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Sample records for assembly ligand recognition

  1. Molecular Recognition and Ligand Association

    Science.gov (United States)

    Baron, Riccardo; McCammon, J. Andrew

    2013-04-01

    We review recent developments in our understanding of molecular recognition and ligand association, focusing on two major viewpoints: (a) studies that highlight new physical insight into the molecular recognition process and the driving forces determining thermodynamic signatures of binding and (b) recent methodological advances in applications to protein-ligand binding. In particular, we highlight the challenges posed by compensating enthalpic and entropic terms, competing solute and solvent contributions, and the relevance of complex configurational ensembles comprising multiple protein, ligand, and solvent intermediate states. As more complete physics is taken into account, computational approaches increase their ability to complement experimental measurements, by providing a microscopic, dynamic view of ensemble-averaged experimental observables. Physics-based approaches are increasingly expanding their power in pharmacology applications.

  2. Layer by layer assembly of albumin nanoparticles with selective recognition of tumor necrosis factor-related apoptosis-inducing ligand (TRAIL).

    Science.gov (United States)

    Cui, Wei; Wang, Anhe; Zhao, Jie; Yang, Xiaoke; Cai, Peng; Li, Junbai

    2016-03-01

    Crosslinked albumin nanoparticles which loaded with doxorubicin (DOX) were fabricated with tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) and biocompatible polysaccharide, alginate (ALG), using layer-by-layer technique. Albumin nanoparticles exhibited narrow size distribution and fluorescent property. The assembled core/shell structure of the nanoparticles can be internalized more easily with the cancer cells, which attributes to TRAIL binding with death receptors. TRAIL still hold bioactive properties after assembled onto the particles. In addition, after loaded into the albumin core nanoparticles, DOX (as the chemotherapeutics) display a synergistic cytotoxic effect on cytotoxicity in combination with TRAIL in vitro. The core/shell nanostructured nanoparticles realized in this study would be used as a promising candidate for novel drug carriers.

  3. Ligand inducible assembly of a DNA tetrahedron.

    Science.gov (United States)

    Dohno, Chikara; Atsumi, Hiroshi; Nakatani, Kazuhiko

    2011-03-28

    Here we show that a small synthetic ligand can be used as a key building component for DNA nanofabrication. Using naphthyridinecarbamate dimer (NCD) as a molecular glue for DNA hybridization, we demonstrate NCD-triggered formation of a DNA tetrahedron.

  4. RESEARCH OF MOVEMENT NAVIGATION BASED ON ASSEMBLY CONSTRAINT RECOGNITION

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The requirements and features of virtual assembly movement navigator are analyzed to help operators flexibly manipulate virtual objects, precisely locate or assemble virtual parts in virtual environment. With the degree-of-freedom analysis, the assembly constraint hierarchical model is constructed and the system's constraints are built dynamically. Thus, all objects in virtual environment can be located reasonally by the navigator. Moreover, the assembly constraint recognition in the process of assembly and movement correction is also discussed.

  5. Photocontrol over cooperative porphyrin self-assembly with phenylazopyridine ligands.

    Science.gov (United States)

    Hirose, Takashi; Helmich, Floris; Meijer, E W

    2013-01-02

    The cooperative self-assembly of chiral zinc porphyrins is regulated by a photoresponsive phenylazopyridine ligand. Porphyrin stacks depolymerize into dimers upon axial ligation and the strength of the coordination is regulated by its photoinduced isomerization, which shows more than 95 % conversion ratio for both photostationary states.

  6. Structure and ligand recognition of class C GPCRs

    Institute of Scientific and Technical Information of China (English)

    Lei CHUN; Wen-hua ZHANG; Jian-feng LIU

    2012-01-01

    The G-protein-coupled receptors (GPCRs) are one of the largest super families of cell-surface receptors and play crucial roles in virtu-ally every organ system.One particular family of GPCRs,the class C GPCRs,is distinguished by a characteristically large extracellular domain and constitutive dimerization.The structure and activation mechanism of this family result in potentially unique ligand recognition sites,thereby offering a variety of possibilities by which receptor activity might be modulated using novel compounds.In the present article,we aim to provide an overview of the exact sites and structural features involved in ligand recognition of the class C GPCRs.Furthermore,we demonstrate the precise steps that occur during the receptor activation process,which underlie the possibilities by which receptor function may be altered by different approaches.Finally,we use four typical family members to illustrate orthosteric and allosteric sites with representative ligands and their corresponding therapeutic potential.

  7. Structures of pattern recognition receptors reveal molecular mechanisms of autoinhibition, ligand recognition and oligomerization.

    Science.gov (United States)

    Chuenchor, Watchalee; Jin, Tengchuan; Ravilious, Geoffrey; Xiao, T Sam

    2014-02-01

    Pattern recognition receptors (PRRs) are essential sentinels for pathogens or tissue damage and integral components of the innate immune system. Recent structural studies have provided unprecedented insights into the molecular mechanisms of ligand recognition and signal transduction by several PRR families at distinct subcellular compartments. Here we highlight some of the recent discoveries and summarize the common themes that are emerging from these exciting studies. Better mechanistic understanding of the structure and function of the PRRs will improve future prospects of therapeutic targeting of these important innate immune receptors.

