construct an understanding of the influence of solution environment on biomolecular equilibria at the molecular level using computer simulation are discussed. First, the application of the formal statistical thermodynamic program for investigating biomolecular equilibria in solution is presented, addressing modeling and conceptual simplications such as perturbative methods, long-range interaction approximations, surface thermodynamics, and hydration shell. Then, Monte Carlo calculations on the associations of nucleic acid bases in both polar and nonpolar solvents such as water and carbon tetrachloride are carried out. The solvent contribution to the enthalpy of base association is positive (destabilizing) in both polar and nonpolar solvents while negative enthalpies for stacked complexes are obtained only when the solute-solute in vacuo energy is added to the total energy. The release upon association of solvent molecules from the first hydration layer around a solute to the bulk is accompanied by an increase in solute-solvent energy and decrease in solvent-solvent energy. The techniques presented are expectd to displace less molecular and more heuristic modeling of biomolecular equilibria in solution.

  12. Single-Molecule Pull-down FRET (SiMPull-FRET) to dissect the mechanisms of biomolecular machines (United States)

    Kahlscheuer, Matthew L.; Widom, Julia; Walter, Nils G.


    Spliceosomes are multi-megadalton RNA-protein complexes responsible for the faithful removal of non-coding segments (introns) from pre-messenger RNAs (pre-mRNAs), a process critical for the maturation of eukaryotic mRNAs for subsequent translation by the ribosome. Both the spliceosome and ribosome, as well as many other RNA and DNA processing machineries, contain central RNA components that endow biomolecular complexes with precise, sequence-specific nucleic acid recognition and versatile structural dynamics. Single molecule fluorescence (or Förster) resonance energy transfer (smFRET) microscopy is a powerful tool for the study of local and global conformational changes of both simple and complex biomolecular systems involving RNA. The integration of biochemical tools such as immunoprecipitation with advanced methods in smFRET microscopy and data analysis has opened up entirely new avenues towards studying the mechanisms of biomolecular machines isolated directly from complex biological specimens such as cell extracts. Here we detail the general steps for using prism-based total internal reflection fluorescence (TIRF) microscopy in exemplary single molecule pull-down FRET (SiMPull-FRET) studies of the yeast spliceosome and discuss the broad application potential of this technique. PMID:26068753

  13. SiBr4--prediction and determination of crystal structures. (United States)

    Wolf, Alexandra K; Glinnemann, Jürgen; Schmidt, Martin U; Tong, Jianwei; Dinnebier, Robert E; Simon, Arndt; Köhler, Jürgen


    For SiBr4 no crystal structures have been reported yet. In this work the crystal structures of SiBr4 were predicted by global lattice-energy minimizations using force-field methods. Over an energy range of 5 kJ mol(-1) above the global minimum ten possible structures were found. Two of these structures were experimentally determined from X-ray synchrotron powder diffraction data: The low-temperature beta phase crystallizes in P2(1)/c, the high-temperature alpha phase in Pa3. Temperature-dependant X-ray powder diffraction shows that the phase transition occurs at 168 K.

  14. SiBr4 - Prediction and Determination of Crystal Structures

    Energy Technology Data Exchange (ETDEWEB)

    Wolf, A.; Glinnemann, J; Schmidt, M; Tong, J; Dinnebier, R; Simon, A; Kohler, J


    For SiBr4 no crystal structures have been reported yet. In this work the crystal structures of SiBr4 were predicted by global lattice-energy minimizations using force-field methods. Over an energy range of 5 kJ mol-1 above the global minimum ten possible structures were found. Two of these structures were experimentally determined from X-ray synchrotron powder diffraction data: The low-temperature [beta] phase crystallizes in P21/c, the high-temperature [alpha] phase in Pa overline3. Temperature-dependant X-ray powder diffraction shows that the phase transition occurs at 168 K.

  15. Molecular Models of Genetic and Organismic Structures

    CERN Document Server

    Baianu, I C


    In recent studies we showed that the earlier relational theories of organismic sets (Rashevsky,1967), Metabolic-Replication (M,R)-systems (Rosen,1958)and molecular sets (Bartholomay,1968) share a joint foundation that can be studied within a unified categorical framework of functional organismic structures (Baianu,1980. This is possible because all relational theories have a biomolecular basis, that is, complex structures such as genomes, cells,organs and biological organisms are mathematically represented in terms of biomolecular properties and entities,(that are often implicit in their representation axioms. The definition of organismic sets, for example, requires that certain essential quantities be determined from experiment: these are specified by special sets of values of general observables that are derived from physicochemical measurements(Baianu,1970; Baianu,1980; Baianu et al, 2004a.)Such observables are context-dependent and lead directly to natural transformations in categories and Topoi, that are...

  16. Birthday Cake Activity Structured Arrangement for Helping Children Determining Quantities

    Directory of Open Access Journals (Sweden)

    Neni Mariana


    Full Text Available Few researches have been concerned about relation between children’s spatial thinking and number sense. Narrowing for this small research, we focused on one component of spatial thinking, that is structuring objects, and one component of number senses, that is cardinality by determining quantities. This study focused on a design research that was conducted in Indonesia in which we investigated pre-school children’s (between 2 and 3.5 years old ability in making structured arrangement and their ability to determine the quantities by looking at the arrangements. The result shows us that some of the children were able to make such arrangement. However, the children found difficulties either to determine quantities from those arrangements or to compare some structures to easily recognize number of objects.

  17. In cellulo structure determination of a novel cypovirus polyhedrin

    Energy Technology Data Exchange (ETDEWEB)

    Axford, Danny [Diamond Light Source Ltd, Harwell Oxford, Didcot OX11 0DE (United Kingdom); Ji, Xiaoyun [University of Oxford, Oxford OX3 7BN (United Kingdom); Stuart, David I. [Diamond Light Source Ltd, Harwell Oxford, Didcot OX11 0DE (United Kingdom); University of Oxford, Oxford OX3 7BN (United Kingdom); Sutton, Geoff, E-mail: [University of Oxford, Oxford OX3 7BN (United Kingdom); Diamond Light Source Ltd, Harwell Oxford, Didcot OX11 0DE (United Kingdom)


    The crystal structure of a previously unsolved type of cypovirus polyhedrin has been determined from data collected directly from frozen live insect cells. This work demonstrates that with the use of a microfocus synchrotron beam the structure of a novel viral polyhedrin could be successfully determined from microcrystals within cells, removing the preparatory step of sample isolation and maintaining a favourable biological environment. The data obtained are of high quality, comparable to that obtained from isolated crystals, and enabled a facile structure determination. A small but significant difference is observed between the unit-cell parameters and the mosaic spread of in cellulo and isolated crystals, suggesting that even these robust crystals are adversely affected by removal from the cell.

  18. Biomolecular transport and separation in nanotubular networks.

    Energy Technology Data Exchange (ETDEWEB)

    Stachowiak, Jeanne C.; Stevens, Mark Jackson (Sandia National Laboratories, Albuquerque, NM); Robinson, David B.; Branda, Steven S.; Zendejas, Frank; Meagher, Robert J.; Sasaki, Darryl Yoshio; Bachand, George David (Sandia National Laboratories, Albuquerque, NM); Hayden, Carl C.; Sinha, Anupama; Abate, Elisa; Wang, Julia; Carroll-Portillo, Amanda (Sandia National Laboratories, Albuquerque, NM); Liu, Haiqing (Sandia National Laboratories, Albuquerque, NM)


    Cell membranes are dynamic substrates that achieve a diverse array of functions through multi-scale reconfigurations. We explore the morphological changes that occur upon protein interaction to model membrane systems that induce deformation of their planar structure to yield nanotube assemblies. In the two examples shown in this report we will describe the use of membrane adhesion and particle trajectory to form lipid nanotubes via mechanical stretching, and protein adsorption onto domains and the induction of membrane curvature through steric pressure. Through this work the relationship between membrane bending rigidity, protein affinity, and line tension of phase separated structures were examined and their relationship in biological membranes explored.

  19. Resolution-Adapted All-Atomic and Coarse-Grained Model for Biomolecular Simulations. (United States)

    Shen, Lin; Hu, Hao


    We develop here an adaptive multiresolution method for the simulation of complex heterogeneous systems such as the protein molecules. The target molecular system is described with the atomistic structure while maintaining concurrently a mapping to the coarse-grained models. The theoretical model, or force field, used to describe the interactions between two sites is automatically adjusted in the simulation processes according to the interaction distance/strength. Therefore, all-atomic, coarse-grained, or mixed all-atomic and coarse-grained models would be used together to describe the interactions between a group of atoms and its surroundings. Because the choice of theory is made on the force field level while the sampling is always carried out in the atomic space, the new adaptive method preserves naturally the atomic structure and thermodynamic properties of the entire system throughout the simulation processes. The new method will be very useful in many biomolecular simulations where atomistic details are critically needed.

  20. Advances in biomolecular surface meshing and its applications to mathematical modeling

    Institute of Scientific and Technical Information of China (English)

    CHEN MinXin; LU BenZhuo


    In the field of molecular modeling and simulation,molecular surface meshes are necessary for many problems,such as molecular structure visualization and analysis,docking problem and implicit solvent modeling and simulation.Recently,with the developments of advanced mathematical modeling in the field of implicit solvent modeling and simulation,providing surface meshes with good qualities efficiently for large real biomolecular systems becomes an urgent issue beyond its traditional purposes for visualization and geometry analyses for molecular structure.In this review,we summarize recent works on this issue.First,various definitions of molecular surfaces and corresponding meshing methods are introduced.Second,our recent meshing tool,TMSmesh,and its performances are presented.Finally,we show the applications of the molecular surface mesh in implicit solvent modeling and simulations using boundary element method (BEM) and finite element method (FEM).

  1. Optimizing an emperical scoring function for transmembrane protein structure determination.

    Energy Technology Data Exchange (ETDEWEB)

    Young, Malin M.; Sale, Kenneth L.; Gray, Genetha Anne; Kolda, Tamara Gibson


    We examine the problem of transmembrane protein structure determination. Like many other questions that arise in biological research, this problem cannot be addressed by traditional laboratory experimentation alone. An approach that integrates experiment and computation is required. We investigate a procedure which states the transmembrane protein structure determination problem as a bound constrained optimization problem using a special empirical scoring function, called Bundler, as the objective function. In this paper, we describe the optimization problem and some of its mathematical properties. We compare and contrast results obtained using two different derivative free optimization algorithms.

  2. Determinants of Market Structure and the Airline Industry (United States)

    Raduchel, W.


    The general economic determinants of market structure are outlined with special reference to the airline industry. Included are the following facets: absolute size of firms; distributions of firms by size; concentration; entry barriers; product and service differentiation; diversification; degrees of competition; vertical integration; market boundaries; and economies of scale. Also examined are the static and dynamic properties of market structure in terms of mergers, government policies, and economic growth conditions.

  3. Condutância molecular e biomolecular

    Directory of Open Access Journals (Sweden)

    Gama A. Arnóbio S. da


    Full Text Available The concept of molecular conductance is discussed in terms of the propagation of an electronic interaction, between electron donor and acceptor groups, through the bonds of a molecular structure where these groups are embedded. The electronic interaction propagation is described by a Green's function matrix element, in a donor-bridge-acceptor molecular system reduced to a two-level representation.

  4. Slavnov determinants, Yang-Mills structure constants, and discrete KP

    CERN Document Server

    Foda, O


    Using Slavnov's scalar product of a Bethe eigenstate and a generic state in closed XXZ spin-1/2 chains, with possibly twisted boundary conditions, we obtain determinant expressions for tree-level structure constants in 1-loop conformally-invariant sectors in various planar (super) Yang-Mills theories. When certain rapidity variables are allowed to be free rather than satisfy Bethe equations, these determinants become discrete KP tau-functions.

  5. High-resolution protein structure determination by serial femtosecond crystallography. (United States)

    Boutet, Sébastien; Lomb, Lukas; Williams, Garth J; Barends, Thomas R M; Aquila, Andrew; Doak, R Bruce; Weierstall, Uwe; DePonte, Daniel P; Steinbrener, Jan; Shoeman, Robert L; Messerschmidt, Marc; Barty, Anton; White, Thomas A; Kassemeyer, Stephan; Kirian, Richard A; Seibert, M Marvin; Montanez, Paul A; Kenney, Chris; Herbst, Ryan; Hart, Philip; Pines, Jack; Haller, Gunther; Gruner, Sol M; Philipp, Hugh T; Tate, Mark W; Hromalik, Marianne; Koerner, Lucas J; van Bakel, Niels; Morse, John; Ghonsalves, Wilfred; Arnlund, David; Bogan, Michael J; Caleman, Carl; Fromme, Raimund; Hampton, Christina Y; Hunter, Mark S; Johansson, Linda C; Katona, Gergely; Kupitz, Christopher; Liang, Mengning; Martin, Andrew V; Nass, Karol; Redecke, Lars; Stellato, Francesco; Timneanu, Nicusor; Wang, Dingjie; Zatsepin, Nadia A; Schafer, Donald; Defever, James; Neutze, Richard; Fromme, Petra; Spence, John C H; Chapman, Henry N; Schlichting, Ilme


    Structure determination of proteins and other macromolecules has historically required the growth of high-quality crystals sufficiently large to diffract x-rays efficiently while withstanding radiation damage. We applied serial femtosecond crystallography (SFX) using an x-ray free-electron laser (XFEL) to obtain high-resolution structural information from microcrystals (less than 1 micrometer by 1 micrometer by 3 micrometers) of the well-characterized model protein lysozyme. The agreement with synchrotron data demonstrates the immediate relevance of SFX for analyzing the structure of the large group of difficult-to-crystallize molecules.

  6. Novel genetic algorithm search procedure for LEED surface structure determination. (United States)

    Viana, M L; dos Reis, D D; Soares, E A; Van Hove, M A; Moritz, W; de Carvalho, V E


    Low Energy Electron Diffraction (LEED) is one of the most powerful experimental techniques for surface structure analysis but until now only a trial-and-error approach has been successful. So far, fitting procedures developed to optimize structural and nonstructural parameters-by minimization of the R-factor-have had a fairly small convergence radius, suitable only for local optimization. However, the identification of the global minimum among the several local minima is essential for complex surface structures. Global optimization methods have been applied to LEED structure determination, but they still require starting from structures that are relatively close to the correct one, in order to find the final structure. For complex systems, the number of trial structures and the resulting computation time increase so rapidly that the task of finding the correct model becomes impractical using the present methodologies. In this work we propose a new search method, based on Genetic Algorithms, which is able to determine the correct structural model starting from completely random structures. This method-called here NGA-LEED for Novel Genetic Algorithm for LEED-utilizes bond lengths and symmetry criteria to select reasonable trial structures before performing LEED calculations. This allows a reduction of the parameter space and, consequently of the calculation time, by several orders of magnitude. A refinement of the parameters by least squares fit of simulated annealing is performed only at some intermediate stages and in the final step. The method was successfully tested for two systems, Ag(1 1 1)(4 × 4)-O and Au(1 1 0)-(1 × 2), both in theory versus theory and in theory versus experiment comparisons. Details of the implementation as well as the results for these two systems are presented.

  7. Determining the Cognitive Structures of Geography Teacher Candidates on "Earthquake" (United States)

    Kaya, Bastürk; Aladag, Caner


    The objective of this study is to determine the cognitive structures of the students of geography teaching department by identifying their conceptual frameworks about the concept of earthquake. A case study design from qualitative research approaches was used in this research. Sample group of the study constitutes 155 students from the Department…

  8. Synthesis and structure determination of novel hexasubstituted cyclohexadienes

    Institute of Scientific and Technical Information of China (English)

    Hong Mei Qu; Xin Hui Niu; Juan Li; Jun Liu; Li Li Jiang; Jian Ke Tang; Li Shan Zhou


    The linear trienes were obtained in high yields by copper-mediated cycloaddition of 2,5-bis(trimethylsilyl)zirconacyclopentadienes with dimethyl acetylenedicarboxylate (DMAD) which can be quantitatively converted to novel asymmetric hexasubstituted cyclohexadienes with high (E)-stereoselectivity.The structure of cyclohexadienes was determined via X-ray analysis.

  9. A Laboratory Exercise in the Determination of Carbohydrate Structures. (United States)

    White, Bernard J.; Robyt, John F.


    Describes an experiment in which students are given a naturally occurring oligosaccharide as an unknown and are asked to determine both its monosaccharide composition and its structure. Discusses methods and experimental techniques including thin layer chromatography and the use of enzymes. (CW)

  10. Birthday Cake Activity Structured Arrangement for Helping Children Determining Quantities (United States)

    Mariana, Neni


    Few researches have been concerned about relation between children's spatial thinking and number sense. Narrowing for this small research, we focused on one component of spatial thinking, that is structuring objects, and one component of number senses, that is cardinality by determining quantities. This study focused on a design research that was…

  11. Generative probabilistic models extend the scope of inferential structure determination

    DEFF Research Database (Denmark)

    Olsson, Simon; Boomsma, Wouter; Frellsen, Jes


    rigorous approach was developed which treats structure determination as a problem of Bayesian inference. In this case, the forcefields are brought in as a prior distribution in the form of a Boltzmann factor. Due to high computational cost, the approach has been only sparsely applied in practice. Here, we...

  12. Minimal metabolic pathway structure is consistent with associated biomolecular interactions

    DEFF Research Database (Denmark)

    Bordbar, Aarash; Nagarajan, Harish; Lewis, Nathan E.;


    Pathways are a universal paradigm for functionally describing cellular processes. Even though advances in high-throughput data generation have transformed biology, the core of our biological understanding, and hence data interpretation, is still predicated on human-defined pathways. Here, we intr...

  13. Raman microspectroscopic study of biomolecular structure inside living adhesive cells

    Institute of Scientific and Technical Information of China (English)

    李光; 杨红英; 许以明; 张志义


    Cells adhesion is very important for many physiological processes. Using advanced Raman microspectroscopic technique, we selected T Leukemia cells (Jurkat) as the materials and obtained simultaneously conformation information of various biomolecules inside the whole living cells. By comparing the Raman microspectroscopic spectra of single and adhesive cancer cells, we found for the first time that when cells adhered, the conformation of the biomolecules (DNA, protein, carbohydrates and lipids) inside the cells had different changes: (i) the backbone of double-stranded DNA maintained orderly B-form or modified B-form conformation, whereas the groups of its deoxyribose and bases were modified; (ii) the conformational changes of the main chain and the side chain in the protein were obviously variant. The lines intensity belonging to α-helix andβ-sheet decreased, while that ofβ-turn increased. Tyrosine and tryptophane residues of the protein changed from "buried state" to "exposed state"; the lines intensity of its sulfhydryl group also increased; the conformation of its disulfide bond changed from two kinds to three kinds. These facts suggest that the cells adhesion causes changes in H-bonds organization of the main chain and environment of the side chain in the protein; (iii) the groups of the carbohydrates were also modified simultaneously; (iv) the conformation of the lipids bilayers of the membranes changed obviously; the order parameter for lateral interaction between chains decreased gradually with the increase of number of the adhesive cells. So cells adhesion resulted in an increase in fluidity of the membrane and ion permeability on the membrane.

  14. From bacterial to human dihydrouridine synthase: automated structure determination

    Energy Technology Data Exchange (ETDEWEB)

    Whelan, Fiona, E-mail:; Jenkins, Huw T., E-mail: [The University of York, Heslington, York YO10 5DD (United Kingdom); Griffiths, Samuel C. [University of Oxford, Headington, Oxford OX3 7BN (United Kingdom); Byrne, Robert T. [Ludwig-Maximilians-University Munich, Feodor-Lynen-Strasse 25, 81377 Munich (Germany); Dodson, Eleanor J.; Antson, Alfred A., E-mail: [The University of York, Heslington, York YO10 5DD (United Kingdom)


    The crystal structure of a human dihydrouridine synthase, an enzyme associated with lung cancer, with 18% sequence identity to a T. maritima enzyme, has been determined at 1.9 Å resolution by molecular replacement after extensive molecular remodelling of the template. The reduction of uridine to dihydrouridine at specific positions in tRNA is catalysed by dihydrouridine synthase (Dus) enzymes. Increased expression of human dihydrouridine synthase 2 (hDus2) has been linked to pulmonary carcinogenesis, while its knockdown decreased cancer cell line viability, suggesting that it may serve as a valuable target for therapeutic intervention. Here, the X-ray crystal structure of a construct of hDus2 encompassing the catalytic and tRNA-recognition domains (residues 1–340) determined at 1.9 Å resolution is presented. It is shown that the structure can be determined automatically by starting from a bacterial Dus enzyme with only 18% sequence identity and a significantly divergent structure. The overall fold of the human Dus2 is similar to that of bacterial enzymes, but has a larger recognition domain and a unique three-stranded antiparallel β-sheet insertion into the catalytic domain that packs next to the recognition domain, contributing to domain–domain interactions. The structure may inform the development of novel therapeutic approaches in the fight against lung cancer.

  15. The determinism and boundedness of self-assembling structures

    CERN Document Server

    Tesoro, S


    Self-assembly processes are widespread in nature, and lie at the heart of many biological and physical phenomena. The characteristics of self-assembly building blocks determine the structures that they form. Among the most important of these properties are whether the self-assembly is deterministic or nondeterministic, and whether it is bound or unbound. The former tells us whether the same set of building blocks always generates the same structure, and the latter whether it grows indefinitely. These properties are highly relevant in the context of protein structures, as the difference between deterministic protein self-assembly and nondeterministic protein aggregation is central to a number of diseases. Here we introduce a graph-based approach that can determine, with a few restrictions, whether a set of self-assembly building blocks is deterministic or nondeterministic, and whether it is bound or unbound. We apply this methodology to a previously studied lattice self-assembly model and discuss generalisatio...

  16. Programming biomolecular self-assembly pathways. (United States)

    Yin, Peng; Choi, Harry M T; Calvert, Colby R; Pierce, Niles A


    In nature, self-assembling and disassembling complexes of proteins and nucleic acids bound to a variety of ligands perform intricate and diverse dynamic functions. In contrast, attempts to rationally encode structure and function into synthetic amino acid and nucleic acid sequences have largely focused on engineering molecules that self-assemble into prescribed target structures, rather than on engineering transient system dynamics. To design systems that perform dynamic functions without human intervention, it is necessary to encode within the biopolymer sequences the reaction pathways by which self-assembly occurs. Nucleic acids show promise as a design medium for engineering dynamic functions, including catalytic hybridization, triggered self-assembly and molecular computation. Here, we program diverse molecular self-assembly and disassembly pathways using a 'reaction graph' abstraction to specify complementarity relationships between modular domains in a versatile DNA hairpin motif. Molecular programs are executed for a variety of dynamic functions: catalytic formation of branched junctions, autocatalytic duplex formation by a cross-catalytic circuit, nucleated dendritic growth of a binary molecular 'tree', and autonomous locomotion of a bipedal walker.

  17. Scanning probe and optical tweezer investigations of biomolecular interactions

    Energy Technology Data Exchange (ETDEWEB)

    Rigby-Singleton, Shellie


    A complex array of intermolecular forces controls the interactions between and within biological molecules. The desire to empirically explore the fundamental forces has led to the development of several biophysical techniques. Of these, the atomic force microscope (AFM) and the optical tweezers have been employed throughout this thesis to monitor the intermolecular forces involved in biomolecular interactions. The AFM is a well-established force sensing technique capable of measuring biomolecular interactions at a single molecule level. However, its versatility has not been extrapolated to the investigation of a drug-enzyme complex. The energy landscape for the force induced dissociation of the DHFR-methotrexate complex was studied. Revealing an energy barrier to dissociation located {approx}0.3 nm from the bound state. Unfortunately, the AFM has a limited range of accessible loading rates and in order to profile the complete energy landscape alternative force sensing instrumentation should be considered, for example the BFP and optical tweezers. Thus, this thesis outlines the development and construction an optical trap capable of measuring intermolecular forces between biomolecules at the single molecule level. To demonstrate the force sensing abilities of the optical set up, proof of principle measurements were performed which investigate the interactions between proteins and polymer surfaces subjected to varying degrees of argon plasma treatment. Complementary data was gained from measurements performed independently by the AFM. Changes in polymer resistance to proteins as a response to changes in polymer surface chemistry were detected utilising both AFM and optical tweezers measurements. Finally, the AFM and optical tweezers were employed as ultrasensitive biosensors. Single molecule investigations of the antibody-antigen interaction between the cardiac troponin I marker and its complementary antibody, reveals the impact therapeutic concentrations of heparin

  18. Gold nanoshells with gain-assisted silica core for ultra-sensitive bio-molecular sensors (United States)

    Tao, Yifei; Guo, Zhongyi; Zhang, Anjun; Zhang, Jingran; Wang, Benyang; Qu, Shiliang


    A novel bio-molecular nanostructured sensor composed of Au spherical nanoshell and gain-assisted silica-core has been proposed and investigated theoretically, which shows a superior performance compared to the existing structured sensor. Using quasi-static approximation calculation, it is found that the scattering efficiency and the quality factor of SPR can be enhanced greatly by introducing proper amount of gain. The simulated results demonstrate that our designed Au spherical nanoshell and gain-assisted silica-core can obtain as high as 166.7 nm/RIU for the sensitivity of refractive index, and the sensors' figure of merit is enhanced 2000 times nearly compared to that of g=0, which indicates that the designed spherical core-shell sensors have the powerful ability to detect a subtle change in the concentration of its background medium.

  19. Overconfidence, Managerial Optimism, and the Determinants of Capital Structure

    Directory of Open Access Journals (Sweden)

    Alexandre di Miceli da Silveira


    Full Text Available This research examines the determinants of the capital structure of firms introducing a behavioral perspective that has received little attention in corporate finance literature. The following central hypothesis emerges from a set of recently developed theories: firms managed by optimistic and/or overconfident people will choose more levered financing structures than others, ceteris paribus. We propose different proxies for optimism/overconfidence, based on the manager’s status as an entrepreneur or non-entrepreneur, an idea that is supported by theories and solid empirical evidence, as well as on the pattern of ownership of the firm’s shares by its manager. The study also includes potential determinants of capital structure used in earlier research. We use a sample of Brazilian firms listed in the Sao Paulo Stock Exchange (Bovespa in the years 1998 to 2003. The empirical analysis suggests that the proxies for the referred cognitive biases are important determinants of capital structure. We also found as relevant explanatory variables: profitability, size, dividend payment and tangibility, as well as some indicators that capture the firms’ corporate governance standards. These results suggest that behavioral approaches based on human psychology research can offer relevant contributions to the understanding of corporate decision making.

  20. Engineering biomolecular microenvironments for cell instructive biomaterials. (United States)

    Custódio, Catarina A; Reis, Rui L; Mano, João F


    Engineered cell instructive microenvironments with the ability to stimulate specific cellular responses are a topic of high interest in the fabrication and development of biomaterials for application in tissue engineering. Cells are inherently sensitive to the in vivo microenvironment that is often designed as the cell "niche." The cell "niche" comprising the extracellular matrix and adjacent cells, influences not only cell architecture and mechanics, but also cell polarity and function. Extensive research has been performed to establish new tools to fabricate biomimetic advanced materials for tissue engineering that incorporate structural, mechanical, and biochemical signals that interact with cells in a controlled manner and to recapitulate the in vivo dynamic microenvironment. Bioactive tunable microenvironments using micro and nanofabrication have been successfully developed and proven to be extremely powerful to control intracellular signaling and cell function. This Review is focused in the assortment of biochemical signals that have been explored to fabricate bioactive cell microenvironments and the main technologies and chemical strategies to encode them in engineered biomaterials with biological information.

  1. Biomolecular mechanisms in varicose veins development. (United States)

    Segiet, Oliwia Anna; Brzozowa-Zasada, Marlena; Piecuch, Adam; Dudek, Damian; Reichman-Warmusz, Edyta; Wojnicz, Romuald


    Varicose veins (VVs) can be described as tortuous and dilated palpable veins, which are more than 3 mm in diameter. They are one of the clinical presentations of chronic venous disorders, which are a significant cause of morbidity. The prevalence of VVs has been estimated at 25-33% in women and 10-20% in men and is still increasing at an alarming rate. Family history, older age, female, pregnancy, obesity, standing occupations, and a history of deep venous thrombosis are the predominant risk factors. A great amount of factors are implicated in the pathogenesis of VVs, including changes in hydrostatic pressure, valvular incompetence, deep venous obstruction, ineffective function of calf muscle pump, biochemical and structural alterations of the vessel wall, extracellular matrix abnormalities, impaired balance between growth factors or cytokines, genetic alterations, and several other mechanisms. Nevertheless, the issue of pathogenesis in VVs is still not completely known, even if a great progress has been made in understanding their molecular basis. This kind of studies appears promising and should be encouraged, and perhaps the new insight in this matter may result in targeted therapy or possibly prevention.

  2. Sulfated oligosaccharide structures, as determined by NMR techniques

    Energy Technology Data Exchange (ETDEWEB)

    Noseda, M.D.; Duarte, M.E.R.; Tischer, C.A.; Gorin, P.A.J. [Parana Univ., Curitiba, PR (Brazil). Dept. De Bioquimica; Cerezo, A.S. [Buenos Aires Univ. Nacional (Argentina). Dept. de Quimica Organica


    Carrageenans are sulfated polysaccharides, produced by red seaweeds (Rhodophyta), that have important biological and physico-chemical properties. Using partial autohydrolysis, we obtained sulfated oligosaccharides from a {lambda}-carrageenan (Noseda and Cerezo, 1993). These oligosaccharides are valuable not only for the study of the structures of the parent carrageenans but also for their possible biological activities. In this work we determined the chemical structure of one of the sulfated oligosaccharides using 1D and 2D NMR techniques. (author) 4 refs., 8 figs., 1 tabs.

  3. Differential geometry-based solvation and electrolyte transport models for biomolecular modeling: a review

    Energy Technology Data Exchange (ETDEWEB)

    Wei, Guowei; Baker, Nathan A.


    This chapter reviews the differential geometry-based solvation and electrolyte transport for biomolecular solvation that have been developed over the past decade. A key component of these methods is the differential geometry of surfaces theory, as applied to the solvent-solute boundary. In these approaches, the solvent-solute boundary is determined by a variational principle that determines the major physical observables of interest, for example, biomolecular surface area, enclosed volume, electrostatic potential, ion density, electron density, etc. Recently, differential geometry theory has been used to define the surfaces that separate the microscopic (solute) domains for biomolecules from the macroscopic (solvent) domains. In these approaches, the microscopic domains are modeled with atomistic or quantum mechanical descriptions, while continuum mechanics models (including fluid mechanics, elastic mechanics, and continuum electrostatics) are applied to the macroscopic domains. This multiphysics description is integrated through an energy functional formalism and the resulting Euler-Lagrange equation is employed to derive a variety of governing partial differential equations for different solvation and transport processes; e.g., the Laplace-Beltrami equation for the solvent-solute interface, Poisson or Poisson-Boltzmann equations for electrostatic potentials, the Nernst-Planck equation for ion densities, and the Kohn-Sham equation for solute electron density. Extensive validation of these models has been carried out over hundreds of molecules, including proteins and ion channels, and the experimental data have been compared in terms of solvation energies, voltage-current curves, and density distributions. We also propose a new quantum model for electrolyte transport.

  4. Thermal coupling at aqueous and biomolecular interfaces (United States)

    Shenogina, Natalia B.

    structural characterization tools. We followed up with studies of models of heterogeneous interfaces where we addressed the issue of independent vs. correlated contributions of hydrophobic and hydrophilic interfacial regions to thermal transfer. Finally we simulated heat flow across lipid bilayers which involve hydrophilic interfaces, but are characterized by relatively high surface roughness and non-saturated hydrocarbon chains. We found that roughness of the interface can significantly enhance thermal transport across the lipid membranes.

  5. The potential for biological structure determination with pulsed neutrons

    Energy Technology Data Exchange (ETDEWEB)

    Wilson, C.C. [CLRC Rutherford Appleton Laboratory, Chilton Didcot Oxon (United Kingdom)


    The potential of pulsed neutron diffraction in structural determination of biological materials is discussed. The problems and potential solutions in this area are outlined, with reference to both current and future sources and instrumentation. The importance of developing instrumentation on pulsed sources in emphasized, with reference to the likelihood of future expansion in this area. The possibilities and limitations of single crystal, fiber and powder diffraction in this area are assessed.


    Ünlü, Ali; Dettweiler, Ulrich


    Self-determination theory, as proposed by Deci and Ryan, postulated different types of motivation regulation. As to the introjected and identified regulation of extrinsic motivation, their internalizations were described as "somewhat external" and "somewhat internal" and remained undetermined in the theory. This paper introduces a constrained regression analysis that allows these vaguely expressed motivations to be estimated in an "optimal" manner, in any given empirical context. The approach was even generalized and applied for simplex structure analysis in self-determination theory. The technique was exemplified with an empirical study comparing science teaching in a classical school class versus an expeditionary outdoor program. Based on a sample of 84 German pupils (43 girls, 41 boys, 10 to 12 years old), data were collected using the German version of the Academic Self-Regulation Questionnaire. The science-teaching format was seen to not influence the pupils' internalization of identified regulation. The internalization of introjected regulation differed and shifted more toward the external pole in the outdoor teaching format. The quantification approach supported the simplex structure of self-determination theory, whereas correlations may disconfirm the simplex structure.

  7. Knowledge based cluster ensemble for cancer discovery from biomolecular data. (United States)

    Yu, Zhiwen; Wongb, Hau-San; You, Jane; Yang, Qinmin; Liao, Hongying


    The adoption of microarray techniques in biological and medical research provides a new way for cancer diagnosis and treatment. In order to perform successful diagnosis and treatment of cancer, discovering and classifying cancer types correctly is essential. Class discovery is one of the most important tasks in cancer classification using biomolecular data. Most of the existing works adopt single clustering algorithms to perform class discovery from biomolecular data. However, single clustering algorithms have limitations, which include a lack of robustness, stability, and accuracy. In this paper, we propose a new cluster ensemble approach called knowledge based cluster ensemble (KCE) which incorporates the prior knowledge of the data sets into the cluster ensemble framework. Specifically, KCE represents the prior knowledge of a data set in the form of pairwise constraints. Then, the spectral clustering algorithm (SC) is adopted to generate a set of clustering solutions. Next, KCE transforms pairwise constraints into confidence factors for these clustering solutions. After that, a consensus matrix is constructed by considering all the clustering solutions and their corresponding confidence factors. The final clustering result is obtained by partitioning the consensus matrix. Comparison with single clustering algorithms and conventional cluster ensemble approaches, knowledge based cluster ensemble approaches are more robust, stable and accurate. The experiments on cancer data sets show that: 1) KCE works well on these data sets; 2) KCE not only outperforms most of the state-of-the-art single clustering algorithms, but also outperforms most of the state-of-the-art cluster ensemble approaches.

  8. Photochirogenesis: Photochemical Models on the Origin of Biomolecular Homochirality

    Directory of Open Access Journals (Sweden)

    Cornelia Meinert


    Full Text Available Current research focuses on a better understanding of the origin of biomolecular asymmetry by the identification and detection of the possibly first chiral molecules that were involved in the appearance and evolution of life on Earth. We have reasons to assume that these molecules were specific chiral amino acids. Chiral amino acids have been identified in both chondritic meteorites and simulated interstellar ices. Present research reasons that circularly polarized electromagnetic radiation was identified in interstellar environments and an asymmetric interstellar photon-molecule interaction might have triggered biomolecular symmetry breaking. We review on the possible prebiotic interaction of ‘chiral photons’ in the form of circularly polarized light, with early chiral organic molecules. We will highlight recent studies on enantioselective photolysis of racemic amino acids by circularly polarized light and experiments on the asymmetric photochemical synthesis of amino acids from only one C and one N containing molecules by simulating interstellar environments. Both approaches are based on circular dichroic transitions of amino acids that will be presented as well.

  9. Programming in Biomolecular Computation: Programs, Self-Interpretation and Visualisation

    Directory of Open Access Journals (Sweden)

    J.G. Simonsen


    Full Text Available Our goal is to provide a top-down approach to biomolecular computation. In spite of widespread discussion about connections between biology and computation, one question seems notable by its absence: Where are the programs? We identify a number of common features in programming that seem conspicuously absent from the literature on biomolecular computing; to partially redress this absence, we introduce a model of computation that is evidently programmable, by programs reminiscent of low-level computer machine code; and at the same time biologically plausible: its functioning is defined by a single and relatively small set of chemical-like reaction rules. Further properties: the model is stored-program: programs are the same as data, so programs are not only executable, but are also compilable and interpretable. It is universal: all computable functions can be computed (in natural ways and without arcane encodings of data and algorithm; it is also uniform: new ``hardware'' is not needed to solve new problems; and (last but not least it is Turing complete in a strong sense: a universal algorithm exists, that is able to execute any program, and is not asymptotically inefficient.

  10. Electron Crystallographic Study on Structure Determination for Minute Crystals

    Institute of Scientific and Technical Information of China (English)

    LI Fanghua; FAN Haifu; WAN Zhenghua; HU Jianjun; TANG Dong


    @@ In the 1970s the development of high-resolution electron microscopy (HREM) provided a new approach to structure determination for minute crystals, which is thoroughly different from the diffraction methods.However, the previous method of trial and error has its own limits, such as some preliminary structural information must be known in advance; the crystals must be sufficient strong under the electron beam irradiation;and not all atoms can be seen in the image. Two ideas were proposed to initiate the present research project:one is to transform an arbitrary image into the crystal structure map, and the other is to enhance the image resolution by combining the information contained in the image and the corresponding electron diffraction pattern. These ideas have been realized via the combination of electron microscopy and diffraction crystallography.

  11. Structure determines medication errors in nursing units: a mechanistic approach. (United States)

    Hung, Chang-Chiao; Lee, Bih-O; Tsai, Shu-Ling; Tseng, Yun Shan; Chang, Chia-Hao


    Medication errors have long been considered critical in global health care systems. However, few studies have been conducted to explore the effects of nursing unit structure on medication errors. The purpose of this study, therefore, was to determine the effects of structural factors on medication errors in nursing units. A total of 977 staff nurses and 62 head nurses participated in this cross-sectional design study. The findings show that professional autonomy (β = .53, t = 6.03, p nursing experts (β = .52, t = 5.99, p medication error rates. This study shows that the structural factors influence medication administration and the mechanistic approach is specifically in relation of low medication error rates. The author suggests that head nurses should consider strategies that require adjustments to unit control mechanisms.

  12. Local magnetic structure determination using polarized neutron holography

    Energy Technology Data Exchange (ETDEWEB)

    Szakál, Alex, E-mail:; Markó, Márton, E-mail:; Cser, László, E-mail: [Wigner Research Centre for Physics, Konkoly Thege M. út 29-33, H-1121 Budapest (Hungary)


    A unique and important property of the neutron is that it possesses magnetic moment. This property is widely used for determination of magnetic structure of crystalline samples observing the magnetic components of the diffraction peaks. Investigations of diffraction patterns give information only about the averaged structure of a crystal but for discovering of local spin arrangement around a specific (e.g., impurity) nucleus remains still a challenging problem. Neutron holography is a useful tool to investigate the local structure around a specific nucleus embedded in a crystal lattice. The method has been successfully applied experimentally in several cases using non-magnetic short range interaction of the neutron and the nucleus. A mathematical model of the hologram using interaction between magnetic moment of the atom and the neutron spin for polarized neutron holography is provided. Validity of a polarized neutron holographic experiment is demonstrated by applying the proposed method on model systems.

  13. Clathrate Structure Determination by Combining Crystal Structure Prediction with Computational and Experimental (129) Xe NMR Spectroscopy. (United States)

    Selent, Marcin; Nyman, Jonas; Roukala, Juho; Ilczyszyn, Marek; Oilunkaniemi, Raija; Bygrave, Peter J; Laitinen, Risto; Jokisaari, Jukka; Day, Graeme M; Lantto, Perttu


    An approach is presented for the structure determination of clathrates using NMR spectroscopy of enclathrated xenon to select from a set of predicted crystal structures. Crystal structure prediction methods have been used to generate an ensemble of putative structures of o- and m-fluorophenol, whose previously unknown clathrate structures have been studied by (129) Xe NMR spectroscopy. The high sensitivity of the (129) Xe chemical shift tensor to the chemical environment and shape of the crystalline cavity makes it ideal as a probe for porous materials. The experimental powder NMR spectra can be used to directly confirm or reject hypothetical crystal structures generated by computational prediction, whose chemical shift tensors have been simulated using density functional theory. For each fluorophenol isomer one predicted crystal structure was found, whose measured and computed chemical shift tensors agree within experimental and computational error margins and these are thus proposed as the true fluorophenol xenon clathrate structures.

  14. Determination of organic crystal structures by X ray powder diffraction

    CERN Document Server

    McBride, L


    The crystal structure of Ibuprofen has been solved from synchrotron X-ray powder diffraction data using a genetic algorithm (GA). The performance of the GA is improved by incorporating prior chemical information in the form of hard limits on the values that can be taken by the flexible torsion angles within the molecule. Powder X-ray diffraction data were collected for the anti-convulsant compounds remacemide, remacemide nitrate and remacemide acetate at 130 K on BM 16 at the X-ray European Synchrotron Radiation Facility (ESRF) at Grenoble. High quality crystal structures were obtained using data collected to a resolution of typically 1.5 A. The structure determinations were performed using a simulated annealing (SA) method and constrained Rietveld refinements for the structures converged to chi sup 2 values of 1.64, 1.84 and 1.76 for the free base, nitrate and acetate respectively. The previously unknown crystal structure of the drug famotidine Form B has been solved using X-ray powder diffraction data colle...

  15. Velocity Structure Determination Through Seismic Waveform Modeling and Time Deviations (United States)

    Savage, B.; Zhu, L.; Tan, Y.; Helmberger, D. V.


    Through the use of seismic waveforms recorded by TriNet, a dataset of earthquake focal mechanisms and deviations (time shifts) relative to a standard model facilitates the investigation of the crust and uppermost mantle of southern California. The CAP method of focal mechanism determination, in use by TriNet on a routine basis, provides time shifts for surface waves and Pnl arrivals independently relative to the reference model. These shifts serve as initial data for calibration of local and regional seismic paths. Time shifts from the CAP method are derived by splitting the Pnl section of the waveform, the first arriving Pn to just before the arrival of the S wave, from the much slower surface waves then cross-correlating the data with synthetic waveforms computed from a standard model. Surface waves interact with the entire crust, but the upper crust causes the greatest effect. Whereas, Pnl arrivals sample the deeper crust, upper mantle, and source region. This natural division separates the upper from lower crust for regional calibration and structural modeling and allows 3-D velocity maps to be created using the resulting time shifts. Further examination of Pnl and other arrivals which interact with the Moho illuminate the complex nature of this boundary. Initial attempts at using the first 10 seconds of the Pnl section to determine upper most mantle structure have proven insightful. Two large earthquakes north of southern California in Nevada and Mammoth Lakes, CA allow the creation of record sections from 200 to 600 km. As the paths swing from east to west across southern California, simple 1-D models turn into complex structure, dramatically changing the waveform character. Using finite difference models to explain the structure, we determine that a low velocity zone is present at the base of the crust and extends to 100 km in depth. Velocity variations of 5 percent of the mantle in combination with steeply sloping edges produces complex waveform variations

  16. Structure Determination of Natural Products by Nuclear Magnetic Resonance Spectroscopy (United States)

    Li, Du.

    High-field NMR experiments were used to determine the full structures of six new natural products extracted from plants. These are: four saponins (PT-2, P1, P2 and P3) from the plant Alphitonia zizyphoides found in Samoa; one sesquiterpene (DF-4) from Douglas fir and one diterpene derivative (E-2) from a Chinese medicinal herb. By concerted use of various 1D and 2D NMR techniques, the structures of the above compounds were established and complete resonance assignments were achieved. The 2D INADEQUATE technique coupled with a computerized spectral analysis was extensively used. When carried out on concentrations as low as 60 mg of sample, this technique provided absolute confirmation of the assignments for 35 of the possible 53 C-C bonds for PT-2. On 30 mg of sample of E-21, it revealed 22 of 28 possible C-C bonds.

  17. Structure determination of spider silk from X-ray images

    Energy Technology Data Exchange (ETDEWEB)

    Ulrich, Stephan; Zippelius, Annette [Universitaet Goettingen, Institut fuer Theoretische Physik (Germany); Meling, Martin [Max-Planck-Institut fuer biophysikalische Chemie, Goettingen (Germany); Glisovic, Anja; Salditt, Tim [Universitaet Goettingen, Institut fuer Roentgenphysik (Germany)


    Spider silk consists of interconnected crystallites, which are typically aligned along the fiber axis. We present a method to systematically determine the structure of these crystallites. Hereby we introduce a model that calculates the scattering function G(q) which is fitted to the measured X-ray image (silk from nephila clavipes). With it, the crystallites' size, the constitution and dimensions of their unit cell, as well as their tilt with respect to the fiber axis is identified, and furthermore the effect of coherent scattering from different crystallites is investigated. The shown methods and the presented model can easily be generalized to a wide class of composite materials.

  18. Crystal structure determination of anti-DNA Fab A52. (United States)

    Stanfield, Robyn L; Eilat, Dan


    A52 is a murine monoclonal antibody isolated from autoimmune New Zealand Black/New Zealand White F1 mice that recognizes single and double stranded DNA. This mouse strain spontaneously develops systemic lupus erythematosus-like symptoms and has served as a model for that disease for many years. The 1.62 Å crystal structure of the A52 Fab fragment reveals an H3 complementarity determining region with four closely spaced arginine residues, creating a positively charged surface to accommodate bound DNA.

  19. Simulation of Parallel Logical Operations with Biomolecular Computing

    Directory of Open Access Journals (Sweden)

    Mahnaz Kadkhoda


    Full Text Available Biomolecular computing is the computational method that uses the potential of DNA as a parallel computing device. DNA computing can be used to solve NP-complete problems. An appropriate application of DNA computation is large-scale evaluation of parallel computation models such as Boolean Circuits. In this study, we present a molecular-based algorithm for evaluation of Nand-based Boolean Circuits. The contribution of this paper is that the proposed algorithm has been implemented using only three molecular operations and the number of passes in each level is decreased to less than half of previously addressed in the literature. Thus, the proposed algorithm is much easier to implement in the laboratory.

  20. Biomolecular Network-Based Synergistic Drug Combination Discovery

    Directory of Open Access Journals (Sweden)

    Xiangyi Li


    Full Text Available Drug combination is a powerful and promising approach for complex disease therapy such as cancer and cardiovascular disease. However, the number of synergistic drug combinations approved by the Food and Drug Administration is very small. To bridge the gap between urgent need and low yield, researchers have constructed various models to identify synergistic drug combinations. Among these models, biomolecular network-based model is outstanding because of its ability to reflect and illustrate the relationships among drugs, disease-related genes, therapeutic targets, and disease-specific signaling pathways as a system. In this review, we analyzed and classified models for synergistic drug combination prediction in recent decade according to their respective algorithms. Besides, we collected useful resources including databases and analysis tools for synergistic drug combination prediction. It should provide a quick resource for computational biologists who work with network medicine or synergistic drug combination designing.

  1. Biomolecular decision-making process for self assembly.

    Energy Technology Data Exchange (ETDEWEB)

    Osbourn, Gordon Cecil


    The brain is often identified with decision-making processes in the biological world. In fact, single cells, single macromolecules (proteins) and populations of molecules also make simple decisions. These decision processes are essential to survival and to the biological self-assembly and self-repair processes that we seek to emulate. How do these tiny systems make effective decisions? How do they make decisions in concert with a cooperative network of other molecules or cells? How can we emulate the decision-making behaviors of small-scale biological systems to program and self-assemble microsystems? This LDRD supported research to answer these questions. Our work included modeling and simulation of protein populations to help us understand, mimic, and categorize molecular decision-making mechanisms that nonequilibrium systems can exhibit. This work is an early step towards mimicking such nanoscale and microscale biomolecular decision-making processes in inorganic systems.