  8. Consequences of Morphology on Molecularly Imprinted Polymer-Ligand Recognition

    Directory of Open Access Journals (Sweden)

    Annika M. Rosengren

    2013-01-01

    Full Text Available The relationship between molecularly imprinted polymer (MIP morphology and template-rebinding over a series of warfarin-imprinted methacrylic acid co(ethylene dimethacrylate polymers has been explored. Detailed investigations of the nature of template recognition revealed that an optimal template binding was obtained with polymers possessing a narrow population of pores (~3–4 nm in the mesopore size range. Importantly, the warfarin-polymer rebinding analyses suggest strategies for regulating ligand binding capacity and specificity through variation of the degree of cross-linking, where polymers prepared with a lower degree of cross-linking afford higher capacity though non-specific in character. In contrast, the co-existence of specific and non-specific binding was found in conjunction with higher degrees of cross-linking and resultant meso- and macropore size distributions.

  9. Eph family receptors and ligands in vascular cell targeting and assembly.

    Science.gov (United States)

    Stein, E; Schoecklmann, H; Daniel, T O

    1997-11-01

    Members of the Eph family of receptor tyrosine kinases determine neural cell aggregation and targeting behavior, functions that are also critical in vascular assembly and remodeling. Among this class of diverse receptors, EphA2 (Eck) and EphB1 (ELK) represent prototypes for two receptor subfamilies distinguished by high-affinity interaction with either glycerophosphatidylinositol (GPI)-linked or transmembrane ligands, respectively. EphA2 participates in angiogenic responses to tumor necrosis factor (TNF) through an autocrine loop affecting endothelial cell migration. EphB1 and its ligand Ephrin-B1 (LERK-2) are important determinants of assembly of endothelial cells from the microvasculature of the kidney, where both are expressed in endothelial progenitors and in glomerular microvascular endothelial cells. Ephrin-B1 activation of EphB1 promotes assembly of these cells into capillary-like structures. Interaction trap approaches have identified downstream signaling proteins that complex with ligand-activated EphA2 or EphB1, including nonreceptor tyrosine kinases and SH2 domain-containing adapter proteins. The Grb 10 adapter is one of a subset that binds activated EphB1, but not EphA2, defining distinct signaling mechanisms for these related endothelial receptors. On the basis of observations in vascular endothelial cells and recent results defining Eph receptor and ligand roles in neural cell targeting, we propose that these receptors direct cell-cell recognition events that are critical in vasculogenesis and angiogenesis. (Trends Cardiovasc Med 1997;7:329-334). © 1997, Elsevier Science Inc.

  10. Functional self-assembled DNA nanostructures for molecular recognition

    Science.gov (United States)

    Zhang, Xiaojuan; Yadavalli, Vamsi K.

    2012-03-01

    Nucleic acids present a wonderful toolkit of structural motifs for nanoconstruction. Functional DNA nanostructures can enable protein recognition by the use of aptamers attached to a basic core shape formed by DNA self-assembly. Here, we present a facile, programmable strategy for the assembly of discrete aptamer-tagged DNA shapes and nanostructures that can function for molecular recognition and binding in an aqueous environment. These nanostructures, presented here to bind two different protein targets, are easily synthesized in large numbers, and are portable and stable over long periods of time. This construction modality can facilitate on-demand production of libraries of diverse shapes to recognize and bind proteins or catalyze reactions via functional nucleic acid tags.Nucleic acids present a wonderful toolkit of structural motifs for nanoconstruction. Functional DNA nanostructures can enable protein recognition by the use of aptamers attached to a basic core shape formed by DNA self-assembly. Here, we present a facile, programmable strategy for the assembly of discrete aptamer-tagged DNA shapes and nanostructures that can function for molecular recognition and binding in an aqueous environment. These nanostructures, presented here to bind two different protein targets, are easily synthesized in large numbers, and are portable and stable over long periods of time. This construction modality can facilitate on-demand production of libraries of diverse shapes to recognize and bind proteins or catalyze reactions via functional nucleic acid tags. Electronic supplementary information (ESI) available. See DOI: 10.1039/c2nr11711h

  11. Ligand and Metalloligand Design for Macrocycles, Multimetallic Arrays, Coordination Polymers and Assemblies

    OpenAIRE

    E. C. Constable; Housecroft, C. E.

    2016-01-01

    This overview of ligand design focuses on three areas: (i) principles of ligand binding, the formation of complexes, and popular strategies for ligand synthesis; (ii) ligand design in macrocyclic complexes, coordination polymers and networks and metallopolygons, and assembly strategies based upon the use of metalloligand building blocks; (iii) ligand design for the extraction and transport of metals. This area of coordination chemistry is too large to permit a comprehensive survey in the spac...

  12. Integration of screening and identifying ligand(s) from medicinal plant extracts based on target recognition by using NMR spectroscopy

    OpenAIRE

    2015-01-01

    Authors: Yalin Tang, Qian Shang, Junfeng Xiang, Qianfan Yang, Qiuju Zhou, Lin Li, Hong Zhang, Qian Li, Hongxia Sun, Aijiao Guan, Wei Jiang & Wei Gai ### Abstract This protocol presents the screening of ligand(s) from medicinal plant extracts based on target recognition by using NMR spectroscopy. A detailed description of sample preparation and analysis process is provided. NMR spectroscopies described here are 1H NMR, diffusion-ordered spectroscopy (DOSY), relaxation-edited NMR, ...

  13. The Recognition of Identical Ligands by Unrelated Proteins.

    Science.gov (United States)

    Barelier, Sarah; Sterling, Teague; O'Meara, Matthew J; Shoichet, Brian K

    2015-12-18

    The binding of drugs and reagents to off-targets is well-known. Whereas many off-targets are related to the primary target by sequence and fold, many ligands bind to unrelated pairs of proteins, and these are harder to anticipate. If the binding site in the off-target can be related to that of the primary target, this challenge resolves into aligning the two pockets. However, other cases are possible: the ligand might interact with entirely different residues and environments in the off-target, or wholly different ligand atoms may be implicated in the two complexes. To investigate these scenarios at atomic resolution, the structures of 59 ligands in 116 complexes (62 pairs in total), where the protein pairs were unrelated by fold but bound an identical ligand, were examined. In almost half of the pairs, the ligand interacted with unrelated residues in the two proteins (29 pairs), and in 14 of the pairs wholly different ligand moieties were implicated in each complex. Even in those 19 pairs of complexes that presented similar environments to the ligand, ligand superposition rarely resulted in the overlap of related residues. There appears to be no single pattern-matching "code" for identifying binding sites in unrelated proteins that bind identical ligands, though modeling suggests that there might be a limited number of different patterns that suffice to recognize different ligand functional groups.

  14. Narcissistic self-sorting in self-assembled cages of rare Earth metals and rigid ligands.

    Science.gov (United States)

    Johnson, Amber M; Wiley, Calvin A; Young, Michael C; Zhang, Xing; Lyon, Yana; Julian, Ryan R; Hooley, Richard J

    2015-05-04

    Highly selective, narcissistic self-sorting can be achieved in the formation of self-assembled cages of rare earth metals with multianionic salicylhydrazone ligands. The assembly process is highly sensitive to the length of the ligand and the coordination geometry. Most surprisingly, high-fidelity sorting is possible between ligands of identical coordination angle and geometry, differing only in a single functional group on the ligand core, which is not involved in the coordination. Supramolecular effects allow discrimination between pendant functions as similar as carbonyl or methylene groups in a complex assembly process.

  15. Ionic interaction as a powerful driving force for the formation of heterobidentate assembly ligands.

    Science.gov (United States)

    Gulyás, Henrik; Benet-Buchholz, Jordi; Escudero-Adan, Eduardo C; Freixa, Zoraida; van Leeuwen, Piet W N M

    2007-01-01

    An ionic interaction has been used for the first time to assemble monophosphane ligands. NMR spectroscopy and X-ray studies show that cationic and anionic triphenylphosphane derivatives form ion pairs and subsequently act as a ligand in various transition-metal complexes. The position of the ionic functional groups allows both cis and trans coordination of the novel assembly ligand in square-planar transition-metal complexes.

  16. Structural basis for ligand recognition of incretin receptors

    DEFF Research Database (Denmark)

    Underwood, Christina Rye; Parthier, Christoph; Reedtz-Runge, Steffen

    2010-01-01

    been solved recently by X-ray crystallography. The crystal structures reveal a similar fold of the ECD and a similar mechanism of ligand binding, where the ligand adopts an α-helical conformation. Residues in the C-terminal part of the ligand interact directly with the ECD and hydrophobic interactions...... appear to be the main driving force for ligand binding to the ECD of incretin receptors. Obviously, the-still missing-structures of full-length incretin receptors are required to construct a complete picture of receptor function at the molecular level. However, the progress made recently in structural...

  17. A Ferrocene-Based Catecholamide Ligand: the Consequences of Ligand Swivel for Directed Supramolecular Self-Assembly

    Energy Technology Data Exchange (ETDEWEB)

    Mugridge, Jeffrey; Fiedler, Dorothea; Raymond, Kenneth

    2010-02-04

    A ferrocene-based biscatecholamide ligand was prepared and investigated for the formation of metal-ligand supramolecular assemblies with different metals. Reaction with Ge(IV) resulted in the formation of a variety of Ge{sub n}L{sub m} coordination complexes, including [Ge{sub 2}L{sub 3}]{sup 4-} and [Ge{sub 2}L{sub 2}({mu}-OMe){sub 2}]{sup 2-}. The ligand's ability to swivel about the ferrocenyl linker and adopt different conformations accounts for formation of many different Ge{sub n}L{sub m} species. This study demonstrates why conformational ligand rigidity is essential in the rational design and directed self-assembly of supramolecular complexes.