  2. Design and implementation of a biomolecular concentration tracker. (United States)

    Hsiao, Victoria; de los Santos, Emmanuel L C; Whitaker, Weston R; Dueber, John E; Murray, Richard M


    As a field, synthetic biology strives to engineer increasingly complex artificial systems in living cells. Active feedback in closed loop systems offers a dynamic and adaptive way to ensure constant relative activity independent of intrinsic and extrinsic noise. In this work, we use synthetic protein scaffolds as a modular and tunable mechanism for concentration tracking through negative feedback. Input to the circuit initiates scaffold production, leading to colocalization of a two-component system and resulting in the production of an inhibitory antiscaffold protein. Using a combination of modeling and experimental work, we show that the biomolecular concentration tracker circuit achieves dynamic protein concentration tracking in Escherichia coli and that steady state outputs can be tuned.

  3. Ion irradiation and biomolecular radiation damage II. Indirect effect

    CERN Document Server

    Wang, Wei; Su, Wenhui


    It has been reported that damage of genome in a living cell by ionizing radiation is about one-third direct and two-thirds indirect. The former which has been introduced in our last paper, concerns direct energy deposition and ionizing reactions in the biomolecules; the latter results from radiation induced reactive species (mainly radicals) in the medium (mainly water) surrounding the biomolecules. In this review, a short description of ion implantation induced radical formation in water is presented. Then we summarize the aqueous radical reaction chemistry of DNA, protein and their components, followed by a brief introduction of biomolecular damage induced by secondary particles (ions and electron). Some downstream biological effects are also discussed.

  4. Structural determinants of tobacco vein mottling virus protease substrate specificity. (United States)

    Sun, Ping; Austin, Brian P; Tözsér, József; Waugh, David S


    Tobacco vein mottling virus (TVMV) is a member of the Potyviridae, one of the largest families of plant viruses. The TVMV genome is translated into a single large polyprotein that is subsequently processed by three virally encoded proteases. Seven of the nine cleavage events are carried out by the NIa protease. Its homolog from the tobacco etch virus (TEV) is a widely used reagent for the removal of affinity tags from recombinant proteins. Although TVMV protease is a close relative of TEV protease, they exhibit distinct sequence specificities. We report here the crystal structure of a catalytically inactive mutant TVMV protease (K65A/K67A/C151A) in complex with a canonical peptide substrate (Ac-RETVRFQSD) at 1.7-Å resolution. As observed in several crystal structures of TEV protease, the C-terminus (∼20 residues) of TVMV protease is disordered. Unexpectedly, although deleting the disordered residues from TEV protease reduces its catalytic activity by ∼10-fold, an analogous truncation mutant of TVMV protease is significantly more active. Comparison of the structures of TEV and TVMV protease in complex with their respective canonical substrate peptides reveals that the S3 and S4 pockets are mainly responsible for the differing substrate specificities. The structure of TVMV protease suggests that it is less tolerant of variation at the P1' position than TEV protease. This conjecture was confirmed experimentally by determining kinetic parameters k(cat) and K(m) for a series of oligopeptide substrates. Also, as predicted by the cocrystal structure, we confirm that substitutions in the P6 position are more readily tolerated by TVMV than TEV protease.

  5. The Vibration Impact Determination of the Helicopter Structural Components

    Directory of Open Access Journals (Sweden)

    Khaksar Zeinab


    Full Text Available This paper presents the determination of the vibration impact of the helicopter structural components and skin repairs in terms of frequency characteristics. To address this issue, a 3D Finite Element Method (FEM model of 349 Gazelle helicopter has been developed in ABAQUS and the frequency analysis is conducted. The results on the natural frequencies of the full structure reasonably match with the literature giving confidence in the baseline model. The main advantage of this FEM model is that, it can be used to predict the natural frequencies of the full structure, precisely. In addition, the material properties and conditions of the components can be updated based on the applied conditions during the repair and maintenance period. Thus, the model gives a comprehensive design tool for analysing the frequencies of the helicopter with differing components. The effective variations in the frequency changes due to repair are predicted numerically. The discussion of these results helps in developing leads to improved selection of replacement materials and their properties.

  6. Simple surface structure determination from Fourier transforms of angle-resolved photoemission extended fine structure

    Energy Technology Data Exchange (ETDEWEB)

    Zheng, Y. [Pennsylvania State Univ., University Park, PA (United States)]|[Lawrence Berkeley Lab., CA (United States); Shirley, D.A. [Pennsylvania State Univ., University Park, PA (United States)


    The authors show by Fourier analyses of experimental data, with no further treatment, that the positions of all the strong peaks in Fourier transforms of angle-resolved photoemission extended fine structure (ARPEFS) from adsorbed surfaces can be explicitly predicted from a trial structure with an accuracy of about {+-} 0.3 {angstrom} based on a single-scattering cluster model together with the concept of a strong backscattering cone, and without any additional analysis. This characteristic of ARPEFS Fourier transforms can be developed as a simple method for determining the structures of adsorbed surfaces to an accuracy of about {+-} 0.1 {angstrom}.

  7. Nanoscale structural features determined by AFM for single virus particles. (United States)

    Chen, Shu-wen W; Odorico, Michael; Meillan, Matthieu; Vellutini, Luc; Teulon, Jean-Marie; Parot, Pierre; Bennetau, Bernard; Pellequer, Jean-Luc


    In this work, we propose "single-image analysis", as opposed to multi-image averaging, for extracting valuable information from AFM images of single bio-particles. This approach allows us to study molecular systems imaged by AFM under general circumstances without restrictions on their structural forms. As feature exhibition is a resolution correlation, we have performed AFM imaging on surfaces of tobacco mosaic virus (TMV) to demonstrate variations of structural patterns with probing resolution. Two AFM images were acquired with the same tip at different probing resolutions in terms of pixel width, i.e., 1.95 and 0.49 nm per pixel. For assessment, we have constructed an in silico topograph based on the three-dimensional crystal structure of TMV as a reference. The prominent artifacts observed in the AFM-determined shape of TMV were attributed to tip convolutions. The width of TMV rod was systematically overestimated by ~10 nm at both probing resolutions of AFM. Nevertheless, the effects of tip convolution were less severe in vertical orientation so that the estimated height of TMV by AFM imaging was in close agreement with the in silico X-ray topograph. Using dedicated image processing algorithms, we found that at low resolution (i.e., 1.95 nm per pixel), the extracted surface features of TMV can be interpreted as a partial or full helical repeat (three complete turns with ~7.0 nm in length), while individual protein subunits (~2.5 nm) were perceivable only at high resolution. The present study shows that the scales of revealed structural features in AFM images are subject to both probing resolution and processing algorithms for image analysis.

  8. Structural Determinants of Clostridium difficile Toxin A Glucosyltransferase Activity

    Energy Technology Data Exchange (ETDEWEB)

    Pruitt, Rory N.; Chumbler, Nicole M.; Rutherford, Stacey A.; Farrow, Melissa A.; Friedman, David B.; Spiller, Ben; Lacy, D. Borden (Vanderbilt)


    The principle virulence factors in Clostridium difficile pathogenesis are TcdA and TcdB, homologous glucosyltransferases capable of inactivating small GTPases within the host cell. We present crystal structures of the TcdA glucosyltransferase domain in the presence and absence of the co-substrate UDP-glucose. Although the enzymatic core is similar to that of TcdB, the proposed GTPase-binding surface differs significantly. We show that TcdA is comparable with TcdB in its modification of Rho family substrates and that, unlike TcdB, TcdA is also capable of modifying Rap family GTPases both in vitro and in cells. The glucosyltransferase activities of both toxins are reduced in the context of the holotoxin but can be restored with autoproteolytic activation and glucosyltransferase domain release. These studies highlight the importance of cellular activation in determining the array of substrates available to the toxins once delivered into the cell.

  9. Determinants of capital structure: New evidence from Portuguese small firms

    Directory of Open Access Journals (Sweden)

    Zélia Serrasqueiro


    Full Text Available This paper studies the determinants of capital structure of 2,329 Portuguese small firms, decomposing total liabilities in long and short-term debt. The results of 2007-2011 panel data suggest that information asymmetry and agency problems seem to be important for small firms in accessing long-term debt. Greater size and a higher level of collateral are quite important in accessing long-term debt. Liquidity is positively associated with long-term debt, although it is negatively related to short-term debt. Higher profitability is related to lower levels of debt. When internal finance is insufficient, these firms seem to be strongly dependent on short-term debt, due to the difficulties in accessing long-term. The main conclusion of the current study is that the predicitons of POT and TOT are followed by small firms in their capital structure, which is in accordance with the results of previous studies focusing on SMEs.

  10. The determinants of capital structure choice: Evidence from Western Europe

    Directory of Open Access Journals (Sweden)

    Ana Mugosa


    Full Text Available This paper examines corporate leverage and its determinants on panel of 921 large Western European companies from 2003 to 2010. The results proved a substantial influence of estimated variables on changes in target debt or leverage ratio. Apart of the determinants from the “core” model, I test the influence of stock price variations on changes in capital structure to conclude if companies “time” the market. The estimation procedure of target debt ratio was performed using Fixed-Effect and FGLS methods. The results were compared to the results of often used methodology in previous research – OLS and Tobit regression. I found statistically significant and negative correlation between target leverage ratio and tangibility, market to book, profitability, product uniqueness and total return (average stock return and statistically significant and positive correlation between target leverage ratio and size. The results suggest the mix of trade-off and pecking order theory predictions and are consistent with findings of previous studies. Future research should focus on impact of leverage deficit (deviations from target leverage ratio on corporate decisions in Europe.

  11. The Detection of Structural Deformation Errors in Attitude Determination

    Institute of Scientific and Technical Information of China (English)

    M. J. Moore; C. Rizos; J. Wang


    In the determination of the attitude parameters from a multi-antenna GPS array, one of the major assumptions is that the body frame is rigid at all times. If this assumption is not true then the derived attitude parameters will be in error. It is well known that in airborne platforms the wings often experience some displacement during flight, especially during periods of initializing maneouvres, such as taking off, landing,and banking. Often it is at these points in time that it is most critical to have the most precise attitude parameters.There are a number of techniques available for the detection of modeling errors.The CUSUM algorithm has successfully been implemented in the past to detect small persistent changes. In this paper the authors investigate different methods of generating the residuals, to be tested by the CUSUM algorithm, in an effort to determine which technique is best suited for the detection of structural deformation of an airborne platform. The methods investigated include monitoring the mean of the residuals generated from the difference between the known body frame coordinates, and those calculated from the derived attitude parameters. The generated residuals are then passed to a CUSUM algorithm to detect any small persistent changes. An alternative method involves transforming the generated residuals into the frequency domain through the use of the Fast Fourier Transform. The CUSUM algorithm is then used to detect any frequency changes. The final technique investigated involves transforming the generated residuals using the Haar wavelet. The wavelet coefficients are then monitored by the CUSUM algorithm in order to detect any significant change to the rigidity of the body frame.Detecting structural deformation, and quantifying the degree of deformation, during flight will ensure that these effects can be removed from the system, thus ensuring the most precise and reliable attitude parameter solutions. This paper, through a series

  12. Unraveling the biomolecular snapshots of mitosis in healthy and cancer cells using plasmonically-enhanced Raman spectroscopy. (United States)

    Panikkanvalappil, Sajanlal R; Hira, Steven M; Mahmoud, Mahmoud A; El-Sayed, Mostafa A


    Owing to the dynamic and complex nature of mitosis, precise and timely executions of biomolecular events are critical for high fidelity cell division. In this context, visualization of such complex events at the molecular level can provide vital information on the biomolecular processes in abnormal cells. Here, we explored the plasmonically enhanced light scattering properties of functionalized gold nanocubes (AuNCs) together with surface-enhanced Raman spectroscopy (SERS) to unravel the complex and dynamic biological processes involved in mitosis of healthy and cancerous cells from its molecular perspectives. By monitoring various stages of mitosis using SERS, we noticed that relatively high rate of conversion of mitotic proteins from their α-helix structure to β-sheet conformation is likely in the cancer cells during meta-, ana-, and telophases. Unique biochemical modifications to the lipid and amino acid moieties, associated with the observed protein conformational modifications, were also identified. However, in healthy cells, the existence of proteins in their β conformation was momentary and was largely in the α-helix form. The role of abnormal conformational modifications of mitotic proteins on the development of anomalous mitotic activities was further confirmed by looking at plasmonic nanoparticle-induced cytokinesis failure in cancer cells. Our findings illustrate the vast possibilities of SERS in real-time tracking of complex, subtle, and momentary modifications of biomolecules in live cells, which could provide new insights to the role of protein conformation dynamics during mitosis on the development of cancer and many other diseases.

  13. Automatic Structure Determination of Organic Molecules: Principle and Implementation of the LSD Program

    Institute of Scientific and Technical Information of China (English)



    The LSD (Logic for Structure Determination) program generates organic molecular structures from 1D and 2D NMR data without resorting to chemical shift databases. Its use in the resolution of natural product structure determination problems has been already reported in the literature. This paper describes how data and structures are internally represented and processed by LSD to build solution structures.

  14. Computational Recipe for Efficient Description of Large-Scale Conformational Changes in Biomolecular Systems. (United States)

    Moradi, Mahmoud; Tajkhorshid, Emad


    Characterizing large-scale structural transitions in biomolecular systems poses major technical challenges to both experimental and computational approaches. On the computational side, efficient sampling of the configuration space along the transition pathway remains the most daunting challenge. Recognizing this issue, we introduce a knowledge-based computational approach toward describing large-scale conformational transitions using (i) nonequilibrium, driven simulations combined with work measurements and (ii) free energy calculations using empirically optimized biasing protocols. The first part is based on designing mechanistically relevant, system-specific reaction coordinates whose usefulness and applicability in inducing the transition of interest are examined using knowledge-based, qualitative assessments along with nonequilirbrium work measurements which provide an empirical framework for optimizing the biasing protocol. The second part employs the optimized biasing protocol resulting from the first part to initiate free energy calculations and characterize the transition quantitatively. Using a biasing protocol fine-tuned to a particular transition not only improves the accuracy of the resulting free energies but also speeds up the convergence. The efficiency of the sampling will be assessed by employing dimensionality reduction techniques to help detect possible flaws and provide potential improvements in the design of the biasing protocol. Structural transition of a membrane transporter will be used as an example to illustrate the workings of the proposed approach.

  15. Crystal and molecular structures of some organophosphorus insecticides and computer methods for structure determination. [Dissertation

    Energy Technology Data Exchange (ETDEWEB)

    Lapp, R.L.


    Molecular structure investigations of a set of organophosphorus insecticides have been carried out in order to acquire the data base to develop correlations between such parameters and their toxicities. The crystal and molecular structures of dimethoate (LD/sub 50/ (rats) = 600 mg/kg), IPAT, and leptophos (LD/sub 50/ (rats) = 90 mg/kg) have been determined via three-dimensional x-ray analysis. The crystal and molecular structure of (-)-..cap alpha..-phenylethylammonium (-)-0-methyl-phenylphosphonothioate was solved by conventional Patterson and Fourier techniques to a final R value of 0.057. The crystal and molecular structures of two crystalline forms of calcium formate were determined. A new least-squares refinement program was written which is much more general and efficient than any previous program. In particular, a new block-diagonal approximation has been devised which is much more economical than full-matrix refinement and appears to work much better than previous block-diagonal methods. A Howells, Phillips and Rogers test for a center of symmetry and a Wilson plot have been programmed into the data collection algorithm. Some approximations and special problems are discussed relative to implementing these routines in a real-time mode on a minicomputer. A mathematical background and program description are included for each program.

  16. [Biobanking and Biomolecular Resources Research Infrastructure (BBMRI). Implications for pathology]. (United States)

    Viertler, C; Zatloukal, K


    High quality human biological samples (e.g. blood, tissue or DNA) with associated, well documented clinical and research data are key resources for advancement of life sciences, biotechnology, clinical medicine, drug development and also molecular pathology. Millions of samples of diseased tissues have been collected in the context of routine histopathological diagnosis and are stored in the archives of hospitals and institutes of pathology. A concerted effort is necessary to overcome the current fragmentation of the European biobanking community in order to tap the full research potential of existing biobanks. A pan-European research infrastructure for biobanking and biomolecular resources (BBMRI) is currently in its planning phase. The mission is to link and provide access to local biobanks of different formats, including tissue collections, harmonize standards, establish operational procedures which properly consider ethical, legal, societal aspects, and to secure sustainable funding. Pathology plays a key role in development and administration of tissue banks and is, thus, a major partner for collaboration, expertise and construction of this pan-European research infrastructure.

  17. Biomolecular Evidence of Silk from 8,500 Years Ago. (United States)

    Gong, Yuxuan; Li, Li; Gong, Decai; Yin, Hao; Zhang, Juzhong


    Pottery, bone implements, and stone tools are routinely found at Neolithic sites. However, the integrity of textiles or silk is susceptible to degradation, and it is therefore very difficult for such materials to be preserved for 8,000 years. Although previous studies have provided important evidence of the emergence of weaving skills and tools, such as figuline spinning wheels and osseous lamellas with traces of filament winding, there is a lack of direct evidence proving the existence of silk. In this paper, we explored evidence of prehistoric silk fibroin through the analysis of soil samples collected from three tombs at the Neolithic site of Jiahu. Mass spectrometry was employed and integrated with proteomics to characterize the key peptides of silk fibroin. The direct biomolecular evidence reported here showed the existence of prehistoric silk fibroin, which was found in 8,500-year-old tombs. Rough weaving tools and bone needles were also excavated, indicating the possibility that the Jiahu residents may possess the basic weaving and sewing skills in making textile. This finding may advance the study of the history of silk, and the civilization of the Neolithic Age.

  18. Label-free screening of bio-molecular interactions. (United States)

    Cooper, Matthew A


    The majority of techniques currently employed to interrogate a biomolecular interaction require some type of radio- or enzymatic- or fluorescent-labelling to report the binding event. However, there is an increasing awareness of novel techniques that do not require labelling of the ligand or the receptor, and that allow virtually any complex to be screened with minimal assay development. This review focuses on three major label-free screening platforms: surface plasmon resonance biosensors, acoustic biosensors, and calorimetric biosensors. Scientists in both academia and industry are using biosensors in areas that encompass almost all areas drug discovery, diagnostics, and the life sciences. The capabilities and advantages of each technique are compared and key applications involving small molecules, proteins, oligonucleotides, bacteriophage, viruses, bacteria, and cells are reviewed. The role of the interface between the biosensor surface (in the case of SPR and acoustic biosensors) and the chemical or biological systems to be studied is also covered with attention to the covalent and non-covalent coupling chemistries commonly employed.

  19. Microscale thermophoresis quantifies biomolecular interactions under previously challenging conditions. (United States)

    Seidel, Susanne A I; Dijkman, Patricia M; Lea, Wendy A; van den Bogaart, Geert; Jerabek-Willemsen, Moran; Lazic, Ana; Joseph, Jeremiah S; Srinivasan, Prakash; Baaske, Philipp; Simeonov, Anton; Katritch, Ilia; Melo, Fernando A; Ladbury, John E; Schreiber, Gideon; Watts, Anthony; Braun, Dieter; Duhr, Stefan


    Microscale thermophoresis (MST) allows for quantitative analysis of protein interactions in free solution and with low sample consumption. The technique is based on thermophoresis, the directed motion of molecules in temperature gradients. Thermophoresis is highly sensitive to all types of binding-induced changes of molecular properties, be it in size, charge, hydration shell or conformation. In an all-optical approach, an infrared laser is used for local heating, and molecule mobility in the temperature gradient is analyzed via fluorescence. In standard MST one binding partner is fluorescently labeled. However, MST can also be performed label-free by exploiting intrinsic protein UV-fluorescence. Despite the high molecular weight ratio, the interaction of small molecules and peptides with proteins is readily accessible by MST. Furthermore, MST assays are highly adaptable to fit to the diverse requirements of different biomolecules, such as membrane proteins to be stabilized in solution. The type of buffer and additives can be chosen freely. Measuring is even possible in complex bioliquids like cell lysate allowing close to in vivo conditions without sample purification. Binding modes that are quantifiable via MST include dimerization, cooperativity and competition. Thus, its flexibility in assay design qualifies MST for analysis of biomolecular interactions in complex experimental settings, which we herein demonstrate by addressing typically challenging types of binding events from various fields of life science.

  20. A fast mollified impulse method for biomolecular atomistic simulations (United States)

    Fath, L.; Hochbruck, M.; Singh, C. V.


    Classical integration methods for molecular dynamics are inherently limited due to resonance phenomena occurring at certain time-step sizes. The mollified impulse method can partially avoid this problem by using appropriate filters based on averaging or projection techniques. However, existing filters are computationally expensive and tedious in implementation since they require either analytical Hessians or they need to solve nonlinear systems from constraints. In this work we follow a different approach based on corotation for the construction of a new filter for (flexible) biomolecular simulations. The main advantages of the proposed filter are its excellent stability properties and ease of implementation in standard softwares without Hessians or solving constraint systems. By simulating multiple realistic examples such as peptide, protein, ice equilibrium and ice-ice friction, the new filter is shown to speed up the computations of long-range interactions by approximately 20%. The proposed filtered integrators allow step sizes as large as 10 fs while keeping the energy drift less than 1% on a 50 ps simulation.

  1. Indirect readout in protein-peptide recognition: a different story from classical biomolecular recognition. (United States)

    Yu, Hua; Zhou, Peng; Deng, Maolin; Shang, Zhicai


    Protein-peptide interactions are prevalent and play essential roles in many living activities. Peptides recognize their protein partners by direct nonbonded interactions and indirect adjustment of conformations. Although processes of protein-peptide recognition have been comprehensively studied in both sequences and structures recently, flexibility of peptides and the configuration entropy penalty in recognition did not get enough attention. In this study, 20 protein-peptide complexes and their corresponding unbound peptides were investigated by molecular dynamics simulations. Energy analysis revealed that configurational entropy penalty introduced by restriction of the degrees of freedom of peptides in indirect readout process of protein-peptide recognition is significant. Configurational entropy penalty has become the main content of the indirect readout energy in protein-peptide recognition instead of deformation energy which is the main source of the indirect readout energy in classical biomolecular recognition phenomena, such as protein-DNA binding. These results provide us a better understanding of protein-peptide recognition and give us some implications in peptide ligand design.

  2. A method for rapid quantitative assessment of biofilms with biomolecular staining and image analysis. (United States)

    Larimer, Curtis; Winder, Eric; Jeters, Robert; Prowant, Matthew; Nettleship, Ian; Addleman, Raymond Shane; Bonheyo, George T


    The accumulation of bacteria in surface-attached biofilms can be detrimental to human health, dental hygiene, and many industrial processes. Natural biofilms are soft and often transparent, and they have heterogeneous biological composition and structure over micro- and macroscales. As a result, it is challenging to quantify the spatial distribution and overall intensity of biofilms. In this work, a new method was developed to enhance the visibility and quantification of bacterial biofilms. First, broad-spectrum biomolecular staining was used to enhance the visibility of the cells, nucleic acids, and proteins that make up biofilms. Then, an image analysis algorithm was developed to objectively and quantitatively measure biofilm accumulation from digital photographs and results were compared to independent measurements of cell density. This new method was used to quantify the growth intensity of Pseudomonas putida biofilms as they grew over time. This method is simple and fast, and can quantify biofilm growth over a large area with approximately the same precision as the more laborious cell counting method. Stained and processed images facilitate assessment of spatial heterogeneity of a biofilm across a surface. This new approach to biofilm analysis could be applied in studies of natural, industrial, and environmental biofilms.

  3. A Quick-responsive DNA Nanotechnology Device for Bio-molecular Homeostasis Regulation. (United States)

    Wu, Songlin; Wang, Pei; Xiao, Chen; Li, Zheng; Yang, Bing; Fu, Jieyang; Chen, Jing; Wan, Neng; Ma, Cong; Li, Maoteng; Yang, Xiangliang; Zhan, Yi


    Physiological processes such as metabolism, cell apoptosis and immune responses, must be strictly regulated to maintain their homeostasis and achieve their normal physiological functions. The speed with which bio-molecular homeostatic regulation occurs directly determines the ability of an organism to adapt to conditional changes. To produce a quick-responsive regulatory system that can be easily utilized for various types of homeostasis, a device called nano-fingers that facilitates the regulation of physiological processes was constructed using DNA origami nanotechnology. This nano-fingers device functioned in linked open and closed phases using two types of DNA tweezers, which were covalently coupled with aptamers that captured specific molecules when the tweezer arms were sufficiently close. Via this specific interaction mechanism, certain physiological processes could be simultaneously regulated from two directions by capturing one biofactor and releasing the other to enhance the regulatory capacity of the device. To validate the universal application of this device, regulation of the homeostasis of the blood coagulant thrombin was attempted using the nano-fingers device. It was successfully demonstrated that this nano-fingers device achieved coagulation buffering upon the input of fuel DNA. This nano-device could also be utilized to regulate the homeostasis of other types of bio-molecules.

  4. Co-Immobilization of Proteins and DNA Origami Nanoplates to Produce High-Contrast Biomolecular Nanoarrays. (United States)

    Hager, Roland; Burns, Jonathan R; Grydlik, Martyna J; Halilovic, Alma; Haselgrübler, Thomas; Schäffler, Friedrich; Howorka, Stefan


    The biofunctionalization of nanopatterned surfaces with DNA origami nanostructures is an important topic in nanobiotechnology. An unexplored challenge is, however, to co-immobilize proteins with DNA origami at pre-determined substrate sites in high contrast relative to the nontarget areas. The immobilization should, in addition, preferably be achieved on a transparent substrate to allow ultrasensitive optical detection. If successful, specific co-binding would be a step towards stoichiometrically defined arrays with few to individual protein molecules per site. Here, we successfully immobilize with high specificity positively charged avidin proteins and negatively charged DNA origami nanoplates on 100 nm-wide carbon nanoislands while suppressing undesired adsorption to surrounding nontarget areas. The arrays on glass slides achieve unprecedented selectivity factors of up to 4000 and allow ultrasensitive fluorescence read-out. The co-immobilization onto the nanoislands leads to layered biomolecular architectures, which are functional because bound DNA origami influences the number of capturing sites on the nanopatches for other proteins. The novel hybrid DNA origami-protein nanoarrays allow the fabrication of versatile research platforms for applications in biosensing, biophysics, and cell biology, and, in addition, represent an important step towards single-molecule protein arrays.

  5. Amplified Immunoassay of Human IgG Using Real-time Biomolecular Interaction Analysis (BIA) Technology

    Institute of Scientific and Technical Information of China (English)

    PEI,Ren-Jun(裴仁军); CUI,Xiao-Qiang(崔小强); YANG,Xiu-Rong(杨秀荣); WANG,Er-Kang(汪尔康)


    An automated biomolecular interaction analysis instrument (BIAcore) based on surface plasmon resonance (SPR) has been used to determine human immunoglobulin G (IgG) in real time. Polyclonal anti-human IgG antibody was covalently immobilized to a carboxymethyldextran-modified gold film surface. The samples of human IgG prepared in HBS buffer were poured over the immobilized surface. The signal amplification antibody was applied to amplify the response signal. After each measurement, the surface was regenerated with 0.1 mol/L H3PO4. The assay was rapid, requiring only 30 min for antibody immobilization and 20 min for each subsequent process of immune binding, antibody amplification and regeneration. The antibody immobilized surface had good response to human IgG in the range of 0.12-60 nmol/L with a detection limit of 60 pmoL/L. The same antibody immobilized surface could be used for more than 110 cycles of binding, amplificafion and regeneration. The results demonstrate that the sensitivity, specificity and reproducibility of amplified immunoassay using real-time BIA technology are satisfactory.

  6. Market power versus capital structure determinants: Do they impact leverage?

    Directory of Open Access Journals (Sweden)

    Agha Jahanzeb


    Full Text Available The purpose of this study is to investigate the association between market power and capital structure. This study will further provide a logical explanation towards the factors affecting capital structure. This study analysed 176 non-financial Pakistani companies listed on Karachi Stock Exchange over the period of 2003–2012. Capital structure has been tried to investigate with a different perspective by investigating its association with market power. It has been seen that there is a significant and positive relation between market power and capital structure. Size and liquidity remained significantly negative with capital structure, whereas profitability and dividend payout remained significantly positive with capital structure. To the best of authors’ knowledge, this is the first study that investigates the relationship between market power and capital structure in any developing economy by employing the data of non-financial Pakistani firms.

  7. An Analysis of Biomolecular Force Fields for Simulations of Polyglutamine in Solution

    Energy Technology Data Exchange (ETDEWEB)

    Fluitt, Aaron M. [Univ. of Chicago, IL (United States); de Pablo, Juan J. [Argonne National Lab. (ANL), Argonne, IL (United States)


    Polyglutamine (polyQ) peptides are a useful model system for biophysical studies of protein folding and aggregation, both for their intriguing aggregation properties and their own relevance to human disease. The genetic expansion of a polyQ tract triggers the formation of amyloid aggregates associated with nine neurodegenerative diseases. Several clearly identifiable and separable factors, notably the length of the polyQ tract, influence the mechanism of aggregation, its associated kinetics, and the ensemble of structures formed. Atomistic simulations are well positioned to answer open questions regarding the thermodynamics and kinetics of polyQ folding and aggregation. The additional, explicit representation of water permits deeper investigation of the role of solvent dynamics, and it permits a direct comparison of simulation results with infrared spectroscopy experiments. The generation of meaningful simulation results hinges on satisfying two essential criteria: achieving sufficient conformational sampling to draw statistically valid conclusions, and accurately reproducing the intermolecular forces that govern system structure and dynamics. In this work, we examine the ability of 12 biomolecular force fields to reproduce the properties of a simple, 30-residue polyQ peptide (Q30) in explicit water. In addition to secondary and tertiary structure, we consider generic structural properties of polymers that provide additional dimensions for analysis of the highly degenerate disordered states of the molecule. We find that the 12 force fields produce a wide range of predictions. We identify AMBER ff99SB, AMBER ff99SB*, and OPLS-AA/L to be most suitable for studies of polyQ folding and aggregation.

  8. Synthesis and structure determination of uranyl peroxide nanospheres in the presence of organic structure directing agents (United States)

    Forbes, T. Z.; Burns, P. C.


    Recently, actinyl peroxide nanoclusters containing 20, 24, 28, or 32 actinyl polyhedra have been synthesized and their structures identified with single crystal X-ray diffraction [1]. Most nanomaterials are composed of main group elements or transition metals, therefore, these actinyl nanospheres may display vastly different chemical and physical properties due to the presence of filled f-orbitals. A major goal of our research group is to create novel actinyl materials, focusing on nano- and mesoporous materials. The original nanosphere syntheses were limited to inorganic crystallization agents, such as monovalent cations. Over the last decade, the use of organic compounds and surfactants have received increased attention as structure-directing agents for the generation of novel inorganic materials. Using structure-directing organic amines we have successfully synthesized and determined the structures of uranyl nanospheres containing 40 and 50 uranyl polyhedra. The topology of the skeletal U-50 nanosphere is identical to the C50Cl10 fullerene [2]. The topographical relationship between the actinyl nanospheres and fullerene or fullerene-like material may provide additional insight into stable configurations for lower fullerenes. [1] Burns et al., Actinyl peroxide nanospheres. Angewandte Chemie, International Edition, 2005. 44(14): p. 2135. [2] Xie et al., Capturing the Labile Fullerene[50] as C50Cl10. Science, (2004) 305(5671): p. 699.

  9. Biomolecular detection using a metal semiconductor field effect transistor (United States)

    Estephan, Elias; Saab, Marie-Belle; Buzatu, Petre; Aulombard, Roger; Cuisinier, Frédéric J. G.; Gergely, Csilla; Cloitre, Thierry


    In this work, our attention was drawn towards developing affinity-based electrical biosensors, using a MESFET (Metal Semiconductor Field Effect Transistor). Semiconductor (SC) surfaces must be prepared before the incubations with biomolecules. The peptides route was adapted to exceed and bypass the limits revealed by other types of surface modification due to the unwanted unspecific interactions. As these peptides reveal specific recognition of materials, then controlled functionalization can be achieved. Peptides were produced by phage display technology using a library of M13 bacteriophage. After several rounds of bio-panning, the phages presenting affinities for GaAs SC were isolated; the DNA of these specific phages were sequenced, and the peptide with the highest affinity was synthesized and biotinylated. To explore the possibility of electrical detection, the MESFET fabricated with the GaAs SC were used to detect the streptavidin via the biotinylated peptide in the presence of the bovine Serum Albumin. After each surface modification step, the IDS (current between the drain and the source) of the transistor was measured and a decrease in the intensity was detected. Furthermore, fluorescent microscopy was used in order to prove the specificity of this peptide and the specific localisation of biomolecules. In conclusion, the feasibility of producing an electrical biosensor using a MESFET has been demonstrated. Controlled placement, specific localization and detection of biomolecules on a MESFET transistor were achieved without covering the drain and the source. This method of functionalization and detection can be of great utility for biosensing application opening a new way for developing bioFETs (Biomolecular Field-Effect Transistor).

  10. Fundamental behavior of a model biomolecular amphiphile system (United States)

    Haverstick, Kraig Leonard

    An interest in the fundamental interactions between protein components, in the form of either single amino acids or peptides, unifies the work represented in this thesis. These fundamental interactions drive protein folding, enzyme-substrate binding, and cell adhesion to extracellular ligands. The technology of lipidation was used to isolate these protein interactions. Lipidation of a water-soluble amino acid or peptide sequence confined the protein component to the air-water interface or to a self-assembled structure in water. Compression of the molecules at the air-water interface ordered them into a solid-like monolayer, and Langmuir-Blodgett deposition produced a surface modification with protein component presented in a controlled, orderly manner. These molecules have potential applications as biomaterials coatings or drug delivery devices. A method for determination of specific hydrogen bonding interactions through cocrystallization of two complementary peptide sequences is also described. In order to understand the effect of lipidation and lipid structure on peptide behavior, a comprehensive study of tail designs was first undertaken. Tail length, linkage group, linker, spacer length, and headgroup chirality, orientation, and terminal group were systematically varied in simple amino acid amphiphiles. Monolayer assembly, thermal stability, and structure were studied with Langmuir isotherms and Fourier transform infrared spectroscopy. Each part of the tail structure was found to affect monolayer behavior. With lipid effects better understood, peptide amphiphiles were designed, synthesized, and studied using peptide sequences of importance for cell adhesion. The sequences [IV-H1] from type IV collagen and Arg-Gly-Asp (RGD) were lipidated and characterized in monolayers by Langmuir isotherms and Fourier transform infrared spectroscopy. Biological functionality was determined by melanoma cell spreading assays. Peptide presentation was found to be critical for

  11. Diffusion Monte Carlo applied to weak interactions - hydrogen bonding and aromatic stacking in (bio-)molecular model systems (United States)

    Fuchs, M.; Ireta, J.; Scheffler, M.; Filippi, C.


    Dispersion (Van der Waals) forces are important in many molecular phenomena such as self-assembly of molecular crystals or peptide folding. Calculating this nonlocal correlation effect requires accurate electronic structure methods. Usual density-functional theory with generalized gradient functionals (GGA-DFT) fails unless empirical corrections are added that still need extensive validation. Quantum chemical methods like MP2 and coupled cluster are more accurate, yet limited to rather small systems by their unfavorable computational scaling. Diffusion Monte Carlo (DMC) can provide accurate molecular total energies and remains feasible also for larger systems. Here we apply the fixed-node DMC method to (bio-)molecular model systems where dispersion forces are significant: (dimethyl-) formamide and benzene dimers, and adenine-thymine DNA base pairs. Our DMC binding energies agree well with data from coupled cluster (CCSD(T)), in particular for stacked geometries where GGA-DFT fails qualitatively and MP2 predicts too strong binding.

  12. Protein Structure Determination by Assembling Super-Secondary Structure Motifs Using Pseudocontact Shifts. (United States)

    Pilla, Kala Bharath; Otting, Gottfried; Huber, Thomas


    Computational and nuclear magnetic resonance hybrid approaches provide efficient tools for 3D structure determination of small proteins, but currently available algorithms struggle to perform with larger proteins. Here we demonstrate a new computational algorithm that assembles the 3D structure of a protein from its constituent super-secondary structural motifs (Smotifs) with the help of pseudocontact shift (PCS) restraints for backbone amide protons, where the PCSs are produced from different metal centers. The algorithm, DINGO-PCS (3D assembly of Individual Smotifs to Near-native Geometry as Orchestrated by PCSs), employs the PCSs to recognize, orient, and assemble the constituent Smotifs of the target protein without any other experimental data or computational force fields. Using a universal Smotif database, the DINGO-PCS algorithm exhaustively enumerates any given Smotif. We benchmarked the program against ten different protein targets ranging from 100 to 220 residues with different topologies. For nine of these targets, the method was able to identify near-native Smotifs.

  13. Recent applications of AC electrokinetics in biomolecular analysis on microfluidic devices. (United States)

    Sasaki, Naoki


    AC electrokinetics is a generic term that refers to an induced motion of particles and fluids under nonuniform AC electric fields. The AC electric fields are formed by application of AC voltages to microelectrodes, which can be easily integrated into microfluidic devices by standard microfabrication techniques. Moreover, the magnitude of the motion is large enough to control the mass transfer on the devices. These advantages are attractive for biomolecular analysis on the microfluidic devices, in which the characteristics of small space and microfluidics have been mainly employed. In this review, I describe recent applications of AC electrokinetics in biomolecular analysis on microfluidic devices. The applications include fluid pumping and mixing by AC electrokinetic flow, and manipulation of biomolecules such as DNA and proteins by various AC electrokinetic techniques. Future prospects for highly functional biomolecular analysis on microfluidic devices with the aid of AC electrokinetics are also discussed.

  14. Mining, modeling, and evaluation of subnetworks from large biomolecular networks and its comparison study. (United States)

    Hu, Xiaohua; Ng, Michael; Wu, Fang-Xiang; Sokhansanj, Bahrad A


    In this paper, we present a novel method to mine, model, and evaluate a regulatory system executing cellular functions that can be represented as a biomolecular network. Our method consists of two steps. First, a novel scale-free network clustering approach is applied to such a biomolecular network to obtain various subnetworks. Second, computational models are generated for the subnetworks and simulated to predict their behavior in the cellular context. We discuss and evaluate some of the advanced computational modeling approaches, in particular, state-space modeling, probabilistic Boolean network modeling, and fuzzy logic modeling. The modeling and simulation results represent hypotheses that are tested against high-throughput biological datasets (microarrays and/or genetic screens) under normal and perturbation conditions. Experimental results on time-series gene expression data for the human cell cycle indicate that our approach is promising for subnetwork mining and simulation from large biomolecular networks.


    Directory of Open Access Journals (Sweden)

    Floriniţa Duca


    Full Text Available This paper examines the relative importance of four factors in the capital structure decisions of Romanian listed firms. The existing empirical research on capital structure has been largely confined to developed countries. The Romanian Financial Market has been developing at an exponential rate and dedicated research in the field is required. We used 100 firms listed in 2010 at the Bucharest Stock Exchange. The objective of this paper is to build on previous studies model all the important factors affecting capital structure decisions. We find that factors such as tangibility of assets, firm size, liquidity, and profitability have significant influences on the leverage structure chosen by firms.These results are believed to have significant implications for the theory of finance and to be of importance to the corporate treasure in choice of new financing and to the financial analyst.

  16. Crystal Structure of Mitochondrial Respiratory Membrane Protein Complex Ⅱ Determined

    Institute of Scientific and Technical Information of China (English)


    @@ Scientists at the CAS Institute of Biophysics (IBP) and Tsinghua University have gained new insights into the mechanism of mitochondria, the subcellular structures which generate energy for living cells.

  17. Structural determinants of Smad function in TGF-β signaling. (United States)

    Macias, Maria J; Martin-Malpartida, Pau; Massagué, Joan


    Smad transcription factors are central to the signal transduction pathway that mediates the numerous effects of the transforming growth factor β (TGF-β) superfamily of cytokines in metazoan embryo development as well as in adult tissue regeneration and homeostasis. Although Smad proteins are conserved, recent genome-sequencing projects have revealed their sequence variation in metazoan evolution, human polymorphisms, and cancer. Structural studies of Smads bound to partner proteins and target DNA provide a framework for understanding the significance of these evolutionary and pathologic sequence variations. We synthesize the extant mutational and structural data to suggest how genetic variation in Smads may affect the structure, regulation, and function of these proteins. We also present a web application that compares Smad sequences and displays Smad protein structures and their disease-associated variants.

  18. iBIOMES: managing and sharing biomolecular simulation data in a distributed environment. (United States)

    Thibault, Julien C; Facelli, Julio C; Cheatham, Thomas E


    Biomolecular simulations, which were once batch queue or compute limited, have now become data analysis and management limited. In this paper we introduce a new management system for large biomolecular simulation and computational chemistry data sets. The system can be easily deployed on distributed servers to create a mini-grid at the researcher's site. The system not only offers a simple data deposition mechanism but also a way to register data into the system without moving the data from their original location. Any registered data set can be searched and downloaded using a set of defined metadata for molecular dynamics and quantum mechanics and visualized through a dynamic Web interface.

  19. Structural Determinants of Cadherin-23 Function in Hearing and Deafness

    Energy Technology Data Exchange (ETDEWEB)

    Sotomayor, Marcos; Weihofen, Wilhelm A.; Gaudet, Rachelle; Corey, David P. (Harvard-Med); (Harvard)


    The hair-cell tip link, a fine filament directly conveying force to mechanosensitive transduction channels, is composed of two proteins, protocadherin-15 and cadherin-23, whose mutation causes deafness. However, their molecular structure, elasticity, and deafness-related structural defects are unknown. We present crystal structures of the first and second extracellular cadherin repeats of cadherin-23. Overall, structures show typical cadherin folds, but reveal an elongated N terminus that precludes classical cadherin interactions and contributes to an N-terminal Ca{sup 2+}-binding site. The deafness mutation D101G, in the linker region between the repeats, causes a slight bend between repeats and decreases Ca{sup 2+} affinity. Molecular dynamics simulations suggest that cadherin-23 repeats are stiff and that either removing Ca{sup 2+} or mutating Ca{sup 2+}-binding residues reduces rigidity and unfolding strength. The structures define an uncharacterized cadherin family and, with simulations, suggest mechanisms underlying inherited deafness and how cadherin-23 may bind with itself and with protocadherin-15 to form the tip link.

  20. Structure Determination of Unknown Organic Liquids Using NMR and IR Spectroscopy: A General Chemistry Laboratory (United States)

    Pavel, John T.; Hyde, Erin C.; Bruch, Martha D.


    This experiment introduced general chemistry students to the basic concepts of organic structures and to the power of spectroscopic methods for structure determination. Students employed a combination of IR and NMR spectroscopy to perform de novo structure determination of unknown alcohols, without being provided with a list of possible…

  1. Structure determination of T-cell protein-tyrosine phosphatase

    DEFF Research Database (Denmark)

    Iversen, L.F.; Møller, K. B.; Pedersen, A.K.;


    homologous T cell protein-tyrosine phosphatase (TC-PTP) has received much less attention, and no x-ray structure has been provided. We have previously co-crystallized PTP1B with a number of low molecular weight inhibitors that inhibit TC-PTP with similar efficiency. Unexpectedly, we were not able to co...... the high degree of functional and structural similarity between TC-PTP and PTP1B, we have been able to identify areas close to the active site that might be addressed to develop selective inhibitors of each enzyme....

  2. First-principles determination of the structure of magnesium borohydride. (United States)

    Zhou, Xiang-Feng; Oganov, Artem R; Qian, Guang-Rui; Zhu, Qiang


    The energy landscape of Mg(BH(4))(2) under pressure is explored by ab initio evolutionary calculations. Two new tetragonal structures, with space groups P4 and I4(1)/acd, are predicted to be lower in enthalpy by 15.4 and 21.2 kJ/mol, respectively, than the earlier proposed P4(2)nm phase. We have simulated x-ray diffraction spectra, lattice dynamics, and equations of state of these phases. The density, volume contraction, bulk modulus, and simulated x-ray diffraction patterns of I4(1)/acd and P4 structures are in excellent agreement with the experimental results.

  3. Unified approach for determining tetragonal tungsten bronze crystal structures. (United States)

    Smirnov, M; Saint-Grégoire, P


    Tetragonal tungsten bronze (TTB) oxides are one of the most important classes of ferroelectrics. Many of these framework structures undergo ferroelastic transformations related to octahedron tilting deformations. Such tilting deformations are closely related to the rigid unit modes (RUMs). This paper discusses the whole set of RUMs in an ideal TTB lattice and possible crystal structures which can emerge owing to the condensation of some of them. Analysis of available experimental data for the TTB-like niobates lends credence to the obtained theoretical predictions.

  4. Engineering intracellular active transport systems as in vivo biomolecular tools.

    Energy Technology Data Exchange (ETDEWEB)

    Bachand, George David; Carroll-Portillo, Amanda


    Active transport systems provide essential functions in terms of cell physiology and metastasis. These systems, however, are also co-opted by invading viruses, enabling directed transport of the virus to and from the cell's nucleus (i.e., the site of virus replication). Based on this concept, fundamentally new approaches for interrogating and manipulating the inner workings of living cells may be achievable by co-opting Nature's active transport systems as an in vivo biomolecular tool. The overall goal of this project was to investigate the ability to engineer kinesin-based transport systems for in vivo applications, specifically the collection of effector proteins (e.g., transcriptional regulators) within single cells. In the first part of this project, a chimeric fusion protein consisting of kinesin and a single chain variable fragment (scFv) of an antibody was successfully produced through a recombinant expression system. The kinesin-scFv retained both catalytic and antigenic functionality, enabling selective capture and transport of target antigens. The incorporation of a rabbit IgG-specific scFv into the kinesin established a generalized system for functionalizing kinesin with a wide range of target-selective antibodies raised in rabbits. The second objective was to develop methods of isolating the intact microtubule network from live cells as a platform for evaluating kinesin-based transport within the cytoskeletal architecture of a cell. Successful isolation of intact microtubule networks from two distinct cell types was demonstrated using glutaraldehyde and methanol fixation methods. This work provides a platform for inferring the ability of kinesin-scFv to function in vivo, and may also serve as a three-dimensional scaffold for evaluating and exploiting kinesin-based transport for nanotechnological applications. Overall, the technology developed in this project represents a first-step in engineering active transport system for in vivo

  5. Output-input ratio in thermally fluctuating biomolecular machines. (United States)

    Kurzynski, Michal; Torchala, Mieczyslaw; Chelminiak, Przemyslaw


    Biological molecular machines are proteins that operate under isothermal conditions and hence are referred to as free energy transducers. They can be formally considered as enzymes that simultaneously catalyze two chemical reactions: the free energy-donating (input) reaction and the free energy-accepting (output) one. Most if not all biologically active proteins display a slow stochastic dynamics of transitions between a variety of conformational substates composing their native state. This makes the description of the enzymatic reaction kinetics in terms of conventional rate constants insufficient. In the steady state, upon taking advantage of the assumption that each reaction proceeds through a single pair (the gate) of transition conformational substates of the enzyme-substrates complex, the degree of coupling between the output and the input reaction fluxes has been expressed in terms of the mean first-passage times on a conformational transition network between the distinguished substates. The theory is confronted with the results of random-walk simulations on the five-dimensional hypercube. The formal proof is given that, for single input and output gates, the output-input degree of coupling cannot exceed unity. As some experiments suggest such exceeding, looking for the conditions for increasing the degree of coupling value over unity challenges the theory. Performed simulations of random walks on several model networks involving more extended gates indicate that the case of the degree of coupling value higher than 1 is realized in a natural way on critical branching trees extended by long-range shortcuts. Such networks are scale-free and display the property of the small world. For short-range shortcuts, the networks are scale-free and fractal, representing a reasonable model for biomolecular machines displaying tight coupling, i.e., the degree of coupling equal exactly to unity. A hypothesis is stated that the protein conformational transition networks, as

  6. Compressed Sensing Electron Tomography for Determining Biological Structure (United States)

    Guay, Matthew D.; Czaja, Wojciech; Aronova, Maria A.; Leapman, Richard D.