  18. Cyclic Peptide-Decorated Self-Assembled Nanohybrids for Selective Recognition and Detection of Multivalent RNAs.

    Science.gov (United States)

    Choi, Jun Shik; Han, So-hee; Kim, Hyoseok; Lim, Yong-Beom

    2016-03-16

    Although there has been substantial advancement in the development of nanostructures, the development of self-assembled nanostructures that can selectively recognize multivalent targets has been very difficult. Here we show the proof of concept that topology-controlled peptide nanoassemblies can selectively recognize and detect a multivalent RNA target. We compared the differential behaviors of peptides in a linear or cyclic topology in terms of peptide-gold nanoparticle hybrid nanostructure formation, conformational stabilization, monovalent and multivalent RNA binding in vitro, and multivalent RNA recognition in live cells. When the topology-dependent selectivity amplification of the cyclic peptide hybrids is combined with the noninvasive nature of dark-field microscopy, the cellular localization of the viral Rev response element (RRE) RNA can be monitored in situ. Because intracellular interactions are often mediated by overlapping binding partners with weak affinity, the topology-controlled peptide assemblies can provide a versatile means to convert weak ligands into multivalent ligands with high affinity and selectivity.

  19. Computational studies of protein-ligand molecular recognition

    NARCIS (Netherlands)

    Gillies, M.B.

    2001-01-01

    Structure-based drug design is made possible by our understanding of molecular recognition. The utility of this approach was apparent in the development of the clinically e V ective HIV-1 PR inhibitors, where crystal structures of complexes of HIV-1 protease and inhibitors gave pivotal information.

  20. Self-assembly of heteroleptic dinuclear metallosupramolecular kites from multivalent ligands via social self-sorting

    Directory of Open Access Journals (Sweden)

    Christian Benkhäuser

    2015-05-01

    Full Text Available A Tröger's base-derived racemic bis(1,10-phenanthroline ligand (rac-1 and a bis(2,2'-bipyridine ligand with a central 1,3-diethynylbenzene unit 2 were synthesized. Each of these ligands acts as a multivalent entity for the binding of two copper(I ions. Upon coordination to the metal ions these two ligands undergo selective self-assembly into heteroleptic dinuclear metallosupramolecular kites in a high-fidelity social self-sorting manner as evidenced by NMR spectroscopy and mass spectrometry.

  1. RNA gymnastics in mammalian signal recognition particle assembly.

    Science.gov (United States)

    Wild, Klemens; Sinning, Irmgard

    2014-01-01

    More than one third of the cellular proteome is destined for incorporation into cell membranes or export from the cell. In all domains of life, the signal recognition particle (SRP) delivers these proteins to the membrane and protein traffic falls apart without SRP logistics. With the aid of a topogenic transport signal, SRP retrieves its cargo right at the ribosome, from where they are sorted to the translocation channel. Mammalian SRP is a ribonucleoprotein complex consisting of an SRP RNA of 300 nucleotides and 6 proteins bound to it. Assembly occurs in a hierarchical manner mainly in the nucleolus and only SRP54, which recognizes the signal sequence and regulates the targeting process, is added as the last component in the cytosol. Here we present an update on recent insights in the structure, function and dynamics of SRP RNA in SRP assembly with focus on the S domain, and present SRP as an example for the complex biogenesis of a rather small ribonucleoprotein particle.

  2. Structural and Functional Insights into Endoglin Ligand Recognition and Binding

    Science.gov (United States)

    Alt, Aaron; Miguel-Romero, Laura; Donderis, Jordi; Aristorena, Mikel; Blanco, Francisco J.; Round, Adam; Rubio, Vicente; Bernabeu, Carmelo; Marina, Alberto

    2012-01-01

    Endoglin, a type I membrane glycoprotein expressed as a disulfide-linked homodimer on human vascular endothelial cells, is a component of the transforming growth factor (TGF)-β receptor complex and is implicated in a dominant vascular dysplasia known as hereditary hemorrhagic telangiectasia as well as in preeclampsia. It interacts with the type I TGF-β signaling receptor activin receptor-like kinase (ALK)1 and modulates cellular responses to Bone Morphogenetic Protein (BMP)-9 and BMP-10. Structurally, besides carrying a zona pellucida (ZP) domain, endoglin contains at its N-terminal extracellular region a domain of unknown function and without homology to any other known protein, therefore called the orphan domain (OD). In this study, we have determined the recognition and binding ability of full length ALK1, endoglin and constructs encompassing the OD to BMP-9 using combined methods, consisting of surface plasmon resonance and cellular assays. ALK1 and endoglin ectodomains bind, independently of their glycosylation state and without cooperativity, to different sites of BMP-9. The OD comprising residues 22 to 337 was identified among the present constructs as the minimal active endoglin domain needed for partner recognition. These studies also pinpointed to Cys350 as being responsible for the dimerization of endoglin. In contrast to the complete endoglin ectodomain, the OD is a monomer and its small angle X-ray scattering characterization revealed a compact conformation in solution into which a de novo model was fitted. PMID:22347366

  3. Structural and functional insights into endoglin ligand recognition and binding.

    Directory of Open Access Journals (Sweden)

    Aaron Alt

    Full Text Available Endoglin, a type I membrane glycoprotein expressed as a disulfide-linked homodimer on human vascular endothelial cells, is a component of the transforming growth factor (TGF-β receptor complex and is implicated in a dominant vascular dysplasia known as hereditary hemorrhagic telangiectasia as well as in preeclampsia. It interacts with the type I TGF-β signaling receptor activin receptor-like kinase (ALK1 and modulates cellular responses to Bone Morphogenetic Protein (BMP-9 and BMP-10. Structurally, besides carrying a zona pellucida (ZP domain, endoglin contains at its N-terminal extracellular region a domain of unknown function and without homology to any other known protein, therefore called the orphan domain (OD. In this study, we have determined the recognition and binding ability of full length ALK1, endoglin and constructs encompassing the OD to BMP-9 using combined methods, consisting of surface plasmon resonance and cellular assays. ALK1 and endoglin ectodomains bind, independently of their glycosylation state and without cooperativity, to different sites of BMP-9. The OD comprising residues 22 to 337 was identified among the present constructs as the minimal active endoglin domain needed for partner recognition. These studies also pinpointed to Cys350 as being responsible for the dimerization of endoglin. In contrast to the complete endoglin ectodomain, the OD is a monomer and its small angle X-ray scattering characterization revealed a compact conformation in solution into which a de novo model was fitted.

  4. Synthesis of nanoparticle/ligand composite thin films by sequential ligand self assembly and surface complex reduction.

    Science.gov (United States)

    Muench, Falk; Fuchs, Anne; Mankel, Eric; Rauber, Markus; Lauterbach, Stefan; Kleebe, Hans-Joachim; Ensinger, Wolfgang

    2013-01-01

    Nanocomposite thin films consisting of ligand-connected metal nanoparticles were deposited by iteration of ligand assembly, surface complex formation and reduction. This novel and convenient approach combines characteristics of the layer-by-layer (LbL) and the successive ion layer adsorption and reaction (SILAR) techniques. In contrast to classical LbL assembly, the nanoparticle formation is performed in situ, avoiding separate reduction, protection and attachment steps. To demonstrate the versatility of the approach, different metal precursors (Pd, Ag and Au salts) and linkers (1,2-ethanedithiol, 1,4-benzenedithiol and polythiol) were applied. The formation of dithiol-linked nanoparticle films was confirmed by TEM and XPS. By combining the deposition protocol with ion track etched polycarbonate templates, nanotubes and nanowires with high aspect ratios of up to 300 could be fabricated.

  5. Human NKG2D-ligands: cell biology strategies to ensure immune recognition

    Directory of Open Access Journals (Sweden)

    Lola eFernández-Messina

    2012-09-01

    Full Text Available Immune recognition mediated by the activating receptor NKG2D plays an important role for the elimination of stressed cells, including tumours and virus-infected cells. On the other hand, the ligands for NKG2D can also be shed into the sera of cancer patients where they weaken the immune response by downmodulating the receptor on effector cells, mainly NK and T cells. Although both families of NKG2D-ligands, MICA/B and ULBPs, are related to MHC molecules and their expression is increased after stress, many differences are observed in terms of their biochemical properties and cell trafficking. In this paper, we summarise the variety of NKG2D-ligands and propose that selection pressure has driven evolution of diversity in their trafficking and shedding, but not receptor binding affinity. However, it is also possible to identify functional properties common to individual ULBP molecules and MICA/B alleles, but not generally conserved within the MIC or ULBP families. These characteristics likely represent examples of convergent evolution for efficient immune recognition, but are also attractive targets for pathogen immune evasion strategies. Categorization of NKG2D-ligands according to their biological features, rather than their genetic family, may help to achieve a better understanding of NKG2D-ligand association with disease.

  6. A Self-Assembled Electro-Active M8L4 Cage Based on Tetrathiafulvalene Ligands

    Directory of Open Access Journals (Sweden)

    Sébastien Goeb

    2014-01-01

    Full Text Available Two self-assembled redox-active cages are presented. They are obtained by coordination-driven self-assembly of a tetra-pyridile tetrathiafulvalene ligand with cis-M(dppf(OTf2 (M = Pd or Pt; dppf = 1,1′-bis(diphenylphosphinoferrocene; OTf = trifluoromethane-sulfonate complexes. Both species are fully characterized and are constituted of 12 electro-active subunits that can be reversibly oxidized.

  7. Roles for ordered and bulk solvent in ligand recognition and docking in two related cavities.

    Directory of Open Access Journals (Sweden)

    Sarah Barelier

    Full Text Available A key challenge in structure-based discovery is accounting for modulation of protein-ligand interactions by ordered and bulk solvent. To investigate this, we compared ligand binding to a buried cavity in Cytochrome c Peroxidase (CcP, where affinity is dominated by a single ionic interaction, versus a cavity variant partly opened to solvent by loop deletion. This opening had unexpected effects on ligand orientation, affinity, and ordered water structure. Some ligands lost over ten-fold in affinity and reoriented in the cavity, while others retained their geometries, formed new interactions with water networks, and improved affinity. To test our ability to discover new ligands against this opened site prospectively, a 534,000 fragment library was docked against the open cavity using two models of ligand solvation. Using an older solvation model that prioritized many neutral molecules, three such uncharged docking hits were tested, none of which was observed to bind; these molecules were not highly ranked by the new, context-dependent solvation score. Using this new method, another 15 highly-ranked molecules were tested for binding. In contrast to the previous result, 14 of these bound detectably, with affinities ranging from 8 µM to 2 mM. In crystal structures, four of these new ligands superposed well with the docking predictions but two did not, reflecting unanticipated interactions with newly ordered waters molecules. Comparing recognition between this open cavity and its buried analog begins to isolate the roles of ordered solvent in a system that lends itself readily to prospective testing and that may be broadly useful to the community.