    There has been growing interest in applying compressed sensing (CS) theory and practice to reconstruct 3D volumes at the nanoscale from electron tomography datasets of inorganic materials, based on known sparsity in the structure of interest. Here we explore the application of CS for visualizing the 3D structure of biological specimens from tomographic tilt series acquired in the scanning transmission electron microscope (STEM). CS-ET reconstructions match or outperform commonly used alternative methods in full and undersampled tomogram recovery, but with less significant performance gains than observed for the imaging of inorganic materials. We propose that this disparity stems from the increased structural complexity of biological systems, as supported by theoretical CS sampling considerations and numerical results in simulated phantom datasets. A detailed analysis of the efficacy of CS-ET for undersampled recovery is therefore complicated by the structure of the object being imaged. The numerical nonlinear decoding process of CS shares strong connections with popular regularized least-squares methods, and the use of such numerical recovery techniques for mitigating artifacts and denoising in reconstructions of fully sampled datasets remains advantageous. This article provides a link to the software that has been developed for CS-ET reconstruction of electron tomographic data sets.

  7. Structural Determinants of Intergroup Association: Interracial Marriage and Crime. (United States)

    South, Scott J.; Messner, Steven F.


    Using data from a sample of 25 U. S. metropolitan cities, this study investigates the relationship between interracial marriage and violent interracial crime. Results show a positive relationship, one which was predicted by Blau's macrosociological theory of social structure. (Author/JDH)

  8. Some structural determinants of Pavlovian conditioning in artificial neural networks

    NARCIS (Netherlands)

    Sanchez, Jose M.; Galeazzi, Juan M.; Burgos, Jose E.


    This paper investigates the possible role of neuroanatomical features in Pavlovian conditioning, via computer simulations with layered, feedforward artificial neural networks. The networks' structure and functioning are described by a strongly bottom-up model that takes into account the roles of hip

  9. Novel test structures for dedicated temperature budget determination

    NARCIS (Netherlands)

    Faber, Erik J.; Wolters, Rob A.M.; Schmitz, Jurriaan


    We present a novel method for determining the temperature budget of the process side of silicon substrates and chips, based on well-known silicide formation reactions of metal–Si systems and (four-point probe) resistance measurements. In this paper, we focus on the Pd–Si system that is most temperat

  10. Fractal structure and fractal dimension determination at nanometer scale

    Institute of Scientific and Technical Information of China (English)

    张跃; 李启楷; 褚武扬; 王琛; 白春礼


    Three-dimensional fractures of different fractal dimensions have been constructed with successive random addition algorithm, the applicability of various dimension determination methods at nanometer scale has been studied. As to the metallic fractures, owing to the limited number of slit islands in a slit plane or limited datum number at nanometer scale, it is difficult to use the area-perimeter method or power spectrum method to determine the fractal dimension. Simulation indicates that box-counting method can be used to determine the fractal dimension at nanometer scale. The dimensions of fractures of valve steel 5Cr21Mn9Ni4N have been determined with STM. Results confirmed that fractal dimension varies with direction at nanometer scale. Our study revealed that, as to theoretical profiles, the dependence of fractal dimension with direction is simply owing to the limited data set number, i.e. the effect of boundaries. However, the dependence of fractal dimension with direction at nanometer scale in rea

  11. Iron phosphate glasses: Structure determination and radiation tolerance (United States)

    Jolley, Kenny; Smith, Roger


    Iron phosphate glass (IPG) has gained recent interest for use in encapsulating radioactive waste for long term storage. In this work, we investigate 5 different compositions of iron phosphate glass. We consider amorphous structures of 3 known crystalline phases: Fe2+ Fe23+ (P2O7)2, Fe43 + (P2O7)3 and Fe3+(PO3)3, and structures of IPG (40 mol% Fe2O3 and 60 mol% P2O5), with 4% and 17% Fe2+ ion concentrations. Using constant volume molecular dynamics (MD), we quench a set of structures for each glass composition, to find the optimal density structure. We found that the lowest energy structures of IPG with 4% and 17% concentration of Fe2+, have a density of 3.25 and 3.28 g/cm3 respectively. This is slightly higher than the experimentally measured values of 2.9 and 2.95 g/cm3 respectively. We also estimate an upper and lower bound on the melting temperatures of each glass, then for each glass, we simulate radiation damage cascades at 4 keV. The cascade structures can be in the form of either a concentrated thermal spike or more diffuse with sub-cascade branching. We found that the glass compositions with a higher Fe/P atomic ratio, contained a greater number of displacements after the cascade. We also found that the IPG with 4% Fe2+, contained slightly fewer displacements than the IPG with 17% Fe2+. This is consistent with our previous work, which showed that the threshold displacement energies are lower for glasses with a lower Fe2+ content. In all the simulations, many PO4 polyhedra are destroyed during the early stages of irradiation, but recover strongly over a time scale of picoseconds, leaving very few over or under co-ordinated P atoms at the end of the ballistic phase. This is in contrast to recent work in apatite. The strong recovery indicates that phosphate glasses with a low Fe2+ content could be good materials for waste encapsulation.

  12. Spectroscopic infrared ellipsometry to determine the structure of layered samples

    Energy Technology Data Exchange (ETDEWEB)

    Korte, Ernst-Heiner; Hinrichs, Karsten; Roeseler, Arnulf


    This contribution outlines investigations in our laboratory in the course of developing spectroscopic infrared ellipsometry into an analytical tool for structure elucidation of a given solid sample with one single experimental technique. The term 'structure' is meant here to comprise the layer or stack geometry of a sample along with the thicknesses, as well as the optical properties of the individual layers. The latter ones--expressed as optical constants--serve as a basis to characterize the layer material, from the identity of the compound to specific molecular interactions and order. There are no general restrictions as to the physical properties of the materials; the individual layers or films should advantageously be thin enough to transmit infrared radiation at least within spectral windows. The sensitivity of infrared ellipsometry to films as thin as a few nanometers or less is illustrated by experimental examples.

  13. Determination of channeling perspectives for complex crystal structures

    Energy Technology Data Exchange (ETDEWEB)

    Allen, W.R.


    Specification of the atomic arrangement for axes and planes of high symmetry is essential for crystal alignment using Rutherford backscattering and for studies of the lattice location of impurities in single crystals. By rotation of an inscribed orthogonal coordinate system, a visual image for a given perspective of a crystal structure can be specified. Knowledge of the atomic arrangement permits qualitative channeling perspectives to be visualized and calculation of continuum potentials for channeling. Channeling angular-yield profiles can then be analytically modeled and, subsequently, shadowing by host atoms of positions within the unit cell predicted. Software to calculate transformed atom positions for a channeling perspective in a single crystal are described and illustrated for the spinel crystal structure.

  14. Structural determinants of reductive terpene cyclization in iridoid biosynthesis

    DEFF Research Database (Denmark)

    Kries, Hajo; Caputi, Lorenzo; Stevenson, Clare E M;


    The carbon skeleton of ecologically and pharmacologically important iridoid monoterpenes is formed in a reductive cyclization reaction unrelated to canonical terpene cyclization. Here we report the crystal structure of the recently discovered iridoid cyclase (from Catharanthus roseus) bound to a ...... to a mechanism-inspired inhibitor that illuminates substrate binding and catalytic function of the enzyme. Key features that distinguish iridoid synthase from its close homolog progesterone 5β-reductase are highlighted....

  15. Determination of the pion and kaon structure functions

    Energy Technology Data Exchange (ETDEWEB)

    Aitkenhead, W.; Barton, D.S.; Brandenburg, G.W.; Busza, W.; Dobrowolski, T.; Friedman, J.I.; Kendall, H.W.; Lyons, T.; Nelson, B.; Rosenson, L.; Toy, W.; Verdier, R.; Votta, L.; Chiaradia, M.T.; DeMarzo, C.; Favuzzi, C.; Germinario, G.; Guerriero, L.; LaVopa, P.; Maggi, G.; Posa, F.; Selvaggi, G.; Spinelli, P.; Waldner, F.; Brenner, A.E.; Carey, D.C.; Elias, J.E.; Garbincius, P.H.; Mikenberg, G.; Polychronakos, V.A.; Meunier, R.; Cutts, D.; Dulude, R.S.; Lanou, R.E. Jr.; Massimo, J.T.


    Quark structure functions have been extracted from low-p/sub T/ inclusive hadron production data for the pion and kaon with use of the recombination model. n/sup ..pi../=1.0 +- 0.1 and n/sup K/=2.5 +- 0.6 is obtained, where n is the leading (1-x) power of the nonstrange--valence-quark distribution. Both the pion and kaon nonstrange--sea-quark functions have napprox. =3.5.

  16. Structural foundations of optogenetics: Determinants of channelrhodopsin ion selectivity. (United States)

    Berndt, Andre; Lee, Soo Yeun; Wietek, Jonas; Ramakrishnan, Charu; Steinberg, Elizabeth E; Rashid, Asim J; Kim, Hoseok; Park, Sungmo; Santoro, Adam; Frankland, Paul W; Iyer, Shrivats M; Pak, Sally; Ährlund-Richter, Sofie; Delp, Scott L; Malenka, Robert C; Josselyn, Sheena A; Carlén, Marie; Hegemann, Peter; Deisseroth, Karl


    The structure-guided design of chloride-conducting channelrhodopsins has illuminated mechanisms underlying ion selectivity of this remarkable family of light-activated ion channels. The first generation of chloride-conducting channelrhodopsins, guided in part by development of a structure-informed electrostatic model for pore selectivity, included both the introduction of amino acids with positively charged side chains into the ion conduction pathway and the removal of residues hypothesized to support negatively charged binding sites for cations. Engineered channels indeed became chloride selective, reversing near -65 mV and enabling a new kind of optogenetic inhibition; however, these first-generation chloride-conducting channels displayed small photocurrents and were not tested for optogenetic inhibition of behavior. Here we report the validation and further development of the channelrhodopsin pore model via crystal structure-guided engineering of next-generation light-activated chloride channels (iC++) and a bistable variant (SwiChR++) with net photocurrents increased more than 15-fold under physiological conditions, reversal potential further decreased by another ∼ 15 mV, inhibition of spiking faithfully tracking chloride gradients and intrinsic cell properties, strong expression in vivo, and the initial microbial opsin channel-inhibitor-based control of freely moving behavior. We further show that inhibition by light-gated chloride channels is mediated mainly by shunting effects, which exert optogenetic control much more efficiently than the hyperpolarization induced by light-activated chloride pumps. The design and functional features of these next-generation chloride-conducting channelrhodopsins provide both chronic and acute timescale tools for reversible optogenetic inhibition, confirm fundamental predictions of the ion selectivity model, and further elucidate electrostatic and steric structure-function relationships of the light-gated pore.

  17. Music structure determines heart rate variability of singers (United States)

    Vickhoff, Björn; Malmgren, Helge; Åström, Rickard; Nyberg, Gunnar; Ekström, Seth-Reino; Engwall, Mathias; Snygg, Johan; Nilsson, Michael; Jörnsten, Rebecka


    Choir singing is known to promote wellbeing. One reason for this may be that singing demands a slower than normal respiration, which may in turn affect heart activity. Coupling of heart rate variability (HRV) to respiration is called Respiratory sinus arrhythmia (RSA). This coupling has a subjective as well as a biologically soothing effect, and it is beneficial for cardiovascular function. RSA is seen to be more marked during slow-paced breathing and at lower respiration rates (0.1 Hz and below). In this study, we investigate how singing, which is a form of guided breathing, affects HRV and RSA. The study comprises a group of healthy 18 year olds of mixed gender. The subjects are asked to; (1) hum a single tone and breathe whenever they need to; (2) sing a hymn with free, unguided breathing; and (3) sing a slow mantra and breathe solely between phrases. Heart rate (HR) is measured continuously during the study. The study design makes it possible to compare above three levels of song structure. In a separate case study, we examine five individuals performing singing tasks (1–3). We collect data with more advanced equipment, simultaneously recording HR, respiration, skin conductance and finger temperature. We show how song structure, respiration and HR are connected. Unison singing of regular song structures makes the hearts of the singers accelerate and decelerate simultaneously. Implications concerning the effect on wellbeing and health are discussed as well as the question how this inner entrainment may affect perception and behavior. PMID:23847555

  18. Neural Network Enhanced Structure Determination of Osteoporosis, Immune System, and Radiation Repair Proteins Project (United States)

    National Aeronautics and Space Administration — We propose a dual objective innovation that has valuable NASA applicability and tremendous commercial potential. The first innovation is the structure determination...

  19. Neural Network Enhanced Structure Determination of Osteoporosis, Immune System, and Radiation Repair Proteins Project (United States)

    National Aeronautics and Space Administration — The proposed innovation will utilize self learning neural network technology to determine the structure of osteoporosis, immune system disease, and excess radiation...

  20. Variability of Protein Structure Models from Electron Microscopy. (United States)

    Monroe, Lyman; Terashi, Genki; Kihara, Daisuke


    An increasing number of biomolecular structures are solved by electron microscopy (EM). However, the quality of structure models determined from EM maps vary substantially. To understand to what extent structure models are supported by information embedded in EM maps, we used two computational structure refinement methods to examine how much structures can be refined using a dataset of 49 maps with accompanying structure models. The extent of structure modification as well as the disagreement between refinement models produced by the two computational methods scaled inversely with the global and the local map resolutions. A general quantitative estimation of deviations of structures for particular map resolutions are provided. Our results indicate that the observed discrepancy between the deposited map and the refined models is due to the lack of structural information present in EM maps and thus these annotations must be used with caution for further applications.

  1. Determining the Spectral Signature of Spatial Coherent Structures

    CERN Document Server

    Pastur, L R; Fraigneau, Y; Podvin, B


    We applied to an open flow a proper orthogonal decomposition (pod) technique, on 2D snapshots of the instantaneous velocity field, to reveal the spatial coherent structures responsible of the self-sustained oscillations observed in the spectral distribution of time series. We applied the technique to 2D planes out of 3D direct numerical simulations on an open cavity flow. The process can easily be implemented on usual personal computers, and might bring deep insights on the relation between spatial events and temporal signature in (both numerical or experimental) open flows.

  2. Understanding chlorophylls: central magnesium ion and phytyl as structural determinants. (United States)

    Fiedor, Leszek; Kania, Agnieszka; Myśliwa-Kurdziel, Beata; Orzeł, Łukasz; Stochel, Grazyna


    Phytol, a C20 alcohol esterifying the C-17(3) propionate, and Mg2+ ion chelated in the central cavity, are conservative structural constituents of chlorophylls. To evaluate their intramolecular structural effects we prepared a series of metal- and phytyl-free derivatives of bacteriochlorophyll a and applied them as model chlorophylls. A detailed spectroscopic study on the model pigments reveals meaningful differences in the spectral characteristics of the phytylated and non-phytylated pigments. Their analysis in terms of solvatochromism and axial coordination shows how the central Mg and phytyl residue shape the properties of the pigment. Surprisingly, the presence/absence of the central Mg has no effect on the solvatochromism of (bacterio)chlorophyll pi-electron system and the hydrophobicity of phytyl does not interfere with the first solvation shell of the chromophore. However, both residues significantly influence the conformation of the pigment macrocycle and the removal of either residue increases the macrocycle flexibility. The chelation of Mg has a flattening effect on the macrocycle whereas bulky phytyl residue seems to control the conformation of the chromophore via steric interactions with ring V and its substituents. The analysis of spectroscopic properties of bacteriochlorophyllide (free acid) shows that esterification of the C-17(3) propionate is necessary in chlorophylls because the carboxyl group may act as a strong chelator of the central Mg. These observations imply that the truncated chlorophylls used in theoretical studies are not adequate as models of native chromophores, especially when fine effects are to be modeled.

  3. Molecular Determinants of Staphylococcal Biofilm Dispersal and Structuring

    Directory of Open Access Journals (Sweden)

    Katherine Y Le


    Full Text Available Staphylococci are frequently implicated in human infections, and continue to pose a therapeutic dilemma due to their ability to form deeply seated microbial communities, known as biofilms, on the surfaces of implanted medical devices and host tissues. Biofilm development has been proposed to occur in three stages: 1 attachment, 2 proliferation/structuring, and 3 detachment/dispersal. Although research within the last several decades has implicated multiple molecules in the roles as effectors of staphylococcal biofilm proliferation/structuring and detachment/dispersal, to date, only phenol soluble modulins (PSMs have been consistently demonstrated to serve in this role under both in-vitro and in-vivo settings. PSMs are regulated directly through a density-dependent manner by the accessory gene regulator (Agr system. They disrupt the non-covalent forces holding the biofilm extracellular matrix together, which is necessary for the formation of channels, a process essential for the delivery of nutrients to deeper biofilm layers, and for dispersal/dissemination of clusters of biofilm to distal organs in acute infection. Given their relevance in both acute and chronic biofilm-associated infections, the Agr system and the psm genes hold promise as potential therapeutic targets.

  4. Using Dust as Probes to Determine Sheath Extent and Structure

    CERN Document Server

    Douglass, Angela; Qiao, Ke; Matthews, Lorin; Hyde, Truell


    Two in-situ experimental methods are presented in which dust particles are used to determine the extent of the sheath and gain information about the time-averaged electric force profile within a RF plasma sheath. These methods are advantageous because they are not only simple and quick to carry out, but they also can be performed using standard dusty plasma experimental equipment. In the first method, dust particles are tracked as they fall through the plasma toward the lower electrode. These trajectories are then used to determine the electric force on the particle as a function of height as well as the extent of the sheath. In the second method, dust particle levitation height is measured across a wide range of RF voltages. Similarities were observed between the two experiments, but in order to understand the underlying physics behind these observations, the same conditions were replicated using a self-consistent fluid model. Through comparison of the fluid model and experimental results, it is shown that t...

  5. g_contacts: Fast contact search in bio-molecular ensemble data (United States)

    Blau, Christian; Grubmuller, Helmut


    Short-range interatomic interactions govern many bio-molecular processes. Therefore, identifying close interaction partners in ensemble data is an essential task in structural biology and computational biophysics. A contact search can be cast as a typical range search problem for which efficient algorithms have been developed. However, none of those has yet been adapted to the context of macromolecular ensembles, particularly in a molecular dynamics (MD) framework. Here a set-decomposition algorithm is implemented which detects all contacting atoms or residues in maximum O(Nlog(N)) run-time, in contrast to the O(N2) complexity of a brute-force approach. Catalogue identifier: AEQA_v1_0 Program summary URL: Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, No. of lines in distributed program, including test data, etc.: 8945 No. of bytes in distributed program, including test data, etc.: 981604 Distribution format: tar.gz Programming language: C99. Computer: PC. Operating system: Linux. RAM: ≈Size of input frame Classification: 3, 4.14. External routines: Gromacs 4.6[1] Nature of problem: Finding atoms or residues that are closer to one another than a given cut-off. Solution method: Excluding distant atoms from distance calculations by decomposing the given set of atoms into disjoint subsets. Running time:≤O(Nlog(N)) References: [1] S. Pronk, S. Pall, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R. Shirts, J.C. Smith, P. M. Kasson, D. van der Spoel, B. Hess and Erik Lindahl, Gromacs 4.5: a high-throughput and highly parallel open source molecular simulation toolkit, Bioinformatics 29 (7) (2013).

  6. Biomolecularly capped uniformly sized nanocrystalline materials: glutathione-capped ZnS nanocrystals (United States)

    Torres-Martínez, Claudia L.; Nguyen, Liem; Kho, Richard; Bae, Weon; Bozhilov, Krassimir; Klimov, Victor; Mehra, Rajesh K.


    Micro-organisms such as bacteria and yeasts form CdS to detoxify toxic cadmium ions. Frequently, CdS particles formed in yeasts and bacteria were found to be associated with specific biomolecules. It was later determined that these biomolecules were present at the surface of CdS. This coating caused a restriction in the growth of CdS particles and resulted in the formation of nanometre-sized semiconductors (NCs) that exhibited typical quantum confinement properties. Glutathione and related phytochelatin peptides were shown to be the biomolecules that capped CdS nanocrystallites synthesized by yeasts Candida glabrata and Schizosaccharomyces pombe. Although early studies showed the existence of specific biochemical pathways for the synthesis of biomolecularly capped CdS NCs, these NCs could be formed in vitro under appropriate conditions. We have recently shown that cysteine and cysteine-containing peptides such as glutathione and phytochelatins can be used in vitro to dictate the formation of discrete sizes of CdS and ZnS nanocrystals. We have evolved protocols for the synthesis of ZnS or CdS nanocrystals within a narrow size distribution range. These procedures involve three steps: (1) formation of metallo-complexes of cysteine or cysteine-containing peptides, (2) introduction of stoichiometric amounts of inorganic sulfide into the metallo-complexes to initiate the formation of nanocrystallites and finally (3) size-selective precipitation of NCs with ethanol in the presence of Na+. The resulting NCs were characterized by optical spectroscopy, high-resolution transmission electron microscopy (HRTEM), x-ray diffraction and electron diffraction. HRTEM showed that the diameter of the ZnS-glutathione nanocrystals was 3.45+/-0.5 nm. X-ray diffraction and electron diffraction analyses indicated ZnS-glutathione to be hexagonal. Photocatalytic studies suggest that glutathione-capped ZnS nanocrystals prepared by our procedure are highly efficient in degrading a test model

  7. Electron Crystallography Novel Approaches for Structure Determination of Nanosized Materials

    CERN Document Server

    Weirich, Thomas E; Zou, Xiaodong


    During the last decade we have been witness to several exciting achievements in electron crystallography. This includes structural and charge density studies on organic molecules complicated inorganic and metallic materials in the amorphous, nano-, meso- and quasi-crystalline state and also development of new software, tailor-made for the special needs of electron crystallography. Moreover, these developments have been accompanied by a now available new generation of computer controlled electron microscopes equipped with high-coherent field-emission sources, cryo-specimen holders, ultra-fast CCD cameras, imaging plates, energy filters and even correctors for electron optical distortions. Thus, a fast and semi-automatic data acquisition from small sample areas, similar to what we today know from imaging plates diffraction systems in X-ray crystallography, can be envisioned for the very near future. This progress clearly shows that the contribution of electron crystallography is quite unique, as it enables to r...

  8. Extracellular matrix structure and nano-mechanics determine megakaryocyte function. (United States)

    Malara, Alessandro; Gruppi, Cristian; Pallotta, Isabella; Spedden, Elise; Tenni, Ruggero; Raspanti, Mario; Kaplan, David; Tira, Maria Enrica; Staii, Cristian; Balduini, Alessandra


    Cell interactions with matrices via specific receptors control many functions, with chemistry, physics, and membrane elasticity as fundamental elements of the processes involved. Little is known about how biochemical and biophysical processes integrate to generate force and, ultimately, to regulate hemopoiesis into the bone marrow-matrix environment. To address this hypothesis, in this work we focus on the regulation of MK development by type I collagen. By atomic force microscopy analysis, we demonstrate that the tensile strength of fibrils in type I collagen structure is a fundamental requirement to regulate cytoskeleton contractility of human MKs through the activation of integrin-α2β1-dependent Rho-ROCK pathway and MLC-2 phosphorylation. Most importantly, this mechanism seemed to mediate MK migration, fibronectin assembly, and platelet formation. On the contrary, a decrease in mechanical tension caused by N-acetylation of lysine side chains in type I collagen completely reverted these processes by preventing fibrillogenesis.

  9. Mesopore quality determines the lifetime of hierarchically structured zeolite catalysts (United States)

    Milina, Maria; Mitchell, Sharon; Crivelli, Paolo; Cooke, David; Pérez-Ramírez, Javier


    Deactivation due to coking limits the lifetime of zeolite catalysts in the production of chemicals and fuels. Superior performance can be achieved through hierarchically structuring the zeolite porosity, yet no relation has been established between the mesopore architecture and the catalyst lifetime. Here we introduce a top-down demetallation strategy to locate mesopores in different regions of MFI-type crystals with identical bulk porous and acidic properties. In contrast, well-established bottom-up strategies as carbon templating and seed silanization fail to yield materials with matching characteristics. Advanced characterization tools capable of accurately discriminating the mesopore size, distribution and connectivity are applied to corroborate the concept of mesopore quality. Positron annihilation lifetime spectroscopy proves powerful to quantify the global connectivity of the intracrystalline pore network, which, as demonstrated in the conversions of methanol or of propanal to hydrocarbons, is closely linked to the lifetime of zeolite catalysts. The findings emphasize the need to aptly tailor hierarchical materials for maximal catalytic advantage.

  10. Structural determinants allowing endolysosomal sorting and degradation of endosomal GTPases. (United States)

    Valero, Ruth A; Oeste, Clara L; Stamatakis, Konstantinos; Ramos, Irene; Herrera, Mónica; Boya, Patricia; Pérez-Sala, Dolores


    Rapid control of protein degradation is usually achieved through the ubiquitin-proteasome pathway. We recently found that the short-lived GTPase RhoB is degraded in lysosomes. Moreover, the fusion of the RhoB C-terminal sequence CINCCKVL, containing the isoprenylation and palmitoylation sites, to other proteins directs their sorting into multivesicular bodies (MVBs) and rapid lysosomal degradation. Here, we show that this process is highly specific for RhoB. Alteration of late endosome lipid dynamics produced the accumulation of RhoB, but not of other endosomal GTPases, including Rab5, Rab7, Rab9 or Rab11, into enlarged MVB. Other isoprenylated and bipalmitoylated GTPases, such as H-Ras, Rap2A, Rap2B and TC10, were not accumulated into MVB and were stable. Remarkably, although TC10, which is highly homologous to RhoB, was stable, a sequence derived from its C-terminus (CINCCLIT) elicited MVB sorting and degradation of a green fluorescent protein (GFP)-chimeric protein. This led us to identify a cluster of basic amino acids (KKH) in the TC10 hypervariable region, constituting a secondary signal potentially involved in electrostatic interactions with membrane lipids. Mutation of this cluster allowed TC10 MVB sorting and degradation, whereas inserting it into RhoB hypervariable region rescued this protein from its lysosomal degradation pathway. These findings define a highly specific structural module for entering the MVB pathway and rapid lysosomal degradation.

  11. Benzofuranyl Esters: Synthesis, Crystal Structure Determination, Antimicrobial and Antioxidant Activities

    Directory of Open Access Journals (Sweden)

    C. S. Chidan Kumar


    Full Text Available A series of five new 2‐(1‐benzofuran‐2‐yl‐2‐oxoethyl 4-(un/substitutedbenzoates 4(a–e, with the general formula of C8H5O(C=OCH2O(C=OC6H4X, X = H, Cl, CH3, OCH3 or NO2, was synthesized in high purity and good yield under mild conditions. The synthesized products 4(a–e were characterized by FTIR, 1H-, 13C- and 1H-13C HMQC NMR spectroscopic analysis and their 3D structures were confirmed by single-crystal X-ray diffraction studies. These compounds were screened for their antimicrobial and antioxidant activities. The tested compounds showed antimicrobial ability in the order of 4b < 4a < 4c < 4d < 4e and the highest potency with minimum inhibition concentration (MIC value of 125 µg/mL was observed for 4e. The results of antioxidant activities revealed the highest activity for compound 4e (32.62% ± 1.34% in diphenyl-2-picrylhydrazyl (DPPH radical scavenging, 4d (31.01% ± 4.35% in ferric reducing antioxidant power (FRAP assay and 4a (27.11% ± 1.06% in metal chelating (MC activity.

  12. Genetic and perinatal determinants of structural brain deficits in schizophrenia. (United States)

    Cannon, T D; Mednick, S A; Parnas, J


    Using a subsample from the Copenhagen schizophrenia high-risk project, we examined the contributions of schizophrenic genetic liability and perinatal complications to computed tomographic (CT) measurements of ventricular enlargement and cortical and cerebellar abnormalities. A factor analysis of six CT measurements yielded two significant factors. One factor reflected multisite neural deficits as evidenced by abnormality of the cerebellar vermis and widening of the sylvian and interhemispheric fissures and cortical sulci. The other factor reflected periventricular damage as evidenced by enlargement of the third and lateral ventricles. Because all of the subjects had schizophrenic mothers, the major source of genetic variation is contributed by the diagnostic status of their fathers. In a stepwise multiple-regression analysis, it was determined that the multisite neural deficits factor was significantly related to genetic risk for schizophrenia (as measured by schizophrenia spectrum illness in the subjects' fathers) but was unrelated to pregnancy or delivery complications or to weight at birth. Periventricular damage was highly and significantly correlated with the number of complications suffered at delivery, but only among subjects with an elevated genetic risk. Although limited by a small sample size, these results suggest that the two types of CT abnormalities in schizophrenia may reflect partially independent processes based on different combinations of genetic and perinatal influences.

  13. Determination of pair-structure factor of scattering potential of a collection of particles. (United States)

    Wang, Tao; Zhao, Daomu


    The method of determination of the pair-structure factor of a collection of particles has been discussed. It is shown that the pair-structure factor of scattering potential of the collection of particles can be determined from the cross-spectral density function of the scattered field.

  14. Fourier Analysis and Structure Determination--Part III: X-ray Crystal Structure Analysis. (United States)

    Chesick, John P.


    Discussed is single crystal X-ray crystal structure analysis. A common link between the NMR imaging and the traditional X-ray crystal structure analysis is reported. Claims that comparisons aid in the understanding of both techniques. (MVL)

  15. Crystallization of an achiral cyclohexanone ethylene ketal in enantiomorphs and determination of the absolute structure. (United States)

    Graus, Sara; Tejedor, Rosa M; Uriel, Santiago; Serrano, José Luis; Alkorta, Ibon; Elguero, José


    The achiral 4-methoxy-4-(p-methoxyphenyl)-cyclohexanone ethylene ketal (1) resolves spontaneously. The crystal structure is solved in chiral spatial group P2(1). Because compound 1 is composed of only light atoms (C, H, O) it is not possible to determine its absolute structure configuration. An efficient procedure for the absolute structure configuration determination of flexible molecules containing only light atoms is proposed, based on the combination of X-ray diffraction, solid-state VCD, and DFT calculations.

  16. New improvements in automatic structure elucidation using the LSD (Logic for Structure Determination) and the SISTEMAT expert systems. (United States)

    Plainchont, Bertrand; Nuzillard, Jean-Marc; Rodrigues, Gilberto V; Ferreira, Marcelo J P; Scotti, Marcus T; Emerenciano, Vicente P


    This article describes the integration of the LSD (Logic for Structure Determination) and SISTEMAT expert systems that were both designed for the computer-assisted structure elucidation of small organic molecules. A first step has been achieved towards the linking of the SISTEMAT database with the LSD structure generator. The skeletal descriptions found by the SISTEMAT programs are now easily transferred to LSD as substructural constraints. Examples of the synergy between these expert systems are given for recently reported natural products.

  17. Toward a structure determination method for biomineral-associated protein using combined solid- state NMR and computational structure prediction. (United States)

    Masica, David L; Ash, Jason T; Ndao, Moise; Drobny, Gary P; Gray, Jeffrey J


    Protein-biomineral interactions are paramount to materials production in biology, including the mineral phase of hard tissue. Unfortunately, the structure of biomineral-associated proteins cannot be determined by X-ray crystallography or solution nuclear magnetic resonance (NMR). Here we report a method for determining the structure of biomineral-associated proteins. The method combines solid-state NMR (ssNMR) and ssNMR-biased computational structure prediction. In addition, the algorithm is able to identify lattice geometries most compatible with ssNMR constraints, representing a quantitative, novel method for investigating crystal-face binding specificity. We use this method to determine most of the structure of human salivary statherin interacting with the mineral phase of tooth enamel. Computation and experiment converge on an ensemble of related structures and identify preferential binding at three crystal surfaces. The work represents a significant advance toward determining structure of biomineral-adsorbed protein using experimentally biased structure prediction. This method is generally applicable to proteins that can be chemically synthesized.

  18. Inferential protein structure determination and refinement using fast, electronic structure based backbone amide chemical shift predictions

    CERN Document Server

    Christensen, Anders S


    This report covers the development of a new, fast method for calculating the backbone amide proton chemical shifts in proteins. Through quantum chemical calculations, structure-based forudsiglese the chemical shift for amidprotonen in protein has been parameterized. The parameters are then implemented in a computer program called Padawan. The program has since been implemented in protein folding program Phaistos, wherein the method andvendes to de novo folding of the protein structures and to refine the existing protein structures.

  19. Blind testing of routine, fully automated determination of protein structures from NMR data. (United States)

    Rosato, Antonio; Aramini, James M; Arrowsmith, Cheryl; Bagaria, Anurag; Baker, David; Cavalli, Andrea; Doreleijers, Jurgen F; Eletsky, Alexander; Giachetti, Andrea; Guerry, Paul; Gutmanas, Aleksandras; Güntert, Peter; He, Yunfen; Herrmann, Torsten; Huang, Yuanpeng J; Jaravine, Victor; Jonker, Hendrik R A; Kennedy, Michael A; Lange, Oliver F; Liu, Gaohua; Malliavin, Thérèse E; Mani, Rajeswari; Mao, Binchen; Montelione, Gaetano T; Nilges, Michael; Rossi, Paolo; van der Schot, Gijs; Schwalbe, Harald; Szyperski, Thomas A; Vendruscolo, Michele; Vernon, Robert; Vranken, Wim F; Vries, Sjoerd de; Vuister, Geerten W; Wu, Bin; Yang, Yunhuang; Bonvin, Alexandre M J J


    The protocols currently used for protein structure determination by nuclear magnetic resonance (NMR) depend on the determination of a large number of upper distance limits for proton-proton pairs. Typically, this task is performed manually by an experienced researcher rather than automatically by using a specific computer program. To assess whether it is indeed possible to generate in a fully automated manner NMR structures adequate for deposition in the Protein Data Bank, we gathered 10 experimental data sets with unassigned nuclear Overhauser effect spectroscopy (NOESY) peak lists for various proteins of unknown structure, computed structures for each of them using different, fully automatic programs, and compared the results to each other and to the manually solved reference structures that were not available at the time the data were provided. This constitutes a stringent "blind" assessment similar to the CASP and CAPRI initiatives. This study demonstrates the feasibility of routine, fully automated protein structure determination by NMR.

  20. Determination of the experimental equilibrium structure of solid nitromethane using path-integral molecular dynamics simulations (United States)

    Reilly, Anthony M.; Habershon, Scott; Morrison, Carole A.; Rankin, David W. H.


    Path-integral molecular dynamics (PIMD) simulations with an empirical interaction potential have been used to determine the experimental equilibrium structure of solid nitromethane at 4.2 and 15 K. By comparing the time-averaged molecular structure determined in a PIMD simulation to the calculated minimum-energy (zero-temperature) molecular structure, we have derived structural corrections that describe the effects of thermal motion. These corrections were subsequently used to determine the equilibrium structure of nitromethane from the experimental time-averaged structure. We find that the corrections to the intramolecular and intermolecular bond distances, as well as to the torsion angles, are quite significant, particularly for those atoms participating in the anharmonic motion of the methyl group. Our results demonstrate that simple harmonic models of thermal motion may not be sufficiently accurate, even at low temperatures, while molecular simulations employing more realistic potential-energy surfaces can provide important insight into the role and magnitude of anharmonic atomic motions.

  1. Application of Nuclear Magnetic Resonance and Hybrid Methods to Structure Determination of Complex Systems. (United States)

    Prischi, Filippo; Pastore, Annalisa


    The current main challenge of Structural Biology is to undertake the structure determination of increasingly complex systems in the attempt to better understand their biological function. As systems become more challenging, however, there is an increasing demand for the parallel use of more than one independent technique to allow pushing the frontiers of structure determination and, at the same time, obtaining independent structural validation. The combination of different Structural Biology methods has been named hybrid approaches. The aim of this review is to critically discuss the most recent examples and new developments that have allowed structure determination or experimentally-based modelling of various molecular complexes selecting them among those that combine the use of nuclear magnetic resonance and small angle scattering techniques. We provide a selective but focused account of some of the most exciting recent approaches and discuss their possible further developments.

  2. Roof structure theory and support resistance determination of longwall face in shallow seam

    Institute of Scientific and Technical Information of China (English)

    HUANG Qing-xiang(黄庆享)


    This paper presents the structure models founded in shallow seam, the roof asymmetry arch with three articulations in roof first weighting and the step voussoir beam in roof periodic weighting. These structure models are differ from classic theory, it establishes the new roof control theory of instability structure roof, especially in shallow seam. Based on the new roof structure theory, the support working state of "given sliding load" is put forward, and the factor of load transmitting is introduced to determine the load on roof structure. Therefore, the proper and accurate calculating methods of support resistance are established. Based on this, the dynamic structure theory in shallow seam could be predicted.

  3. SMEs capital structure determinants during severe economic crisis: The case of Greece

    Directory of Open Access Journals (Sweden)

    D. Balios


    Full Text Available The objective of this paper was to explore whether and how the main capital structure determinants of SMEs affected capital structure determination in different ways during the years of economic crisis. We used panel data of 8,052 SMEs operating in Greece during 2009–2012. We found that the effect of capital structure determinants on leverage does not change in an environment of economic crisis; larger SMEs continued to show higher debt ratios, the relationship between profitability and tangibility of assets with leverage continued to be negative, and growth was positively related to leverage.

  4. PREFACE: India-Japan Workshop on Biomolecular Electronics & Organic Nanotechnology for Environment Preservation (United States)

    Onoda, Mitsuyoshi; Malhotra, Bansi D.


    The 'India-Japan Workshop on Biomolecular Electronics & Organic Nanotechnology for Environment Preservation' (IJWBME 2011) will be held on 7-10 December 2011 at EGRET Himeji, Himeji, Hyogo, Japan. This workshop was held for the first time on 17-19 December 2009 at NPL, New Delhi. Keeping in mind the importance of organic nanotechnology and biomolecular electronics for environmental preservation and their anticipated impact on the economics of both the developing and the developed world, IJWBME 2009 was jointly organized by the Department of Biological Functions, Graduate School of Life Sciences and Systems Engineering, the Kyushu Institute of Technology (KIT), Kitakyushu, Japan, and the Department of Science & Technology Centre on Biomolecular Electronics (DSTCBE), National Physical Laboratory (NPL). Much progress in the field of biomolecular electronics and organic nanotechnology for environmental preservation is expected for the 21st Century. Organic optoelectronic devices, such as organic electroluminescent devices, organic thin-film transistors, organic sensors, biological systems and so on have especially attracted much attention. The main purpose of this workshop is to provide an opportunity for researchers interested in biomolecular electronics and organic nanotechnology for environmental preservation, to come together in an informal and friendly atmosphere and exchange technical knowledge and experience. We are sure that this workshop will be very useful and fruitful for all participants in summarizing the recent progress in biomolecular electronics and organic nanotechnology for environmental preservation and preparing new ground for the next generation. Many papers have been submitted from India and Japan and more than 30 papers have been accepted for presentation. The main topics of interest are as follows: Bioelectronics Biomolecular Electronics Fabrication Techniques Self-assembled Monolayers Nano-sensors Environmental Monitoring Organic Devices

  5. Specificity quantification of biomolecular recognition and its implication for drug discovery (United States)

    Yan, Zhiqiang; Wang, Jin


    Highly efficient and specific biomolecular recognition requires both affinity and specificity. Previous quantitative descriptions of biomolecular recognition were mostly driven by improving the affinity prediction, but lack of quantification of specificity. We developed a novel method SPA (SPecificity and Affinity) based on our funneled energy landscape theory. The strategy is to simultaneously optimize the quantified specificity of the ``native'' protein-ligand complex discriminating against ``non-native'' binding modes and the affinity prediction. The benchmark testing of SPA shows the best performance against 16 other popular scoring functions in industry and academia on both prediction of binding affinity and ``native'' binding pose. For the target COX-2 of nonsteroidal anti-inflammatory drugs, SPA successfully discriminates the drugs from the diversity set, and the selective drugs from non-selective drugs. The remarkable performance demonstrates that SPA has significant potential applications in identifying lead compounds for drug discovery.

  6. Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks

    DEFF Research Database (Denmark)

    Soberano de Oliveira, Ana Paula; Patil, Kiran Raosaheb; Nielsen, Jens


    Background: Uncovering the operating principles underlying cellular processes by using 'omics' data is often a difficult task due to the high-dimensionality of the solution space that spans all interactions among the bio-molecules under consideration. A rational way to overcome this problem...... is to use the topology of bio-molecular interaction networks in order to constrain the solution space. Such approaches systematically integrate the existing biological knowledge with the 'omics' data. Results: Here we introduce a hypothesis-driven method that integrates bio-molecular network topology...... with transcriptome data, thereby allowing the identification of key biological features (Reporter Features) around which transcriptional changes are significantly concentrated. We have combined transcriptome data with different biological networks in order to identify Reporter Gene Ontologies, Reporter Transcription...

  7. Biochemical filter with sigmoidal response: increasing the complexity of biomolecular logic. (United States)

    Privman, Vladimir; Halámek, Jan; Arugula, Mary A; Melnikov, Dmitriy; Bocharova, Vera; Katz, Evgeny


    The first realization of a designed, rather than natural, biochemical filter process is reported and analyzed as a promising network component for increasing the complexity of biomolecular logic systems. Key challenge in biochemical logic research has been achieving scalability for complex network designs. Various logic gates have been realized, but a "toolbox" of analog elements for interconnectivity and signal processing has remained elusive. Filters are important as network elements that allow control of noise in signal transmission and conversion. We report a versatile biochemical filtering mechanism designed to have sigmoidal response in combination with signal-conversion process. Horseradish peroxidase-catalyzed oxidation of chromogenic electron donor by H(2)O(2) was altered by adding ascorbate, allowing to selectively suppress the output signal, modifying the response from convex to sigmoidal. A kinetic model was developed for evaluation of the quality of filtering. The results offer improved capabilities for design of scalable biomolecular information processing systems.

  8. Constructing Bio-molecular Databases on a DNA-based Computer

    CERN Document Server

    Chang, Weng-Long; Ho,; Guo, Minyi


    Codd [Codd 1970] wrote the first paper in which the model of a relational database was proposed. Adleman [Adleman 1994] wrote the first paper in which DNA strands in a test tube were used to solve an instance of the Hamiltonian path problem. From [Adleman 1994], it is obviously indicated that for storing information in molecules of DNA allows for an information density of approximately 1 bit per cubic nm (nanometer) and a dramatic improvement over existing storage media such as video tape which store information at a density of approximately 1 bit per 1012 cubic nanometers. This paper demonstrates that biological operations can be applied to construct bio-molecular databases where data records in relational tables are encoded as DNA strands. In order to achieve the goal, DNA algorithms are proposed to perform eight operations of relational algebra (calculus) on bio-molecular relational databases, which include Cartesian product, union, set difference, selection, projection, intersection, join and division. Fu...

  9. Conformation of bovine submaxillary mucin layers on hydrophobic surface as studied by biomolecular probes

    DEFF Research Database (Denmark)

    Pakkanen, Kirsi I.; Madsen, Jan Busk; Lee, Seunghwan


    In the present study, the conformational changes of bovine submaxillary mucin (BSM) adsorbed on a hydrophobic surface (polystyrene (PS)) as a function of concentration in bulk solution (up to 2mg/mL) have been investigated with biomolecular probe-based approaches, including bicinchoninic acid (BCA...... solution. Adsorbed masses of BSM onto hydrophobic surface, as probe by BCA, showed a continuously increasing trend up to 2mg/mL. But, the signals from EIA and ELLA, which probe the concentration of available unglycosylatedC-terminals and the central glycosylated regions, respectively, showed complicated...... non-linear responses with increasing surface concentration. The results from this study support the conventional amphiphilic, triblock model of BSM in the adsorption onto hydrophobic surface from aqueous solution.The biomolecular probe-based approaches employed in this study, however, provided further...

  10. Solving the Phase Problem in Crystal Structure Determination: A Simple Introduction to Direct Methods. (United States)

    Schenk, H.


    Presents a simple way to introduce Direct Methods program systems to solve phase problems in x-ray crystal structure determination. It is intended for the undergraduate chemistry student laboratory. (Author/SA)

  11. Parity Violation in Chiral Molecules: From Theory towards Spectroscopic Experiment and the Evolution of Biomolecular Homochirality

    CERN Document Server

    CERN. Geneva


    The observation of biomolecular homochirality can be considered as a quasi-fossil of the evolution of life [1], the interpretation of which has been an open question for more than a century, with numerous related hypotheses, but no definitive answers. We shall briefly discuss the current status and the relation to the other two questions. The discovery of parity violation led to important developm...

  12. Colloid-in-Liquid Crystal Gels that Respond to Biomolecular Interactions


    Agarwal, Ankit; Sidiq, Sumyra; Setia, Shilpa; Bukusoglu, Emre; de Pablo, Juan J.; Pal, Santanu Kumar; Abbott, Nicholas L.


    This paper advances the design of stimuli-responsive materials based on colloidal particles dispersed in liquid crystals (LCs). Specifically, we report that thin films of colloid-in-liquid crystal (CLC) gels can undergo easily visualized ordering transitions in response to reversible and irreversible (enzymatic) biomolecular interactions occurring at aqueous interfaces of the gels. In particular, we demonstrate that LC ordering transitions can propagate across the entire thickness of the gels...

  13. Determining the velocity fine structure by a laser anemometer with fixed orientation

    Energy Technology Data Exchange (ETDEWEB)

    Kristensen, Leif; Kirkegaard, P.; Mikkelsen, Torben


    We have studied the velocity structure functions and spectra which can be determined by a CW-laser anemometer and a (pulsed) lidar anemometer. We have found useful theoretical expressions for both types of anemometers and compared their filtering of the along-beam turbulent velocity. The purpose has been to establish a basis for remote determining of turbulence fine-structure in terms of the rate of dissipation of specific kinetic energy in the atmospheric boundary layer. (Author)

  14. Vegetation structure determination using LIDAR data and the forest growth parameters (United States)

    Rybansky, M.; Brenova, M.; Cermak, J.; van Genderen, J.; Sivertun, Å.


    The goal of this paper is to identify the main vegetation factors in the terrain, which are important for the analysis of forest structure. Such an analysis is important for forestry, rescue operations management during crises situations and disasters such as fires, storms, earthquakes and military analysis (transportation, cover, concealment, etc.). For the forest structure determination, both LIDAR and the forest growth prediction analysis were used. As main results, the vegetation height, tree spacing and stem diameters were determined

  15. Structure and partitioning of bacterial DNA: determined by a balance of competion and expansion forces?

    DEFF Research Database (Denmark)

    Woldringh, C. L.; Jensen, Peter Ruhdal; Westerhoff, H. V.


    The mechanisms that determine chromosome structure and chromosome partitioning in bacteria are largely unknown. Here we discuss two hypotheses: (i) the structure of the Escherichia coli nucleoid is determined by DNA binding proteins and DNA supercoiling, representing a compaction force on the one...... hand, and by the coupled transcription/translation/translocation of plasma membrane and cell wall proteins, representing an expansion force on the other hand; (ii) the two forces are important for the partitioning process of chromosomes....

  16. Rational Design of Biomolecular Templates for Synthesizing Multifunctional Noble Metal Nanoclusters toward Personalized Theranostic Applications. (United States)

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


    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.