  8. Simultaneous recognition of a carboxylate-containing ligand and an intramolecular surrogate ligand in the crystal structure of an asymmetric vancomycin dimer

    Energy Technology Data Exchange (ETDEWEB)

    Loll, P.J.; Bevivino, A.E.; Korty, B.D.; Axelsen, P.H. [Univ. of Pennsylvania School of Medicine, Philadelphia, PA (United States)

    1997-02-19

    Vancomycin is one of the most important and commonly used antibiotics in hospitals. Despite numerous investigations, however, it is not clear how vancomycin recognizes its site of action in the bacterial cell wall. The increasing incidence of bacterial resistance to vancomycin makes it imperative to understand these recognition determinants so that alternative agents may be developed. Herein we report the first crystal structure of vancomycin. The structure resolves a long-standing controversy about carboxylate recognition by vancomycin, suggests a possible cooperative mechanism linking ligand binding and dimerization, and demonstrates the operation of a novel intramolecular flap which occupies the binding site in the absence of ligand. 45 refs., 5 figs., 1 tab.

  9. Light-Induced Reversible Self-Assembly of Gold Nanoparticles Surface-Immobilized with Coumarin Ligands.

    Science.gov (United States)

    He, Huibin; Feng, Miao; Chen, Qidi; Zhang, Xinqi; Zhan, Hongbing

    2016-01-18

    A novel light-induced reversible self-assembly (LIRSA) system is based on the reversible photodimerization and photocleavage of coumarin groups on the surface of gold nanoparticles (AuNPs) in THF solution. Facilitated by coumarin groups, light irradiation at 365 nm triggers the stable assembly of monodisperse AuNPs; the resulting self-assembly system can be disassembled back to the disassembled state by a relatively short exposure to benign UV light. The reversible self-assembly cycle can be repeated 4 times. A specific concentration range of coumarin ligand and the THF solvent were identified to be the two predominant factors that contribute to the LIRSA of AuNPs. This is the first successful application of reversible photodimerization based on a coumarin derivative in the field of AuNP LIRSA. This LIRSA system may provide unique opportunities for the photoregulated synthesis of many adjustable nanostructures and devices.

  10. Polyphospholyl ligands as building blocks for the formation of polymeric and spherical assemblies

    OpenAIRE

    Heindl, Claudia

    2016-01-01

    This thesis is concerned with polyphospholyl ligands as building blocks for the formation of polymeric and spherical assemblies. Within the scope of this work, the coordination chemistry of 1,2,4-triphosphaferrocenes, 1,2,4-triphospholyl anions and pentaphosphaferrocenes towards Cu(I) halides is investigated. Thereby, the first two substance classes preferably tend to the build-up of novel one-, two- and three-dimensional polymers bearing rather uncommon or even unprecedented structural motif...

  11. Molecular Recognition Directed Self-Assembly of Supramolecular Polymers

    Science.gov (United States)

    1994-06-30

    demonstrated that various substituted gallic acid derivatives can be used to constmict exo-receptors with a tapered shape. "Tihis paper will review...understood self-assembled biological system [3ab.5]. Therefore, we believe it provides an ideal model to be used for the understanding of the principles...governing the self-assembly of synthetic supraimolecular architectures. Synthetic Strategy Used In The Design Of TMV-Like Supramolecular Architectures fl

  12. Molecular recognition in helix-loop-helix and helix-loop-helix-leucine zipper domains. Design of repertoires and selection of high affinity ligands for natural proteins.

    Science.gov (United States)

    Ciarapica, Roberta; Rosati, Jessica; Cesareni, Gianni; Nasi, Sergio

    2003-04-04

    Helix-loop-helix (HLH) and helix-loop-helix-leucine zipper (HLHZip) are dimerization domains that mediate selective pairing among members of a large transcription factor family involved in cell fate determination. To investigate the molecular rules underlying recognition specificity and to isolate molecules interfering with cell proliferation and differentiation control, we assembled two molecular repertoires obtained by directed randomization of the binding surface in these two domains. For this strategy we selected the Heb HLH and Max Zip regions as molecular scaffolds for the randomization process and displayed the two resulting molecular repertoires on lambda phage capsids. By affinity selection, many domains were isolated that bound to the proteins Mad, Rox, MyoD, and Id2 with different levels of affinity. Although several residues along an extended surface within each domain appeared to contribute to dimerization, some key residues critically involved in molecular recognition could be identified. Furthermore, a number of charged residues appeared to act as switch points facilitating partner exchange. By successfully selecting ligands for four of four HLH or HLHZip proteins, we have shown that the repertoires assembled are rather general and possibly contain elements that bind with sufficient affinity to any natural HLH or HLHZip molecule. Thus they represent a valuable source of ligands that could be used as reagents for molecular dissection of functional regulatory pathways.