  17. Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks

    Directory of Open Access Journals (Sweden)

    Nielsen Jens


    Full Text Available Abstract Background Uncovering the operating principles underlying cellular processes by using 'omics' data is often a difficult task due to the high-dimensionality of the solution space that spans all interactions among the bio-molecules under consideration. A rational way to overcome this problem is to use the topology of bio-molecular interaction networks in order to constrain the solution space. Such approaches systematically integrate the existing biological knowledge with the 'omics' data. Results Here we introduce a hypothesis-driven method that integrates bio-molecular network topology with transcriptome data, thereby allowing the identification of key biological features (Reporter Features around which transcriptional changes are significantly concentrated. We have combined transcriptome data with different biological networks in order to identify Reporter Gene Ontologies, Reporter Transcription Factors, Reporter Proteins and Reporter Complexes, and use this to decipher the logic of regulatory circuits playing a key role in yeast glucose repression and human diabetes. Conclusion Reporter Features offer the opportunity to identify regulatory hot-spots in bio-molecular interaction networks that are significantly affected between or across conditions. Results of the Reporter Feature analysis not only provide a snapshot of the transcriptional regulatory program but also are biologically easy to interpret and provide a powerful way to generate new hypotheses. Our Reporter Features analyses of yeast glucose repression and human diabetes data brings hints towards the understanding of the principles of transcriptional regulation controlling these two important and potentially closely related systems.

  18. Application of isothermal titration calorimetry and column chromatography for identification of biomolecular targets. (United States)

    Zhou, Xingding; Kini, R Manjunatha; Sivaraman, J


    This protocol describes a method for identifying unknown target proteins from a mixture of biomolecules for a given drug or a lead compound. This method is based on a combination of chromatography and isothermal titration calorimetry (ITC) where ITC is used as a tracking tool. The first step involves the use of ITC to confirm the binding of ligand to a component in the biomolecular mixture. Subsequently, the biomolecular mixture is fractionated by chromatography, and the binding of the ligand with individual fractions (or subfractions) is verified by ITC. The iteration of chromatographic purification on the fractions combined with ITC results in identifying the target protein. This method is useful when the target protein or ligand is unknown and/or not amenable to labeling, chemical modification or immobilization. This protocol has been successfully used by our team and by others to identify both low-abundance and highly abundant target proteins present in biomolecular mixtures. With this protocol, it takes approximately 3-5 d to identify the target protein from a mixture.

  19. An improved simple polarisable water model for use in biomolecular simulation

    Energy Technology Data Exchange (ETDEWEB)

    Bachmann, Stephan J.; Gunsteren, Wilfred F. van, E-mail: [Laboratory of Physical Chemistry, ETH Zürich, CH-8093 Zürich (Switzerland)


    The accuracy of biomolecular simulations depends to some degree on the accuracy of the water model used to solvate the biomolecules. Because many biomolecules such as proteins are electrostatically rather inhomogeneous, containing apolar, polar, and charged moieties or side chains, a water model should be able to represent the polarisation response to a local electrostatic field, while being compatible with the force field used to model the biomolecules or protein. The two polarisable water models, COS/G2 and COS/D, that are compatible with the GROMOS biomolecular force fields leave room for improvement. The COS/G2 model has a slightly too large dielectric permittivity and the COS/D model displays a much too slow dynamics. The proposed COS/D2 model has four interaction sites: only one Lennard-Jones interaction site, the oxygen atom, and three permanent charge sites, the two hydrogens, and one massless off-atom site that also serves as charge-on-spring (COS) polarisable site with a damped or sub-linear dependence of the induced dipole on the electric field strength for large values of the latter. These properties make it a cheap and yet realistic water model for biomolecular solvation.

  20. Determining protein structures by combining semireliable data with atomistic physical models by Bayesian inference. (United States)

    MacCallum, Justin L; Perez, Alberto; Dill, Ken A


    More than 100,000 protein structures are now known at atomic detail. However, far more are not yet known, particularly among large or complex proteins. Often, experimental information is only semireliable because it is uncertain, limited, or confusing in important ways. Some experiments give sparse information, some give ambiguous or nonspecific information, and others give uncertain information-where some is right, some is wrong, but we don't know which. We describe a method called Modeling Employing Limited Data (MELD) that can harness such problematic information in a physics-based, Bayesian framework for improved structure determination. We apply MELD to eight proteins of known structure for which such problematic structural data are available, including a sparse NMR dataset, two ambiguous EPR datasets, and four uncertain datasets taken from sequence evolution data. MELD gives excellent structures, indicating its promise for experimental biomolecule structure determination where only semireliable data are available.

  1. Imaging and chemical surface analysis of biomolecular functionalization of monolithically integrated on silicon Mach-Zehnder interferometric immunosensors (United States)

    Gajos, Katarzyna; Angelopoulou, Michailia; Petrou, Panagiota; Awsiuk, Kamil; Kakabakos, Sotirios; Haasnoot, Willem; Bernasik, Andrzej; Rysz, Jakub; Marzec, Mateusz M.; Misiakos, Konstantinos; Raptis, Ioannis; Budkowski, Andrzej


    Time-of-flight secondary ion mass spectrometry (imaging, micro-analysis) has been employed to evaluate biofunctionalization of the sensing arm areas of Mach-Zehnder interferometers monolithically integrated on silicon chips for the immunochemical (competitive) detection of bovine κ-casein in goat milk. Biosensor surfaces are examined after: modification with (3-aminopropyl)triethoxysilane, application of multiple overlapping spots of κ-casein solutions, blocking with 100-times diluted goat milk, and reaction with monoclonal mouse anti-κ-casein antibodies in blocking solution. The areas spotted with κ-casein solutions of different concentrations are examined and optimum concentration providing homogeneous coverage is determined. Coverage of biosensor surfaces with biomolecules after each of the sequential steps employed in immunodetection is also evaluated with TOF-SIMS, supplemented by Atomic force microscopy and X-ray photoelectron spectroscopy. Uniform molecular distributions are observed on the sensing arm areas after spotting with optimum κ-casein concentration, blocking and immunoreaction. The corresponding biomolecular compositions are determined with a Principal Component Analysis that distinguished between protein amino acids and milk glycerides, as well as between amino acids characteristic for Mabs and κ-casein, respectively. Use of the optimum conditions (κ-casein concentration) for functionalization of chips with arrays of ten Mach-Zehnder interferometers provided on-chips assays with dramatically improved both intra-chip response repeatability and assay detection sensitivity.

  2. Determining the Velocity Fine Structure by a Laser Anemometer in VAD operation

    DEFF Research Database (Denmark)

    Kristensen, Leif; Kirkegaard, Peter; Mikkelsen, Torben

    The theoretical basis for determining the dissipation ε, by measuring the velocity structure function with a CW-laser anemometer has been derived in the case of calm wind conditions. If there is a well defined mean wind speed the structure function can be obtained by having the laser beam pointing...

  3. Determination of the Cu(110)-c(6X2)-O structure by x-ray diffraction

    DEFF Research Database (Denmark)

    Feidenhans'l, R.; Grey, F.; Johnson, R.L.


    We have performed a structural determination of the Cu(110)-c(6 X 2)-O surface by x-ray diffraction. A model including only copper atoms is found on the basis of the Patterson function; the positions of the oxygen atoms are revealed in an electron-density-difference map. The final structure has a...

  4. Re‐Determination of the Crystal Structure of MIL‐91(Al) (United States)

    Hermer, Nele


    The structure of one of the first permanently porous metal phosphonates, MIL‐91(Al) was re‐determined using high resolution synchrotron powder X‐ray diffraction data. The new model is in a lower symmetry space group, with no disordered ligands in the structure, whilst remaining otherwise consistent with the reported compound. New milder synthetic conditions were also developed.

  5. Solution Structure Determination of Proteins by Solution NMR: Application to a Envelope Protein, LAP2

    Institute of Scientific and Technical Information of China (English)


    @@ Recent advances in multidimensional NMR to obtain resonance assignments, interproton distance and torsion angle restraints, and restraints that characterize long range order, coupled with new methods of structure refinement, have permitted solution structures of proteins to be rapidly and quickly determined.

  6. Determinants of Rural Industrial Entrepreneurship of Farmers in West Bengal : A Structural Equations Approach

    NARCIS (Netherlands)

    Folmer, Henk; Dutta, Subrata; Oud, Han


    This article presents a structural equations model of rural industrial entrepreneurship (RIE) among farmers in the Bardhaman district, West Bengal, India. It identifies the determinants of RIE but also analyzes impacts of RIE on its endogenous determinants. Age, education, marital status, number of

  7. Blind testing of routine, fully automated determination of protein structures from NMR data.

    NARCIS (Netherlands)

    Rosato, A.; Aramini, J.M.; Arrowsmith, C.; Bagaria, A.; Baker, D.; Cavalli, A.; Doreleijers, J.; Eletsky, A.; Giachetti, A.; Guerry, P.; Gutmanas, A.; Guntert, P.; He, Y.; Herrmann, T.; Huang, Y.J.; Jaravine, V.; Jonker, H.R.; Kennedy, M.A.; Lange, O.F.; Liu, G.; Malliavin, T.E.; Mani, R.; Mao, B.; Montelione, G.T.; Nilges, M.; Rossi, P.; Schot, G. van der; Schwalbe, H.; Szyperski, T.A.; Vendruscolo, M.; Vernon, R.; Vranken, W.F.; Vries, S.D. de; Vuister, G.W.; Wu, B.; Yang, Y.; Bonvin, A.M.


    The protocols currently used for protein structure determination by nuclear magnetic resonance (NMR) depend on the determination of a large number of upper distance limits for proton-proton pairs. Typically, this task is performed manually by an experienced researcher rather than automatically by us


    NARCIS (Netherlands)



    The modulated structure of nickel telluride Ni3+/-xTe2 (Ni2.76Te2) is stabilized at 300 K by the substitution of a small amount of Fe (prepared as Ni2.57Fe0.29Te2). The structure of this compound has been determined by X-ray diffraction at room temperature (1311 unique reflections). The structure is

  9. Analysis and Report on SD2000: A Workshop to Determine Structural Dynamics Research for the Millenium (United States)


    This ONR grant was to facilitate the meeting of an international group of researchers to examine the future of structural dynamics . A group of about...promptly dismissed it as an intellectual pursuit not useful in structural dynamics . In reflecting back over his career, he now views this as a materials, mechatronics, etc.) and determining the appropriate interaction between these new advances and structural dynamics was one of the

  10. Polymorph identification and crystal structure determination by a combined crystal structure prediction and transmission electron microscopy approach. (United States)

    Eddleston, Mark D; Hejczyk, Katarzyna E; Bithell, Erica G; Day, Graeme M; Jones, William


    Electron diffraction offers advantages over X-ray based methods for crystal structure determination because it can be applied to sub-micron sized crystallites, and picogram quantities of material. For molecular organic species, however, crystal structure determination with electron diffraction is hindered by rapid crystal deterioration in the electron beam, limiting the amount of diffraction data that can be collected, and by the effect of dynamical scattering on reflection intensities. Automated electron diffraction tomography provides one possible solution. We demonstrate here, however, an alternative approach in which a set of putative crystal structures of the compound of interest is generated by crystal structure prediction methods and electron diffraction is used to determine which of these putative structures is experimentally observed. This approach enables the advantages of electron diffraction to be exploited, while avoiding the need to obtain large amounts of diffraction data or accurate reflection intensities. We demonstrate the application of the methodology to the pharmaceutical compounds paracetamol, scyllo-inositol and theophylline.

  11. Direct methods determination of the Si(111)-(6x6)Au surface structure

    DEFF Research Database (Denmark)

    Grozea, D.; Landree, E.; Marks, L.D.;


    The atomic structure of the Au 6 x 6 on Si(111) phase has been determined using direct methods and surface X-ray diffraction data. This surface structure is very complicated, with 14 independent gold atoms, relaxations in 24 independent silicon sites and three partially occupied gold sites. In on...... the gold structures in the coverage range 0.8-1.5 monolayers as pseudo-glasses with strong short-range order but varying degrees of long-range order. (C) 1998 Elsevier Science B.V. All rights reserved.......The atomic structure of the Au 6 x 6 on Si(111) phase has been determined using direct methods and surface X-ray diffraction data. This surface structure is very complicated, with 14 independent gold atoms, relaxations in 24 independent silicon sites and three partially occupied gold sites. In one...

  12. Protein crystallography for aspiring crystallographers or how to avoid pitfalls and traps in macromolecular structure determination. (United States)

    Wlodawer, Alexander; Minor, Wladek; Dauter, Zbigniew; Jaskolski, Mariusz


    The number of macromolecular structures deposited in the Protein Data Bank now approaches 100,000, with the vast majority of them determined by crystallographic methods. Thousands of papers describing such structures have been published in the scientific literature, and 20 Nobel Prizes in chemistry or medicine have been awarded for discoveries based on macromolecular crystallography. New hardware and software tools have made crystallography appear to be an almost routine (but still far from being analytical) technique and many structures are now being determined by scientists with very limited experience in the practical aspects of the field. However, this apparent ease is sometimes illusory and proper procedures need to be followed to maintain high standards of structure quality. In addition, many noncrystallographers may have problems with the critical evaluation and interpretation of structural results published in the scientific literature. The present review provides an outline of the technical aspects of crystallography for less experienced practitioners, as well as information that might be useful for users of macromolecular structures, aiming to show them how to interpret (but not overinterpret) the information present in the coordinate files and in their description. A discussion of the extent of information that can be gleaned from the atomic coordinates of structures solved at different resolution is provided, as well as problems and pitfalls encountered in structure determination and interpretation.

  13. On Explorative and Integrative Modeling of Biomolecular Complexes

    NARCIS (Netherlands)

    van Zundert, G.C.P.


    This thesis introduces and showcases novel approaches for explorative and integrative modeling in the presence of cryo-EM data and distance restraints. In it the PowerFit software is presented, a Python package for fast cross correlation based rigid body fitting of high-resolution structures in low-

  14. A novel strategy for NMR resonance assignment and protein structure determination

    Energy Technology Data Exchange (ETDEWEB)

    Lemak, Alexander [University of Toronto, Ontario Cancer Institute and Campbell Family Cancer Research Institute, Department of Medical Biophysics (Canada); Gutmanas, Aleksandras [European Bioinformatics Institute, Protein Data Bank Europe (United Kingdom); Chitayat, Seth; Karra, Murthy [University of Toronto, Ontario Cancer Institute and Campbell Family Cancer Research Institute, Department of Medical Biophysics (Canada); Fares, Christophe [Max-Planck-Institut f. Kohlenforschung (Germany); Sunnerhagen, Maria [Linkoeping University, Division of Molecular Biotechnology, Department of Physics, Chemistry and Biology (Sweden); Arrowsmith, Cheryl H., E-mail: [University of Toronto, Ontario Cancer Institute and Campbell Family Cancer Research Institute, Department of Medical Biophysics (Canada)


    The quality of protein structures determined by nuclear magnetic resonance (NMR) spectroscopy is contingent on the number and quality of experimentally-derived resonance assignments, distance and angular restraints. Two key features of protein NMR data have posed challenges for the routine and automated structure determination of small to medium sized proteins; (1) spectral resolution - especially of crowded nuclear Overhauser effect spectroscopy (NOESY) spectra, and (2) the reliance on a continuous network of weak scalar couplings as part of most common assignment protocols. In order to facilitate NMR structure determination, we developed a semi-automated strategy that utilizes non-uniform sampling (NUS) and multidimensional decomposition (MDD) for optimal data collection and processing of selected, high resolution multidimensional NMR experiments, combined it with an ABACUS protocol for sequential and side chain resonance assignments, and streamlined this procedure to execute structure and refinement calculations in CYANA and CNS, respectively. Two graphical user interfaces (GUIs) were developed to facilitate efficient analysis and compilation of the data and to guide automated structure determination. This integrated method was implemented and refined on over 30 high quality structures of proteins ranging from 5.5 to 16.5 kDa in size.

  15. Determining molecular structures and conformations directly from electron diffraction using a genetic algorithm. (United States)

    Habershon, Scott; Zewail, Ahmed H


    A global optimization strategy, based upon application of a genetic algorithm (GA), is demonstrated as an approach for determining the structures of molecules possessing significant conformational flexibility directly from gas-phase electron diffraction data. In contrast to the common approach to molecular structure determination, based on trial-and-error assessment of structures available from quantum chemical calculations, the GA approach described here does not require expensive quantum mechanical calculations or manual searching of the potential energy surface of the sample molecule, relying instead upon simple comparison between the experimental and calculated diffraction pattern derived from a proposed trial molecular structure. Structures as complex as all-trans retinal and p-coumaric acid, both important chromophores in photosensing processes, may be determined by this approach. In the examples presented here, we find that the GA approach can determine the correct conformation of a flexible molecule described by 11 independent torsion angles. We also demonstrate applications to samples comprising a mixture of two distinct molecular conformations. With these results we conclude that applications of this approach are very promising in elucidating the structures of large molecules directly from electron diffraction data.

  16. Towards a calculus of biomolecular complexes at equilibrium. (United States)

    Mjolsness, Eric


    An overview is presented of the construction and use of algebraic partition functions to represent the equilibrium statistical mechanics of multimolecular complexes and their action within a larger regulatory network. Unlike many applications of equilibrium statistical mechanics, multimolecular complexes may operate with various subsets of their components present and connected to the others, the rest remaining in solution. Thus they are variable-structure systems. This aspect of their behavior may be accounted for by the use of 'fugacity' variables as a representation within the partition functions. Four principles are proposed by which the combinatorics of molecular complex construction can be reflected in the construction of their partition functions. The corresponding algebraic operations on partition functions are multiplication, addition, function composition and a less commonly used operation called contraction. Each has a natural interpretation in terms of probability distributions on multimolecular structures. Possible generalizations to nonequilibrium statistical mechanics are briefly discussed.

  17. Crystal structure of pentapeptide-independent chemotaxis receptor methyltransferase (CheR) reveals idiosyncratic structural determinants for receptor recognition. (United States)

    Batra, Monu; Sharma, Rajesh; Malik, Anjali; Dhindwal, Sonali; Kumar, Pravindra; Tomar, Shailly


    Chemotactic methyltransferase, CheR catalyse methylation of specific glutamate residues in the cytoplasmic domain of methyl-accepting chemotactic protein receptors (MCPRs). The methylation of MCPRs is essential for the chemical sensing and chemotactic bacterial mobility towards favorable chemicals or away from unfavorable ones. In this study, crystal structure of B. subtilis CheR (BsCheR) in complex with S-adenosyl-l-homocysteine (SAH) has been determined to 1.8Å resolution. This is the first report of crystal structure belonging to the pentapeptide-independent CheR (PICheR) class. Till date, only one crystal structure of CheR from S. typhimurium (StCheR) belonging to pentapeptide-dependent CheR (PDCheR) class is available. Structural analysis of BsCheR reveals a helix-X-helix motif (HXH) with Asp53 as the linker residue in the N-terminal domain. The key structural features of the PDCheR β-subdomain involved in the formation of a tight complex with the pentapeptide binding motif in MCPRs were found to be absent in the structure of BsCheR. Additionally, isothermal titration calorimetry (ITC) experiments were performed to investigate S-adenosyl-(l)-methionine (SAM) binding affinity and KD was determined to be 0.32mM. The structure of BsCheR reveals that mostly residues of the large C-terminal domain contribute to SAH binding, with contributions of few residues from the linker region and the N-terminal domain. Structural investigations and sequence analysis carried out in this study provide critical insights into the distinct receptor recognition mechanism of the PDCheR and PICheR methyltransferase classes.

  18. Accurate structural correlations from maximum likelihood superpositions.

    Directory of Open Access Journals (Sweden)

    Douglas L Theobald


    Full Text Available The cores of globular proteins are densely packed, resulting in complicated networks of structural interactions. These interactions in turn give rise to dynamic structural correlations over a wide range of time scales. Accurate analysis of these complex correlations is crucial for understanding biomolecular mechanisms and for relating structure to function. Here we report a highly accurate technique for inferring the major modes of structural correlation in macromolecules using likelihood-based statistical analysis of sets of structures. This method is generally applicable to any ensemble of related molecules, including families of nuclear magnetic resonance (NMR models, different crystal forms of a protein, and structural alignments of homologous proteins, as well as molecular dynamics trajectories. Dominant modes of structural correlation are determined using principal components analysis (PCA of the maximum likelihood estimate of the correlation matrix. The correlations we identify are inherently independent of the statistical uncertainty and dynamic heterogeneity associated with the structural coordinates. We additionally present an easily interpretable method ("PCA plots" for displaying these positional correlations by color-coding them onto a macromolecular structure. Maximum likelihood PCA of structural superpositions, and the structural PCA plots that illustrate the results, will facilitate the accurate determination of dynamic structural correlations analyzed in diverse fields of structural biology.

  19. Integration of XAS and NMR techniques for the structure determination of metalloproteins. Examples from the study of copper transport proteins. (United States)

    Banci, Lucia; Bertini, Ivano; Mangani, Stefano


    Nuclear magnetic resonance (NMR) is a powerful technique for protein structure determination in solution. However, when dealing with metalloproteins, NMR methods are unable to directly determine the structure of the metal site and its coordination geometry. The capability of X-ray absorption spectroscopy (XAS) to provide the structure of a metal ion bound to a protein is then perfectly suited to complement the process of the structure determination. This aspect is particularly relevant in structural genomic projects where high throughput of structural results is the main goal. The synergism of the two techniques has been exploited in the structure determination of bacterial copper transport proteins.

  20. Developments of the neutron scattering analysis method for the determination of magnetic structures

    Energy Technology Data Exchange (ETDEWEB)

    Park, Je-Geun; Chung, Jae Gwan; Park, Jung Hwan; Kong, Ung Girl [Inha Univ., Incheon (Korea); So, Ji Yong [Seoul National University, Seoul(Korea)


    Neutron diffraction is up to now almost the only and very important experimental method of determining the magnetic structure of materials. Unlike the studies of crystallographic structure, however to use neutron diffraction for magnetic structure determination is not easily accessible to non-experts because of the complexity of magnetic group theory: which is very important in the magnetic structure analysis. With the recent development of computer code for magnetic group, it is now time to rethink of these difficulties. In this work, we have used the computer code of the magnetic group (Mody-2) and Fullprof refinement program in order to study the magnetic structure of YMnO{sub 3} and other interesting materials. YMnO{sub 3} forms in the hexagonal structure and show both ferroelectric and antiferromagnetic phase transitions. Since it was recently found that YMnO{sub 3} can be used as a nonvolatile memory device, there has been many numbers of applied research on this material. We used neutron diffraction to determine the magnetic structure, and, in particular, to investigate the correlation between the order parameters of the ferroelectric and antiferromagnetic phase transitions. From this study, we have demonstrated that with a proper use of the computer code of the magnetic group one can overcome most of difficulties arising from the magnetic group theory. 4 refs., 8 figs., 5 tabs. (Author)

  1. Determining Orientational Structure of Diamondoid Thiols Attached to Silver Using Near Edge X-ray Absorption Fine Structure Spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Willey, T M; Lee, J I; Fabbri, J D; Wang, D; Nielsen, M; Randel, J C; Schreiner, P R; Fokin, A A; Tkachenko, B A; Fokina, N A; Dahl, J P; Carlson, R K; Terminello, L J; Melosh, N A; van Buuren, T


    Near-edge x-ray absorption fine structure spectroscopy (NEXAFS) is a powerful tool for determination of molecular orientation in self-assembled monolayers and other surface-attached molecules. A general framework for using NEXAFS to simultaneously determine molecular tilt and twist of rigid molecules attached to surfaces is presented. This framework is applied to self-assembled monolayers of higher diamondoid, hydrocarbon molecules with cubic-diamond-cage structures. Diamondoid monolayers chemisorbed on metal substrates are known to exhibit interesting electronic and surface properties. This work compares molecular orientation in monolayers prepared on silver substrates using two different thiol positional isomers of [121]tetramantane, and thiols derived from two different pentamantane structural isomers, [1212]pentamantane and [1(2,3)4]pentamantane. The observed differences in monolayer structure demonstrate the utility and limitations of NEXAFS spectroscopy and the framework. The results also demonstrate the ability to control diamondoid assembly, in particular the molecular orientational structure, providing a flexible platform for the modification of surface properties with this exciting new class of nanodiamond materials.

  2. The three-dimensional structure of Infectious flacherie virus capsid determined by cryo-electron microscopy

    Institute of Scientific and Technical Information of China (English)


    Cryo-electron microscopy and image reconstruction were used to determine the three-dimensional structure of Infectious flacherie virus (IFV). 5047 particles were selected for the final reconstruction. The FSC curve showed that the resolution of this capsid structure was 18 ·. The structure is a psuedo T=3 (P=3) icosahedral capsid with a diameter of 302.4 · and a single shell thickness of 15 ·. The density map showed that IFV has a smooth surface without any prominent protrude or depression. Comparison of the IFV structure with those of the insect picorna-like virus-Cricket paralysis virus (CrPV)and human picornavirus-Human rhinovirus 14 (HRV 14) revealed that the IFV structure resembles the CrPV structure. The "Rossmann canyon" is absent in both IFV and CrPV particles. The polypeptide topology of IFV VP2, IFV VP3 was predicted and the subunit location at the capsid surface was further analyzed.

  3. Structure determination of archaea-specific ribosomal protein L46a reveals a novel protein fold

    Energy Technology Data Exchange (ETDEWEB)

    Feng, Yingang, E-mail: [Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101 (China); Song, Xiaxia [Department of Biological Science and Engineering, School of Chemical and Biological Engineering, University of Science and Technology Beijing, Beijing 100083 (China); Lin, Jinzhong [National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China); Xuan, Jinsong [Department of Biological Science and Engineering, School of Chemical and Biological Engineering, University of Science and Technology Beijing, Beijing 100083 (China); Cui, Qiu [Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101 (China); Wang, Jinfeng [National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China)


    Highlights: • The archaea-specific ribosomal protein L46a has no homology to known proteins. • Three dimensional structure and backbone dynamics of L46a were determined by NMR. • The structure of L46a represents a novel protein fold. • A potential rRNA-binding surface on L46a was identified. • The potential position of L46a on the ribosome was proposed. - Abstract: Three archaea-specific ribosomal proteins recently identified show no sequence homology with other known proteins. Here we determined the structure of L46a, the most conserved one among the three proteins, from Sulfolobus solfataricus P2 using NMR spectroscopy. The structure presents a twisted β-sheet formed by the N-terminal part and two helices at the C-terminus. The L46a structure has a positively charged surface which is conserved in the L46a protein family and is the potential rRNA-binding site. Searching homologous structures in Protein Data Bank revealed that the structure of L46a represents a novel protein fold. The backbone dynamics identified by NMR relaxation experiments reveal significant flexibility at the rRNA binding surface. The potential position of L46a on the ribosome was proposed by fitting the structure into a previous electron microscopy map of the ribosomal 50S subunit, which indicated that L46a contacts to domain I of 23S rRNA near a multifunctional ribosomal protein L7ae.

  4. Goadsporin, a chemical substance which promotes secondary metabolism and Morphogenesis in streptomycetes. II. Structure determination. (United States)

    Igarashi, Y; Kan, Y; Fujii, K; Fujita, T; Harada, K; Naoki, H; Tabata, H; Onaka, H; Furumai, T


    The structure of goadsporin was determined by using spectroscopic techniques. NMR analysis revealed that goadsporin consists of 19 amino acids, two of which are dehydroalanines (Deala), and six of which are cyclized to oxazoles (Oxz) and thiazoles (Thz) by dehydrative cyclization and dehydrogenation from serine, threonine and cysteine. NMR analysis established seven partial structures, and their sequence was determined by CID-MS/MS. Negative mode FAB-MS/MS gave product ions arising from charge-remote fragmentation that allowed determination of the sequence of the amino acid components as AcNH-Ala-MeOxz-Val-Deala-MeOxz-Ile-Leu-Thz-Ser-Gly-Gly-MeOxz-Leu-Deala-Oxz-Ala-Gly-Thz-Val-OH. The chiral amino acids were determined by the advanced Marfey's method to have L-configurations.


    Directory of Open Access Journals (Sweden)

    Ena Mostarac


    Full Text Available This paper analysis capital structure determinants of Croatian enterprises based on a cross-sectional data for pre-recession 2007 and recession 2010 comprising about 10,000 firms. Determinants are selected with reference to the relevant capital structure theories and include asset tangibility, profitability, firm size and business risk. The results indicate highly positive significant impact of tangibility and negative significant impact of profitability on financial leverage in both observed years. Firm size seems to be statistically significant at higher level in crisis period, but at the same time no relationship can be found between business risk and financial leverage that is of economic significance.

  6. Determining the size-dependent structure of ligand-free gold-cluster ions. (United States)

    Schooss, Detlef; Weis, Patrick; Hampe, Oliver; Kappes, Manfred M


    Ligand-free metal clusters can be prepared over a wide size range, but only in comparatively small amounts. Determining their size-dependent properties has therefore required the development of experimental methods that allow characterization of sample sizes comprising only a few thousand mass-selected particles under well-defined collision-free conditions. In this review, we describe the application of these methods to the geometric structural determination of Au(n)(+) and Au(n)(-) with n = 3-20. Geometries were assigned by comparing experimental data, primarily from ion-mobility spectrometry and trapped ion electron diffraction, to structural models from quantum chemical calculations.



    Pereira, Hélder; Tavares, Fernando; Luís Pacheco, Luís; Carvalho, Cláudia


    The main objective of this paper is to study the determinants of capital structure of SMEs in “Vinho Verde” sector and the way that can influence their level of indebtedness. Through the multiple linear regression models methodology, it is studied the behavior of the capital structure determinants between 2003 and 2012, considering a sample of 13 “Vinho Verde” SMEs obtained through the SABI data base. This study intends to examine the indebtedness level, with two main theories that practice t...

  8. In situ proteolysis to generate crystals for structure determination: an update.

    Directory of Open Access Journals (Sweden)

    Amy Wernimont

    Full Text Available For every 100 purified proteins that enter crystallization trials, an average of 30 form crystals, and among these only 13-15 crystallize in a form that enables structure determination. In 2007, Dong et al reported that the addition of trace amounts of protease to crystallization trials--in situ proteolysis--significantly increased the number of proteins in a given set that produce diffraction quality crystals. 69 proteins that had previously resisted structure determination were subjected to crystallization with in situ proteolysis and ten crystallized in a form that led to structure determination (14.5% success rate. Here we apply in situ proteolysis to over 270 new soluble proteins that had failed in the past to produce crystals suitable for structure determination. These proteins had produced no crystals, crystals that diffracted poorly, or produced twinned and/or unmanageable diffraction data. The new set includes yeast and prokaryotic proteins, enzymes essential to protozoan parasites, and human proteins such as GTPases, chromatin remodeling proteins, and tyrosine kinases. 34 proteins yielded deposited crystal structures of 2.8 A resolution or better, for an overall 12.6% success rate, and at least ten more yielded well-diffracting crystals presently in refinement. The success rate among proteins that had previously crystallized was double that of those that had never before yielded crystals. The overall success rate is similar to that observed in the smaller study, and appears to be higher than any other method reported to rescue stalled protein crystallography projects.

  9. Present and future of membrane protein structure determination by electron crystallography. (United States)

    Ubarretxena-Belandia, Iban; Stokes, David L


    Membrane proteins are critical to cell physiology, playing roles in signaling, trafficking, transport, adhesion, and recognition. Despite their relative abundance in the proteome and their prevalence as targets of therapeutic drugs, structural information about membrane proteins is in short supply. This chapter describes the use of electron crystallography as a tool for determining membrane protein structures. Electron crystallography offers distinct advantages relative to the alternatives of X-ray crystallography and NMR spectroscopy. Namely, membrane proteins are placed in their native membranous environment, which is likely to favor a native conformation and allow changes in conformation in response to physiological ligands. Nevertheless, there are significant logistical challenges in finding appropriate conditions for inducing membrane proteins to form two-dimensional arrays within the membrane and in using electron cryo-microscopy to collect the data required for structure determination. A number of developments are described for high-throughput screening of crystallization trials and for automated imaging of crystals with the electron microscope. These tools are critical for exploring the necessary range of factors governing the crystallization process. There have also been recent software developments to facilitate the process of structure determination. However, further innovations in the algorithms used for processing images and electron diffraction are necessary to improve throughput and to make electron crystallography truly viable as a method for determining atomic structures of membrane proteins.

  10. Structure determination of an integral membrane protein at room temperature from crystals in situ

    Energy Technology Data Exchange (ETDEWEB)

    Axford, Danny [Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE (United Kingdom); Foadi, James [Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE (United Kingdom); Imperial College London, London SW7 2AZ (United Kingdom); Hu, Nien-Jen; Choudhury, Hassanul Ghani [Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE (United Kingdom); Imperial College London, London SW7 2AZ (United Kingdom); Rutherford Appleton Laboratory, Oxfordshire OX11 0FA (United Kingdom); Iwata, So [Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE (United Kingdom); Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE (United Kingdom); Imperial College London, London SW7 2AZ (United Kingdom); Rutherford Appleton Laboratory, Oxfordshire OX11 0FA (United Kingdom); Kyoto University, Kyoto 606-8501 (Japan); Beis, Konstantinos [Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE (United Kingdom); Imperial College London, London SW7 2AZ (United Kingdom); Rutherford Appleton Laboratory, Oxfordshire OX11 0FA (United Kingdom); Evans, Gwyndaf, E-mail: [Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE (United Kingdom); Alguel, Yilmaz, E-mail: [Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE (United Kingdom); Imperial College London, London SW7 2AZ (United Kingdom); Rutherford Appleton Laboratory, Oxfordshire OX11 0FA (United Kingdom)


    The X-ray structure determination of an integral membrane protein using synchrotron diffraction data measured in situ at room temperature is demonstrated. The structure determination of an integral membrane protein using synchrotron X-ray diffraction data collected at room temperature directly in vapour-diffusion crystallization plates (in situ) is demonstrated. Exposing the crystals in situ eliminates manual sample handling and, since it is performed at room temperature, removes the complication of cryoprotection and potential structural anomalies induced by sample cryocooling. Essential to the method is the ability to limit radiation damage by recording a small amount of data per sample from many samples and subsequently assembling the resulting data sets using specialized software. The validity of this procedure is established by the structure determination of Haemophilus influenza TehA at 2.3 Å resolution. The method presented offers an effective protocol for the fast and efficient determination of membrane-protein structures at room temperature using third-generation synchrotron beamlines.

  11. Identification and determination of solitary wave structures in nonlinear wave propagation

    Energy Technology Data Exchange (ETDEWEB)

    Newman, W.I.; Campbell, D.K.; Hyman, J.M.


    Nonlinear wave phenomena are characterized by the appearance of solitary wave coherent structures'' traveling at speeds determined by their amplitudes and morphologies. Assuming that these structures are briefly noninteracting, we propose a method for the identification of the number of independent features and their respective speeds. Using data generated from an exact two-soliton solution to the Korteweg-de-Vries equation, we test the method and discuss its strengths and limitations. 41 refs., 2 figs.

  12. Determination of Structural Parameters of Thin-Film Photocatalytic Materials by BDS (United States)

    Korte, Dorota; Franko, Mladen


    A method for determination of structural parameters of some thin-film photocatalytic materials is presented. The analysis was based on the material's thermal parameter dependences on its surface structure or porosity and was thus performed by the use of beam deflection spectroscopy (BDS) supported by theoretical analysis made in the framework of complex geometrical optics. The results obtained by BDS were than compared with those received on the basis of AFM and SEM measurements and found to be in good agreement.

  13. Ab Initio structure determination of vaterite by automated electron diffraction. (United States)

    Mugnaioli, Enrico; Andrusenko, Iryna; Schüler, Timo; Loges, Niklas; Dinnebier, Robert E; Panthöfer, Martin; Tremel, Wolfgang; Kolb, Ute


    "This is a mineral about which there has been much discussion" is a typical statement about vaterite in older standard textbooks of inorganic chemistry. This polymorph of CaCO(3) was first mentioned by H. Vater in 1897, plays key roles in weathering and biomineralization processes, but occurs only in the form of nanosized crystals, unsuitable for structure determination. Its structure could now be solved by automated electron diffraction tomography from 50 nm sized nanocrystals.

  14. Phase Structures of Microemulsions Determined by the Steady-State Fluorescence Method

    Institute of Scientific and Technical Information of China (English)


    The steady-state fluorescence method has been tentatively used to determine the phase structures of microemulsion systems consisting of cetyltrimethylammonium bromide (CTAB), n-butanol (n-C4H9OH), octane (n-C5H18), and water. The excimer/monomer intensity ratio (Ie/Im) of pyrene has demonstrated that the various structures in the microemulsion phase region can be distinguished. The results are consistent with electrical conductivity data already reported.

  15. Workshop on Measurement Needs for Local-Structure Determination in Inorganic Materials


    Levin, Igor; Vanderah, Terrell


    The functional responses (e. g., dielectric, magnetic, catalytic, etc.) of many industrially-relevant materials are controlled by their local structure-a term that refers to the atomic arrangements on a scale ranging from atomic (sub-nanometer) to several nanometers. Thus, accurate knowledge of local structure is central to understanding the properties of nanostructured materials, thereby placing the problem of determining atomic positions on the nanoscale-the so-called "nanostructure problem...

  16. Scattering pulse of label free fine structure cells to determine the size scale of scattering structures (United States)

    Zhang, Lu; Chen, Xingyu; Zhang, Zhenxi; Chen, Wei; Zhao, Hong; Zhao, Xin; Li, Kaixing; Yuan, Li


    Scattering pulse is sensitive to the morphology and components of each single label-free cell. The most direct detection result, label free cell's scattering pulse is studied in this paper as a novel trait to recognize large malignant cells from small normal cells. A set of intrinsic scattering pulse calculation method is figured out, which combines both hydraulic focusing theory and small particle's scattering principle. Based on the scattering detection angle ranges of widely used flow cytometry, the scattering pulses formed by cell scattering energy in forward scattering angle 2°-5° and side scattering angle 80°-110° are discussed. Combining the analysis of cell's illuminating light energy, the peak, area, and full width at half maximum (FWHM) of label free cells' scattering pulses for fine structure cells with diameter 1-20 μm are studied to extract the interrelations of scattering pulse's features and cell's morphology. The theoretical and experimental results show that cell's diameter and FWHM of its scattering pulse agree with approximate linear distribution; the peak and area of scattering pulse do not always increase with cell's diameter becoming larger, but when cell's diameter is less than about 16 μm the monotone increasing relation of scattering pulse peak or area with cell's diameter can be obtained. This relationship between the features of scattering pulse and cell's size is potentially a useful but very simple criterion to distinguishing malignant and normal cells by their sizes and morphologies in label free cells clinical examinations.

  17. Exploration and analysis of the structural and intermediate social determinants of the HIV/AIDS pandemic

    Directory of Open Access Journals (Sweden)

    Yesica Daniela Liscano Pinzón


    Full Text Available Understanding distribution, epidemiology and the Social Determinants of Health related with HIV/AIDS are the basis on which we must work to achieve full containment of the epidemic in taking preventive measures such as clinical measures implemented for this purpose. Objective: To analyse intermediate and structural social determinants related to the HIV / AIDS reported in the national and international literature in the period 1993-2013. Material and methods: This research is hermeneutic, was developed in three phases: 1 Literature search and classification results. 2 Revision 3 Analysis of this literature with subsequent preparation of the final report. Results: met inclusion criteria 119 items. Eighty-four were for structural studies of determinants, 33 related to socioeconomic status, gender 25 and 26 with other structural determinants. Thirty-five were for intermediate DDS, 22 related to the conduct and 13 with the material conditions of life. Discussion: the structural determinants (gender and socioeconomic status are those with a high probability of exercising greater constraint on the behaviour of HIV, and therefore require considerable efforts in this field to combat the pandemic. 

  18. Protein Secondary Structure Determination by Constrained Single-Particle Cryo-Electron Tomography


    Bartesaghi, Alberto; Lecumberry, Federico; Sapiro, Guillermo; Subramaniam, Sriram


    Cryo-electron microscopy (cryo-EM) is a powerful technique for 3D structure determination of protein complexes by averaging information from individual molecular images. The resolutions that can be achieved with single-particle cryo-EM are frequently limited by inaccuracies in assigning molecular orientations based solely on 2D projection images. Tomographic data collection schemes, however, provide powerful constraints that can be used to more accurately determine molecular orientations nece...

  19. Theoretical description of biomolecular hydration - Application to A-DNA

    Energy Technology Data Exchange (ETDEWEB)

    Garcia, A.E.; Hummer, G. [Los Alamos National Laboratory, NM (United States); Soumpasis, D.M. [Max Planck Inst. for Biophysical Chemistry, Goettingen (Germany)


    The local density of water molecules around a biomolecule is constructed from calculated two- and three-points correlation functions of polar solvents in water using a Potential-of-Mean-Force (PMF) expansion. As a simple approximation, the hydration of all polar (including charged) groups in a biomolecule is represented by the hydration of water oxygen in bulk water, and the effect of non-polar groups on hydration are neglected, except for excluded volume effects. Pair and triplet correlation functions are calculated by molecular dynamics simulations. We present calculations of the structural hydration for ideal A-DNA molecules with sequences [d(CG){sub 5}]{sub 2} and [d(C{sub 5}G{sub 5})]{sub 2}. We find that this method can accurately reproduce the hydration patterns of A-DNA observed in neutron diffraction experiments on oriented DNA fibers.

  20. Anisotropy spectra for enantiomeric differentiation of biomolecular building blocks. (United States)

    Evans, A C; Meinert, C; Bredehöft, J H; Giri, C; Jones, N C; Hoffmann, S V; Meierhenrich, U J


    All biopolymers are composed of homochiral building blocks, and both D-sugars and L-amino acids uniquely constitute life on Earth. These monomers were originally enantiomerically differentiated under prebiotic conditions. Particular progress has recently been made in support of the photochemical model for this differentiation: the interaction of circularly polarized light with racemic molecules is currently thought to have been the original source for life's biological homochirality. The differential asymmetric photoreactivity of particular small molecules can be characterized by both circular dichroism and anisotropy spectroscopy. Anisotropy spectroscopy, a novel derivative of circular dichroism spectroscopy, records the anisotropy factor g = Δε/ε as a function of the wavelength. Anisotropy spectroscopy promisingly affords the wavelength-dependent determination of the enantiomeric excess (ee) inducible into chiral organic molecules by photochemical irradiation with circularly polarized light. Anisotropy spectra of small molecules therefore provide unique means for characterizing the different photochemical behaviors between enantiomers upon exposure to various wavelengths of circularly polarized light. This chapter will: (1) present the theory and configuration of anisotropy spectroscopy; (2) explain experimentally recorded anisotropy spectra of selected chiral biomolecules such as amino acids; and (3) discuss the relevance of these spectra for the investigation of the origin of the molecular homochirality observed in living organisms. This review describes a new chiroptical technique that is of significance for advances in asymmetric photochemistry and that is also highly relevant for the European Space Agency Rosetta Mission, which will determine enantiomeric excesses (ees) in chiral organic molecules in cometary ices when it lands on Comet 67P/Churyumov-Gerasimenko in November 2014.

  1. The universal statistical distributions of the affinity, equilibrium constants, kinetics and specificity in biomolecular recognition.

    Directory of Open Access Journals (Sweden)

    Xiliang Zheng


    Full Text Available We uncovered the universal statistical laws for the biomolecular recognition/binding process. We quantified the statistical energy landscapes for binding, from which we can characterize the distributions of the binding free energy (affinity, the equilibrium constants, the kinetics and the specificity by exploring the different ligands binding with a particular receptor. The results of the analytical studies are confirmed by the microscopic flexible docking simulations. The distribution of binding affinity is Gaussian around the mean and becomes exponential near the tail. The equilibrium constants of the binding follow a log-normal distribution around the mean and a power law distribution in the tail. The intrinsic specificity for biomolecular recognition measures the degree of discrimination of native versus non-native binding and the optimization of which becomes the maximization of the ratio of the free energy gap between the native state and the average of non-native states versus the roughness measured by the variance of the free energy landscape around its mean. The intrinsic specificity obeys a Gaussian distribution near the mean and an exponential distribution near the tail. Furthermore, the kinetics of binding follows a log-normal distribution near the mean and a power law distribution at the tail. Our study provides new insights into the statistical nature of thermodynamics, kinetics and function from different ligands binding with a specific receptor or equivalently specific ligand binding with different receptors. The elucidation of distributions of the kinetics and free energy has guiding roles in studying biomolecular recognition and function through small-molecule evolution and chemical genetics.

  2. The Universal Statistical Distributions of the Affinity, Equilibrium Constants, Kinetics and Specificity in Biomolecular Recognition (United States)

    Zheng, Xiliang; Wang, Jin


    We uncovered the universal statistical laws for the biomolecular recognition/binding process. We quantified the statistical energy landscapes for binding, from which we can characterize the distributions of the binding free energy (affinity), the equilibrium constants, the kinetics and the specificity by exploring the different ligands binding with a particular receptor. The results of the analytical studies are confirmed by the microscopic flexible docking simulations. The distribution of binding affinity is Gaussian around the mean and becomes exponential near the tail. The equilibrium constants of the binding follow a log-normal distribution around the mean and a power law distribution in the tail. The intrinsic specificity for biomolecular recognition measures the degree of discrimination of native versus non-native binding and the optimization of which becomes the maximization of the ratio of the free energy gap between the native state and the average of non-native states versus the roughness measured by the variance of the free energy landscape around its mean. The intrinsic specificity obeys a Gaussian distribution near the mean and an exponential distribution near the tail. Furthermore, the kinetics of binding follows a log-normal distribution near the mean and a power law distribution at the tail. Our study provides new insights into the statistical nature of thermodynamics, kinetics and function from different ligands binding with a specific receptor or equivalently specific ligand binding with different receptors. The elucidation of distributions of the kinetics and free energy has guiding roles in studying biomolecular recognition and function through small-molecule evolution and chemical genetics. PMID:25885453

  3. Raman spectroscopy detects biomolecular changes associated with nanoencapsulated hesperetin treatment in experimental oral carcinogenesis (United States)

    Gurushankar, K.; Gohulkumar, M.; Kumar, Piyush; Krishna, C. Murali; Krishnakumar, N.


    Recently it has been shown that Raman spectroscopy possesses great potential in the investigation of biomolecular changes of tumor tissues with therapeutic drug response in a non-invasive and label-free manner. The present study is designed to investigate the antitumor effect of hespertin-loaded nanoparticles (HETNPs) relative to the efficacy of native hesperetin (HET) in modifying the biomolecular changes during 7,12-dimethyl benz(a)anthracene (DMBA)-induced oral carcinogenesis using a Raman spectroscopic technique. Significant differences in the intensity and shape of the Raman spectra between the control and the experimental tissues at 1800-500 cm-1 were observed. Tumor tissues are characterized by an increase in the relative amount of proteins, nucleic acids, tryptophan and phenylalanine and a decrease in the percentage of lipids when compared to the control tissues. Further, oral administration of HET and its nanoparticulates restored the status of the lipids and significantly decreased the levels of protein and nucleic acid content. Treatment with HETNPs showed a more potent antitumor effect than treatment with native HET, which resulted in an overall reduction in the intensity of several biochemical Raman bands in DMBA-induced oral carcinogenesis being observed. Principal component and linear discriminant analysis (PC-LDA), together with leave-one-out cross validation (LOOCV) on Raman spectra yielded diagnostic sensitivities of 100%, 80%, 91.6% and 65% and specificities of 100%, 65%, 60% and 55% for classification of control versus DMBA, DMBA versus DMBA  +  HET, DMBA versus DMBA  +  HETNPs and DMBA  +  HET versus DMBA  +  HETNPs treated tissue groups, respectively. These results further demonstrate that Raman spectroscopy associated with multivariate statistical algorithms could be a valuable tool for developing a comprehensive understanding of the process of biomolecular changes, and could reveal the signatures of the

  4. Determination of conduction and valence band electronic structure of anatase and rutile TiO2

    Indian Academy of Sciences (India)

    Jakub Szlachetko; Katarzyna Michalow-Mauke; Maarten Nachtegaal; Jacinto Sá


    Electronic structures of rutile and anatase polymorph of TiO2 were determined by resonant inelastic X-ray scattering measurements and FEFF9.0 calculations. Difference between crystalline structures led to shifts in the rutile Ti -band to lower energy with respect to anatase, i.e., decrease in band gap. Anatase possesses localized states located in the band gap where electrons can be trapped, which are almost absent in the rutile structure. This could well explain the reported longer lifetimes in anatase. It was revealed that HR-XAS is insufficient to study in-depth unoccupied states of investigated materials because it overlooks the shallow traps.