  13. Nanoparticle assembly on topographical polymer templates: effects of spin rate, nanoparticle size, ligand, and concentration.

    Science.gov (United States)

    Pavan, Mariela J; Ploshnik, Elina; Shenhar, Roy

    2012-11-29

    The ability to assemble nanoparticles (NPs) into desired patterns in a controlled fashion is crucial for the study of collective properties and for the fabrication of a variety of NP-based devices. Drying-mediated assembly directed by a template provides a facile route for organizing NPs in predefined patterns. We utilize the branched topographical landscapes displayed by partially crystallized poly(ethylene glycol) (PEG) films as a generic template for studying the drying-mediated organization of dodecanethiol- and polystyrene thiol-protected gold NPs (Au-DT and Au-PS), and explore the combined effects of NP size and ligand, concentration, and spin rate on the distribution of NPs inside the channels. We show how NP concentration and the spin rate applied during NP deposition can be used to influence the tendency of NPs either to fill the channel uniformly or to localize near the channel edges, explain the important role of the enhanced aggregation tendency of larger NPs on the resulting morphologies, and demonstrate how this tendency can be tuned by the proper choice of ligands. The different effects are explained in the context of possible scenarios of drying-mediated assembly by analyzing the relevant interactions and forces acting on the NPs during solvent evaporation.

  14. Creation of recognition sites for organophosphate esters based on charge transfer and ligand exchange imprinting methods.

    Science.gov (United States)

    Say, Ridvan

    2006-10-01

    This manuscript describes a method for the selective binding behavior of paraoxan and parathion compounds on surface imprinted polymers which were prepared using both charge transfer (CT) (methacryloyl-antipyrine, MAAP) and ligand-exchange (LE) (methacryloyl-antipyrine-gadalonium, MAAP-Gd) monomers. These polymers were prepared in the presence of azobisisobutyronitrile (AIBN) as an initiator and crosslinking EDMA and were imprinted with organophosphate esters. Influence of CT and LE imprinting on the creation of recognition sites toward paraoxan and parathion was determined applying adsorption isotherms. The effect of initial concentration of paraoxan and parathion, adsorption time and imprinting efficiency on adsorption selectivity for MIP-CT and MIP-LE was investigated. Association constant (K(ass)), number of accessible sites (Q(max)), relative selectivity coefficient (k') and binding ability were also evaluated.

  15. Photoassisted photoluminescence fine-tuning of gold nanodots through free radical-mediated ligand-assembly

    Science.gov (United States)

    Tseng, Yu-Ting; Cherng, Rochelle; Harroun, Scott G.; Yuan, Zhiqin; Lin, Tai-Yuan; Wu, Chien-Wei; Chang, Huan-Tsung; Huang, Chih-Ching

    2016-05-01

    In this study, we have developed a simple photoassisted ligand assembly to fine-tune the photoluminescence (PL) of (11-mercaptoundecyl)-N,N,N-trimethylammonium bromide-capped gold nanodots (11-MUTAB-Au NDs). The 11-MUTAB-Au NDs (size: ca. 1.8 nm), obtained from the reaction of gold nanoparticles (ca. 3 nm) and 11-MUTAB, exhibited weak, near-infrared (NIR) PL at 700 nm with a quantum yield (QY) of 0.37% upon excitation at 365 nm. The PL QY of the Au NDs increased to 11.43% after reaction with 11-mercaptoundecanoic acid (11-MUA) for 30 min under ultraviolet (UV) light, which was accompanied by a PL wavelength shift to the green region (~520 nm). UV-light irradiation accelerates 11-MUA assembly on the 11-MUTABAu NDs (11-MUA/11-MUTAB-Au NDs) through a radical-mediated reaction. Furthermore, the PL wavelength of the 11-MUA/11-MUTAB-Au NDs can be switched to 640 nm via cysteamine under UV-light irradiation. We propose that the PL of the Au NDs with NIR and visible emissions was originally from the surface thiol-Au complexes and the Au core, respectively. These dramatically different optical properties of the Au NDs were due to variation in the surface ligands, as well as the densities and surface oxidant states of the surface Au atoms/ions. These effects can be controlled by assembling surface thiol ligands and accelerated by UV irradiation.In this study, we have developed a simple photoassisted ligand assembly to fine-tune the photoluminescence (PL) of (11-mercaptoundecyl)-N,N,N-trimethylammonium bromide-capped gold nanodots (11-MUTAB-Au NDs). The 11-MUTAB-Au NDs (size: ca. 1.8 nm), obtained from the reaction of gold nanoparticles (ca. 3 nm) and 11-MUTAB, exhibited weak, near-infrared (NIR) PL at 700 nm with a quantum yield (QY) of 0.37% upon excitation at 365 nm. The PL QY of the Au NDs increased to 11.43% after reaction with 11-mercaptoundecanoic acid (11-MUA) for 30 min under ultraviolet (UV) light, which was accompanied by a PL wavelength shift to the green region

  16. Sequential Block Copolymer Self-Assemblies Controlled by Metal-Ligand Stoichiometry.

    Science.gov (United States)