  5. In situ monitoring of biomolecular processes in living systems using surface-enhanced Raman scattering (United States)

    Altunbek, Mine; Kelestemur, Seda; Culha, Mustafa


    Surface-enhanced Raman scattering (SERS) continues to strive to gather molecular level information from dynamic biological systems. It is our ongoing effort to utilize the technique for understanding of the biomolecular processes in living systems such as eukaryotic and prokaryotic cells. In this study, the technique is investigated to identify cell death mechanisms in 2D and 3D in vitro cell culture models, which is a very important process in tissue engineering and pharmaceutical applications. Second, in situ biofilm formation monitoring is investigated to understand how microorganisms respond to the environmental stimuli, which inferred information can be used to interfere with biofilm formation and fight against their pathogenic activity.

  6. Force sensors based on piezoresistive and MOSFET cantilevers for biomolecular sensing


    Tosolini, Giordano


    Los procesos de reconocimiento biomolecular entre receptores y ligandos son muy importantes en biología. Estas biomoléculas pueden desarrollar complejos muy específicos y tener una variedad de funciones como replicación y transcripción genómica, actividad enzimática, respuesta inmune, señalamiento celular, etc. La complementariedad inequívoca mostrada por estos componentes biológicos es ampliamente utilizada para desarrollar biosensores. Dependiendo de la naturaleza de las señales que se conv...

  7. Workshop on Measurement Needs for Local-Structure Determination in Inorganic Materials

    Directory of Open Access Journals (Sweden)

    Levin, Igor


    Full Text Available The functional responses (e. g., dielectric, magnetic, catalytic, etc. of many industrially-relevant materials are controlled by their local structure-a term that refers to the atomic arrangements on a scale ranging from atomic (sub-nanometer to several nanometers. Thus, accurate knowledge of local structure is central to understanding the properties of nanostructured materials, thereby placing the problem of determining atomic positions on the nanoscale-the so-called "nanostructure problem"-at the center of modern materials development. Today, multiple experimental techniques exist for probing local atomic arrangements; nonetheless, finding accurate comprehensive, and robust structural solutions for the nanostructured materials still remains a formidable challenge because any one of these methods yields only a partial view of the local structure. The primary goal of this 2-day NIST-sponsored workshop was to bring together experts in the key experimental and theoretical areas relevant to local-structure determination to devise a strategy for the collaborative effort required to develop a comprehensive measurement solution on the local scale. The participants unanimously agreed that solving the nanostructure problem-an ultimate frontier in materials characterization-necessitates a coordinated interdisciplinary effort that transcends the existing capabilities of any single institution, including national laboratories, centers, and user facilities. The discussions converged on an institute dedicated to local structure determination as the most viable organizational platform for successfully addressing the nanostructure problem. The proposed "institute" would provide an intellectual infrastructure for local structure determination by (1 developing and maintaining relevant computer software integrated in an open-source global optimization framework (Fig. 2, (2 connecting industrial and academic users with experts in measurement techniques, (3

  8. Determination of crystallographic and macroscopic orientation of planar structures in TEM

    DEFF Research Database (Denmark)

    Huang, X.; Liu, Q.


    With the aid of a double-tilt holder in a transmission electron microscope (TEM), simple methods are described for determination of the crystallographic orientation of a planar structure and for calculation of the macroscopic orientation of the planar structure. The correlation between a planar s...... taken at tilted positions, can be transformed to the real macroscopic orientation of the planar structures with estimated error of about +/- 2 degrees. (C) 1998 Elsevier Science B.V. All rights reserved....... structure and a crystallographic plane can be found by comparing the differences in their trace directions on the projection plane and inclination angles with respect to that plane. The angles between the traces of planar structures and the sample axis measured from the TEM micrographs, which have been...

  9. Ownership and Determinants Capital Structure of Public Listed Companies in Indonesia: a Panel Data Analysis

    Directory of Open Access Journals (Sweden)

    Arief Tri Hardiyanto


    Full Text Available Capital structure is a mix of debts and equities used by a company to finance its investment. Debt offers benefit of tax shield from interest expenses that can be deducted in calculating company income tax. Unfortunately, company can not use debts in unlimited amount because it will lead to risk of bankcrupt. Therefore, company needs to establish a target (unobserved capital structure which will optimize the value of the firm. The purpose of this study is to investigate the determinant of capital structure and ownership in public listed companies in Indonesia Stock Exchange using Time-Series CrossSection Regression (TSCSREG and supported with a balanced panel data. Data used are financial statements of 228 public listed companies from group of eight industry sectors. Research finding confirms that tax shield and fixed financial burden are significantly influence the capital structure and state ownership also significantly influence the capital structure of the state owned enterprises.

  10. Determining the Velocity Fine Structure by a Laser Anemometer with Fixed Orientation

    DEFF Research Database (Denmark)

    Kristensen, Leif; Kirkegaard, Peter; Mikkelsen, Torben

    We have studied the velocity structure functions and spectra which can be determined by a CW-laser anemometer and a (pulsed) lidar anemometer. We have found useful theoretical expressions for both types of anemometers and compared their filtering of the alongbeam turbulent velocity. The purpose has...

  11. The determination of the in situ structure by nuclear spin contrast variation

    Energy Technology Data Exchange (ETDEWEB)

    Stuhrmann, H.B. [GKSS Forschungszentrum, Geesthacht (Germany); Nierhaus, K.H. [Max-Planch-Institut fuer Molekulare Genetik, Berlin (Germany)


    Polarized neutron scattering from polarized nuclear spins in hydrogenous substances opens a new way of contrast variation. The enhanced contrast due to proton spin polarization was used for the in situ structure determination of tRNA of the functional complex of the E.coli ribosome.

  12. Processing visual rhetoric in advertisements: Interpretations determined by verbal anchoring and visual structure

    NARCIS (Netherlands)

    Lagerwerf, L.; Hooijdonk, van C.M.J.; Korenberg, A.


    This research investigated meaning operation in relation to verbal anchoring and visual structure of visual rhetoric in advertisements. Meaning operation refers to the relation between meaningful visual elements, and determines the number of interpretations of an image. Meaning operation ‘connection

  13. Biomolecular modification of zirconia surfaces for enhanced biocompatibility

    Energy Technology Data Exchange (ETDEWEB)

    Hsu, Shih-Kuang; Hsu, Hsueh-Chuan [Department of Dental Technology and Materials Science, Central Taiwan University of Science and Technology, Taichung 40601, Taiwan, ROC (China); Ho, Wen-Fu [Department of Chemical and Materials Engineering, National University of Kaohsiung, Taiwan, ROC (China); Yao, Chun-Hsu [Department of Biomedical Imaging and Radiological Science, China Medical University, Taichung 40402, Taiwan, ROC (China); Chang, Pai-Ling [Taoyuan General Hospital, Taoyuan 33004, Taiwan, ROC (China); Wu, Shih-Ching, E-mail: [Department of Dental Technology and Materials Science, Central Taiwan University of Science and Technology, Taichung 40601, Taiwan, ROC (China)


    Yttria-tetragonal zirconia polycrystal (Y-TZP) is a preferred biomaterial due to its good mechanical properties. In order to improve the biocompatibility of zirconia, RGD-peptide derived from extracellular matrix proteins was employed to modify the surface of Y-TZP to promote cell adhesion in this study. The surface of Y-TZP specimens was first modified using a hydrothermal method for different lengths of time. The topographies of modified Y-TZP specimens were analyzed by contact angle, XRD, FTIR, AFM, and FE-SEM. The mechanical properties were evaluated using Vickers hardness and three point bending strength. Then, the RGD-peptide was immobilized on the surface of the Y-TZP by chemical treatment. These RGD-peptide immobilized Y-TZP specimens were characterized by FTIR and AFM, and then were cocultured with MG-63 osteoblast cells for biocompatibility assay. The cell morphology and proliferation were evaluated by SEM, WST-1, and ALP activity assay. The XRD results indicated that the phase transition, from tetragonal phase to monoclinic phase, was increased with a longer incubation time of hydrothermal treatment. However, there were no significant differences in mechanical strengths after RGD-peptide was successfully grafted onto the Y-TZP surface. The SEM images showed that the MG-63 cells appeared polygonal, spindle-shaped, and attached on the RGD-peptide immobilized Y-TZP. The proliferation and cellular activities of MG-63 cells on the RGD-peptide immobilized Y-TZP were better than that on the unmodified Y-TZP. From the above results, the RGD-peptide can be successfully grafted onto the hydrothermal modified Y-TZP surface. The RGD-peptide immobilized Y-TZP can increase cell adhesion, and thus, improve the biocompatibility of Y-TZP. - Highlights: • Covalent bonding between peptide and Y-TZP was proposed. • Stable biomimetic structures produced on the surface of zirconia. • The biocompatibility was improved.

  14. ALMOST: an all atom molecular simulation toolkit for protein structure determination. (United States)

    Fu, Biao; Sahakyan, Aleksandr B; Camilloni, Carlo; Tartaglia, Gian Gaetano; Paci, Emanuele; Caflisch, Amedeo; Vendruscolo, Michele; Cavalli, Andrea


    Almost (all atom molecular simulation toolkit) is an open source computational package for structure determination and analysis of complex molecular systems including proteins, and nucleic acids. Almost has been designed with two primary goals: to provide tools for molecular structure determination using various types of experimental measurements as conformational restraints, and to provide methods for the analysis and assessment of structural and dynamical properties of complex molecular systems. The methods incorporated in Almost include the determination of structural and dynamical features of proteins using distance restraints derived from nuclear Overhauser effect measurements, orientational restraints obtained from residual dipolar couplings and the structural restraints from chemical shifts. Here, we present the first public release of Almost, highlight the key aspects of its computational design and discuss the main features currently implemented. Almost is available for the most common Unix-based operating systems, including Linux and Mac OS X. Almost is distributed free of charge under the GNU Public License, and is available both as a source code and as a binary executable from the project web site at Interested users can follow and contribute to the further development of Almost on

  15. Advanced Structural Determination of Diterpene Esters Using Molecular Modeling and NMR Spectroscopy. (United States)

    Nothias-Scaglia, Louis-Félix; Gallard, Jean-François; Dumontet, Vincent; Roussi, Fanny; Costa, Jean; Iorga, Bogdan I; Paolini, Julien; Litaudon, Marc


    Three new jatrophane esters (1-3) were isolated from Euphorbia amygdaloides ssp. semiperfoliata, including an unprecedented macrocyclic jatrophane ester bearing a hemiketal substructure, named jatrohemiketal (3). The chemical structures of compounds 1-3 and their relative configurations were determined by spectroscopic analysis. The absolute configuration of compound 3 was determined unambiguously through an original strategy combining NMR spectroscopy and molecular modeling. Conformational search calculations were performed for the four possible diastereomers 3a-3d differing in their C-6 and C-9 stereocenters, and the lowest energy conformer was used as input structure for geometry optimization. The prediction of NMR parameters ((1)H and (13)C chemical shifts and (1)H-(1)H coupling constants) by density functional theory (DFT) calculations allowed identifying the most plausible diastereomer. Finally, the stereostructure of 3 was solved by comparison of the structural features obtained by molecular modeling for 3a-3d with NMR-derived data (the values of dihedral angles deduced from the vicinal proton-proton coupling constants ((3)JHH) and interproton distances determined by ROESY). The methodology described herein provides an efficient way to solve or confirm structural elucidation of new macrocyclic diterpene esters, in particular when no crystal structure is available.

  16. Requirements on paramagnetic relaxation enhancement data for membrane protein structure determination by NMR. (United States)

    Gottstein, Daniel; Reckel, Sina; Dötsch, Volker; Güntert, Peter


    Nuclear magnetic resonance (NMR) structure calculations of the α-helical integral membrane proteins DsbB, GlpG, and halorhodopsin show that distance restraints from paramagnetic relaxation enhancement (PRE) can provide sufficient structural information to determine their structure with an accuracy of about 1.5 Å in the absence of other long-range conformational restraints. Our systematic study with simulated NMR data shows that about one spin label per transmembrane helix is necessary for obtaining enough PRE distance restraints to exclude wrong topologies, such as pseudo mirror images, if only limited other NMR restraints are available. Consequently, an experimentally realistic amount of PRE data enables α-helical membrane protein structure determinations that would not be feasible with the very limited amount of conventional NOESY data normally available for these systems. These findings are in line with our recent first de novo NMR structure determination of a heptahelical integral membrane protein, proteorhodopsin, that relied extensively on PRE data.

  17. Designing synthetic RNAs to determine the relevance of structural motifs in picornavirus IRES elements (United States)

    Fernandez-Chamorro, Javier; Lozano, Gloria; Garcia-Martin, Juan Antonio; Ramajo, Jorge; Dotu, Ivan; Clote, Peter; Martinez-Salas, Encarnacion


    The function of Internal Ribosome Entry Site (IRES) elements is intimately linked to their RNA structure. Viral IRES elements are organized in modular domains consisting of one or more stem-loops that harbor conserved RNA motifs critical for internal initiation of translation. A conserved motif is the pyrimidine-tract located upstream of the functional initiation codon in type I and II picornavirus IRES. By computationally designing synthetic RNAs to fold into a structure that sequesters the polypyrimidine tract in a hairpin, we establish a correlation between predicted inaccessibility of the pyrimidine tract and IRES activity, as determined in both in vitro and in vivo systems. Our data supports the hypothesis that structural sequestration of the pyrimidine-tract within a stable hairpin inactivates IRES activity, since the stronger the stability of the hairpin the higher the inhibition of protein synthesis. Destabilization of the stem-loop immediately upstream of the pyrimidine-tract also decreases IRES activity. Our work introduces a hybrid computational/experimental method to determine the importance of structural motifs for biological function. Specifically, we show the feasibility of using the software RNAiFold to design synthetic RNAs with particular sequence and structural motifs that permit subsequent experimental determination of the importance of such motifs for biological function.

  18. Structural determinants of glutathione transferases with azathioprine activity identified by DNA shuffling of alpha class members. (United States)

    Kurtovic, Sanela; Modén, Olof; Shokeer, Abeer; Mannervik, Bengt


    A library of alpha class glutathione transferases (GSTs), composed of chimeric enzymes derived from human (A1-1, A2-2 and A3-3), bovine (A1-1) and rat (A2-2 and A3-3) cDNA sequences was constructed by the method of DNA shuffling. The GST variants were screened in bacterial lysates for activity with the immunosuppressive agent azathioprine, a prodrug that is transformed into its active form, 6-mercaptopurine, by reaction with the tripeptide glutathione catalyzed by GSTs. Important structural determinants for activity with azathioprine were recognized by means of primary structure analysis and activities of purified enzymes chosen from the screening. The amino acid sequences could be divided into 23 exchangeable segments on the basis of the primary structures of 45 chosen clones. Segments 2, 20, 21, and 22 were identified as primary determinants of the azathioprine activity representing two of the regions forming the substrate-binding H-site. Segments 21 and 22 are situated in the C-terminal helix characterizing alpha class GSTs, which is instrumental in their catalytic function. The study demonstrates the power of DNA shuffling in identifying segments of primary structure that are important for catalytic activity with a targeted substrate. GSTs in combination with azathioprine have potential as selectable markers for use in gene therapy. Knowledge of activity-determining segments in the structure is valuable in the protein engineering of glutathione transferase for enhanced or suppressed activity.

  19. Biomolecular interactions probed by fluorescence resonance energy transfer (United States)

    Lange, Daniela Charlotte


    trafficking, with emphasis on defining the role of apoD in this disease. In vitro FRET studies on the dynamic structure of apoD and its close relative, β-lactoglobulin, are presented. FRET combined with conventional fluorescence microscopy established a direct association between apoD and cholesterol in situ. No evidence was found for interaction between apoD and the NPC1 protein.

  20. Ab initio determination of dark structures in radiationless transitions for aromatic carbonyl compounds. (United States)

    Fang, Wei-Hai


    Mechanistic photodissociation of a polyatomic molecule has long been regarded as an intellectually challenging area of chemical physics, the results of which are relevant to atmospheric chemistry, biological systems, and many application fields. Carbonyl compounds play a unique role in the development of our understanding of the spectroscopy, photochemistry, and photophysics of polyatomic molecules and their photodissociation has been the subject of numerous studies over many decades. Upon irradiation, a molecule can undergo internal conversion (IC) and intersystem crossing (ISC) processes, besides photochemical and other photophysical processes. Transient intermediates formed in the IC and ISC radiationless processes, which are termed "dark", are not amenable to detection by conventional light absorption or emission. However, these dark intermediates play critical roles in IC and ISC processes and thus are essential to understanding mechanistic photochemistry of a polyatomic molecule. We have applied the multiconfiguration complete active space self-consistent field (CASSCF) method to determine the dark transient structures involved in radiationless processes for acetophenone and the related aromatic carbonyl compounds. The electronic and geometric structures predicted for the dark states are in a good agreement with those determined by ultrafast electron diffraction experiments. Intersection structure of different electronic states provides a very efficient "funnel" for the IC or ISC process. However, experimental determination of the intersection structure involved in radiationless transitions of a polyatomic molecule is impossible at present. We have discovered a minimum energy crossing point among the three potential energy surfaces (S1, T1, and T2) that appears to be common to a wide variety of aromatic carbonyl compounds with a constant structure. This new type of crossing point holds the key to understanding much about radiationless processes after

  1. Effective Method for Determining Environmental Loads on Supporting Structures for Offshore Wind Turbines

    Directory of Open Access Journals (Sweden)

    Dymarski Paweł


    Full Text Available This paper presents a description of an effective method for determining loads due to waves and current acting on the supporting structures of the offshore wind turbines. This method is dedicated to the structures consisting of the cylindrical or conical elements as well as (truncates pyramids of polygon with a large number of sides (8 or more. The presented computational method is based on the Morison equation, which was originally developed only for cylindrically shaped structures. The new algorithm shown here uses the coefficients of inertia and drag forces that were calculated for non-cylindrical shapes. The analysed structure consists of segments which are truncated pyramids on the basis of a hex decagon. The inertia coefficients, CM, and drag coefficients, CD, were determined using RANSE-CFD calculations. The CFD simulations were performed for a specific range of variation of the period, and for a certain range of amplitudes of the velocity. In addition, the analysis of influence of the surface roughness on the inertia and drag coefficients was performed. In the next step, the computations of sea wave, current and wind load on supporting structure for the fifty-year storm were carried out. The simulations were performed in the time domain and as a result the function of forces distribution along the construction elements was obtained. The most unfavourable distribution of forces will be used, to analyse the strength of the structure, as the design load.

  2. Virological control of groundwater quality using biomolecular tests. (United States)

    Carducci, A; Casini, B; Bani, A; Rovini, E; Verani, M; Mazzoni, F; Giuntini, A


    Deep groundwater, even if generally protected, could be contaminated by surface or rain water infiltration through soil fractures, septic tanks, cesspits, land irrigation, disposal of wastewater and disposal of muds from depuration systems. The sanitary importance of such possible contamination is related to the different uses of the water and it is at the maximum level when it is intended for human use. Routine microbiological analyses do not consider viruses, only bacterial parameters, as contamination indicators. However, it is known that enteric viruses can survive a long time in deep aquifers and that they may not always be associated with bacterial indicators. The virological analysis of waters intended for drinking use is provided only as an occasional control exercised at the discretion of the sanitary authority. Technological difficulties with obtaining data about groundwater viral contamination led to a study to devise rapid and efficient methods for their detection and the application of these methods to samples from different sources. Four acid nucleic extraction techniques have been tested (classic proteinase K- phenol/chloroform, QIAamp Viral RNA Kit (Qiagen), SV Total RNA Isolation System (Promega) and NucleoSpin Virus L (Macherey-Nagel). Sensitivity and specificity of RT-PCR protocols for entero- (EV), hepatitis A (HAV) and small round structured (SRSV) viruses have been verified. Deep groundwater samples (100 L) were concentrated (2-step tangential flow ultrafiltration) and the concentrate contaminated with serial 10-fold dilutions of a known titre of poliovirus type 3. Extracted RNA was concentrated (microcon-100) and analysed by RT-PCR using specific EV primers and visualising amplification products by agarose gel electrophoresis. In addition, two different methods of RT-PCR for non-cultivable viruses have been tested: (a) RT-PCR and nested RT-PCR for HAV and (b) RT-PCR with generic primers and RT-PCR with specific primers for SRSV. Different

  3. Imaging and chemical surface analysis of biomolecular functionalization of monolithically integrated on silicon Mach-Zehnder interferometric immunosensors

    Energy Technology Data Exchange (ETDEWEB)

    Gajos, Katarzyna, E-mail: [M. Smoluchowski Institute of Physics, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków (Poland); Angelopoulou, Michailia; Petrou, Panagiota [Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety, NCSR Demokritos, P. Grigoriou & Neapoleos St, Aghia Paraksevi 15310, Athens (Greece); Awsiuk, Kamil [M. Smoluchowski Institute of Physics, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków (Poland); Kakabakos, Sotirios [Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety, NCSR Demokritos, P. Grigoriou & Neapoleos St, Aghia Paraksevi 15310, Athens (Greece); Haasnoot, Willem [RIKILT Wageningen UR, Akkermaalsbos 2, 6708 WB Wageningen (Netherlands); Bernasik, Andrzej [Faculty of Physics and Applied Computer Science, AGH University of Science and Technology, Mickiewicza 30, 30-059 Kraków (Poland); Academic Centre for Materials and Nanotechnology, AGH University of Science and Technology, Mickiewicza 30, 30-059 Kraków (Poland); Rysz, Jakub [M. Smoluchowski Institute of Physics, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków (Poland); Marzec, Mateusz M. [Academic Centre for Materials and Nanotechnology, AGH University of Science and Technology, Mickiewicza 30, 30-059 Kraków (Poland); Misiakos, Konstantinos; Raptis, Ioannis [Department of Microelectronics, Institute of Nanoscience and Nanotechnology, NCSR Demokritos, P. Grigoriou & Neapoleos St, Aghia Paraksevi 15310, Athens (Greece); Budkowski, Andrzej [M. Smoluchowski Institute of Physics, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków (Poland)


    Highlights: • Optimization of probe immobilization with robotic spotter printing overlapping spots. • In-situ inspection of microstructured surfaces of biosensors integrated on silicon. • Imaging and chemical analysis of immobilization, surface blocking and immunoreaction. • Insight with molecular discrimination into step-by-step sensor surface modifications. • Optimized biofunctionalization improves sensor sensitivity and response repeatability. - Abstract: Time-of-flight secondary ion mass spectrometry (imaging, micro-analysis) has been employed to evaluate biofunctionalization of the sensing arm areas of Mach-Zehnder interferometers monolithically integrated on silicon chips for the immunochemical (competitive) detection of bovine κ-casein in goat milk. Biosensor surfaces are examined after: modification with (3-aminopropyl)triethoxysilane, application of multiple overlapping spots of κ-casein solutions, blocking with 100-times diluted goat milk, and reaction with monoclonal mouse anti-κ-casein antibodies in blocking solution. The areas spotted with κ-casein solutions of different concentrations are examined and optimum concentration providing homogeneous coverage is determined. Coverage of biosensor surfaces with biomolecules after each of the sequential steps employed in immunodetection is also evaluated with TOF-SIMS, supplemented by Atomic force microscopy and X-ray photoelectron spectroscopy. Uniform molecular distributions are observed on the sensing arm areas after spotting with optimum κ-casein concentration, blocking and immunoreaction. The corresponding biomolecular compositions are determined with a Principal Component Analysis that distinguished between protein amino acids and milk glycerides, as well as between amino acids characteristic for Mabs and κ-casein, respectively. Use of the optimum conditions (κ-casein concentration) for functionalization of chips with arrays of ten Mach-Zehnder interferometers provided on-chips assays

  4. Photochemical functionalization of gallium nitride thin films with molecular and biomolecular layers. (United States)

    Kim, Heesuk; Colavita, Paula E; Metz, Kevin M; Nichols, Beth M; Sun, Bin; Uhlrich, John; Wang, Xiaoyu; Kuech, Thomas F; Hamers, Robert J


    We demonstrate that photochemical functionalization can be used to functionalize and photopattern the surface of gallium nitride crystalline thin films with well-defined molecular and biomolecular layers. GaN(0001) surfaces exposed to a hydrogen plasma will react with organic molecules bearing an alkene (C=C) group when illuminated with 254 nm light. Using a bifunctional molecule with an alkene group at one end and a protected amine group at the other, this process can be used to link the alkene group to the surface, leaving the protected amine exposed. Using a simple contact mask, we demonstrate the ability to directly pattern the spatial distribution of these protected amine groups on the surface with a lateral resolution of <12 mum. After deprotection of the amines, single-stranded DNA oligonucleotides were linked to the surface using a bifunctional cross-linker. Measurements using fluorescently labeled complementary and noncomplementary sequences show that the DNA-modified GaN surfaces exhibit excellent selectivity, while repeated cycles of hybridization and denaturation in urea show good stability. These results demonstrate that photochemical functionalization can be used as an attractive starting point for interfacing molecular and biomolecular systems with GaN and other compound semiconductors.

  5. A new approach to implement absorbing boundary condition in biomolecular electrostatics. (United States)

    Goni, Md Osman


    This paper discusses a novel approach to employ the absorbing boundary condition in conjunction with the finite-element method (FEM) in biomolecular electrostatics. The introduction of Bayliss-Turkel absorbing boundary operators in electromagnetic scattering problem has been incorporated by few researchers. However, in the area of biomolecular electrostatics, this boundary condition has not been investigated yet. The objective of this paper is twofold. First, to solve nonlinear Poisson-Boltzmann equation using Newton's method and second, to find an efficient and acceptable solution with minimum number of unknowns. In this work, a Galerkin finite-element formulation is used along with a Bayliss-Turkel absorbing boundary operator that explicitly accounts for the open field problem by mapping the Sommerfeld radiation condition from the far field to near field. While the Bayliss-Turkel condition works well when the artificial boundary is far from the scatterer, an acceptable tolerance of error can be achieved with the second order operator. Numerical results on test case with simple sphere show that the treatment is able to reach the same level of accuracy achieved by the analytical method while using a lower grid density. Bayliss-Turkel absorbing boundary condition (BTABC) combined with the FEM converges to the exact solution of scattering problems to within discretization error.

  6. Biomolecular detection at ssDNA-conjugated nanoparticles by nano-impact electrochemistry. (United States)

    Karimi, Anahita; Hayat, Akhtar; Andreescu, Silvana


    We describe the use of ssDNA functionalized silver nanoparticle (AgNP) probes for quantitative investigation of biorecognition and real time detection of biomolecular targets using nano-impact electrochemistry. The method is based on measurements of the individual collision events between ssDNA aptamer-functionalized AgNPs and a carbon fiber miroelectrode (CFME). Specific binding events of target analyte induced collision frequency changes enabling ultrasensitive detection of the aptamer target in a single step. These changes are assigned to the surface coverage of the NP by the ssDNA aptamers and subsequent conformational changes of the aptamer probe which affect the electron transfer between the NP and the electrode surface. The method enables sensitive and selective detection of ochratoxin A (OTA), chosen here as a model target, with a limit of detection of 0.05nM and a relative standard deviation of 4.9%. The study provides a means of characterizing bioconjugation of AgNPs with aptamers and assessing biomolecular recognition events with high sensitivity and without the use of exogenous reagents or enzyme amplification steps. This methodology can be broadly applicable to other bioconjugated systems, biosensing and related bioanalytical applications.

  7. Optimizing water hyperpolarization and dissolution for sensitivity-enhanced 2D biomolecular NMR (United States)

    Olsen, Greg; Markhasin, Evgeny; Szekely, Or; Bretschneider, Christian; Frydman, Lucio


    A recent study explored the use of hyperpolarized water, to enhance the sensitivity of nuclei in biomolecules thanks to rapid proton exchanges with labile amide backbone and sidechain groups. Further optimizations of this approach have now allowed us to achieve proton polarizations approaching 25% in the water transferred into the NMR spectrometer, effective water T1 times approaching 40 s, and a reduction in the dilution demanded for the cryogenic dissolution process. Further hardware developments have allowed us to perform these experiments, repeatedly and reliably, in 5 mm NMR tubes. All these ingredients - particularly the ⩾3000× 1H polarization enhancements over 11.7 T thermal counterparts, long T1 times and a compatibility with high-resolution biomolecular NMR setups - augur well for hyperpolarized 2D NMR studies of peptides, unfolded proteins and intrinsically disordered systems undergoing fast exchanges of their protons with the solvent. This hypothesis is here explored by detailing the provisions that lead to these significant improvements over previous reports, and demonstrating 1D coherence transfer experiments and 2D biomolecular HMQC acquisitions delivering NMR spectral enhancements of 100-500× over their optimized, thermally-polarized, counterparts.

  8. Time-resolved methods in biophysics. 9. Laser temperature-jump methods for investigating biomolecular dynamics. (United States)

    Kubelka, Jan


    Many important biochemical processes occur on the time-scales of nanoseconds and microseconds. The introduction of the laser temperature-jump (T-jump) to biophysics more than a decade ago opened these previously inaccessible time regimes up to direct experimental observation. Since then, laser T-jump methodology has evolved into one of the most versatile and generally applicable methods for studying fast biomolecular kinetics. This perspective is a review of the principles and applications of the laser T-jump technique in biophysics. A brief overview of the T-jump relaxation kinetics and the historical development of laser T-jump methodology is presented. The physical principles and practical experimental considerations that are important for the design of the laser T-jump experiments are summarized. These include the Raman conversion for generating heating pulses, considerations of size, duration and uniformity of the temperature jump, as well as potential adverse effects due to photo-acoustic waves, cavitation and thermal lensing, and their elimination. The laser T-jump apparatus developed at the NIH Laboratory of Chemical Physics is described in detail along with a brief survey of other laser T-jump designs in use today. Finally, applications of the laser T-jump in biophysics are reviewed, with an emphasis on the broad range of problems where the laser T-jump methodology has provided important new results and insights into the dynamics of the biomolecular processes.

  9. Biomolecular Systems of Disease Buried Across Multiple GWAS Unveiled by Information Theory and Ontology (United States)

    Lee, Younghee; Li, Jianrong; Gamazon, Eric; Chen, James L.; Tikhomirov, Anna; Cox, Nancy J.; Lussier, Yves A.


    A key challenge for genome-wide association studies (GWAS) is to understand how single nucleotide polymorphisms (SNPs) mechanistically underpin complex diseases. While this challenge has been addressed partially by Gene Ontology (GO) enrichment of large list of host genes of SNPs prioritized in GWAS, these enrichment have not been formally evaluated. Here, we develop a novel computational approach anchored in information theoretic similarity, by systematically mining lists of host genes of SNPs prioritized in three adult-onset diabetes mellitus GWAS. The “gold-standard” is based on GO associated with 20 published diabetes SNPs’ host genes and on our own evaluation. We computationally identify 69 similarity-predicted GO independently validated in all three GWAS (FDR<5%), enriched with those of the gold-standard (odds ratio=5.89, P=4.81e-05), and these terms can be organized by similarity criteria into 11 groupings termed “biomolecular systems”. Six biomolecular systems were corroborated by the gold-standard and the remaining five were previously uncharacterized. PMID:21347143

  10. fireball/amber: An Efficient Local-Orbital DFT QM/MM Method for Biomolecular Systems. (United States)

    Mendieta-Moreno, Jesús I; Walker, Ross C; Lewis, James P; Gómez-Puertas, Paulino; Mendieta, Jesús; Ortega, José


    In recent years, quantum mechanics/molecular mechanics (QM/MM) methods have become an important computational tool for the study of chemical reactions and other processes in biomolecular systems. In the QM/MM technique, the active region is described by means of QM calculations, while the remainder of the system is described using a MM approach. Because of the complexity of biomolecules and the desire to achieve converged sampling, it is important that the QM method presents a good balance between accuracy and computational efficiency. Here, we report on the implementation of a QM/MM technique that combines a DFT approach specially designed for the study of complex systems using first-principles molecular dynamics simulations (fireball) with the amber force fields and simulation programs. We also present examples of the application of this QM/MM approach to three representative biomolecular systems: the analysis of the effect of electrostatic embedding in the behavior of a salt bridge between an aspartic acid and a lysine residue, a study of the intermediate states for the triosephosphate isomerase catalyzed conversion of dihydroxyacetone phosphate into glyceraldehyde 3-phosphate, and the detailed description, using DFT QM/MM molecular dynamics, of the cleavage of a phosphodiester bond in RNA catalyzed by the enzyme RNase A.

  11. The interplay of intrinsic and extrinsic bounded noises in biomolecular networks.

    Directory of Open Access Journals (Sweden)

    Giulio Caravagna

    Full Text Available After being considered as a nuisance to be filtered out, it became recently clear that biochemical noise plays a complex role, often fully functional, for a biomolecular network. The influence of intrinsic and extrinsic noises on biomolecular networks has intensively been investigated in last ten years, though contributions on the co-presence of both are sparse. Extrinsic noise is usually modeled as an unbounded white or colored gaussian stochastic process, even though realistic stochastic perturbations are clearly bounded. In this paper we consider Gillespie-like stochastic models of nonlinear networks, i.e. the intrinsic noise, where the model jump rates are affected by colored bounded extrinsic noises synthesized by a suitable biochemical state-dependent Langevin system. These systems are described by a master equation, and a simulation algorithm to analyze them is derived. This new modeling paradigm should enlarge the class of systems amenable at modeling. We investigated the influence of both amplitude and autocorrelation time of a extrinsic Sine-Wiener noise on: (i the Michaelis-Menten approximation of noisy enzymatic reactions, which we show to be applicable also in co-presence of both intrinsic and extrinsic noise, (ii a model of enzymatic futile cycle and (iii a genetic toggle switch. In (ii and (iii we show that the presence of a bounded extrinsic noise induces qualitative modifications in the probability densities of the involved chemicals, where new modes emerge, thus suggesting the possible functional role of bounded noises.

  12. Submicrometer Hall sensors for detection of magnetic nanoparticles in biomolecular sensing (United States)

    Mihajlovic, Goran; Xiong, P.; von Molnar, S.; Ohtani, K.; Ohno, H.; Field, M.; Sullivan, G. J.


    Significant progress has been made in the recent years in synthesis and biomolecular functionalization of magnetic nanoparticles. These magnetic bio-nanolabels can be utilized as protein or gene markers in biomolecular sensing assays, in contrast to the much larger micron sized magnetic beads that are usually limited to cell labeling. However, the low magnetic moments of individual nanoparticles (10^4-10^5 μB) render their sensitive detection still a challenging task. In order to address this issue we are developing miniaturized Hall sensors from InAs/AlSb quantum well semiconductor heterostructures with active Hall cross areas down to 300 nm x 300 nm. Our preliminary characterization measurements performed at room temperature show functional devices with magnetic field resolution < 100 μT/√Hz at frequencies above 100 Hz, yielding a moment sensitivity ˜ 10^5 μB. In addition to the progress in improving the moment sensitivity of the submicrometer Hall detectors, we will also present efforts in device integration with on-chip microcoils for the generation of local magnetic excitation fields. Results on nanoparticle detection will also be presented.

  13. The detection of specific biomolecular interactions with micro-Hall magnetic sensors (United States)

    Manandhar, Pradeep; Chen, Kan-Sheng; Aledealat, Khaled; Mihajlović, Goran; Yun, C. Steven; Field, Mark; Sullivan, Gerard J.; Strouse, Geoffrey F.; Bryant Chase, P.; von Molnár, Stephan; Xiong, Peng


    The detection of reagent-free specific biomolecular interactions through sensing of nanoscopic magnetic labels provides one of the most promising routes to biosensing with solid-state devices. In particular, Hall sensors based on semiconductor heterostructures have shown exceptional magnetic moment sensitivity over a large dynamic field range suitable for magnetic biosensing using superparamagnetic labels. Here we demonstrate the capability of such micro-Hall sensors to detect specific molecular binding using biotin-streptavidin as a model system. We apply dip-pen nanolithography to selectively biotinylate the active areas of InAs micro-Hall devices with nanoscale precision. Specific binding of complementarily functionalized streptavidin-coated superparamagnetic beads to the Hall crosses occurs via molecular recognition, and magnetic detection of the assembled beads is achieved at room temperature using phase sensitive micro-Hall magnetometry. The experiment constitutes the first unambiguous demonstration of magnetic detection of specific biomolecular interactions with semiconductor micro-Hall sensors, and the selective molecular functionalization and resulting localized bead assembly demonstrate the possibility of multiplexed sensing of multiple target molecules using a single device with an array of micro-Hall sensors.

  14. Structural determinants of nuclear export signal orientation in binding to exportin CRM1. (United States)

    Fung, Ho Yee Joyce; Fu, Szu-Chin; Brautigam, Chad A; Chook, Yuh Min


    The Chromosome Region of Maintenance 1 (CRM1) protein mediates nuclear export of hundreds of proteins through recognition of their nuclear export signals (NESs), which are highly variable in sequence and structure. The plasticity of the CRM1-NES interaction is not well understood, as there are many NES sequences that seem incompatible with structures of the NES-bound CRM1 groove. Crystal structures of CRM1 bound to two different NESs with unusual sequences showed the NES peptides binding the CRM1 groove in the opposite orientation (minus) to that of previously studied NESs (plus). Comparison of minus and plus NESs identified structural and sequence determinants for NES orientation. The binding of NESs to CRM1 in both orientations results in a large expansion in NES consensus patterns and therefore a corresponding expansion of potential NESs in the proteome.

  15. Experimental determination of excitonic band structures of single-walled carbon nanotubes using circular dichroism spectra (United States)

    Wei, Xiaojun; Tanaka, Takeshi; Yomogida, Yohei; Sato, Naomichi; Saito, Riichiro; Kataura, Hiromichi


    Experimental band structure analyses of single-walled carbon nanotubes have not yet been reported, to the best of our knowledge, except for a limited number of reports using scanning tunnelling spectroscopy. Here we demonstrate the experimental determination of the excitonic band structures of single-chirality single-walled carbon nanotubes using their circular dichroism spectra. In this analysis, we use gel column chromatography combining overloading selective adsorption with stepwise elution to separate 12 different single-chirality enantiomers. Our samples show higher circular dichroism intensities than the highest values reported in previous works, indicating their high enantiomeric purity. Excitonic band structure analysis is performed by assigning all observed Eii and Eij optical transitions in the circular dichroism spectra. The results reproduce the asymmetric structures of the valence and conduction bands predicted by density functional theory. Finally, we demonstrate that an extended empirical formula can estimate Eij optical transition energies for any (n,m) species.

  16. Crystal structure determination of alkaline haemorrhagin AaHⅢ from snake venom of Agkistrodon acutus

    Institute of Scientific and Technical Information of China (English)

    龚为民; 滕脉坤; 牛立文


    The haemorrhagin AaH Ⅲ isolated from the snake venom of Agkistrodon acutus is one of the few al-kaline ones in snake venoms. Its crystals belong to space group P212121 with a = 9. 573 4 nm, b = 4. 996 7 nm and c = 4. 728 8 nm. Its crystal structure was determined by the molecular replacement method according to the model of metalloproteinase Adamalysin n from eastern rattlesnake venom. The AaHⅢ structure has been refined by PROLSQ. The final R factor was 0.254 and the RMS deviations of bond lengths and angles were 0. 001 8 nm and 1.5°. The structure comparison suggested that AaHⅢ has a similar structure to other snake venom zinc-metalloproteinases. They all belong to matrix metalloproteinases super-family.

  17. Structural determinants of host defense peptides for antimicrobial activity and target cell selectivity. (United States)

    Takahashi, Daisuke; Shukla, Sanjeev K; Prakash, Om; Zhang, Guolong


    Antimicrobial host defense peptides (HDPs) are a critical component of the innate immunity with microbicidal, endotoxin-neutralizing, and immunostimulatory properties. HDPs kill bacteria primarily through non-specific membrane lysis, therefore with a less likelihood of provoking resistance. Extensive structure-activity relationship studies with a number of HDPs have revealed that net charge, amphipathicity, hydrophobicity, and structural propensity are among the most important physicochemical and structural parameters that dictate their ability to interact with and disrupt membranes. A delicate balance among these factors, rather than a mere alteration of a single factor, is critically important for HDPs to ensure the antimicrobial potency and target cell selectivity. With a better understanding of the structural determinants of HDPs for their membrane-lytic activities, it is expected that novel HDP-based antimicrobials with minimum toxicity to eukaryotic cells can be developed for resistant infections, which have become a global public health crisis.

  18. Detection and use of pseudo-translation in determination of protein structures. (United States)

    Chook, Y M; Lipscomb, W N; Ke, H


    Two types of pseudo-translation symmetry, pseudo-twofold translational symmetry and pseudo-body-centered symmetry, have been found in protein crystals of chorismate mutase and cyclophilin C. Statistics on diffraction intensity from these two crystals showed that the presence of pseudo-translations in atomic space yielded a distribution of systematically strong and weak reflections at low resolution. The diffraction pattern resulting from pseudo-translational symmetry was apparently similar to that from true crystallographic symmetry at 4 A resolution, but was distinct at high resolution. Pseudo-translation can be detected by comparing the average magnitudes of certain parity groups of reflections in three-dimensional hkl space. Based on the structures of chorismate mutase and cyclophilin C, the ratio of >1.2 for the average magnitudes of parity groups is sufficient to indicate the existence of pseudo-translation. Although pseudo-translation often makes structure determination more difficult, the additional information of pseudo-translation has been used successfully in the structure determination of chorismate mutase by multiple isomorphous replacement and of cyclophilin C by molecular replacement. Thus, examination of pseudo-translation is recommended at an early stage of structure determination.

  19. Relationship between Structural and Intermediary Determinants of Health and Preterm Delivery (United States)

    Dolatian, Mahrokh; Mirabzadeh, Arash; Forouzan, Ameneh Setareh; Sajjadi, Homeira; Alavimajd, Hamid; Mahmoodi, Zohreh; Moafi, Farnoosh


    Background Preterm birth is a major health problem that leads to infant morbidity and mortality. The main goal of this study was to find the relationship between social determinants of health and preterm delivery. Methods A prospective longitudinal cohort study was carried out on 500 pregnant women in their 24th to 28th gestational weeks in 2012. The pregnant women filled out a self-report questionnaire on the structural determinant, perceived stress, and perceived social support. The participants were followed up until labor and the data about mother and the newborn were collected after labor. The data were analyzed by SPSS 21 and Lisrel 8.8 software programs using pathway analysis. Results The final path model fit well (CFI=0.96; RMSEA=0.060). Path analysis showed that among structural factors, income had a direct effect (β=0.06) and the factors of income (β=0.00594), number of children (family size) (β=-0.024), as well as mother's education (β=-0.0084) had the greatest overall effect on gestational age at birth respectively. Also, the results showed that among intermediate factors of social determinants of health, stress in the direct path (β=-0.12) and among the overall effects, the perceived stress (β=-0.12) and perceived social support (β=0.0396) affected the gestational age at birth. Conclusion The current study showed that some structural and intermediary determinants such as income and perceived stress had an effect on preterm labor. PMID:24918080

  20. Protein secondary structure determination by constrained single-particle cryo-electron tomography. (United States)

    Bartesaghi, Alberto; Lecumberry, Federico; Sapiro, Guillermo; Subramaniam, Sriram


    Cryo-electron microscopy (cryo-EM) is a powerful technique for 3D structure determination of protein complexes by averaging information from individual molecular images. The resolutions that can be achieved with single-particle cryo-EM are frequently limited by inaccuracies in assigning molecular orientations based solely on 2D projection images. Tomographic data collection schemes, however, provide powerful constraints that can be used to more accurately determine molecular orientations necessary for 3D reconstruction. Here, we propose "constrained single-particle tomography" as a general strategy for 3D structure determination in cryo-EM. A key component of our approach is the effective use of images recorded in tilt series to extract high-resolution information and correct for the contrast transfer function. By incorporating geometric constraints into the refinement to improve orientational accuracy of images, we reduce model bias and overrefinement artifacts and demonstrate that protein structures can be determined at resolutions of ∼8 Å starting from low-dose tomographic tilt series.

  1. Pseudosymmetry, high copy number and twinning complicate the structure determination of Desulfovibrio desulfuricans (ATCC 29577) flavodoxin. (United States)

    Guelker, Megan; Stagg, Loren; Wittung-Stafshede, Pernilla; Shamoo, Yousif


    The crystal structure of oxidized flavodoxin from Desulfovibrio desulfuricans (ATCC 29577) was determined by molecular replacement in two crystal forms, P3(1)21 and P4(3), at 2.5 and 2.0 A resolution, respectively. Structure determination in space group P3(1)21 was challenging owing to the presence of pseudo-translational symmetry and a high copy number in the asymmetric unit (8). Initial phasing attempts in space group P3(1)21 by molecular replacement using a poor search model (46% identity) and multi-wavelength anomalous dispersion were unsuccessful. It was necessary to solve the structure in a second crystal form, space group P4(3), which was characterized by almost perfect twinning, in order to obtain a suitable search model for molecular replacement. This search model with complementary approaches to molecular replacement utilizing the pseudo-translational symmetry operators determined by analysis of the native Patterson map facilitated the selection and manual placement of molecules to generate an initial solution in the P3(1)21 crystal form. During the early stages of refinement, application of the appropriate twin law, (-h, -k, l), was required to converge to reasonable R-factor values despite the fact that in the final analysis the data were untwinned and the twin law could subsequently be removed. The approaches used in structure determination and refinement may be applicable to other crystal structures characterized by these complicating factors. The refined model shows flexibility of the flavin mononucleotide coordinating loops indicated by the isolation of two loop conformations and provides a starting point for the elucidation of the mechanism used for protein-partner recognition.

  2. Distributed computing and NMR constraint-based high-resolution structure determination: applied for bioactive Peptide endothelin-1 to determine C-terminal folding. (United States)

    Takashima, Hiroyuki; Mimura, Norio; Ohkubo, Tadayasu; Yoshida, Takuya; Tamaoki, Haruhiko; Kobayashi, Yuji


    Distributed computing has been implemented to the solution structure determination of endothelin-1 to evaluate efficiency of the method for NMR constraint-based structure calculations. A key target of the investigation was determination of the C-terminal folding of the peptide, which had been dispersed in previous studies of NMR, despite its pharmacological significances. With use of tens of thousands of random initial structures to explore the conformational space comprehensively, we determined high-resolution structures with good convergences of C-terminal as well as previously defined N-terminal structures. The previous studies had missed the C-terminal convergence because of initial structure dependencies trapped in localized folding of the N-terminal region, which are strongly constricted by two disulfide bonds.

  3. Eddy current measurement system evaluation for corrosion depth determination on cast aluminum aircraft structure (United States)

    Singh, Surendra; Greving, Dan; Kinney, Andy; Vensel, Fred; Ohm, Jim; Peeler, Mike


    An eddy current (EC) technique was developed to determine the corrosion depth on a bare flange face of a cast aluminum A356-T6 aircraft engine structure. The EC response and the corrosion depths determined through metallurgical cross sections were used to develop an empirical relation between EC response and depth. The EC technique and depth determination are used to inspect the engine structures during overhaul to determine if they are fit for continued service. An accurate and reliable Non-Destructive Inspection is required to ensure that structures returned to service are safe for continued operation. NDE system reliability demonstrations of the eddy current technique are traditionally reported in terms of Probability of Detection (POD) data using MIL-HDBK-1823A. However, the calculation of POD data is based on a simple linear predictive model that is valid only if certain criteria are met. These are: 1) NDE system response is measurable (i.e. continuous data), 2) Flaw size is known and measurable (i.e. continuous data), 3) relationship between the NDE system response and flaw size is linear (or linear on a log scale), 4) variation in measured responseresponse around a predicted response for a given flaw size is normally distributed, 5) the variation around the predicted response is constant (i.e. variation does not change with flaw size), and 6) inherent variability in the NDE system is known and fully understood. In this work, a Measurement System Evaluation (MSE) of the Eddy Current System was used to address some of these concerns. This work was completed on two aircraft structures having varying corrosion depths. The data were acquired in a random manner at fifty regions of interests (ROIs). Three operators participated in this study, and each operator measured Eddy Current response three times in each ROI. In total, there were four hundred and fifty data points collected. Following this, the two structures were sectioned for measuring corrosion depth. The

  4. Targeting acetylcholinesterase: identification of chemical leads by high throughput screening, structure determination and molecular modeling.

    Directory of Open Access Journals (Sweden)

    Lotta Berg

    Full Text Available Acetylcholinesterase (AChE is an essential enzyme that terminates cholinergic transmission by rapid hydrolysis of the neurotransmitter acetylcholine. Compounds inhibiting this enzyme can be used (inter alia to treat cholinergic deficiencies (e.g. in Alzheimer's disease, but may also act as dangerous toxins (e.g. nerve agents such as sarin. Treatment of nerve agent poisoning involves use of antidotes, small molecules capable of reactivating AChE. We have screened a collection of organic molecules to assess their ability to inhibit the enzymatic activity of AChE, aiming to find lead compounds for further optimization leading to drugs with increased efficacy and/or decreased side effects. 124 inhibitors were discovered, with considerable chemical diversity regarding size, polarity, flexibility and charge distribution. An extensive structure determination campaign resulted in a set of crystal structures of protein-ligand complexes. Overall, the ligands have substantial interactions with the peripheral anionic site of AChE, and the majority form additional interactions with the catalytic site (CAS. Reproduction of the bioactive conformation of six of the ligands using molecular docking simulations required modification of the default parameter settings of the docking software. The results show that docking-assisted structure-based design of AChE inhibitors is challenging and requires crystallographic support to obtain reliable results, at least with currently available software. The complex formed between C5685 and Mus musculus AChE (C5685•mAChE is a representative structure for the general binding mode of the determined structures. The CAS binding part of C5685 could not be structurally determined due to a disordered electron density map and the developed docking protocol was used to predict the binding modes of this part of the molecule. We believe that chemical modifications of our discovered inhibitors, biochemical and biophysical

  5. Guiding automated NMR structure determination using a global optimization metric, the NMR DP score

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Yuanpeng Janet, E-mail:; Mao, Binchen; Xu, Fei; Montelione, Gaetano T., E-mail: [Rutgers, The State University of New Jersey, Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, and Northeast Structural Genomics Consortium (United States)


    ASDP is an automated NMR NOE assignment program. It uses a distinct bottom-up topology-constrained network anchoring approach for NOE interpretation, with 2D, 3D and/or 4D NOESY peak lists and resonance assignments as input, and generates unambiguous NOE constraints for iterative structure calculations. ASDP is designed to function interactively with various structure determination programs that use distance restraints to generate molecular models. In the CASD–NMR project, ASDP was tested and further developed using blinded NMR data, including resonance assignments, either raw or manually-curated (refined) NOESY peak list data, and in some cases {sup 15}N–{sup 1}H residual dipolar coupling data. In these blinded tests, in which the reference structure was not available until after structures were generated, the fully-automated ASDP program performed very well on all targets using both the raw and refined NOESY peak list data. Improvements of ASDP relative to its predecessor program for automated NOESY peak assignments, AutoStructure, were driven by challenges provided by these CASD–NMR data. These algorithmic improvements include (1) using a global metric of structural accuracy, the discriminating power score, for guiding model selection during the iterative NOE interpretation process, and (2) identifying incorrect NOESY cross peak assignments caused by errors in the NMR resonance assignment list. These improvements provide a more robust automated NOESY analysis program, ASDP, with the unique capability of being utilized with alternative structure generation and refinement programs including CYANA, CNS, and/or Rosetta.

  6. First synthesis and structural determination of a monomeric, unsolvated lithium amide, LiNH(2). (United States)

    Grotjahn, D B; Sheridan, P M; Al Jihad, I; Ziurys, L M


    Alkali metal amides typically aggregate in solution and the solid phase, and even in the gas phase. In addition, even in the few known monomeric structures, the coordination number of the alkali metal is raised by binding of Lewis-basic solvent molecules, with concomitant changes in structure. In contrast, the simplest lithium amide LiNH(2) has never been made in a monomeric form, even though its structure has been theoretically predicted several times. Here, the first experimental structural data for a monomeric, unsolvated lithium amide are determined using a combination of gas-phase synthesis and millimeter/submillimeter-wave spectroscopy. All data point to a planar structure for LiNH(2). The r(o) structure of LiNH(2) has a Li-N distance of 1.736(3) A, an N-H distance of 1.022(3) A, and a H-N-H angle of 106.9(1) degrees. These results are compared with theoretical predictions for LiNH(2), and experimental data for oligomeric, solid-phase samples, which could not resolve the question of whether LiNH(2) is planar or not. In addition, comparisons are made with revised gas-phase and solid-phase data and calculated structures of NaNH(2).

  7. Are the Crystal Structures of Enantiopure and Racemic Mandelic Acids Determined by Kinetics or Thermodynamics? (United States)

    Hylton, Rebecca K; Tizzard, Graham J; Threlfall, Terence L; Ellis, Amy L; Coles, Simon J; Seaton, Colin C; Schulze, Eric; Lorenz, Heike; Seidel-Morgenstern, Andreas; Stein, Matthias; Price, Sarah L


    Mandelic acids are prototypic chiral molecules where the sensitivity of crystallized forms (enantiopure/racemic compound/polymorphs) to both conditions and substituents provides a new insight into the factors that may allow chiral separation by crystallization. The determination of a significant number of single crystal structures allows the analysis of 13 enantiopure and 30 racemic crystal structures of 21 (F/Cl/Br/CH3/CH3O) substituted mandelic acid derivatives. There are some common phenyl packing motifs between some groups of racemic and enantiopure structures, although they show very different hydrogen-bonding motifs. The computed crystal energy landscape of 3-chloromandelic acid, which has at least two enantiopure and three racemic crystal polymorphs, reveals that there are many more possible structures, some of which are predicted to be thermodynamically more favorable as well as slightly denser than the known forms. Simulations of mandelic acid dimers in isolation, water, and toluene do not differentiate between racemic and enantiopure dimers and also suggest that the phenyl ring interactions play a major role in the crystallization mechanism. The observed crystallization behavior of mandelic acids does not correspond to any simple "crystal engineering rules" as there is a range of thermodynamically feasible structures with no distinction between the enantiopure and racemic forms. Nucleation and crystallization appear to be determined by the kinetics of crystal growth with a statistical bias, but the diversity of the mandelic acid crystallization behavior demonstrates that the factors that influence the kinetics of crystal nucleation and growth are not yet adequately understood.

  8. Computational tools for experimental determination and theoretical prediction of protein structure

    Energy Technology Data Exchange (ETDEWEB)

    O`Donoghue, S.; Rost, B.


    This tutorial was one of eight tutorials selected to be presented at the Third International Conference on Intelligent Systems for Molecular Biology which was held in the United Kingdom from July 16 to 19, 1995. The authors intend to review the state of the art in the experimental determination of protein 3D structure (focus on nuclear magnetic resonance), and in the theoretical prediction of protein function and of protein structure in 1D, 2D and 3D from sequence. All the atomic resolution structures determined so far have been derived from either X-ray crystallography (the majority so far) or Nuclear Magnetic Resonance (NMR) Spectroscopy (becoming increasingly more important). The authors briefly describe the physical methods behind both of these techniques; the major computational methods involved will be covered in some detail. They highlight parallels and differences between the methods, and also the current limitations. Special emphasis will be given to techniques which have application to ab initio structure prediction. Large scale sequencing techniques increase the gap between the number of known proteins sequences and that of known protein structures. They describe the scope and principles of methods that contribute successfully to closing that gap. Emphasis will be given on the specification of adequate testing procedures to validate such methods.

  9. Application of in situ diffraction in high-throughput structure determination platforms. (United States)

    Aller, Pierre; Sanchez-Weatherby, Juan; Foadi, James; Winter, Graeme; Lobley, Carina M C; Axford, Danny; Ashton, Alun W; Bellini, Domenico; Brandao-Neto, Jose; Culurgioni, Simone; Douangamath, Alice; Duman, Ramona; Evans, Gwyndaf; Fisher, Stuart; Flaig, Ralf; Hall, David R; Lukacik, Petra; Mazzorana, Marco; McAuley, Katherine E; Mykhaylyk, Vitaliy; Owen, Robin L; Paterson, Neil G; Romano, Pierpaolo; Sandy, James; Sorensen, Thomas; von Delft, Frank; Wagner, Armin; Warren, Anna; Williams, Mark; Stuart, David I; Walsh, Martin A


    Macromolecular crystallography (MX) is the most powerful technique available to structural biologists to visualize in atomic detail the macromolecular machinery of the cell. Since the emergence of structural genomics initiatives, significant advances have been made in all key steps of the structure determination process. In particular, third-generation synchrotron sources and the application of highly automated approaches to data acquisition and analysis at these facilities have been the major factors in the rate of increase of macromolecular structures determined annually. A plethora of tools are now available to users of synchrotron beamlines to enable rapid and efficient evaluation of samples, collection of the best data, and in favorable cases structure solution in near real time. Here, we provide a short overview of the emerging use of collecting X-ray diffraction data directly from the crystallization experiment. These in situ experiments are now routinely available to users at a number of synchrotron MX beamlines. A practical guide to the use of the method on the MX suite of beamlines at Diamond Light Source is given.

  10. A Dynamic Analysis of Capital Structure Determinants. Empirical Results for Romanian Capital Market

    Directory of Open Access Journals (Sweden)

    Mihaela Dragota


    Full Text Available The analysis of capital structure and its determinants represents an useful approach for the Romanian and foreign investors and for the companies, at the same time. The main conclusion for capital structure analysis was that Romanian listed companies sustained their assets, in this order, on equity, commercial debt and, finally, on financial debt. The four variables used in the regression model are significant. The pecking order theory seemed to be more appropriate for the Romanian capital market, but the signalling theory was not entirely rejected.

  11. Thermo-responsive cell culture carriers based on poly(vinyl methyl ether)—the effect of biomolecular ligands to balance cell adhesion and stimulated detachment (United States)

    Teichmann, Juliane; Nitschke, Mirko; Pette, Dagmar; Valtink, Monika; Gramm, Stefan; Härtel, Frauke V.; Noll, Thomas; Funk, Richard H. W.; Engelmann, Katrin; Werner, Carsten


    Two established material systems for thermally stimulated detachment of adherent cells were combined in a cross-linked polymer blend to merge favorable properties. Through this approach poly(N-isopropylacrylamide) (PNiPAAm) with its superior switching characteristic was paired with a poly(vinyl methyl ether)-based composition that allows adjusting physico-chemical and biomolecular properties in a wide range. Beyond pure PNiPAAm, the proposed thermo-responsive coating provides thickness, stiffness and swelling behavior, as well as an apposite density of reactive sites for biomolecular functionalization, as effective tuning parameters to meet specific requirements of a particular cell type regarding initial adhesion and ease of detachment. To illustrate the strength of this approach, the novel cell culture carrier was applied to generate transplantable sheets of human corneal endothelial cells (HCEC). Sheets were grown, detached, and transferred onto planar targets. Cell morphology, viability and functionality were analyzed by immunocytochemistry and determination of transepithelial electrical resistance (TEER) before and after sheet detachment and transfer. HCEC layers showed regular morphology with appropriate TEER. Cells were positive for function-associated marker proteins ZO-1, Na+/K+-ATPase, and paxillin, and extracellular matrix proteins fibronectin, laminin and collagen type IV before and after transfer. Sheet detachment and transfer did not impair cell viability. Subsequently, a potential application in ophthalmology was demonstrated by transplantation onto de-endothelialized porcine corneas in vitro. The novel thermo-responsive cell culture carrier facilitates the generation and transfer of functional HCEC sheets. This paves the way to generate tissue engineered human corneal endothelium as an alternative transplant source for endothelial keratoplasty.

  12. Residual dipolar coupling constants and structure determination of large DNA duplexes

    Energy Technology Data Exchange (ETDEWEB)

    Mauffret, Olivier; Tevanian, Georges; Fermandjian, Serge [Institut Gustave-Roussy, Departement de Biologie et Pharmacologie Structurales (France)], E-mail:


    Several NMR works have shown that long-range information provided by residual dipolar couplings (RDCs) significantly improve the global structure definition of RNAs and DNAs. Most of these are based on the use of a large set of RDCs, the collect of which requires samples labeled with {sup 13}C, {sup 15}N, and sometimes, {sup 2}H. Here, we carried out torsion-angle dynamics simulations on a non-self complementary DNA fragment of 17 base-pairs, d(GGAAAATATCTAGCAGT).(ACTGCTAGAGATTTTCC). This reproduces the U5 LTR distal end of the HIV-1 cDNA that contains the enzyme integrase binding site. Simulations aimed at evaluating the impact of RDCs on the structure definition of long oligonucleotides, were performed in incorporating (i) nOe-distances at both < 4.5 A and < 5 A; (ii) a small set of {sup 13}C-{sup 1}H RDCs, easily detectable at the natural abundance, and (iii) a larger set of RDCs only accessible through the {sup 13}C labeling of DNAs. Agreement between a target structure and a simulated structure was measured in terms of precision and accuracy. Results allowed to define conditions in which accurate DNA structures can be determined. We confirmed the strong impact of RDCs on the structure determination, and, above all, we found that a small set of RDC constraints (ca. 50) detectable at the natural abundance is sufficient to accurately derive the global and local DNA duplex structures when used in conjunction with nOe-distances < 5 A.

  13. Magic Angle Spinning NMR Structure Determination of Proteins from Pseudocontact Shifts

    KAUST Repository

    Li, Jianping


    Magic angle spinning solid-state NMR is a unique technique to study atomic-resolution structure of biomacromolecules which resist crystallization or are too large to study by solution NMR techniques. However, difficulties in obtaining sufficient number of long-range distance restraints using dipolar coupling based spectra hamper the process of structure determination of proteins in solid-state NMR. In this study it is shown that high-resolution structure of proteins in solid phase can be determined without the use of traditional dipolar-dipolar coupling based distance restraints by combining the measurements of pseudocontact shifts (PCSs) with Rosetta calculations. The PCSs were generated by chelating exogenous paramagnetic metal ions to a tag 4-mercaptomethyl-dipicolinic acid, which is covalently attached to different residue sites in a 56-residue immunoglobulin-binding domain of protein G (GB1). The long-range structural restraints with metal-nucleus distance of up to ∼20 Å are quantitatively extracted from experimentally observed PCSs, and these are in good agreement with the distances back-calculated using an X-ray structure model. Moreover, we demonstrate that using several paramagnetic ions with varied paramagnetic susceptibilities as well as the introduction of paramagnetic labels at different sites can dramatically increase the number of long-range restraints and cover different regions of the protein. The structure generated from solid-state NMR PCSs restraints combined with Rosetta calculations has 0.7 Å root-mean-square deviation relative to X-ray structure. © 2013 American Chemical Society.

  14. Towards the Structure Determination of a Modulated Protein Crystal: The Semicrystalline State of Profilin:Actin (United States)

    Borgstahl, G.; Lovelace, J.; Snell, E. H.; Bellamy, H.


    One of the remaining challenges to structural biology is the solution of modulated structures. While small molecule crystallographers have championed this type of structure, to date, no modulated macromolecular structures have been determined. Modulation of the molecular structures within the crystal can produce satellite reflections or a superlattice of reflections in reciprocal space. We have developed the data collection methods and strategies that are needed to collect and analyze these data. If the macromolecule's crystal lattice is composed of physiologically relevant packing contacts, structural changes induced under physiological conditions can cause distortion relevant to the function and biophysical processes of the molecule making up the crystal. By careful measurement of the distortion, and the corresponding three-dimensional structure of the distorted molecule, we will visualize the motion and mechanism of the biological macromolecule(s). We have measured the modulated diffraction pattern produced by the semicrystalline state of profilin:actin crystals using highly parallel and highly monochromatic synchrotron radiation coupled with fine phi slicing (0.001-0.010 degrees) for structure determination. These crystals present these crystals present a unique opportunity to address an important question in structural biology. The modulation is believed to be due to the formation of actin helical filaments from the actin beta ribbon upon the pH-induced dissociation of profilin. To date, the filamentous state of actin has resisted crystallization and no detailed structures are available. The semicrystalline state profilin:actin crystals provides a unique opportunity to understand the many conformational states of actin. This knowledge is essential for understanding the dynamics underlying shape changes and motility of eukaryotic cells. Many essential processes, such as cytokinesis, phagocytosis, and cellular migration depend upon the capacity of the actin

  15. New insights into structural determinants of prion protein folding and stability. (United States)

    Benetti, Federico; Legname, Giuseppe


    Prions are the etiological agent of fatal neurodegenerative diseases called prion diseases or transmissible spongiform encephalopathies. These maladies can be sporadic, genetic or infectious disorders. Prions are due to post-translational modifications of the cellular prion protein leading to the formation of a β-sheet enriched conformer with altered biochemical properties. The molecular events causing prion formation in sporadic prion diseases are still elusive. Recently, we published a research elucidating the contribution of major structural determinants and environmental factors in prion protein folding and stability. Our study highlighted the crucial role of octarepeats in stabilizing prion protein; the presence of a highly enthalpically stable intermediate state in prion-susceptible species; and the role of disulfide bridge in preserving native fold thus avoiding the misfolding to a β-sheet enriched isoform. Taking advantage from these findings, in this work we present new insights into structural determinants of prion protein folding and stability.

  16. Evidence against the continuum structure underlying motivation measures derived from self-determination theory. (United States)

    Chemolli, Emanuela; Gagné, Marylène


    Self-determination theory (SDT) proposes a multidimensional conceptualization of motivation in which the different regulations are said to fall along a continuum of self-determination. The continuum has been used as a basis for using a relative autonomy index as a means to create motivational scores. Rasch analysis was used to verify the continuum structure of the Multidimensional Work Motivation Scale and of the Academic Motivation Scale. We discuss the concept of continuum against SDT's conceptualization of motivation and argue against the use of the relative autonomy index on the grounds that evidence for a continuum structure underlying the regulations is weak and because the index is statistically problematic. We suggest exploiting the full richness of SDT's multidimensional conceptualization of motivation through the use of alternative scoring methods when investigating motivational dynamics across life domains.

  17. Serendipitous crystallization and structure determination of cyanase (CynS) from Serratia proteamaculans. (United States)

    Butryn, Agata; Stoehr, Gabriele; Linke-Winnebeck, Christian; Hopfner, Karl Peter


    Cyanate hydratase (CynS) catalyzes the decomposition of cyanate and bicarbonate into ammonia and carbon dioxide. Here, the serendipitous crystallization of CynS from Serratia proteamaculans (SpCynS) is reported. SpCynS was crystallized as an impurity and its identity was determined using mass-spectrometric analysis. The crystals belonged to space group P1 and diffracted to 2.1 Å resolution. The overall structure of SpCynS is very similar to a previously determined structure of CynS from Escherichia coli. Density for a ligand bound to the SpCynS active site was observed, but could not be unambiguously identified. Additionally, glycerol molecules bound at the entry to the active site of the enzyme indicate conserved residues that might be important for the trafficking of substrates and products.

  18. Neutron diffraction stress determination in W-laminates for structural divertor applications

    Directory of Open Access Journals (Sweden)

    R. Coppola


    Full Text Available Neutron diffraction measurements have been carried out to develop a non-destructive experimental tool for characterizing the crystallographic structure and the internal stress field in W foil laminates for structural divertor applications in future fusion reactors. The model sample selected for this study had been prepared by brazing, at 1085 °C, 13 W foils with 12 Cu foils. A complete strain distribution measurement through the brazed multilayered specimen and determination of the corresponding stresses has been obtained, assuming zero stress in the through-thickness direction. The average stress determined from the technique across the specimen (over both ‘phases’ of W and Cu is close to zero at −17 ± 32 MPa, in accordance with the expectations.

  19. Structural determination and physical properties of 4d transitional metal diborides by first-principles calculations (United States)

    Ying, Chun; Zhao, Erjun; Lin, Lin; Hou, Qingyu


    The structural determination, thermodynamic, mechanical, dynamic and electronic properties of 4d transitional metal diborides MB2 (M = Y-Ag) are systematically investigated by first-principles within the density functional theory (DFT). For each diboride, five structures are considered, i.e. AlB2-, ReB2-, OsB2-, MoB2- and WB2-type structures. The calculated lattice parameters are in good agreement with the previously theoretical and experimental studies. The formation enthalpy increases from YB2 to AgB2 in AlB2-type structure (similar to MoB2- and WB2-type). While the formation enthalpy decreases from YB2 to MoB2, reached minimum value to TcB2, and then increases gradually in ReB2-type structure (similar to OsB2-type), which is consistent with the results of the calculated density of states. The structural stability of these materials relates mainly on electronegative of metals, boron structure and bond characters. Among the considered structures, TcB2-ReB2 (TcB2-ReB2 represents TcB2 in ReB2-type structure, the same hereinafter) has the largest shear modulus (248 GPa), and is the hardest compound. The number of electrons transferred from metals to boron atoms and the calculated densities of states (DOS) indicate that each diboride is a complex mixture of metallic, ionic and covalent characteristics. Trends are discussed.

  20. System and method for forming synthetic protein crystals to determine the conformational structure by crystallography (United States)

    Craig, George D.; Glass, Robert; Rupp, Bernhard


    A method for forming synthetic crystals of proteins in a carrier fluid by use of the dipole moments of protein macromolecules that self-align in the Helmholtz layer adjacent to an electrode. The voltage gradients of such layers easily exceed 10.sup.6 V/m. The synthetic protein crystals are subjected to x-ray crystallography to determine the conformational structure of the protein involved.

  1. Purification and Primary Structure Determination of a Novel Polypeptide Isolated from Mistletoe Viscum coloratum

    Institute of Scientific and Technical Information of China (English)

    Jing Lin KONG; Xiu Bao DU; Chong Xu FAN; Ying CAO; Hui JIANG; Jian Fu XU; Xiao Jun ZHENG


    A novel polypeptide was isolated from mistletoe Viscum coloratum. The primary structure of the polypeptide 'named viscotoxin B2' was determined to be KSCCKNTTGRNIYNT CRFAGGSRERCAKLSGCKIISASTCPSDYPK by Edman degradation. Viscotoxin B2 shared high sequence homology with viscotoxins isolated from Viscum album. Pharmacological experiments showed that viscotoxin B2 had distinct cytotoxic activity on tumor cells. Viscotoxin B2 could be used as a leading compound in cancer therapy.

  2. Determining the structure of Higgs couplings at the CERN LargeHadron Collider. (United States)

    Plehn, Tilman; Rainwater, David; Zeppenfeld, Dieter


    Higgs boson production via weak boson fusion at the CERN Large Hadron Collider has the capability to determine the dominant CP nature of a Higgs boson, via the tensor structure of its coupling to weak bosons. This information is contained in the azimuthal angle distribution of the two outgoing forward tagging jets. The technique is independent of both the Higgs boson mass and the observed decay channel.

  3. Three-dimensional structure determination of capsid of Aedes albopicus C6/36 cell densovirus

    Institute of Scientific and Technical Information of China (English)

    CHENG Lingpeng; CHEN Senxiong; Jenifer M.Brannan; Joanita Jakana; ZHANG Qinfen; Z.H.Zhou; ZHANG Jingqiang


    The three-dimensional structure of capsid of Aedes albopictus C6/36 densovirus was determined to 14-(A) resolution by electron cryomicroscopy and computer reconstruction. The triangulation number of the capsid is 1. There are 12 holes in each triangular face and a spike on each 5-fold vertex. The validity of the capsid and nucleic acid densities in the reconstructions was discussed.

  4. On the use of pseudocontact shifts in the structure determination of metalloproteins. (United States)

    Jensen, Malene Ringkjøbing; Hansen, D Flemming; Ayna, Umit; Dagil, Robert; Hass, Mathias A S; Christensen, Hans E M; Led, Jens J


    The utility of pseudocontact shifts in the structure refinement of metalloproteins has been evaluated using a native, paramagnetic Cu(2+) metalloprotein, plastocyanin from Anabaena variabilis (A.v.), as a model protein. First, the possibility of detecting signals of nuclei spatially close to the paramagnetic metal ion is investigated using the WEFT pulse sequence in combination with the conventional TOCSY and (1)H-(15)N HSQC sequences. Second, the importance of the electrical charge of the metal ion for the determination of correct pseudocontact shifts from the obtained chemical shifts is evaluated. Thus, using both the Cu(+) plastocyanin and Cd(2+)-substituted plastocyanin as the diamagnetic references, it is found that the Cd(2+)-substituted protein with the same electrical charge of the metal ion as the paramagnetic Cu(2+) plastocyanin provides the most appropriate diamagnetic reference signals. Third, it is found that reliable pseudocontact shifts cannot be obtained from the chemical shifts of the (15)N nuclei in plastocyanin, most likely because these shifts are highly dependent on even minor differences in the structure of the paramagnetic and diamagnetic proteins. Finally, the quality of the obtained (1)H pseudocontact shifts, as well as the possibility of improving the accuracy of the obtained structure, is demonstrated by incorporating the shifts as restraints in a refinement of the solution structure of A.v. plastocyanin. It is found that incorporation of the pseudocontact shifts enhances the precision of the structure in regions with only few NOE restraints and improves the accuracy of the overall structure.

  5. Flow directionality, mountain barriers and functional traits determine diatom metacommunity structuring of high mountain streams. (United States)

    Dong, Xiaoyu; Li, Bin; He, Fengzhi; Gu, Yuan; Sun, Meiqin; Zhang, Haomiao; Tan, Lu; Xiao, Wen; Liu, Shuoran; Cai, Qinghua


    Stream metacommunities are structured by a combination of local (environmental filtering) and regional (dispersal) processes. The unique characters of high mountain streams could potentially determine metacommunity structuring, which is currently poorly understood. Aiming at understanding how these characters influenced metacommunity structuring, we explored the relative importance of local environmental conditions and various dispersal processes, including through geographical (overland), topographical (across mountain barriers) and network (along flow direction) pathways in shaping benthic diatom communities. From a trait perspective, diatoms were categorized into high-profile, low-profile and motile guild to examine the roles of functional traits. Our results indicated that both environmental filtering and dispersal processes influenced metacommunity structuring, with dispersal contributing more than environmental processes. Among the three pathways, stream corridors were primary pathway. Deconstructive analysis suggested different responses to environmental and spatial factors for each of three ecological guilds. However, regardless of traits, dispersal among streams was limited by mountain barriers, while dispersal along stream was promoted by rushing flow in high mountain stream. Our results highlighted that directional processes had prevailing effects on metacommunity structuring in high mountain streams. Flow directionality, mountain barriers and ecological guilds contributed to a better understanding of the roles that mountains played in structuring metacommunity.

  6. Noncontact interface trap determination of SiO2-4H-SiC structures (United States)

    Oborina, E. I.; Hoff, A. M.


    A sequence of noncontact corona-Kelvin metrology is introduced that enables the determination and monitoring of interface properties in dielectric/wide band gap semiconductor structures. The technique involves the incremental application of precise and measured quantities of corona charge, QC, onto the dielectric surface followed by determination of the contact potential difference, VCPD, as the material structure response. The V-Q characteristics obtained are used to extract the surface barrier, VSB, response related to the applied corona charge. The described approach differs from the common noncontact method applied in the case of dielectric/silicon structures where for each quanta of applied charge the value of surface barrier voltage, VSB, is obtained. Materials with wide band gaps and high concentrations of deep levels, as suggested for silicon carbide, do not permit quick determination of VSB by modulation of the band bending in the semiconductor with light. Light exposure in the case of SiC results in a long recovery time required to approach the nominal value of the preillumination VCPD value. The metrology approach presented determines an intersection of the VCPD-QC characteristic obtained in the dark with the Vox-QC characteristic representing the dielectric response. The specific VSB-QC dependence surrounding the reference VFB value is obtained from this approach and enables the noncontact determination of the dielectric interface trap density and its spectrum. Application of the modified metrology method to thermal oxide on n-type 4H-SiC demonstrates the modification of the Dit distribution by Fowler-Nordheim stress. In addition, an ability to quantify and separate trapped charge components is shown.

  7. Determining the Structure of Biomaterials Interfaces using Synchrotron-based X-ray Diffraction

    Energy Technology Data Exchange (ETDEWEB)

    McBride, M


    The purpose of this project is to explore the feasibility of using surface X-ray diffraction (SXRD) to determine the structure of biomineral surfaces in electrolyte solutions and of the adsorbed layer of acidic amino acids that are believed to play a central role in the control of biomineral formation and function. The work is a critical component in the development of an integrated picture of the physical and chemical basis for deposition and dissolution at solid-liquid interfaces in biological systems, and brings a new and very powerful surface-sensitive capability to LLNL. We have chosen as our model systems calcium carbonate and calcium phosphate in aspartic and glutamic acid-bearing solutions. The calcium compounds are ubiquitous among biomineral structures, both those that are beneficial such as bones and teeth, and those that are pathological such as kidney stones, while the two acidic amino acids--both as simple and poly-amino acids--are the dominant constituents of protein mixtures implicated in the control of biomineralization. The goals of the work are: (1) to determine the surface structure of pure calcium phosphate and calcium carbonate surfaces in aqueous solution using SXRD; (2) to determine how those surfaces are modified by the presence of aspartic and glutamic acid, both as the simple amino acids and as poly-aspartate and poly-glutamate and (3) to model the interactions of acidic amino acids with calcite.

  8. Electrochemical sensor for multiplex screening of genetically modified DNA: identification of biotech crops by logic-based biomolecular analysis. (United States)

    Liao, Wei-Ching; Chuang, Min-Chieh; Ho, Ja-An Annie


    Genetically modified (GM) technique, one of the modern biomolecular engineering technologies, has been deemed as profitable strategy to fight against global starvation. Yet rapid and reliable analytical method is deficient to evaluate the quality and potential risk of such resulting GM products. We herein present a biomolecular analytical system constructed with distinct biochemical activities to expedite the computational detection of genetically modified organisms (GMOs). The computational mechanism provides an alternative to the complex procedures commonly involved in the screening of GMOs. Given that the bioanalytical system is capable of processing promoter, coding and species genes, affirmative interpretations succeed to identify specified GM event in terms of both electrochemical and optical fashions. The biomolecular computational assay exhibits detection capability of genetically modified DNA below sub-nanomolar level and is found interference-free by abundant coexistence of non-GM DNA. This bioanalytical system, furthermore, sophisticates in array fashion operating multiplex screening against variable GM events. Such a biomolecular computational assay and biosensor holds great promise for rapid, cost-effective, and high-fidelity screening of GMO.

  9. Biochemical and biomolecular aspects of oxidative stress due to acute and severe hypoxia in human muscle tissue. (United States)

    Corbucci, G G; Sessego, R; Velluti, C; Salvi, M


    Mitochondrial oxidative stress was investigated in severe and acute hypoxia and in reperfusion applied to human muscle tissues. The biochemical and biomolecular relationship between the response of the respiratory-chain enzymic complexes and the metabolism of specific hypoxia stress proteins (HSP) suggest an adaptive mechanism which antagonizes the oxidative damage due to acute and severe tissue hypoxia.

  10. FTIR microscopy reveals distinct biomolecular profile of crustacean digestive glands upon subtoxic exposure to ZnO nanoparticles. (United States)

    Romih, Tea; Jemec, Anita; Novak, Sara; Vaccari, Lisa; Ferraris, Paolo; Šimon, Martin; Kos, Monika; Susič, Robert; Kogej, Ksenija; Zupanc, Jernej; Drobne, Damjana


    Biomolecular profiling with Fourier-Transform InfraRed Microscopy was performed to distinguish the Zn(2+)-mediated effects on the crustacean (Porcellio scaber) digestive glands from the ones elicited by the ZnO nanoparticles (NPs). The exposure to ZnO NPs or ZnCl2 (1500 and 4000 µg Zn/g of dry food) activated different types of metabolic pathways: some were found in the case of both substances, some only in the case of ZnCl2, and some only upon exposure to ZnO NPs. Both the ZnO NPs and the ZnCl2 increased the protein (∼1312 cm(-1); 1720-1485 cm(-1)/3000-2830 cm(-1)) and RNA concentration (∼1115 cm(-1)). At the highest exposure concentration of ZnCl2, where the effects occurred also at the organismal level, some additional changes were found that were not detected upon the ZnO NP exposure. These included changed carbohydrate (most likely glycogen) concentrations (∼1043 cm(-1)) and the desaturation of cell membrane lipids (∼3014 cm(-1)). The activation of novel metabolic pathways, as evidenced by changed proteins' structure (at 1274 cm(-1)), was found only in the case of ZnO NPs. This proves that Zn(2+) are not the only inducers of the response to ZnO NPs. Low bioavailable fraction of Zn(2+) in the digestive glands exposed to ZnO NPs further supports the role of particles in the ZnO NP-generated effects. This study provides the evidence that ZnO NPs induce their own metabolic responses in the subtoxic range.

  11. Ab initio structure determination of new compound Ba 3(BO 3)(PO 4) (United States)

    Ma, H. W.; Liang, J. K.; Wu, L.; Liu, G. Y.; Rao, G. H.; Chen, X. L.


    The crystal structure of new compound Ba3BPO7 was determined by ab initio method from high-resolution conventional X-ray powder diffraction data. The Rietveld refinement converged to Rp=5.92%, Rwp=8.87%, Rexp=5.00% with the following details: Hexagonal, space group P63mc, a=5.4898 (1) Å, c=14.7551(1) Å, Z=2. The basic unit of the structure is the [BaO10]-[BO3]-[PO4] polar polyhedra-chain composed of Ba1-B-P-O cluster. These chains, running along c-axis, stack in a HCP mode to build the whole structure with triangular prism channels. The channels are parallel to c-axis too, in which Ba2 and Ba3 are located.


    Institute of Scientific and Technical Information of China (English)

    Z.Y.Wu; Y.N.Xie; Q.H.Zhang; L.Gao; Z.Z.Chen; J.Zhang; K.Ibrahim; M.I.Abbas; G.Li; Y.Tao; T.D.Hu; F.Q.Liu; H.J.Qian


    As a potential application of titanium-oxide nanoparticles, it is extremely importantto investigate a detailed picture of the surface and interior structural properties ofnanocrystalline materials, such as rutile and anatase with diameters 7.0 and 4.5nm,respectively. X-ray absorption spectroscopy has been used to identify the local Ti envi-ronment and related electronic structure. We combine the experimental results at theTi edge in both bulk and nano-crystals to determine the lattice distortion in terms ofdifferently characteristic preedge features and the variation in the multiple-scatteringregion of X-ray absorption near-edge structure (XANES) spectra. The relationshipbetween the transition peaks and the surface-to volume ratio is also discussed.

  13. The influence of the stray-light component in determining coronal temperature structures

    Institute of Scientific and Technical Information of China (English)


    We use a few solar partial eclipse observations made by XRT/Hinode to estimate the influence of stray-light component in determining coronal temperature structures. Our analysis shows that the stray light will largely affect the estimation of coronal temperature and change the estimated temperature structure in one coronal hole region. The stray lights mildly influence the estimated temperatures in one quiet Sun region and do not change the estimated temperature structure. This implies that the influence of stray lights differs from one region to another, and definitely needs to be considered in some regions. Whereas a carefully estimated point-spread-function is needed to remove the stray light component, our study shows that by a simple approach such as subtracting the average intensity of distant (e.g. >1.4 solar radius) points from the data values, the influence of stray light can be largely removed, at least for the two regions we study here.

  14. Disorder determined by high-resolution powder diffraction: structure of pentamethylcyclopentadienyllithium. (United States)

    Dinnebier; Schneider; van Smaalen S; Olbrich; Behrens


    The crystal structure of pentamethylcyclopentadienyllithium, [Li(C(10)H(15))] (LiCp*), has been determined from a high-resolution powder pattern by modelling and the maximum entropy method (MEM). The compound crystallizes in space group R3m with lattice parameters a = b = 14.7711 (5), c = 3.82206 (6) Å and V = 722.19 (4) Å(3) (Z = 3). LiCp* forms polymeric 'multidecker' chains along the c axis. The pentamethylcyclopentadienyl anions are coplanar with each other and show threefold rotational disorder. The MEM calculations did not only confirm the structural model and the type of disorder, but also discovered additional symmetry compared with the Rietveld analysis. This is the first solid-state structure of a Lewis-base-free alkali metal Cp* compound.

  15. The influence of the stray-light component in determining coronal temperature structures

    Institute of Scientific and Technical Information of China (English)

    HAO Juan; ZHANG Mei


    We use a few solar partial eclipse observations made by XRT/Hinode to estimate the influence of stray-light component in determining coronal temperature structures. Our analysis shows that the stray light will largely affect the estimation of coronal temperature and change the estimated temperature structure in one coronal hole region. The stray lights mildly influence the estimated temperatures in one quiet Sun region and do not change the estimated temperature structure. This implies that the influence of stray lights differs from one region to another, and definitely needs to be considered in some regions. Whereas a carefully estimated point-spread-function Is needed to remove the stray light component, our study shows that by a simple approach such as subtracting the average intensity of distant (e.g. >1.4 solar radius) points from the data values, the influence of stray light can be largely removed, at least for the two regions we study here.

  16. Stochastic structure determination for conformationally flexible heterogenous molecular clusters: application to ionic liquids. (United States)

    Addicoat, Matthew A; Fukuoka, Syou; Page, Alister J; Irle, Stephan


    We present a novel method that enables accurate and efficient computational determination of conformationally flexible clusters, "Kick(3)" This method uses stochastically generated structures in combination with fast quantum mechanical methods. We demonstrate the power of this method by elucidating the structure of ionic liquid (IL) ([xMIM(+)][NO3(-)])n clusters (x = E, B, D, n = 1-10,15). Dispersion-corrected, third-order self-consistent-charge density-functional tight-binding (DFTB3) is shown to be a computationally efficient, yet reliable approximation to density functional theory for predicting and understanding IL structure and stability. The presented approach, therefore, enables the accurate and efficient screening of ILs with high potential toward practical applications, without recourse to more expensive quantum chemical methods.

  17. Low-energy electron diffraction experiment, theory and surface structure determination

    CERN Document Server

    Hove, Michel A; Chan, Chi-Ming


    Surface crystallography plays the same fundamental role in surface science which bulk crystallography has played so successfully in solid-state physics and chemistry. The atomic-scale structure is one of the most important aspects in the understanding of the behavior of surfaces in such widely diverse fields as heterogeneous catalysis, microelectronics, adhesion, lubrication, cor­ rosion, coatings, and solid-solid and solid-liquid interfaces. Low-Energy Electron Diffraction or LEED has become the prime tech­ nique used to determine atomic locations at surfaces. On one hand, LEED has yielded the most numerous and complete structural results to date (almost 200 structures), while on the other, LEED has been regarded as the "technique to beat" by a variety of other surface crystallographic methods, such as photoemission, SEXAFS, ion scattering and atomic diffraction. Although these other approaches have had impressive successes, LEED has remained the most productive technique and has shown the most versatility...

  18. A systematic review of the main factors that determine agility in sport using structural equation modeling. (United States)

    Hojka, Vladimir; Stastny, Petr; Rehak, Tomas; Gołas, Artur; Mostowik, Aleksandra; Zawart, Marek; Musálek, Martin


    While tests of basic motor abilities such as speed, maximum strength or endurance are well recognized, testing of complex motor functions such as agility remains unresolved in current literature. Therefore, the aim of this review was to evaluate which main factor or factor structures quantitatively determine agility. In methodological detail, this review focused on research that explained or described the relationships between latent variables in a factorial model of agility using approaches such as principal component analysis, factor analysis and structural equation modeling. Four research studies met the defined inclusion criteria. No quantitative empirical research was found that tried to verify the quality of the whole suggested model of the main factors determining agility through the use of a structural equation modeling (SEM) approach or a confirmatory factor analysis. From the whole structure of agility, only change of direction speed (CODS) and some of its subtests were appropriately analyzed. The combination of common CODS tests is reliable and useful to estimate performance in sub-elite athletes; however, for elite athletes, CODS tests must be specific to the needs of a particular sport discipline. Sprinting and jumping tests are stronger factors for CODS than explosive strength and maximum strength tests. The authors suggest the need to verify the agility factorial model by a second generation data analysis technique such as SEM.

  19. Structure determination of an 11-subunit exosome in complex with RNA by molecular replacement

    Energy Technology Data Exchange (ETDEWEB)

    Makino, Debora Lika, E-mail:; Conti, Elena [Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried (Germany)


    The crystallographic steps towards the structure determination of a complete eukaryotic exosome complex bound to RNA are presented. Phasing of this 11-protein subunit complex was carried out via molecular replacement. The RNA exosome is an evolutionarily conserved multi-protein complex involved in the 3′ degradation of a variety of RNA transcripts. In the nucleus, the exosome participates in the maturation of structured RNAs, in the surveillance of pre-mRNAs and in the decay of a variety of noncoding transcripts. In the cytoplasm, the exosome degrades mRNAs in constitutive and regulated turnover pathways. Several structures of subcomplexes of eukaryotic exosomes or related prokaryotic exosome-like complexes are known, but how the complete assembly is organized to fulfil processive RNA degradation has been unclear. An atomic snapshot of a Saccharomyces cerevisiae 420 kDa exosome complex bound to an RNA substrate in the pre-cleavage state of a hydrolytic reaction has been determined. Here, the crystallographic steps towards the structural elucidation, which was carried out by molecular replacement, are presented.

  20. Oligomeric structure of a cathelicidin antimicrobial peptide in dodecylphosphocholine micelle determined by NMR spectroscopy. (United States)

    Saravanan, Rathi; Bhattacharjya, Surajit


    The broad spectrum of antibacterial activities of host defense cationic antimicrobial peptides (AMPs) arises from their ability to perturb membrane integrity of the microbes. The mechanisms are often thought to require assembly of AMPs on the membrane surface to form pores. However, three dimensional structures in the oligomeric form of AMPs in the context of lipid membranes are largely limited. Here, we demonstrate that a 22-residue antimicrobial peptide, termed VK22, derived from fowlicidin-1, a cathelicidin family of AMP from chicken oligomerizes into a predominantly tetrameric state in zwitterionic dodecylphosphocholine (DPC) micelles. An ensemble of NMR structures of VK22 determined in 200mM perdeuterated DPC, from 755 NOE constrains including 19 inter-helical NOEs, had revealed an assembly of four helices arranged in anti-parallel fashion. Hydrogen bonds, C(α)H-O=C types, and van der Waals interactions among the helical sub-units appear to be involved in the stabilization of the quaternary structures. The central region of the barrel shaped tetrameric bundle is non-polar with clusters of aromatic residues, whereas all the cationic residues are positioned at the termini. Paramagnetic spin labeled NMR experiments indicated that the tetrameric structure is embedded into micelles such that the non-polar region located inside the lipid acyl chains. Structure and micelle localization of a monomeric version, obtained from substitution of two Tyr residues with Ala, of the peptide is also compared. The mutated peptide VK22AA has been found be localized at the surface of the micelles. The tetrameric structure of VK22 delineates a small water pore that can be larger in the higher order oligomers. As these results provide structural insights, at atomic resolution, into the oligomeric states of a helical AMP in lipid environment, the structural details may be further utilized for the design of novel self-assembled membrane protein mimics.

  1. PREFACE: Structure and dynamics determined by neutron and x-ray scattering Structure and dynamics determined by neutron and x-ray scattering (United States)

    Müller-Buschbaum, Peter


    Neutron and x-ray scattering have emerged as powerful methods for the determination of structure and dynamics. Driven by emerging new, powerful neutron and synchrotron radiation sources, the continuous development of new instrumentation and novel scattering techniques gives rise to exciting possibilities. For example, in situ observations become possible via a high neutron or x-ray flux at the sample and, as a consequence, morphological transitions with small time constants can be detected. This special issue covers a broad range of different materials from soft to hard condensed matter. Hence, different material classes such as colloids, polymers, alloys, oxides and metals are addressed. The issue is dedicated to the 60th birthday of Professor Winfried Petry, scientific director of the Research Neutron Source Heinz Maier-Leibnitz (FRM-II), Germany, advisor at the physics department for the Bayerische Elite-Akademie, chair person of the Arbeitsgemeinschaft Metall- und Materialphysik of the German Physical Society (DPG) and a member of the professional council of the German Science Foundation (Deutsche Forschungsgemeinschaft, DFG). We would like to acknowledge and thank all contributors for their submissions, which made this special issue possible in the first place. Moreover, we would like to thank the staff at IOP Publishing for helping us with the administrative aspects and for coordinating the refereeing process, and Valeria Lauter for the beautiful cover artwork. Finally, to the readers, we hope that you find this special issue a valuable resource that provides insights into the present possibilities of neutron and x-ray scattering as powerful tools for the investigation of structure and dynamics. Structure and dynamics determined by neutron and x-ray scattering contents In situ studies of mass transport in liquid alloys by means of neutron radiography F Kargl, M Engelhardt, F Yang, H Weis, P Schmakat, B Schillinger, A Griesche and A Meyer Magnetic spin

  2. Determination of irradiation parameters for laser-induced periodic surface structures

    Energy Technology Data Exchange (ETDEWEB)

    Eichstaedt, J., E-mail: [University of Twente, Faculty of Engineering Technology, Chair of Applied Laser Technology, P.O. Box 217, Enschede, 7500 AE (Netherlands); Roemer, G.R.B.E. [University of Twente, Faculty of Engineering Technology, Chair of Applied Laser Technology, P.O. Box 217, Enschede, 7500 AE (Netherlands); Huis in ' t Veld, A.J. [University of Twente, Faculty of Engineering Technology, Chair of Applied Laser Technology, P.O. Box 217, Enschede, 7500 AE (Netherlands); TNO Technical Sciences, Mechatronics, Mechanics and Materials, De Rondom 1, Eindhoven, 5600 HE (Netherlands)


    Highlights: Black-Right-Pointing-Pointer We present an approach for the determination of irradiation parameters for laser-induced periodic surface structures. Black-Right-Pointing-Pointer The approach is based on accumulated fluence and consists of two steps. Black-Right-Pointing-Pointer (1) Determination of fluence domain boundaries and (2) approximation of irradiation parameters. Black-Right-Pointing-Pointer The approach is required to apply LIPSS for surface functionalization. Black-Right-Pointing-Pointer We provide experimental evidence that the accumulated fluence has a decisive role in the spatial emergence of LIPSS. - Abstract: The spatial emergence of laser-induced periodic surface structures (LIPSS) on single-crystalline silicon, upon irradiation with linearly polarized picosecond laser pulses (wavelength {lambda} = 1030 nm, pulse duration {tau} = 6.7 ps, pulse repetition frequency f{sub p} = 1 kHz) was studied theoretically and experimentally, under lateral displacement conditions. An experimental approach is presented for the determination of irradiation parameters of extended surface areas homogenously covered with LIPSS. The approach is based on accumulated fluence and consists of two steps, first the empirical determination of accumulated fluence domain boundaries and second the approximation of irradiation parameters. Such an approach is required for the application of LIPSS in the field of surface functionalization. The approach was successfully applied for structuring extended surface areas, which were homogenously covered with LIPSS. The areas, obtained by different irradiation parameter combinations, satisfying accumulated fluence boundary conditions, show the same type of LIPSS. This observation provides evidence, that the accumulated fluence has a decisive role in the spatial emergence of LIPSS. In the future, further experiments are required to verify the validity and boundaries of the approximations applied.

  3. Fine-scale habitat structure complexity determines insectivorous bird diversity in a tropical forest (United States)

    Castaño-Villa, Gabriel J.; Ramos-Valencia, Santiago A.; Fontúrbel, Francisco E.


    Habitat complexity in reforested stands has been acknowledged as a key factor that influences habitat use by birds, being especially critical for habitat disturbance-sensitive species such as tropical understory insectivorous birds. Most studies regarding the relationship between forest structure and species diversity were conducted at the landscape scale, but different diversity patterns may emerge at a finer scale (i.e., within a habitat patch). We examined a tropical reforested area (State of Caldas, Colombia), hypothesizing that insectivorous bird richness, abundance, and foraging guild abundance would increase as intra-habitat complexity increases. We established 40 monitoring plots within a reforested area, measured their structural features, and determined their relationships with species richness, total abundance, and foraging guild abundance, using Generalized Additive Models. We found that the increasing variation in basal area, stem diameter, and number of stems was positively correlated with species richness, total abundance, and foraging guild abundance. Relationships between richness or abundance and structural features were not lineal, but showing curvilinear responses and thresholds. Our results show that heterogeneity on basal area, stem diameter, and the number of stems was more correlated to insectivorous bird richness and abundance than the average of those structural features. Promoting structural variation on reforested areas by planting species with different growth rates may contribute to increase the richness and abundance of a tropical vulnerable group of species such as the understory insectivorous birds.

  4. Determination of the structure of P II protein from H. seropedicae

    Energy Technology Data Exchange (ETDEWEB)

    Benelli, M.; Souza, E.M.; Delboni, F.; Pedrosa, F.O. [Parana Univ., Curitiba, PR (Brazil). Dept. de Bioquimica; Buck, M. [Imperial Coll. of Science and Technology and Medicine, London (United Kingdom). Dept. of Biology; Moore, M.; Harper, A. [New York Univ., NY (United States). Dept. of Chemistry


    Full text. The P II protein, the product of the glnB gene is involved in a signal transducing cascade that controls nitrogen fixation in diazotrophs. The PII protein of H. seropedicae was over-produced in Escherichia coli RB9065 (glnB, glnD mutant), as PII-His from the plasmid pEMB101.7 and native PII from the plasmid pEMB101.8. Both plasmids yielded soluble proteins which were purified, the PII protein was crystallized and its structure solved at 3.0 A resolution by molecular replacement, using the E. coli PII structure as a model. The protein is a trimer and the monomer has a double bab motif. Comparison of the PII proteins of both organisms showed that the main structural difference was in the C-terminal. The T loop that contains the Tyr 51 residue was not visible in the H. seropedicae PII crystal structure. To determine the T loop structure and improve the resolution, the PII protein from H. seropedicae is being co-crystallized in the presence of small ligands, ATP and 2-ketoglutarate. (author)

  5. Functional analysis and structure determination of alkaline protease from Aspergillus flavus. (United States)

    Syed, Rabbani; Rani, Roja; Sabeena; Masoodi, Tariq Ahmad; Shafi, Gowher; Alharbi, Khalid


    Proteases are one of the highest value commercial enzymes as they have broad applications in food, pharmaceutical, detergent, and dairy industries and serve as vital tools in determination of structure of proteins and polypeptides. Multiple application of these enzymes stimulated interest to discover them with novel properties and considerable advancement of basic research into these enzymes. A broad understanding of the active site of the enzyme and of the mechanism of its inactivation is essential for delineating its structure-function relationship. Primary structure analysis of alkaline protease showed 42% of its content to be alpha helix making it stable for three dimensional structure modeling. Homology model of alkaline protease has been constructed using the X-ray structure (3F7O) as a template and swiss model as the workspace. The model was validated by ProSA, SAVES, PROCHECK, PROSAII and RMSD. The results showed the final refined model is reliable. It has 53% amino acid sequence identity with the template, 0.24 Å as RMSD and has -7.53 as Z-score, the Ramachandran plot analysis showed that conformations for 83.4 % of amino acid residues are within the most favored regions and only 0.4% in the disallowed regions.

  6. Determination of surface structure and the depth profile of silica glass by infrared spectroscopy

    Institute of Scientific and Technical Information of China (English)



    The surface structure and properties are different from those of the bulk, depending on the substrate materials and deposition condition, and playing an important role in precise optical components. The conventional spectroscopic methods to monitor the surface structure are restricted only in several layers of molecules. It is known that the penetration depth of the incident light increases with its wavelength and decreases with the angle of incidence. Thus infrared spectroscopy provides a powerful means for determination of surface structure and the depth profile up to micrometers. By recording the reflection spectra at different angles of incidence, the surface structure and its depth profile can be monitored successively. Further, the incident field has the subcomponents parallel and perpendicular to the surface, which excite the transverse and longitudinal optic modes, respectively. Change of the polarization direction of the incident light provides a practical function to study anisotropic property of the surface and the interaction between the transverse and longitudinal optic modes. In this work, infrared spectrophotometer was applied to investigate the depth profile in microstructure of silica glass. Combining with the glass fiber system, this technique can be used for in-situ control of the deposition process. In comparing with ellipsometry, this method reveals both structural and constitutional information.

  7. From X - rays to Biomolecular Structure: D. Hodgkin, R. Franklin and A. Yonath [Dos Raios - X à Estrutura Biomolecular: D. Hodgkin, R. Franklin e A. Yonath



    Following the discovery of X-rays by Wilhelm Röntgen and Max von Laue’s discovery of X-ray diffraction by crystals, William and Lawrence Bragg made it possible to calculate the positions of the atoms within a crystal from the way in which an X-ray beam is diffracted by a crystal lattice. Since then, several researchers have applied this powerful technique in the study of many molecules of life, such as proteins, vitamins and hormones. In this interdisciplinary field, two women played a very i...

  8. Determining

    Directory of Open Access Journals (Sweden)

    Bahram Andarzian


    Full Text Available Wheat production in the south of Khuzestan, Iran is constrained by heat stress for late sowing dates. For optimization of yield, sowing at the appropriate time to fit the cultivar maturity length and growing season is critical. Crop models could be used to determine optimum sowing window for a locality. The objectives of this study were to evaluate the Cropping System Model (CSM-CERES-Wheat for its ability to simulate growth, development, grain yield of wheat in the tropical regions of Iran, and to study the impact of different sowing dates on wheat performance. The genetic coefficients of cultivar Chamran were calibrated for the CSM-CERES-Wheat model and crop model performance was evaluated with experimental data. Wheat cultivar Chamran was sown on different dates, ranging from 5 November to 9 January during 5 years of field experiments that were conducted in the Khuzestan province, Iran, under full and deficit irrigation conditions. The model was run for 8 sowing dates starting on 25 October and repeated every 10 days until 5 January using long-term historical weather data from the Ahvaz, Behbehan, Dezful and Izeh locations. The seasonal analysis program of DSSAT was used to determine the optimum sowing window for different locations as well. Evaluation with the experimental data showed that performance of the model was reasonable as indicated by fairly accurate simulation of crop phenology, biomass accumulation and grain yield against measured data. The normalized RMSE were 3%, 2%, 11.8%, and 3.4% for anthesis date, maturity date, grain yield and biomass, respectively. Optimum sowing window was different among locations. It was opened and closed on 5 November and 5 December for Ahvaz; 5 November and 15 December for Behbehan and Dezful;and 1 November and 15 December for Izeh, respectively. CERES-Wheat model could be used as a tool to evaluate the effect of sowing date on wheat performance in Khuzestan conditions. Further model evaluations

  9. Determining upper mantle structures using gravity, seismology, and GIA modelling in Fennoscandia (United States)

    Root, B. C.; van der Wal, W.; Vermeersen, B. L. A.


    The 3D structure of the upper mantle plays a large role in Glacial Isostatic Adjustment (GIA). Finite-element software is able to model this 3D structure, but knowledge of the upper mantle is needed to make these models realistic. Nowadays, global maps are made of the crustal structure and temperature of the upper mantle from seismic observations. Also, satellite gravity missions, such as GOCE and GRACE, determine global gravity fields. Combining these data sets could give new insights in Glacial Isostatic Adjustment and explain some discrepancies seen in currents geological observations with 1D rheology Earth models. We obtain upper mantle models that fit gravity observations. Then, the upper mantle seismic velocities are converted to temperature profiles; that are used to determine the amount of strain according to diffusion and dislocation creep in the upper mantle. The obtained 3D rheology models are used in a finite element GIA model to observe the effect of the 3D structures during GIA. The GIA model results are compared to geological observations of the sea level change, GPS uplift rates, and ongoing gravity change in the area. This study specifically studies the effect of compositional differences in the upper mantle on the modelled remaining uplift and gravity signal. Molecular conversion relations for primitive mantle rock composition, Garnet Lherzolite rock composition, and Archon, iron depleted rock composition are used to compute the temperature and density profiles. The Fennoscandian lithosphere is believed to contain these three types of composition, yet, it is not yet known in what relative amounts and locations. An iterative approach is used to find the best compositional structure to fit the GIA observables in the Fenoscandian upper mantle.

  10. Techniques and tactics used in determining the structure of the trimeric ebolavirus glycoprotein

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Jeffrey E.; Fusco, Marnie L.; Abelson, Dafna M.; Hessell, Ann J.; Burton, Dennis R. [Department of Immunology and Microbial Science, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (United States); Saphire, Erica Ollmann, E-mail: [Department of Immunology and Microbial Science, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (United States); The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (United States)


    Here, the techniques, tactics and strategies used to overcome a series of technical roadblocks in crystallization and phasing of the trimeric ebolavirus glycoprotein are described. The trimeric membrane-anchored ebolavirus envelope glycoprotein (GP) is responsible for viral attachment, fusion and entry. Knowledge of its structure is important both for understanding ebolavirus entry and for the development of medical interventions. Crystal structures of viral glycoproteins, especially those in their metastable prefusion oligomeric states, can be difficult to achieve given the challenges in production, purification, crystallization and diffraction that are inherent in the heavily glycosylated flexible nature of these types of proteins. The crystal structure of ebolavirus GP in its trimeric prefusion conformation in complex with a human antibody derived from a survivor of the 1995 Kikwit outbreak has now been determined [Lee et al. (2008 ▶), Nature (London), 454, 177–182]. Here, the techniques, tactics and strategies used to overcome a series of technical roadblocks in crystallization and phasing are described. Glycoproteins were produced in human embryonic kidney 293T cells, which allowed rapid screening of constructs and expression of protein in milligram quantities. Complexes of GP with an antibody fragment (Fab) promoted crystallization and a series of deglycosylation strategies, including sugar mutants, enzymatic deglycosylation, insect-cell expression and glycan anabolic pathway inhibitors, were attempted to improve the weakly diffracting glycoprotein crystals. The signal-to-noise ratio of the search model for molecular replacement was improved by determining the structure of the uncomplexed Fab. Phase combination with Fab model phases and a selenium anomalous signal, followed by NCS-averaged density modification, resulted in a clear interpretable electron-density map. Model building was assisted by the use of B-value-sharpened electron-density maps and the

  11. Interpopulation Variation in Contour Feather Structure Is Environmentally Determined in Great Tits (United States)

    Broggi, Juli; Gamero, Anna; Hohtola, Esa; Orell, Markku; Nilsson, Jan-Åke


    Background The plumage of birds is important for flying, insulation and social communication. Contour feathers cover most of the avian body and among other functions they provide a critical insulation layer against heat loss. Feather structure and composition are known to vary among individuals, which in turn determines variation in the insulation properties of the feather. However, the extent and the proximate mechanisms underlying this variation remain unexplored. Methodology/Principal Findings We analyzed contour feather structure from two different great tit populations adapted to different winter regimes, one northern population in Oulu (Finland) and one southern population in Lund (Sweden). Great tits from the two populations differed significantly in feather structure. Birds from the northern population had a denser plumage but consisting of shorter feathers with a smaller proportion containing plumulaceous barbs, compared with conspecifics from the southern population. However, differences disappeared when birds originating from the two populations were raised and moulted in identical conditions in a common-garden experiment located in Oulu, under ad libitum nutritional conditions. All birds raised in the aviaries, including adult foster parents moulting in the same captive conditions, developed a similar feather structure. These feathers were different from that of wild birds in Oulu but similar to wild birds in Lund, the latter moulting in more benign conditions than those of Oulu. Conclusions/Significance Wild populations exposed to different conditions develop contour feather differences either due to plastic responses or constraints. Environmental conditions, such as nutrient availability during feather growth play a crucial role in determining such differences in plumage structure among populations. PMID:21949798

  12. Interpopulation variation in contour feather structure is environmentally determined in great tits.

    Directory of Open Access Journals (Sweden)

    Juli Broggi

    Full Text Available BACKGROUND: The plumage of birds is important for flying, insulation and social communication. Contour feathers cover most of the avian body and among other functions they provide a critical insulation layer against heat loss. Feather structure and composition are known to vary among individuals, which in turn determines variation in the insulation properties of the feather. However, the extent and the proximate mechanisms underlying this variation remain unexplored. METHODOLOGY/PRINCIPAL FINDINGS: We analyzed contour feather structure from two different great tit populations adapted to different winter regimes, one northern population in Oulu (Finland and one southern population in Lund (Sweden. Great tits from the two populations differed significantly in feather structure. Birds from the northern population had a denser plumage but consisting of shorter feathers with a smaller proportion containing plumulaceous barbs, compared with conspecifics from the southern population. However, differences disappeared when birds originating from the two populations were raised and moulted in identical conditions in a common-garden experiment located in Oulu, under ad libitum nutritional conditions. All birds raised in the aviaries, including adult foster parents moulting in the same captive conditions, developed a similar feather structure. These feathers were different from that of wild birds in Oulu but similar to wild birds in Lund, the latter moulting in more benign conditions than those of Oulu. CONCLUSIONS/SIGNIFICANCE: Wild populations exposed to different conditions develop contour feather differences either due to plastic responses or constraints. Environmental conditions, such as nutrient availability during feather growth play a crucial role in determining such differences in plumage structure among populations.

  13. Using entropy maximization to understand the determinants of structural dynamics beyond native contact topology.

    Directory of Open Access Journals (Sweden)

    Timothy R Lezon


    Full Text Available Comparison of elastic network model predictions with experimental data has provided important insights on the dominant role of the network of inter-residue contacts in defining the global dynamics of proteins. Most of these studies have focused on interpreting the mean-square fluctuations of residues, or deriving the most collective, or softest, modes of motions that are known to be insensitive to structural and energetic details. However, with increasing structural data, we are in a position to perform a more critical assessment of the structure-dynamics relations in proteins, and gain a deeper understanding of the major determinants of not only the mean-square fluctuations and lowest frequency modes, but the covariance or the cross-correlations between residue fluctuations and the shapes of higher modes. A systematic study of a large set of NMR-determined proteins is analyzed using a novel method based on entropy maximization to demonstrate that the next level of refinement in the elastic network model description of proteins ought to take into consideration properties such as contact order (or sequential separation between contacting residues and the secondary structure types of the interacting residues, whereas the types of amino acids do not play a critical role. Most importantly, an optimal description of observed cross-correlations requires the inclusion of destabilizing, as opposed to exclusively stabilizing, interactions, stipulating the functional significance of local frustration in imparting native-like dynamics. This study provides us with a deeper understanding of the structural basis of experimentally observed behavior, and opens the way to the development of more accurate models for exploring protein dynamics.

  14. Ultrafast colorimetric determination of predominant protein structure evolution with gold nanoplasmonic particles (United States)

    Kim, Hye Young; Choi, Inhee


    The intracellular and extracellular accumulation of disordered proteins and aggregated proteins occurs in many protein conformational diseases, such as aging-related neurodegeneration and alcoholic liver diseases. However, the conventional methods to study protein structural changes are limited for the rapid detection and monitoring of protein aggregation because of long incubation times (i.e., usually several days), complicated sample pretreatment steps, and expensive instrumentation. Here, we describe an ultrafast colorimetric method for the real-time monitoring of protein structure evolution and the determination of predominant structures via nanoparticle-assisted protein aggregation. During the aggregation process, nanoparticles act as nucleation cores, which form networks depending on the structures of the protein aggregates, and accelerate the kinetics of the protein aggregation. Simultaneously, these nanoparticles exhibit colorimetric responses according to their embedded shapes (e.g., fibrillar and amorphous) on the protein aggregates. We observed distinct spectral shifts and concomitant colorimetric responses of concentration- and type-dependent protein aggregation with the naked eye within a few minutes (pH levels, high temperature, and chemicals. These findings suggest that the proposed method is an easy way to study the molecular biophysics of protein aggregation and to rapidly screen anti-aggregation drugs for protein conformational diseases.The intracellular and extracellular accumulation of disordered proteins and aggregated proteins occurs in many protein conformational diseases, such as aging-related neurodegeneration and alcoholic liver diseases. However, the conventional methods to study protein structural changes are limited for the rapid detection and monitoring of protein aggregation because of long incubation times (i.e., usually several days), complicated sample pretreatment steps, and expensive instrumentation. Here, we describe an

  15. Polarized Raman spectroscopy unravels the biomolecular structural changes in cervical cancer (United States)

    Daniel, Amuthachelvi; Prakasarao, Aruna; Dornadula, Koteeswaran; Ganesan, Singaravelu


    Polarized Raman spectroscopy has emerged as a promising technique giving a wealth of information about the orientation and symmetry of bond vibrations in addition to the general chemical information from the conventional Raman spectroscopy. In this regard, polarized Raman Spectroscopic technique was employed to study the changes in the orientation of biomolecules in normal and cancerous conditions. This technique was compared to the conventional Raman spectroscopic technique and was found to yield additional information about the orientation of tyrosine, collagen and DNA. The statistically analyzed depolarization ratios by Linear Discriminant Analysis yielded better accuracy than the statistical results of conventional Raman spectroscopy. Thus, this study reveals that polarized Raman spectroscopy has better diagnostic potential than the conventional Raman spectroscopic technique.

  16. Self-chemisorption of azurin on functionalized oxide surfaces for the implementation of biomolecular devices

    Energy Technology Data Exchange (ETDEWEB)

    Biasco, A.; Maruccio, G.; Visconti, P.; Bramanti, A.; Calogiuri, P.; Cingolani, R.; Rinaldi, R


    In this work, we investigate the formation of redox protein Azurin (Az) monolayers on functionalized oxygen exposing surfaces. These metallo-proteins mediate electron transfer in the denitrifying chain of Pseudomonas bacteria and exhibit self-assembly properties, therefore they are good candidates for bio-electronic applications. Azurin monolayers are self-assembled onto silane functionalized surfaces and characterized by atomic force microscopy (AFM). We show also that a biomolecular field effect transistor (FET) in the solid state can be implemented by interconnecting an Azurin monolayer immobilized on SiO{sub 2} with two gold nanoelectrodes. Transport experiments, carried out at room temperature and ambient pressure, show FET behavior with conduction modulated by the gate potential.

  17. In situ characterization of nanoparticle biomolecular interactions in complex biological media by flow cytometry (United States)

    Lo Giudice, Maria Cristina; Herda, Luciana M.; Polo, Ester; Dawson, Kenneth A.


    Nanoparticles interacting with, or derived from, living organisms are almost invariably coated in a variety of biomolecules presented in complex biological milieu, which produce a bio-interface or `biomolecular corona' conferring a biological identity to the particle. Biomolecules at the surface of the nanoparticle-biomolecule complex present molecular fragments that may be recognized by receptors of cells or biological barriers, potentially engaging with different biological pathways. Here we demonstrate that using intense fluorescent reporter binders, in this case antibodies bound to quantum dots, we can map out the availability of such recognition fragments, allowing for a rapid and meaningful biological characterization. The application in microfluidic flow, in small detection volumes, with appropriate thresholding of the detection allows the study of even complex nanoparticles in realistic biological milieu, with the emerging prospect of making direct connection to conditions of cell level and in vivo experiments.

  18. Biomolecular Electrostatics Simulation by an FMM-based BEM on 512 GPUs

    CERN Document Server

    Yokota, Rio; Bardhan, Jaydeep P; Knepley, Matthew G; Barba, L A


    We present simulations of biomolecular electrostatics at a scale not reached before, thanks to both algorithmic and hardware acceleration. The algorithmic acceleration is achieved with the fast multipole method (FMM) in conjunction with a boundary element method (BEM) formulation of the continuum electrostatic model. The hardware acceleration is achieved through graphics processors, GPUs. We demonstrate the power of our algorithms and software for the calculation of the electrostatic interactions between biological molecules in solution. Computational experiments are presented simulating the electrostatics of protein--drug binding and several multi-million atom systems consisting of hundreds to thousands of copies of the problems, which models over 20 million atoms and has more than six billion unknowns, one iteration step requires only a few minutes on 512 GPU nodes. We achieved a sustained performance of 34.6TFlops for the entire BEM calculation. We are currently adapting our solver to model the linearized ...

  19. Towards local electromechanical probing of cellular and biomolecular systems in a liquid environment

    Energy Technology Data Exchange (ETDEWEB)

    Kalinin, Sergei V [Materials Sciences and Technology Division, Oak Ridge National Laboratory, Oak Ridge, TN 37931 (United States); Rodriguez, Brian J [Materials Sciences and Technology Division, Oak Ridge National Laboratory, Oak Ridge, TN 37931 (United States); Jesse, Stephen [Materials Sciences and Technology Division, Oak Ridge National Laboratory, Oak Ridge, TN 37931 (United States); Seal, Katyayani [Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37931 (United States); Proksch, Roger [Asylum Research, Santa Barbara, CA 93117 (United States); Hohlbauch, Sophia [Asylum Research, Santa Barbara, CA 93117 (United States); Revenko, Irene [Asylum Research, Santa Barbara, CA 93117 (United States); Thompson, Gary Lee [Department of Bioengineering, Clemson University, Clemson, SC 29634 (United States); Vertegel, Alexey A [Department of Bioengineering, Clemson University, Clemson, SC 29634 (United States)


    Electromechanical coupling is ubiquitous in biological systems, with examples ranging from simple piezoelectricity in calcified and connective tissues to voltage-gated ion channels, energy storage in mitochondria, and electromechanical activity in cardiac myocytes and outer hair cell stereocilia. Piezoresponse force microscopy (PFM) originally emerged as a technique to study electromechanical phenomena in ferroelectric materials, and in recent years has been employed to study a broad range of non-ferroelectric polar materials, including piezoelectric biomaterials. At the same time, the technique has been extended from ambient to liquid imaging on model ferroelectric systems. Here, we present results on local electromechanical probing of several model cellular and biomolecular systems, including insulin and lysozyme amyloid fibrils, breast adenocarcinoma cells, and bacteriorhodopsin in a liquid environment. The specific features of PFM operation in liquid are delineated and bottlenecks on the route towards nanometre-resolution electromechanical imaging of biological systems are identified.

  20. Biochemical Filter with Sigmoidal Response: Increasing the Complexity of Biomolecular Logic

    CERN Document Server

    Privman, Vladimir; Arugula, Mary A; Melnikov, Dmitriy; Bocharova, Vera; Katz, Evgeny


    The first realization of a designed, rather than natural, biochemical filter process is reported and analyzed as a promising network component for increasing the complexity of biomolecular logic systems. Key challenge in biochemical logic research has been achieving scalability for complex network designs. Various logic gates have been realized, but a "toolbox" of analog elements for interconnectivity and signal processing has remained elusive. Filters are important as network elements that allow control of noise in signal transmission and conversion. We report a versatile biochemical filtering mechanism designed to have sigmoidal response in combination with signal-conversion process. Horseradish peroxidase-catalyzed oxidation of chromogenic electron donor by hydrogen peroxide, was altered by adding ascorbate, allowing to selectively suppress the output signal, modifying the response from convex to sigmoidal. A kinetic model was developed for evaluation of the quality of filtering. The results offer improved...

  1. A Review of Salam Phase Transition in Protein Amino Acids Implication for Biomolecular Homochirality

    CERN Document Server

    Bai, F; Bai, Fan; Wang, Wenqing


    The origin of chirality, closely related to the evolution of life on the earth, has long been debated. In 1991, Abdus Salam suggested a novel approach to achieve biomolecular homochirality by a phase transition. In his subsequent publication, he predicted that this phase transition could eventually change D-amino acids to L-amino acids as C -H bond would break and H atom became a superconductive atom. Since many experiments denied the configuration change in amino acids, Salam hypothesis aroused suspicion. This paper is aimed to provide direct experimental evidence of a phase transition in alanine, valine single crystals but deny the configuration change of D- to L- enantiomers. New views on Salam phase transition are presented to revalidate its great importance in the origin of homochirality.

  2. Effect of temperature and magnetic field on the photocurrent response of biomolecular bulk-hetero junction (United States)

    Tajima, Hiroyuki; Sekiguchi, Yusuke; Matsuda, Masaki


    The photocurrent responses were investigated for the biomolecular bulk-hetero junction of chlorophyll α (Chl-α) and 1-(3-methoxycarbonyl)-propyl-1-phenyl-1-phenyl-(6,6)C61 (PCBM) in the temperature range between 300 K and 1.5 K under the magnetic field up to 8 T. The chopped-light photocurrent decreases on lowering the temperature. Below 10 K, photocurrent decrease was observed under the applied magnetic field. Decay of the photocurrent observed at 10 K was ascribed to the formation of the charged trap under light irradiation. The magnetic field effect (MFE) observed in this device was found to be very similar to that observed in P3HT:PCBM bulk-hetero junction at low temperatures.

  3. 3D structure determination of protein using TEM single particle analysis. (United States)

    Sato, Chikara; Mio, Kazuhiro; Kawata, Masaaki; Ogura, Toshihiko


    Proteins play important roles in cell functions such as enzymes, cell trafficking, neurotransmission, muscle contraction and hormone secretion. However, some proteins are very difficult to be crystallized and their structures are undetermined. Several techniques have been developed to elucidate the structure of macromolecules; X-ray or electron crystallography, nuclear magnetic resonance spectroscopy, and high-resolution electron microscopy. Among them, electron microscopy based single particle reconstruction (SPA) technique is a computer-aided structure determination method. This method reconstructs the 3D structure from projection images of dispersed protein. A large number of two-dimensional particle images are picked up from EM films, aligned and classified to generate 2D averages, and used to reconstruct the 3D structure by assigning the Euler angle of each 2D average. Due to the necessity of elaborate collaboration between the classical biology and the innovative information technology including parallel computing, scientists needed to break unseen barriers to get a start of this analysis. However, recent progresses in electron microscopes, mathematical algorithms, and computational abilities greatly reduced the height of barriers and expanded targets that are considered to be primarily addressable using single particle analysis. Membrane proteins are one of these targets to which the single particle analysis is successfully applied for the understanding of their 3D structures. For this purpose, we have developed various SPA methods [1-5] and applied them to different proteins [6-8].Here, we introduce reconstructed proteins, and discuss the availability of this technique. The intramembrane-cleaving proteases (I-CLiPs) that sever the transmembrane domains of their substrates have been identified in a range of organisms and play a variety of roles in biological conditions. I-CLiPs have been classified into three groups: serine-, aspartyl- and metalloprotease

  4. Structural determinants of phenotypic diversity and replication rate of human prions.

    Directory of Open Access Journals (Sweden)

    Jiri G Safar


    Full Text Available The infectious pathogen responsible for prion diseases is the misfolded, aggregated form of the prion protein, PrPSc. In contrast to recent progress in studies of laboratory rodent-adapted prions, current understanding of the molecular basis of human prion diseases and, especially, their vast phenotypic diversity is very limited. Here, we have purified proteinase resistant PrPSc aggregates from two major phenotypes of sporadic Creutzfeldt-Jakob disease (sCJD, determined their conformational stability and replication tempo in vitro, as well as characterized structural organization using recently emerged approaches based on hydrogen/deuterium (H/D exchange coupled with mass spectrometry. Our data clearly demonstrate that these phenotypically distant prions differ in a major way with regard to their structural organization, both at the level of the polypeptide backbone (as indicated by backbone amide H/D exchange data as well as the quaternary packing arrangements (as indicated by H/D exchange kinetics for histidine side chains. Furthermore, these data indicate that, in contrast to previous observations on yeast and some murine prion strains, the replication rate of sCJD prions is primarily determined not by conformational stability but by specific structural features that control the growth rate of prion protein aggregates.

  5. Versatile single-molecule multi-color excitation and detection fluorescence setup for studying biomolecular dynamics

    KAUST Repository

    Sobhy, M. A.


    Single-molecule fluorescence imaging is at the forefront of tools applied to study biomolecular dynamics both in vitro and in vivo. The ability of the single-molecule fluorescence microscope to conduct simultaneous multi-color excitation and detection is a key experimental feature that is under continuous development. In this paper, we describe in detail the design and the construction of a sophisticated and versatile multi-color excitation and emission fluorescence instrument for studying biomolecular dynamics at the single-molecule level. The setup is novel, economical and compact, where two inverted microscopes share a laser combiner module with six individual laser sources that extend from 400 to 640 nm. Nonetheless, each microscope can independently and in a flexible manner select the combinations, sequences, and intensities of the excitation wavelengths. This high flexibility is achieved by the replacement of conventional mechanical shutters with acousto-optic tunable filter (AOTF). The use of AOTF provides major advancement by controlling the intensities, duration, and selection of up to eight different wavelengths with microsecond alternation time in a transparent and easy manner for the end user. To our knowledge this is the first time AOTF is applied to wide-field total internal reflection fluorescence (TIRF) microscopy even though it has been commonly used in multi-wavelength confocal microscopy. The laser outputs from the combiner module are coupled to the microscopes by two sets of four single-mode optic fibers in order to allow for the optimization of the TIRF angle for each wavelength independently. The emission is split into two or four spectral channels to allow for the simultaneous detection of up to four different fluorophores of wide selection and using many possible excitation and photoactivation schemes. We demonstrate the performance of this new setup by conducting two-color alternating excitation single-molecule fluorescence resonance energy

  6. Mechanism for determining the ecology-economic activity of cluster structure

    Directory of Open Access Journals (Sweden)

    V.V. Gimpel


    Full Text Available The aim of the article. The purpose of the article is proposing methods for determining the components of vectors integral indicator of eco-economic activity of the cluster structure.The results of the analysis. The article offers the author's definition of the cluster of environmental and economic activity. Innovative cluster of ecological and economic activity in the development of the region (ICEEA is a form of interaction that connects businesses and organizations of different forms, which are oriented in their work on ecobalanced management decisions on an innovative basis for sustainable development. Advantages ICEEA is to produce competitive environmental products, to increase the export potential of the region, increasing the share of high technology and knowledge-intensive sectors of the economy, reducing demand for primary resources, the developing of green business and, as a consequence to increase the investment attractiveness of the region. For the ecological and economic evaluation of the enterprises activity within the cluster structure prompted the concept of level of environmental and economic activity cluster. The level of environmental and economic activity cluster refers to the degree of investment attractiveness of the region at different stages of cluster operation taking into account environmental, social, economic and environmental and economic factors. The sequence of ecological and economic evaluation of processes in the enterprises to determine the level of environmental and economic activity takes place in 13 stages. The article describes the key aspects of innovative regional development, namely clustering. The emphasis is on the mathematical evaluation model of ecological-economic activity in cluster formation and determination of integral indicator vectors of ecological and economic activity. The mathematical evaluation model of ecological-economic activity of cluster consists of four vectors: social, economic

  7. Structure determination and biochemical characterization of a putative HNH endonuclease from Geobacter metallireducens GS-15.

    Directory of Open Access Journals (Sweden)

    Shuang-yong Xu

    Full Text Available The crystal structure of a putative HNH endonuclease, Gmet_0936 protein from Geobacter metallireducens GS-15, has been determined at 2.6 Å resolution using single-wavelength anomalous dispersion method. The structure contains a two-stranded anti-parallel β-sheet that are surrounded by two helices on each face, and reveals a Zn ion bound in each monomer, coordinated by residues Cys38, Cys41, Cys73, and Cys76, which likely plays an important structural role in stabilizing the overall conformation. Structural homologs of Gmet_0936 include Hpy99I endonuclease, phage T4 endonuclease VII, and other HNH endonucleases, with these enzymes sharing 15-20% amino acid sequence identity. An overlay of Gmet_0936 and Hpy99I structures shows that most of the secondary structure elements, catalytic residues as well as the zinc binding site (zinc ribbon are conserved. However, Gmet_0936 lacks the N-terminal domain of Hpy99I, which mediates DNA binding as well as dimerization. Purified Gmet_0936 forms dimers in solution and a dimer of the protein is observed in the crystal, but with a different mode of dimerization as compared to Hpy99I. Gmet_0936 and its N77H variant show a weak DNA binding activity in a DNA mobility shift assay and a weak Mn²⁺-dependent nicking activity on supercoiled plasmids in low pH buffers. The preferred substrate appears to be acid and heat-treated DNA with AP sites, suggesting Gmet_0936 may be a DNA repair enzyme.

  8. Analysis of physicochemical and structural properties determining HIV-1 coreceptor usage.

    Directory of Open Access Journals (Sweden)

    Katarzyna Bozek

    Full Text Available The relationship of HIV tropism with disease progression and the recent development of CCR5-blocking drugs underscore the importance of monitoring virus coreceptor usage. As an alternative to costly phenotypic assays, computational methods aim at predicting virus tropism based on the sequence and structure of the V3 loop of the virus gp120 protein. Here we present a numerical descriptor of the V3 loop encoding its physicochemical and structural properties. The descriptor allows for structure-based prediction of HIV tropism and identification of properties of the V3 loop that are crucial for coreceptor usage. Use of the proposed descriptor for prediction results in a statistically significant improvement over the prediction based solely on V3 sequence with 3 percentage points improvement in AUC and 7 percentage points in sensitivity at the specificity of the 11/25 rule (95%. We additionally assessed the predictive power of the new method on clinically derived 'bulk' sequence data and obtained a statistically significant improvement in AUC of 3 percentage points over sequence-based prediction. Furthermore, we demonstrated the capacity of our method to predict therapy outcome by applying it to 53 samples from patients undergoing Maraviroc therapy. The analysis of structural features of the loop informative of tropism indicates the importance of two loop regions and their physicochemical properties. The regions are located on opposite strands of the loop stem and the respective features are predominantly charge-, hydrophobicity- and structure-related. These regions are in close proximity in the bound conformation of the loop potentially forming a site determinant for the coreceptor binding. The method is available via server under

  9. Structural determination of Bi-doped magnetite multifunctional nanoparticles for contrast imaging. (United States)

    Laguna-Marco, M A; Piquer, C; Roca, A G; Boada, R; Andrés-Vergés, M; Veintemillas-Verdaguer, S; Serna, C J; Iadecola, A; Chaboy, J


    To determine with precision how Bi atoms are distributed in Bi-doped iron oxide nanoparticles their structural characterization has been carried out by X-ray absorption spectroscopy (XAS) recorded at the K edge of Fe and at the L3 edge of Bi. The inorganic nanoparticles are nominally hybrid structures integrating an iron oxide core and a bismuth oxide shell. Fe K-edge XAS indicates the formation of a structurally ordered, non-stoichiometric magnetite (Fe3-δO4) phase for all the nanoparticles. The XAS spectra show that, in the samples synthesized by precipitation in aqueous media and laser pyrolysis, the Bi atoms neither enter into the iron oxide spinel lattice nor form any other mixed Bi-Fe oxides. No modification of the local structure around the Fe atoms induced by the Bi atoms is observed at the Fe K edge. In addition, contrary to expectations, our results indicate that the Bi atoms do not form a well-defined Bi oxide structure. The XAS study at the Bi L3 edge indicates that the environment around Bi atoms is highly disordered and only a first oxygen coordination shell is observed. Indefinite [BiO6-x(OH)x] units (isolated or aggregated forming tiny amorphous clusters) bonded through hydroxyl bridges to the nanoparticle, rather than a well defined Bi2O3 shell, surround the nanoparticle. On the other hand, the XAS study indicates that, in the samples synthesized by thermal decomposition, the Bi atoms are embedded in a longer range ordered structure showing the first and second neighbors.

  10. Structural insights into viral determinants of nematode mediated Grapevine fanleaf virus transmission.

    Directory of Open Access Journals (Sweden)

    Pascale Schellenberger


    Full Text Available Many animal and plant viruses rely on vectors for their transmission from host to host. Grapevine fanleaf virus (GFLV, a picorna-like virus from plants, is transmitted specifically by the ectoparasitic nematode Xiphinema index. The icosahedral capsid of GFLV, which consists of 60 identical coat protein subunits (CP, carries the determinants of this specificity. Here, we provide novel insight into GFLV transmission by nematodes through a comparative structural and functional analysis of two GFLV variants. We isolated a mutant GFLV strain (GFLV-TD poorly transmissible by nematodes, and showed that the transmission defect is due to a glycine to aspartate mutation at position 297 (Gly297Asp in the CP. We next determined the crystal structures of the wild-type GFLV strain F13 at 3.0 Å and of GFLV-TD at 2.7 Å resolution. The Gly297Asp mutation mapped to an exposed loop at the outer surface of the capsid and did not affect the conformation of the assembled capsid, nor of individual CP molecules. The loop is part of a positively charged pocket that includes a previously identified determinant of transmission. We propose that this pocket is a ligand-binding site with essential function in GFLV transmission by X. index. Our data suggest that perturbation of the electrostatic landscape of this pocket affects the interaction of the virion with specific receptors of the nematode's feeding apparatus, and thereby severely diminishes its transmission efficiency. These data provide a first structural insight into the interactions between a plant virus and a nematode vector.

  11. Specificity determinants in phosphoinositide dephosphorylation: crystal structure of an archetypal inositol polyphosphate 5-phosphatase. (United States)

    Tsujishita, Y; Guo, S; Stolz, L E; York, J D; Hurley, J H


    Inositol polyphosphate 5-phosphatases are central to intracellular processes ranging from membrane trafficking to Ca(2+) signaling, and defects in this activity result in the human disease Lowe syndrome. The 1.8 resolution structure of the inositol polyphosphate 5-phosphatase domain of SPsynaptojanin bound to Ca(2+) and inositol (1,4)-bisphosphate reveals a fold and an active site His and Asp pair resembling those of several Mg(2+)-dependent nucleases. Additional loops mediate specific inositol polyphosphate contacts. The 4-phosphate of inositol (1,4)-bisphosphate is misoriented by 4.6 compared to the reactive geometry observed in the apurinic/apyrimidinic endonuclease 1, explaining the dephosphorylation site selectivity of the 5-phosphatases. Based on the structure, a series of mutants are described that exhibit altered substrate specificity providing general determinants for substrate recognition.

  12. Crystal structure of thermostable catechol 2,3-dioxygenase determined by multiwavelength anomalous dispersion method

    Institute of Scientific and Technical Information of China (English)


    The selenomethionyl derivative of the thermostable catechol 2,3-dioxygenase (SeMet-TC23O) is expressed,purified and crystallized. By using multiwave length anomalous dispersion (MAD) phasing techniques, the crystal structure of TC23O at 0.3 nm resolutions is determined.TC23O is a homotetramer. Each monomer is composed of N-terminal and C-terminal domains (residues 1~153 and 153~319, respectively). The two domains are proximately symmetric by a non-crystallographic axis. Each domain contains two characteristic motifs which are found in almost all of extradial dioxygenases.Kevwords: multiwavelength anomalous dispersion (MAD), X-ray diffraction, thermostable catechol 2,3-dioxygenase, crystal structure,synchrotron light source.

  13. Determining the structure of dark-matter couplings at the LHC

    CERN Document Server

    Haisch, Ulrich; Re, Emanuele


    The latest LHC mono-jet searches place stringent bounds on the pp -> chibar chi cross section of dark matter. Further properties such as the dark matter mass or the precise structure of the interactions between dark matter and the standard model can however not be determined in this manner. We point out that measurements of the azimuthal angle correlations between the two jets in 2 j + chibar chi events may be used to disentangle whether dark matter pair production proceeds dominantly through tree or loop diagrams. Our general observation is illustrated by considering theories in which dark matter interacts predominantly with the top quark. We show explicitly that in this case the jet-jet azimuthal angle difference is a gold-plated observable to probe the Lorentz structure of the couplings of dark matter to top quarks, thus testing the CP nature of the particle mediating these interactions.

  14. Determination of structure tilting in magnetized plasmas—Time delay estimation in two dimensions

    Energy Technology Data Exchange (ETDEWEB)

    Guszejnov, Dávid [Department of Nuclear Techniques, Budapest University of Technology and Economics, Association EURATOM, Műegyetem rkp. 9., H-1111 Budapest (Hungary); Bencze, Attila; Zoletnik, Sándor [MTA Wigner RCP, EURATOM Association, PO Box 49, H-1525 Budapest (Hungary); Krämer-Flecken, Andreas [Institute of Energy and Climate Research-Plasma Physics, Forschungszentrum Jülich, Association EURATOM-FZJ, D-52425 Jülich (Germany)


    Time delay estimation (TDE) is a well-known technique to investigate poloidal flows in fusion plasmas. The present work is an extension of the earlier works of Bencze and Zoletnik [Phys. Plasmas 12, 052323 (2005)] and Tal et al.[Phys. Plasmas 18, 122304 (2011)]. From the prospective of the comparison of theory and experiment, it seems to be important to estimate the statistical properties of the TDE based on solid mathematical groundings. This paper provides analytic derivation of the variance of the TDE using a two-dimensional model for coherent turbulent structures in the plasma edge and also gives an explicit method for determination of the tilt angle of structures. As a demonstration, this method is then applied to the results of a quasi-2D Beam Emission Spectroscopy measurement performed at the TEXTOR tokamak.

  15. Determination of structure tilting in magnetized plasmas - Time delay estimation in two dimensions

    CERN Document Server

    Guszejnov, Dávid; Zoletnik, Sándor; Andreas-Krämer-Flecken,


    Time delay estimation (TDE) is a well-known technique to investigate poloidal flows in fusion plasmas. The present work is an extension of the earlier works of A. Bencze and S. Zoletnik 2005 and B. T\\'al et al. 2011. From the prospective of the comparison of theory and experiment it seem to be important to estimate the statistical properties of the TDE based on solid mathematical groundings. This paper provides analytic derivation of the variance of the TDE using a two-dimensional model for coherent turbulent structures in the plasma edge and also gives an explicit method for determination of the tilt angle of structures. As a demonstration this method is then applied to the results of a quasi-2D Beam Emission Spectroscopy (BES) measurement performed at the TEXTOR tokamak.

  16. Structural and enzymatic characterization of a host-specificity determinant from Salmonella

    Energy Technology Data Exchange (ETDEWEB)

    Kohler, Amanda C. [Rockefeller University, New York, NY 10065 (United States); Spanò, Stefania; Galán, Jorge E. [Yale University School of Medicine, New Haven, CT 06536 (United States); Stebbins, C. Erec, E-mail: [Rockefeller University, New York, NY 10065 (United States)


    The Salmonella effector protein GtgE functions as a cysteine protease to cleave a subset of the Rab-family GTPases and to prevent delivery of antimicrobial agents to the Salmonella-containing vacuole. GtgE is an effector protein from Salmonella Typhimurium that modulates trafficking of the Salmonella-containing vacuole. It exerts its function by cleaving the Rab-family GTPases Rab29, Rab32 and Rab38, thereby preventing the delivery of antimicrobial factors to the bacteria-containing vacuole. Here, the crystal structure of GtgE at 1.65 Å resolution is presented, and structure-based mutagenesis and in vivo infection assays are used to identify its catalytic triad. A panel of cysteine protease inhibitors were examined and it was determined that N-ethylmaleimide, antipain and chymostatin inhibit GtgE activity in vitro. These findings provide the basis for the development of novel therapeutic strategies to combat Salmonella infections.

  17. Aggregate size and structure determination of nanomaterials in physiological media: importance of dynamic evolution (United States)

    Afrooz, A. R. M. Nabiul; Hussain, Saber M.; Saleh, Navid B.


    Most in vitro nanotoxicological assays are performed after 24 h exposure. However, in determining size and shape effect of nanoparticles in toxicity assays, initial characterization data are generally used to describe experimental outcome. The dynamic size and structure of aggregates are typically ignored in these studies. This brief communication reports dynamic evolution of aggregation characteristics of gold nanoparticles. The study finds that gradual increase in aggregate size of gold nanospheres (AuNS) occurs up to 6 h duration; beyond this time period, the aggregation process deviates from gradual to a more abrupt behavior as large networks are formed. Results of the study also show that aggregated clusters possess unique structural conformation depending on nominal diameter of the nanoparticles. The differences in fractal dimensions of the AuNS samples likely occurred due to geometric differences, causing larger packing propensities for smaller sized particles. Both such observations can have profound influence on dosimetry for in vitro nanotoxicity analyses.

  18. Crystal structure of nitarsone determined from synchrotron X-ray powder diffraction data (United States)

    van der Lee, A.; Richez, P.; Tapiero, C.


    The crystal structure of nitarsone, 4-nitrophenylarsonic acid, a substitute for nifursol and dimetridazole in the prevention and treatment of turkey histomoniasis desease, has been determined from synchrotron X-ray powder diffraction data. Nitarsone crystallizes in the monoclinic space group P2 1/ n with unit cell parameters a=7.46413(5), b=25.68543(17), c=4.657388(32) Å, β=105.4670(5)°. The structure was solved using simulated annealing techniques by treating the molecule as a rigid body for which the configuration resulting from an energy minimization was used in slightly adapted form. Structure refinement treated the NO 2 and the AsO(OH) 2 groups as free groups, leading to final confidence factors Rp=0.059 and Rwp=0.071. The crystal structure contains 4 molecules per unit cell that are hydrogen bonded to form infinite chains of dimers running along the c-axis. Nitarsone's low toxicity when compared with inorganic sources of arsenic is explained by the existence of a partial double C-As bond (1.866(5) Å) which confers greater stability so that under physiological conditions nitarsone is not converted to mineral-like As V or III.

  19. An evolutionary game approach for determination of the structural conflicts in signed networks (United States)

    Tan, Shaolin; Lü, Jinhu


    Social or biochemical networks can often divide into two opposite alliances in response to structural conflicts between positive (friendly, activating) and negative (hostile, inhibiting) interactions. Yet, the underlying dynamics on how the opposite alliances are spontaneously formed to minimize the structural conflicts is still unclear. Here, we demonstrate that evolutionary game dynamics provides a felicitous possible tool to characterize the evolution and formation of alliances in signed networks. Indeed, an evolutionary game dynamics on signed networks is proposed such that each node can adaptively adjust its choice of alliances to maximize its own fitness, which yet leads to a minimization of the structural conflicts in the entire network. Numerical experiments show that the evolutionary game approach is universally efficient in quality and speed to find optimal solutions for all undirected or directed, unweighted or weighted signed networks. Moreover, the evolutionary game approach is inherently distributed. These characteristics thus suggest the evolutionary game dynamic approach as a feasible and effective tool for determining the structural conflicts in large-scale on-line signed networks.

  20. Identification of selectivity determinants in CYP monooxygenases by modelling and systematic analysis of sequence and structure. (United States)

    Seifert, Alexander; Pleiss, Jurgen


    Cytochrome P450 monooxygenases (CYPs) form a large, ubiquitous enzyme family and are of great interest in red and white biotechnology. To investigate the effect of protein structure on selectivity, the binding of substrate molecules near to the active site was modelled by molecular dynamics simulations. From a comprehensive and systematic comparison of more than 6300 CYP sequences and 31 structures using the Cytochrome P450 Engineering Database (CYPED), residues were identified which are predicted to point close to the heme centre and thus restrict accessibility for substrates. As a result, sequence-structure-function relationships are described that can be used to predict selectivity-determining positions from CYP sequences and structures. Based on this analysis, a minimal library consisting of bacterial CYP102A1 (P450(BM3)) and 24 variants was constructed. All variants were functionally expressed in E. coli, and the library was screened with four terpene substrates. Only 3 variants showed no activity towards all 4 terpenes, while 11 variants demonstrated either a strong shift or improved regio- or stereoselectivity during oxidation of at least one substrate as compared to CYP102A1 wild type. The minimal library also contains variants that show interesting side products which are not generated by the wild type enzyme. By two additional rounds of molecular modelling, diversification, and screening, the selectivity of one of these variants for a new product was optimised with a minimal screening effort. We propose this as a generic approach for other CYP substrates.

  1. Structure of the organic crystallite unit in coal as determined by X-ray diffraction

    Institute of Scientific and Technical Information of China (English)

    Song Dangyu; Yang Cunbei; Zhang Xiaokui; Su Xianbo; Zhang Xiaodong


    X-ray diffraction (XRD) was used to study the structure of the organic crystallite unit (La,Lc,d002) in coals collected from Henan and Shanxi Provinces,XRD patterns of coal were collected in a step-scan mode (0.1 °/step) over an angular range of 2-90° (2θ),allowing 8 s at each step.The structure of the crystallite unit was determined from the Scherrer equation and peak parameters deduced from whole pattern fitting.The results show that the structure of the crystallite unit in coal is mainly controlled by the coal rank.As the coal rank increases the average diameter of a coal crystallite unit (La) increases,the interlayer spacing (d002) decreases slightly,and the average height of a coal crystallite unit (Lc) increases at first but then decreases.A new diffraction peak from the crystallite unit in coal was found at a low scattering angle in the XRD pattern (2-10°).This suggests a structure with an inter-layer spacing from 1.9 to 2.8 nm exists in coal crystallites.

  2. Tutorial for Collecting and Processing Images of Composite Structures to Determine the Fiber Volume Fraction (United States)

    Conklin, Lindsey


    Fiber-reinforced composite structures have become more common in aerospace components due to their light weight and structural efficiency. In general, the strength and stiffness of a composite structure are directly related to the fiber volume fraction, which is defined as the fraction of fiber volume to total volume of the composite. The most common method to measure the fiber volume fraction is acid digestion, which is a useful method when the total weight of the composite, the fiber weight, and the total weight can easily be obtained. However, acid digestion is a destructive test, so the material will no longer be available for additional characterization. Acid digestion can also be difficult to machine out specific components of a composite structure with complex geometries. These disadvantages of acid digestion led the author to develop a method to calculate the fiber volume fraction. The developed method uses optical microscopy to calculate the fiber area fraction based on images of the cross section of the composite. The fiber area fraction and fiber volume fraction are understood to be the same, based on the assumption that the shape and size of the fibers are consistent in the depth of the composite. This tutorial explains the developed method for optically determining fiber area fraction performed at NASA Langley Research Center.

  3. Strain-Based Damage Determination Using Finite Element Analysis for Structural Health Management (United States)

    Hochhalter, Jacob D.; Krishnamurthy, Thiagaraja; Aguilo, Miguel A.


    A damage determination method is presented that relies on in-service strain sensor measurements. The method employs a gradient-based optimization procedure combined with the finite element method for solution to the forward problem. It is demonstrated that strains, measured at a limited number of sensors, can be used to accurately determine the location, size, and orientation of damage. Numerical examples are presented to demonstrate the general procedure. This work is motivated by the need to provide structural health management systems with a real-time damage characterization. The damage cases investigated herein are characteristic of point-source damage, which can attain critical size during flight. The procedure described can be used to provide prognosis tools with the current damage configuration.

  4. Uncertainties in the use of periodate oxidation for determination of dextran structure. (United States)

    Leonard, G J


    A glucan of high molecular weight isolated from stale sugar-cane, and previously shown to have a marked effect on sucrose crystallisation processes-1, is a relatively linear dextran. Approximately 96-97% of its D-glucose residues are involved in (1 yields 6)-alpha-D linkages and constitute the linear backbone of the polymer. The remaining 3-4% of D-glucose residues form branch-points by (1 yields 3)-alpha-D linkages. The periodate-oxidation technique, which has been extensively used by other workers to determine dextran structure, gave erroneous results when applied to the dextran from stale sugar-cane.

  5. The Three-Dimensional Spatial Structure of Cirrus Clouds Determined from Lidar Satellite Observations (United States)

    Eloranta, E. W.; Wylie, D.; Wolf, W.


    Simultaneous imagery from the University of Wisconsin Volume Imaging Lidar (VIL) and meteorological satellites were used to quantify the spatial structure of cirrus clouds with 60 m resolution. This data was used to determine the spatial distributions of cloud base altitude, cloud top altitude, and mid-cloud altitude. Two dimensional auto-correlation functions describing the mean shape of cirrus clouds were computed. Because cirrus clouds seldom have distinct edges, these correlation functions are derived as a function of a threshold value which defines the cloud edge.

  6. Structural Determinants Responsible for Substrate Recognition and Mode of Action in Family 11 Polysaccharide Lyases*


    Ochiai, Akihito; Itoh, Takafumi; Mikami, Bunzo; Hashimoto, Wataru; Murata, Kousaku


    A saprophytic Bacillus subtilis secretes two types of rhamnogalacturonan (RG) lyases, endotype YesW and exotype YesX, which are responsible for an initial cleavage of the RG type I (RG-I) region of plant cell wall pectin. Polysaccharide lyase family 11 YesW and YesX with a significant sequence identity (67.8%) cleave glycoside bonds between rhamnose and galacturonic acid residues in RG-I through a β-elimination reaction. Here we show the structural determinants for sub...

  7. Determining optimal pattern sequences for three-dimensional structured light sensory systems. (United States)

    Marin, Veronica E; Nejat, Goldie


    Structured light (SL) techniques are used for three-dimensional (3D) measurements of objects in a wide variety of applications. SL-based sensory systems obtain the 3D surface profile of an object from the deformation of light patterns projected onto the object of interest. The number of fringes used in the projected light patterns has a direct effect on the 3D reconstruction errors. This paper presents a novel methodology for determining the optimal sequence of multi-fringe patterns that minimizes reconstruction errors caused by random noise. Experiments conducted with a variety of objects as well as a comparison study demonstrate the effectiveness of the proposed methodology.

  8. Synthesis and crystal structure determination of Br2SeIBr polyhalogen–chalcogen

    Indian Academy of Sciences (India)

    A A Alemi; E Solaimani


    In this paper polyhalogen–chalcogen Br2SeIBr was synthesized and the crystal structure was determined by single crystal X-ray diffraction method. This compound was prepared in the temperature range 150–50°C which was brownish-red in colour and crystallized in monoclinic crystal system and space group 21/c with four molecules per unit cell. Lattice parameters were: = 6.3711(1), = 6.7522(2), = 16.8850(5) Å, = = 90°, = 95·96°, = 722·45 Å3.

  9. Direct determination of the lamellar structure of peripheral nerve myelin at low resolution (17 A). (United States)

    McIntosh, T J; Worthington, C R


    New X-ray diffraction data from normal nerve and nerve swollen in glycerol solutions have been recorded. Direct methods of structure analysis have been used in the interpretation of the X-ray data, and the phases of the first five orders of diffraction of peripheral nerve myelin have been uniquely determined. The direct methods include deconvolution of the autocorrelation function, sampling theorem reconstructions, and Fourier synthesis comparisons. Electron density profiles of normal and swollen nerve myelin at a resolution of 17 A together with an electron density scale in electrons per cubic angstrom are presented.

  10. Socialist and postsocialist land-use legacies determine farm woodland composition and structure

    DEFF Research Database (Denmark)

    Plieninger, Tobias; Schaich, H.


    European agroecosystems host a variety of farm woodlands that act as primary determinants of biodiversity and ecosystem services. While woodland areas have been in decline worldwide, they have regionally increased, for example, in Eastern Germany. This study performs a quantitative and spatially ...... and structure of presocialist woodlands. We argue that forest conservation planning should actively consider land-use legacies, which are of particular relevance in the landscapes of Central and Eastern Europe, as these have undergone multiple, abrupt, and severe land-use transitions....

  11. Site specific incorporation of heavy atom-containing unnatural amino acids into proteins for structure determination (United States)

    Xie, Jianming; Wang, Lei; Wu, Ning; Schultz, Peter G.


    Translation systems and other compositions including orthogonal aminoacyl tRNA-synthetases that preferentially charge an orthogonal tRNA with an iodinated or brominated amino acid are provided. Nucleic acids encoding such synthetases are also described, as are methods and kits for producing proteins including heavy atom-containing amino acids, e.g., brominated or iodinated amino acids. Methods of determining the structure of a protein, e.g., a protein into which a heavy atom has been site-specifically incorporated through use of an orthogonal tRNA/aminoacyl tRNA-synthetase pair, are also described.

  12. A simple structural power method for determining the vibratory strength of machinery sources

    DEFF Research Database (Denmark)

    Ohlrich, Mogens


    A new simple characterisation of the vibrational source strength of multi-terminal machinery is formulated in terms of a total terminal source power. This single power spectrum is determined from a summation of pairs of mean square velocities and point mobilities of the machine feet. The method...... is tested experimentally for two practical source-receiver configurations. The results clearly demonstrate the simplicity of the method and its high potential for engineering evaluation of machinery source strength and for coarse prediction of power transmission to supporting structures. In principle...

  13. Determination of households fish consumption structure and purchase behaviors in urban areas of Van

    Directory of Open Access Journals (Sweden)

    Mustafa Terin


    Full Text Available This study has been carried out to determine the household fish consumption structure and purchase behaviors in urban areas of Van Province. The main data of this study has been compiled through questionnaires from 260 households. In the analysis of the data, frequency tables, chi-square independence test were used and the relationships between the quantity of fish consumption of the households and some socio–demographic categorical variables have been examined through f and t tests. It has been determined that 89.2 % of the participating households consume fish while 10.8 % do not. Nearly a third (35.7 % of the households that do not consume fish do so for the smell of the fish. 84.1 % of the households consume fish in winter. 87.2 % consume fresh fish while 40 % consume fish by frying. Mostly preferred fish are anchovy, trout and tarek respectively. It has been determined that the amounts of fish consumption per month per household and per person are 6.3 kg and 1.4 kg respectively. It has also been determined that households with children, employed head and owning the house consume more fish than those households without children, unemployed head and tenants.

  14. Determining both surface position and orientation in structured-light-based sensing. (United States)

    Song, Zhan; Chung, Chi-Kit Ronald


    Position and orientation profiles are two principal descriptions of shape in space. We describe how a structured light system, coupled with the illumination of a pseudorandom pattern and a suitable choice of feature points, can allow not only the position but also the orientation of individual surface elements to be determined independently. Unlike traditional designs which use the centroids of the illuminated pattern elements as the feature points, the proposed design uses the grid points between the pattern elements instead. The grid points have the essences that their positions in the image data are inert to the effect of perspective distortion, their individual extractions are not directly dependent on one another, and the grid points possess strong symmetry that can be exploited for their precise localization in the image data. Most importantly, the grid lines of the illuminated pattern that form the grid points can aid in determining surface normals. In this paper, we describe how each of the grid points can be labeled with a unique color code, what symmetry they possess and how the symmetry can be exploited for their precise localization at subpixel accuracy in the image data, and how 3D orientation in addition to 3D position can be determined at each of them. Both the position and orientation profiles can be determined with only a single pattern illumination and a single image capture.

  15. Structure of Csd3 from Helicobacter pylori, a cell shape-determining metallopeptidase

    Energy Technology Data Exchange (ETDEWEB)

    An, Doo Ri [Seoul National University, Seoul 151-742 (Korea, Republic of); Kim, Hyoun Sook [Seoul National University, Seoul 151-742 (Korea, Republic of); Seoul National University, Seoul 151 742 (Korea, Republic of); Kim, Jieun; Im, Ha Na; Yoon, Hye Jin; Yoon, Ji Young; Jang, Jun Young [Seoul National University, Seoul 151-742 (Korea, Republic of); Hesek, Dusan; Lee, Mijoon; Mobashery, Shahriar [University of Notre Dame, Notre Dame, IN 46556 (United States); Kim, Soon-Jong [Mokpo National University, Chonnam 534-729 (Korea, Republic of); Lee, Byung Il [National Cancer Center, Gyeonggi 410-769 (Korea, Republic of); Suh, Se Won, E-mail: [Seoul National University, Seoul 151-742 (Korea, Republic of); Seoul National University, Seoul 151-742 (Korea, Republic of)


    H. pylori Csd3 (HP0506), together with other peptidoglycan hydrolases, plays an important role in determining cell shape. Its crystal structure in the latent state is reported. Helicobacter pylori is associated with various gastrointestinal diseases such as gastritis, ulcers and gastric cancer. Its colonization of the human gastric mucosa requires high motility, which depends on its helical cell shape. Seven cell shape-determining genes (csd1, csd2, csd3/hdpA, ccmA, csd4, csd5 and csd6) have been identified in H. pylori. Their proteins play key roles in determining the cell shape through modifications of the cell-wall peptidoglycan by the alteration of cross-linking or by the trimming of peptidoglycan muropeptides. Among them, Csd3 (also known as HdpA) is a bifunctional enzyme. Its d, d-endopeptidase activity cleaves the d-Ala{sup 4}-mDAP{sup 3} peptide bond between cross-linked muramyl tetrapeptides and pentapeptides. It is also a d, d-carboxypeptidase that cleaves off the terminal d-Ala{sup 5} from the muramyl pentapeptide. Here, the crystal structure of this protein has been determined, revealing the organization of its three domains in a latent and inactive state. The N-terminal domain 1 and the core of domain 2 share the same fold despite a very low level of sequence identity, and their surface-charge distributions are different. The C-terminal LytM domain contains the catalytic site with a Zn{sup 2+} ion, like the similar domains of other M23 metallopeptidases. Domain 1 occludes the active site of the LytM domain. The core of domain 2 is held against the LytM domain by the C-terminal tail region that protrudes from the LytM domain.

  16. Determination of the structure of thiol-specific antioxidant (Tsa 2) of Saccharomyces cerevisiae

    Energy Technology Data Exchange (ETDEWEB)

    Breyer, C.A. [Universidade Federal de Sao Carlos (UFSCar), SP (Brazil); Oliveira, M.A. [Universidade Estadual Paulista Julio de Mesquita Fillho (UNESP), Assis, SP (Brazil)


    Full text: The peroxiredoxin (Prx), is a group of antioxidant proteins that have been widely studied for its role in the decomposition of several species of peroxides such as hydrogen peroxide, peroxynitrite and organic hydroperoxides using two highly reactive cysteines, named cysteine peroxidatic (Cys{sub P} ) and resolve cysteine (Cys{sub R}), present in the active site. In Saccharomyces cerevisiae were identified five Prx isoforms, three cytosolic (Tsa1, Tsa2 and Ahp1), a mitochondrial (mTPx) and a nu- clear one (nTPx). Tsa1 and Tsa2 are homodimers that in heat shock or oxidative stress form complex structures of high molecular-weight with chaperone function. These proteins are very similar (86% identity and 96% similarity) but despite this structural similarity it has been shown that they present different functions: Tsa1 is mainly involved in the response to oxidative stress while Tsa2 is involved in signal transduction. Tsa1 was already crystallized and a structural model was generated, but Tsa2 structural studies were not performed. The research goal is the determination of the structure of Tsa2. The initial screening experiments of crystallization using the kits CS1 and CS2 (Hampton Research) showed favorable results when the conditions were 0,1M sodium acetate trihydrate pH 4.6 and 8% polyethylene glycol 4000. To improve our results the crystallization condition is been refined using variations of pH and concentration of polyethylene glycol 4000. We believe that the results of this study may contribute significantly to the understanding of the formation of over oxidized forms and cellular functions of Tsa2. (author)

  17. Disulfide Trapping for Modeling and Structure Determination of Receptor:Chemokine Complexes (United States)

    Kufareva, Irina; Gustavsson, Martin; Holden, Lauren G.; Qin, Ling; Zheng, Yi; Handel, Tracy M.


    Despite the recent breakthrough advances in GPCR crystallography, structure determination of protein-protein complexes involving chemokine receptors and their endogenous chemokine ligands remains challenging. Here we describe disulfide trapping, a methodology for generating irreversible covalent binary protein complexes from unbound protein partners by introducing two cysteine residues, one per interaction partner, at selected positions within their interaction interface. Disulfide trapping can serve at least two distinct purposes: (i) stabilization of the complex to assist structural studies, and/or (ii) determination of pairwise residue proximities to guide molecular modeling. Methods for characterization of disulfide-trapped complexes are described and evaluated in terms of throughput, sensitivity, and specificity towards the most energetically favorable cross-links. Due to abundance of native disulfide bonds at receptor:chemokine interfaces, disulfide trapping of their complexes can be associated with intramolecular disulfide shuffling and result in misfolding of the component proteins; because of this, evidence from several experiments is typically needed to firmly establish a positive disulfide crosslink. An optimal pipeline that maximizes throughput and minimizes time and costs by early triage of unsuccessful candidate constructs is proposed. PMID:26921956

  18. Structural determinants of protein partitioning into ordered membrane domains and lipid rafts. (United States)

    Lorent, Joseph Helmuth; Levental, Ilya


    Increasing evidence supports the existence of lateral nanoscopic lipid domains in plasma membranes, known as lipid rafts. These domains preferentially recruit membrane proteins and lipids to facilitate their interactions and thereby regulate transmembrane signaling and cellular homeostasis. The functionality of raft domains is intrinsically dependent on their selectivity for specific membrane components; however, while the physicochemical determinants of raft association for lipids are known, very few systematic studies have focused on the structural aspects that guide raft partitioning of proteins. In this review, we describe biophysical and thermodynamic aspects of raft-mimetic liquid ordered phases, focusing on those most relevant for protein partitioning. Further, we detail the variety of experimental models used to study protein-raft interactions. Finally, we review the existing literature on mechanisms for raft targeting, including lipid post-translational modifications, lipid binding, and transmembrane domain features. We conclude that while protein palmitoylation is a clear raft-targeting signal, few other general structural determinants for raft partitioning have been revealed, suggesting that many discoveries lie ahead in this burgeoning field.

  19. The Determinants of Capital Structure: an Empirical Study of Omani Listed Industrial Companies

    Directory of Open Access Journals (Sweden)

    Mawih Al Ani


    Full Text Available This study investigates five determinants of capital structure (leverage in three subsectors of the Omani Industrial companies (food, construction and chemical listed on Muscat Securities Market for the period 2008–2012. According to available information and literature review, the determinants are profitability measured by return on assets (ROA, risk measured by the standard deviation of return on assets, the size of the company measured by the natural logarithm of total assets, rate of growth measured by the market-book value ratio (P/E and assets tangibility measured by fixed assets to total assets ratio. The capital structure or leverage is measured by total debt ratio. In the industrial sector as whole; the findings of the study indicate that there is a statistically positive association between risk and tangibility and leverage. Also, there is a statistically negative association between growth rate and profitability and leverage, while there is no association with size. Regression analysis indicates that size, tangibility and risk have a statistically significant effect on leverage.

  20. Structure determination of bisacetylenic oxylipins in carrots (Daucus carota L.) and enantioselective synthesis of falcarindiol. (United States)

    Schmiech, Ludger; Alayrac, Carole; Witulski, Bernhard; Hofmann, Thomas


    Although bisacetylenic oxylipins have been demonstrated to exhibit diverse biological activities, the chemical structures of many representatives of this class of phytochemicals still remain elusive. As carrots play an important role in our daily diet and are known as a source of bisacetylenes, an extract made from Daucus carota L. was screened for bisacetylenic oxylipins, and, after isolation, their structures were determined by means of LC-MS and 1D/2D NMR spectroscopy. Besides the previously reported falcarinol, falcarindiol, and falcarindiol 3-acetate, nine additional bisacetylenes were identified, among which six derivatives are reported for the first time in literature and three compounds were previously not identified in carrots. To determine the absolute stereochemistry of falcarindiol in carrots, the (3R,8R)-, (3R,8S)-, (3S,8R)-, and (3S,8S)-stereoisomers of falcarindiol were synthesized according to a novel 10-step total synthesis involving a Cadiot-Chodkiewicz cross-coupling reaction of (S)- and (R)-trimethylsilanyl-4-dodecen-1-yn-3-ol and (R)- and (S)-5-bromo-1-penten-4-yn-3-ol, respectively. Comparative chiral HPLC analysis of the synthetic stereoisomers with the isolated phytochemical led to the unequivocal assignment of the (Z)-(3R,8S)-configuration for falcarindiol in carrot extracts from Daucus carota L.

  1. Application of Characteristics of Seismogenic Structures in the Determination of Parameter of Potential Seismic Source Areas

    Institute of Scientific and Technical Information of China (English)

    Zhou Bengang


    The characteristics of seismogenic structures are an important basis for delineating the potential seismic source areas and determining the annual occurrence rate of earthquakes. The potential seismic source area does not only have the intension that "this area has the possibility for destructive earthquakes to occur in the future" but also means that earthquakes of high magnitude interval have the characteristics of similar recurrence. When determining the seismic activity parameters of a statistical unit, some active tectonic blocks in the unit may have different background earthquakes. In order to better reflect the heterogeneity in space of seismic activities, it is necessary to divide the potential seismic source areas into three orders.By analyzing the recurrence characteristics of earthquakes of high magnitude interval in the potential source area and calculating the occurrence probability of earthquakes of high magnitude interval in the potential seismic source area in the time window for prediction, the average annual occurrence rate of earthquakes can be obtained by the method of probability equivalent conversion in the time window for prediction. This would be helpful for considering the recurrence characteristics of strong earthquakes in potential source areas within the framework of seismic risk analysis of China. Besides, the insufficient frequency of characteristic earthquakes of the next high magnitude interval in the potential source area and the heterogeneity of strong earthquakes on seismogenic structures are analyzed to see their application in seismic risk analysis.

  2. Structural determinants of host specificity of complement Factor H recruitment by Streptococcus pneumoniae. (United States)

    Achila, David; Liu, Aizhuo; Banerjee, Rahul; Li, Yue; Martinez-Hackert, Erik; Zhang, Jing-Ren; Yan, Honggao


    Many human pathogens have strict host specificity, which affects not only their epidemiology but also the development of animal models and vaccines. Complement Factor H (FH) is recruited to pneumococcal cell surface in a human-specific manner via the N-terminal domain of the pneumococcal protein virulence factor choline-binding protein A (CbpAN). FH recruitment enables Streptococcus pneumoniae to evade surveillance by human complement system and contributes to pneumococcal host specificity. The molecular determinants of host specificity of complement evasion are unknown. In the present study, we show that a single human FH (hFH) domain is sufficient for tight binding of CbpAN, present the crystal structure of the complex and identify the critical structural determinants for host-specific FH recruitment. The results offer new approaches to the development of better animal models for pneumococcal infection and redesign of the virulence factor for pneumococcal vaccine development and reveal how FH recruitment can serve as a mechanism for both pneumococcal complement evasion and adherence.

  3. Climate effects and feedback structure determining weed population dynamics in a long-term experiment. (United States)

    Lima, Mauricio; Navarrete, Luis; González-Andujar, José Luis


    Pest control is one of the areas in which population dynamic theory has been successfully applied to solve practical problems. However, the links between population dynamic theory and model construction have been less emphasized in the management and control of weed populations. Most management models of weed population dynamics have emphasized the role of the endogenous process, but the role of exogenous variables such as climate have been ignored in the study of weed populations and their management. Here, we use long-term data (22 years) on two annual weed species from a locality in Central Spain to determine the importance of endogenous and exogenous processes (local and large-scale climate factors). Our modeling study determined two different feedback structures and climate effects in the two weed species analyzed. While Descurainia sophia exhibited a second-order feedback and low climate influence, Veronica hederifolia was characterized by a first-order feedback structure and important effects from temperature and rainfall. Our results strongly suggest the importance of theoretical population dynamics in understanding plant population systems. Moreover, the use of this approach, discerning between the effect of exogenous and endogenous factors, can be fundamental to applying weed management practices in agricultural systems and to controlling invasive weedy species. This is a radical change from most approaches currently used to guide weed and invasive weedy species managements.

  4. Determinants of capital structure: An empirical study of companies from selected post-transition economies

    Directory of Open Access Journals (Sweden)

    Sasho Arsov


    Full Text Available The goal of this paper is to examine if there are any determinants that systematically influence the capital structure of the companies in the Balkan countries and to determine if any of the existing capital structure theories are relevant in their case. We apply a panel regression on a sample consisting of the largest and most frequently traded joint-stock companies from four countries. The results show that the larger companies and those with higher fixed asset investments exhibit higher leverage, while the more profitable companies and those with more tangible assets use less debt financing. Other variables, such as the concentration of company ownership, the riskiness of its operating profits and the effective tax rates have not been found statistically significant. These results, supported by the robustness tests, have confirmed our expectation that the managers in these countries do not set specific target leverage ratios, but instead follow a particular order in the selection of the sources of financing. In other words, the companies behave in accordance with the pecking order theory, which is a confirmation of our initial hypothesis. The governments of these countries should put more effort on stimulating the use of other sources of financing to relieve the possible excessive company dependence on the banking sector.

  5. Structural parameters and X-ray Debye temperature determination study on copper-ferrite-aluminates (United States)

    Lakhani, V. K.; Pathak, T. K.; Vasoya, N. H.; Modi, K. B.


    The compositional dependence of structural parameters and X-ray Debye temperature for CuAl xFe 2- xO 4 ( x = 0.0, 0.2, 0.4 and 0.6) spinel ferrite system has been studied by means of X-ray powder diffraction (XRD) patterns analysis at 300 K. The XRD data have been used to determine the lattice constant, X-ray density, distribution of cations among the tetrahedral and octahedral sites of spinel lattice, oxygen positional parameter, site radii, bond angle, bond length and interionic distances. The X-ray Debye temperatures have been determined from integrated intensities of selected Bragg reflections. It is found that Al 3+-substitution has marked influence on various parameters. A deficit of Cu 2+-cations at the octahedral sites of the spinel lattice leads to the absence of co-operative active Jahn-Teller distortion and the crystal structure retains into cubic. The increasing disagreement between observed and calculated intensities and reduction in intensity of diffracted beam with increasing Al-concentration have been explained based on preferred orientation and extinction effects. The effect of oxygen deficiency on intensity ratios of planes has been discussed in brief.

  6. Climate Effects and Feedback Structure Determining Weed Population Dynamics in a Long-Term Experiment (United States)

    Lima, Mauricio; Navarrete, Luis; González-Andujar, José Luis


    Pest control is one of the areas in which population dynamic theory has been successfully applied to solve practical problems. However, the links between population dynamic theory and model construction have been less emphasized in the management and control of weed populations. Most management models of weed population dynamics have emphasized the role of the endogenous process, but the role of exogenous variables such as climate have been ignored in the study of weed populations and their management. Here, we use long-term data (22 years) on two annual weed species from a locality in Central Spain to determine the importance of endogenous and exogenous processes (local and large-scale climate factors). Our modeling study determined two different feedback structures and climate effects in the two weed species analyzed. While Descurainia sophia exhibited a second-order feedback and low climate influence, Veronica hederifolia was characterized by a first-order feedback structure and important effects from temperature and rainfall. Our results strongly suggest the importance of theoretical population dynamics in understanding plant population systems. Moreover, the use of this approach, discerning between the effect of exogenous and endogenous factors, can be fundamental to applying weed management practices in agricultural systems and to controlling invasive weedy species. This is a radical change from most approaches currently used to guide weed and invasive weedy species managements. PMID:22272362

  7. Community structure and soil pH determine chemoautotrophic carbon dioxide fixation in drained paddy soils. (United States)

    Long, Xi-En; Yao, Huaiying; Wang, Juan; Huang, Ying; Singh, Brajesh K; Zhu, Yong-Guan


    Previous studies suggested that microbial photosynthesis plays a potential role in paddy fields, but little is known about chemoautotrophic carbon fixers in drained paddy soils. We conducted a microcosm study using soil samples from five paddy fields to determine the environmental factors and quantify key functional microbial taxa involved in chemoautotrophic carbon fixation. We used stable isotope probing in combination with phospholipid fatty acid (PLFA) and molecular approaches. The amount of microbial (13)CO2 fixation was determined by quantification of (13)C-enriched fatty acid methyl esters and ranged from 21.28 to 72.48 ng of (13)C (g of dry soil)(-1), and the corresponding ratio (labeled PLFA-C:total PLFA-C) ranged from 0.06 to 0.49%. The amount of incorporationof (13)CO2 into PLFAs significantly increased with soil pH except at pH 7.8. PLFA and high-throughput sequencing results indicated a dominant role of Gram-negative bacteria or proteobacteria in (13)CO2 fixation. Correlation analysis indicated a significant association between microbial community structure and carbon fixation. We provide direct evidence of chemoautotrophic C fixation in soils with statistical evidence of microbial community structure regulation of inorganic carbon fixation in the paddy soil ecosystem.

  8. Effect of AVE 0991 angiotensin-(1-7) receptor agonist treatment on elemental and biomolecular content and distribution in atherosclerotic plaques of apoE-knockout mice (United States)

    Kowalska, J.; Gajda, M.; Jawień, J.; Kwiatek, W. M.; Appel, K.; Dumas, P.


    Gene-targeted apolipoprotein E-knockout (apoE-KO) mice display early and highly progressive vascular lesions containing lipid deposits and they became a reliable animal model to study atherosclerosis. The aim of the present study was to investigate the effect of AVE 0991 angiotensin-(1-7) receptor agonist on the distribution of selected pro- and anti- inflammatory elements as well as biomolecules in atherosclerotic plaques of apoE-knockout mice. Synchrotron radiation-based X-ray fluorescence (micro-XRF) and Fourier Transform Infrared (micro-FTIR) microspectroscopies were applied. Two-month-old apoE-KO mice were fed for following four months diet supplemented with AVE 0991 (0.58 μmol/kg b.w. per day). Histological sections of ascending aortas were analyzed spectroscopically. The distribution of P, Ca, Fe and Zn were found to correspond with histological structure of the lesion. Significantly lower contents of P, Ca, Zn and significantly higher content of Fe were observed in animals treated with AVE 0991. Biomolecular analysis showed lower lipids saturation level and lower lipid to protein ratio in AVE 0991 treated group. Protein secondary structure was studied according to the composition of amide I band (1660 cm-1) and it demonstrated higher proportion of β-sheet structure as compared to α-helix in both studied groups.

  9. Application of SAIL phenylalanine and tyrosine with alternative isotope-labeling patterns for protein structure determination

    Energy Technology Data Exchange (ETDEWEB)

    Takeda, Mitsuhiro [Nagoya University, Structural Biology Research Center, Graduate School of Science (Japan); Ono, Akira M.; Terauchi, Tsutomu [SAIL Technologies Co., Inc. (Japan); Kainosho, Masatsune, E-mail: [Nagoya University, Structural Biology Research Center, Graduate School of Science (Japan)


    The extensive collection of NOE constraint data involving the aromatic ring signals is essential for accurate protein structure determination, although it is often hampered in practice by the pervasive signal overlapping and tight spin couplings for aromatic rings. We have prepared various types of stereo-array isotope labeled phenylalanines ({epsilon}- and {zeta}-SAIL Phe) and tyrosine ({epsilon}-SAIL Tyr) to overcome these problems (Torizawa et al. 2005), and proven that these SAIL amino acids provide dramatic spectral simplification and sensitivity enhancement for the aromatic ring NMR signals. In addition to these SAIL aromatic amino acids, we recently synthesized {delta}-SAIL Phe and {delta}-SAIL Tyr, which allow us to observe and assign {delta}-{sup 13}C/{sup 1}H signals very efficiently. Each of the various types of SAIL Phe and SAIL Tyr yields well-resolved resonances for the {delta}-, {epsilon}- or {zeta}-{sup 13}C/{sup 1}H signals, respectively, which can readily be assigned by simple and robust pulse sequences. Since the {delta}-, {epsilon}-, and {zeta}-proton signals of Phe/Tyr residues give rise to complementary NOE constraints, the concomitant use of various types of SAIL-Phe and SAIL-Tyr would generate more accurate protein structures, as compared to those obtained by using conventional uniformly {sup 13}C, {sup 15}N-double labeled proteins. We illustrated this with the case of an 18.2 kDa protein, Escherichia coli peptidyl-prolyl cis-trans isomerase b (EPPIb), and concluded that the combined use of {zeta}-SAIL Phe and {epsilon}-SAIL Tyr would be practically the best choice for protein structural determinations.

  10. Structure and Genetic Variability of the Oceanic Whitetip Shark, Carcharhinus longimanus, Determined Using Mitochondrial DNA (United States)

    Camargo, Sâmia M.; Coelho, Rui; Chapman, Demian; Howey-Jordan, Lucy; Brooks, Edward J.; Fernando, Daniel; Mendes, Natalia J.; Hazin, Fabio H. V.; Oliveira, Claudio; Santos, Miguel N.; Foresti, Fausto; Mendonça, Fernando F.


    Information regarding population structure and genetic connectivity is an important contribution when establishing conservation strategies to manage threatened species. The oceanic whitetip shark, Carcharhinus longimanus, is a highly migratory, large-bodied, pelagic shark listed by the IUCN (International Union for Conservation of Nature) Red List as "vulnerable" throughout its range and “critically endangered” in the western north Atlantic. In 2014, the species was protected globally under Appendix II of CITES (Convention on International Trade in Endangered Species), limiting and regulating trade. This study used partial sequences of mitochondrial DNA (mtDNA) control region to determine the population genetic structure of oceanic whitetip sharks across the Atlantic and Indian Oceans. 724 base pairs were obtained from 215 individuals that identifed nine polymorphic sites and defined 12 distinct haplotypes. Total nucleotide diversity (π) was 0.0013 and haplotype diversity (h) was 0.5953. The Analysis of Molecular Variance (AMOVA) evidenced moderate levels of population structure (ɸST = 0.1039) with restricted gene flow between the western and eastern Atlantic Ocean, and a strong relationship between the latter region and the Indian Ocean. Even though the oceanic whitetip is a highly migratory animal the results presented here show that their genetic variability is slightly below average of other pelagic sharks. Additionally, this study recommends that at least two populations in the Atlantic Ocean should be considered distinct (eastern and western Atlantic) and conservation efforts should be focused in areas with the greatest genetic diversity by environmental managers. PMID:27187497

  11. Determination of Stress Concentration factor in Linearly Elastic Structures with Different Stress-Raisers Using FEM

    Directory of Open Access Journals (Sweden)

    Dheeraj Gunwant


    Full Text Available Stress concentration is the localization of stress around stress raisers. Sudden changes in the geometry of structures give rise to stress values that are higher than those obtained by elementary equations of solid mechanics. Therefore the evaluation of stress state at such locations needs specialized techniques such as Finite Element Method (FEM.The finite element method is a numerical procedure that can be used to obtain solution to a large variety of engineering problems such as structural, thermal, heat transfer, electromagnetism and fluid flow. In the present investigation, focus has been kept on the finite element modeling and determination of stress concentration factor (SCF in linearly elastic structures with different stress-raisers such as circular and elliptical holes and double semicircular notch at different locations in a finite plate. The results obtained from FEM are compared with those obtained by analytical relations as given in literature. A commercially available finite element solver ANSYS has been used for the modeling and analysis in the investigation. Throughout the investigation, plane82, which is an eight node two-dimensional element is used for the discretization.

  12. Crystal structure determination of CoGeTe from powder diffraction data

    Energy Technology Data Exchange (ETDEWEB)

    Laufek, F. [Czech Geological Survey, Geologicka 6, 15200 Praha 5 (Czech Republic)], E-mail:; Navratil, J. [Joint Laboratory of Solid State Chemistry of IMC AS CR and University of Pardubice, Studentska 84, 53210 Pardubice (Czech Republic); Plasil, J. [Faculty of Science, Charles University, Albertov 6, 12843 Praha 2 (Czech Republic); Plechacek, T. [Joint Laboratory of Solid State Chemistry of IMC AS CR and University of Pardubice, Studentska 84, 53210 Pardubice (Czech Republic)


    The crystal structure of cobalt germanium telluride CoGeTe has been determined by direct methods using integrate intensities of conventional X-ray powder diffraction data and subsequently refined with the Rietveld method. The title compound was prepared by heating of stoichiometric amount of Co, Ge and Te in silica glass tube at 670 deg. C. CoGeTe adopts orthorhombic symmetry, space group Pbca with unit cell parameters a = 6.1892(4) A, b = 6.2285(4) A, c = 11.1240(6) A, V = 428.8(1) A{sup 3} and Z = 8. Its crystal structure is formed by [CoGe{sub 3}Te{sub 3}] octahedra sharing both edges and corners. CoGeTe represents a ternary ordered variant of {alpha}-NiAs{sub 2} type structure. An important feature present in CoGeTe is an occurrence of short Co-Co distance across the shared edge of [CoGe{sub 3}Te{sub 3}] octahedra. Differential thermal analysis (DTA) has revealed that CoGeTe melts incongruently at about 725 deg. C; CoGeTe decomposes into GeTe, CoGe and CoTe{sub 2}. Temperature dependence of the electrical conductivity and value of Seebeck coefficient at 300 K are also reported.

  13. Quantifying forest vertical structure to determine bird habitat quality in the Greenbelt Corridor, Denton, TX (United States)

    Matsubayashi, Shiho

    This study presents the integration of light detection and range (LiDAR) and hyperspectral remote sensing to create a three-dimensional bird habitat map in the Greenbelt Corridor of the Elm Fork of the Trinity River. This map permits to examine the relationship between forest stand structure, landscape heterogeneity, and bird community composition. A biannual bird census was conducted at this site during the breeding seasons of 2009 and 2010. Census data combined with the three-dimensional map suggest that local breeding bird abundance, community structure, and spatial distribution patterns are highly influenced by vertical heterogeneity of vegetation surface. For local breeding birds, vertical heterogeneity of canopy surface within stands, connectivity to adjacent forest patches, largest forest patch index, and habitat (vegetation) types proved to be the most influential factors to determine bird community assemblages. Results also highlight the critical role of secondary forests to increase functional connectivity of forest patches. Overall, three-dimensional habitat descriptions derived from integrated LiDAR and hyperspectral data serve as a powerful bird conservation tool that shows how the distribution of bird species relates to forest composition and structure at various scales.

  14. Molecular structure of an apolipoprotein determined at 2. 5- angstrom resolution

    Energy Technology Data Exchange (ETDEWEB)

    Breiter, D.R.; Benning, M.M.; Wesenberg, G.; Holden, H.M.; Rayment, I. (Univ. of Wisconsin, Madison (USA)); Kanost, M.R.; Law, J.H.; Wells, M.A. (Univ. of Arizona, Tucson (USA))


    The three-dimensional structure of an apolipoprotein isolated from the African migratory locust Locusta migratoria has been determined by X-ray analysis to a resolution of 2.5 {angstrom}. The overall molecular architecture of this protein consists of five long {alpha}-helices connected by short loops. As predicted from amino acid sequence analyses, these helices are distinctly amphiphilic with the hydrophobic residues pointing in toward the interior of the protein and the hydrophilic side chains facing outward. The molecule falls into the general category of up-and-down {alpha}-helical bundles as previously observed, for example, in cytochrome c{prime}. Although the structure shows the presence of five long amphiphilic {alpha}-helices, the {alpha}-helical moment and hydrophobicity of the entire molecule fall into the range found for normal globular proteins. Thus, in order for the amphiphilic helices to play a role in the binding of the protein to a lipid surface, there must be a structural reorganization of the protein which exposes the hydrophobic interior to the lipid surface. The three dimensional motif of this apolipoprotein is compatible with a model in which the molecule binds to the lipid surface via a relatively nonpolar end and then spreads on the surface in such a way as to cause the hydrophobic side chains of the helices to come in contact with the lipid surface, the charged and polar residues to remain in contact with water, and the overall helical motif of the protein to be maintained.

  15. Firm, Country and Macroeconomic Determinants of Capital Structure: Evidence from Turkish Banking Sector

    Directory of Open Access Journals (Sweden)

    Nuri Baltacı


    Full Text Available This study explores the significance of firm-specific, country, and macroeconomic factors in explaining variation in leverage using a sample of banks from Turkish banking sector. The analysis is based on quarterly firm-level data from Turkish banking sector in 2002–2012. We aims to contribute to the empirical capital structure literature in the following ways. Our first contribution comes from assessing the importance of firm-specific factors, country-level factors and industrial factors for capital structure decisions in Turkish banking sector. Second, we employ appropriate and advanced dynamic panel data estimators, Blundell and Bond’s (1998 generalized methods of moment’s estimators (GMM System. We find that leverage is significantly and positively associated with average industry leverage, firm size and GDP growth. We find also that leverage is significantly and negatively associated with tangibility, profitability, inflation and financial risk. The regression results for leverage are both theoretically and empirically plausible for banks in Turkey. Moreover, tangibility, profitability and GDP growth are consistent with the predictions of the pecking order theory, while firm size is consistent with the predictions of the trade-off theory. Our findings suggest that the capital structures of financial and non-financial firms are ultimately determined by the same drivers.

  16. Studies of firm capital structure determinants in Poland: an integrative review

    Directory of Open Access Journals (Sweden)

    Andrzej Cwynar


    Full Text Available We investigated 34 empirical studies aimed at examining the capital structure determinants in firms operating in Poland to test to what degree the financing patterns were steady during the observed period (2001-2012. Specifically, in conducting the survey we were motivated by the following research questions which constitute the objectives of the article: (1 which factors – country- or firm-specific – are more relevant in explaining leverage in Poland, (2 which theory – trade-off or pecking order – gains greater support in Poland, and (3 what is the significance of the optimal capital structure notion in Poland. Our results show that financing patterns changed importantly during the last 20 years, which manifests itself mainly in gradual increase in debt ratios with a dominant role of short-term debt, along with the decrease in the importance of country-specific factors (especially in large-sized, listed firms. The signs of the associations between leverage and the key firm-specific factors remained relatively stable during the investigated period, with the exception concerning tangibility. These signs provide greater support for pecking order theory, with at most a moderate role of the target capital structure.

  17. Determining the Structure of an Unliganded and Fully Glycosylated SIV gp120 Envelope Glycoprotein

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Bing; Vogan, Erik M.; Gong, Haiyun; Skehel, John J.; Wiley, Don C.; Harrison, Stephen C. (Harvard-Med); (NIMR)


    HIV/SIV envelope glycoproteins mediate the first steps in viral infection. They are trimers of a membrane-anchored polypeptide chain, cleaved into two fragments known as gp120 and gp41. The structure of HIV gp120 bound with receptor (CD4) has been known for some time. We have now determined the structure of a fully glycosylated SIV gp120 envelope glycoprotein in an unliganded conformation by X-ray crystallography at 4.0 {angstrom} resolution. We describe here our experimental and computational approaches, which may be relevant to other resolution-limited crystallographic problems. Key issues were attention to details of beam geometry mandated by small, weakly diffracting crystals, and choice of strategies for phase improvement, starting with two isomorphous derivatives and including multicrystal averaging. We validated the structure by analyzing composite omit maps, averaged among three distinct crystal lattices, and by calculating model-based, SeMet anomalous difference maps. There are at least four ordered sugars on many of the thirteen oligosaccharides.

  18. Structure and Genetic Variability of the Oceanic Whitetip Shark, Carcharhinus longimanus, Determined Using Mitochondrial DNA. (United States)

    Camargo, Sâmia M; Coelho, Rui; Chapman, Demian; Howey-Jordan, Lucy; Brooks, Edward J; Fernando, Daniel; Mendes, Natalia J; Hazin, Fabio H V; Oliveira, Claudio; Santos, Miguel N; Foresti, Fausto; Mendonça, Fernando F


    Information regarding population structure and genetic connectivity is an important contribution when establishing conservation strategies to manage threatened species. The oceanic whitetip shark, Carcharhinus longimanus, is a highly migratory, large-bodied, pelagic shark listed by the IUCN (International Union for Conservation of Nature) Red List as "vulnerable" throughout its range and "critically endangered" in the western north Atlantic. In 2014, the species was protected globally under Appendix II of CITES (Convention on International Trade in Endangered Species), limiting and regulating trade. This study used partial sequences of mitochondrial DNA (mtDNA) control region to determine the population genetic structure of oceanic whitetip sharks across the Atlantic and Indian Oceans. 724 base pairs were obtained from 215 individuals that identifed nine polymorphic sites and defined 12 distinct haplotypes. Total nucleotide diversity (π) was 0.0013 and haplotype diversity (h) was 0.5953. The Analysis of Molecular Variance (AMOVA) evidenced moderate levels of population structure (ɸST = 0.1039) with restricted gene flow between the western and eastern Atlantic Ocean, and a strong relationship between the latter region and the Indian Ocean. Even though the oceanic whitetip is a highly migratory animal the results presented here show that their genetic variability is slightly below average of other pelagic sharks. Additionally, this study recommends that at least two populations in the Atlantic Ocean should be considered distinct (eastern and western Atlantic) and conservation efforts should be focused in areas with the greatest genetic diversity by environmental managers.

  19. Structure and Genetic Variability of the Oceanic Whitetip Shark, Carcharhinus longimanus, Determined Using Mitochondrial DNA.

    Directory of Open Access Journals (Sweden)

    Sâmia M Camargo

    Full Text Available Information regarding population structure and genetic connectivity is an important contribution when establishing conservation strategies to manage threatened species. The oceanic whitetip shark, Carcharhinus longimanus, is a highly migratory, large-bodied, pelagic shark listed by the IUCN (International Union for Conservation of Nature Red List as "vulnerable" throughout its range and "critically endangered" in the western north Atlantic. In 2014, the species was protected globally under Appendix II of CITES (Convention on International Trade in Endangered Species, limiting and regulating trade. This study used partial sequences of mitochondrial DNA (mtDNA control region to determine the population genetic structure of oceanic whitetip sharks across the Atlantic and Indian Oceans. 724 base pairs were obtained from 215 individuals that identifed nine polymorphic sites and defined 12 distinct haplotypes. Total nucleotide diversity (π was 0.0013 and haplotype diversity (h was 0.5953. The Analysis of Molecular Variance (AMOVA evidenced moderate levels of population structure (ɸST = 0.1039 with restricted gene flow between the western and eastern Atlantic Ocean, and a strong relationship between the latter region and the Indian Ocean. Even though the oceanic whitetip is a highly migratory animal the results presented here show that their genetic variability is slightly below average of other pelagic sharks. Additionally, this study recommends that at least two populations in the Atlantic Ocean should be considered distinct (eastern and western Atlantic and conservation efforts should be focused in areas with the greatest genetic diversity by environmental managers.

  20. Determination of the Structure of the Coronal Magnetic Field Using Microwave Polarization Measurements (United States)

    Bogod, V. M.; Yasnov, L. V.


    An analysis of the oscillatory motions and wave processes in active regions requires knowledge of the structure of the magnetic fields in the chromosphere and corona. We study the magnetic field structure of active regions at coronal heights, as they are determined by means of multiwave observations of polarized radio emission of active regions in the microwave range. Two methods, a stereoscopic method and the analysis of the radio spectrum are used. The method of stereoscopy rotation allows estimating the height of radio sources in a stable active region relative to the photosphere, based on its apparent motion in the image plane recorded over several days of observation. At various times one-dimensional scans at multiple frequencies spanning the 5.98 - 15.95 GHz frequency range from the RATAN-600 instrument are used. The gyroresonance emission mechanism, which is sensitive to the coronal magnetic field strength, is applied to convert the radio source estimated heights at various frequencies, h(f), to information as regards magnetic field vs. height, B(h). Diagrams of longitude - height of some polarized radio sources revealed multiple reversals, suggestive of a spiral magnetic structure. In all cases, the magnetic field strength maintains high values (800 - 1000 G) at the highest altitudes analysed, which reflects a relatively weak divergence in the field of magnetic flux tubes (in the height range 8 - 14 Mm) responsible for the main part of the radio emission of active regions.