    Yin, Liyuan; Wu, Hongwei; Zhu, Mingjie; Zou, Qi; Yan, Qiang; Zhu, Liangliang

    2016-06-28

    While numerous efforts have been devoted to developing easy-to-use probes based on block copolymers for detecting analytes due to their advantages in the fields of self-assembly and sensing, a progressive response on block copolymers in response to a continuing chemical event is not readily achievable. Herein, we report the self-assembly of a 4-piperazinyl-1,8-naphthalimide based functional block copolymer (PS-b-PN), whose self-assembly and photophysics can be controlled by the stoichiometry-dependent metal-ligand interaction upon the side chain. The work takes advantages of (1) stoichiometry-controlled coordination-structural transformation of the piperazinyl moiety on PS-b-PN toward Fe(3+) ions, thereby resulting in a shrinkage-expansion conversion of the self-assembled nanostructures in solution as well as in thin film, and (2) stoichiometry-controlled competition between photoinduced electron transfer and spin-orbital coupling process upon naphthalimide fluorophore leading to a boost-decline emission change of the system. Except Fe(3+) ions, such a stoichiometry-dependent returnable property cannot be observed in the presence of other transition ions. The strategy for realizing the dual-channel sequential response on the basis of the progressively alterable nanomorphologies and emissions might provide deeper insights for the further development of advanced polymeric sensors.

  17. Molecular recognition of DNA by ligands: roughness and complexity of the free energy profile.

    Science.gov (United States)

    Zheng, Wenwei; Vargiu, Attilio Vittorio; Vargiu, Attlio Vittorio; Rohrdanz, Mary A; Carloni, Paolo; Clementi, Cecilia

    2013-10-14

    Understanding the molecular mechanism by which probes and chemotherapeutic agents bind to nucleic acids is a fundamental issue in modern drug design. From a computational perspective, valuable insights are gained by the estimation of free energy landscapes as a function of some collective variables (CVs), which are associated with the molecular recognition event. Unfortunately the choice of CVs is highly non-trivial because of DNA's high flexibility and the presence of multiple association-dissociation events at different locations and/or sliding within the grooves. Here we have applied a modified version of Locally-Scaled Diffusion Map (LSDMap), a nonlinear dimensionality reduction technique for decoupling multiple-timescale dynamics in macromolecular systems, to a metadynamics-based free energy landscape calculated using a set of intuitive CVs. We investigated the binding of the organic drug anthramycin to a DNA 14-mer duplex. By performing an extensive set of metadynamics simulations, we observed sliding of anthramycin along the full-length DNA minor groove, as well as several detachments from multiple sites, including the one identified by X-ray crystallography. As in the case of equilibrium processes, the LSDMap analysis is able to extract the most relevant collective motions, which are associated with the slow processes within the system, i.e., ligand diffusion along the minor groove and dissociation from it. Thus, LSDMap in combination with metadynamics (and possibly every equivalent method) emerges as a powerful method to describe the energetics of ligand binding to DNA without resorting to intuitive ad hoc reaction coordinates.

  18. Structural Diversity of Metallosupramolecular Assemblies Based on the Bent Bridging Ligand 4,4′-Dithiodipyridine

    Directory of Open Access Journals (Sweden)

    Rüdiger W. Seidel

    2013-05-01

    Full Text Available 4,4′-Dithiodipyridine (dtdp, also termed 4,4′-dipyridyldisulfide, is a bridging ligand of the 4,4′-bipyridine type. The introduction of the disulfide moiety inevitably leads to a relatively rigid angular structure, which exhibits axial chirality. More than 90 metal complexes containing the dtdp ligand have been crystallographically characterised until now. This review focuses on the preparation and structural diversity of discrete and polymeric metallosupramolecular assemblies constructed from dtdp as bridging ligands. These encompass metallamacrocycles with M2L2 topology and coordination polymers with periodicity in one or two dimensions. One-dimensional coordination polymers represent the vast majority of the metallosupramolecular structures obtained from dtdp. These include repeated rhomboids, zigzag, helical and arched chains among other types. In this contribution, we make an attempt to provide a comprehensive account of the structural data that are currently available for metallosupramolecular assemblies based on the bent bridging ligand dtdp.

  19. Structural Basis for Ligand Recognition and Discrimination of a Quorum-quenching Antibody

    Energy Technology Data Exchange (ETDEWEB)

    Kirchdoerfer, Robert N.; Garner, Amanda L.; Flack, Caralyn E.; Mee, Jenny M.; Horswill, Alexander R.; Janda, Kim D.; Kaufmann, Gunnar F.; Wilson, Ian A. (Scripps); (Iowa)

    2011-09-16

    In the postantibiotic era, available treatment options for severe bacterial infections caused by methicillin-resistant Staphylococcus aureus have become limited. Therefore, new and innovative approaches are needed to combat such life-threatening infections. Virulence factor expression in S. aureus is regulated in a cell density-dependent manner using 'quorum sensing,' which involves generation and secretion of autoinducing peptides (AIPs) into the surrounding environment to activate a bacterial sensor kinase at a particular threshold concentration. Mouse monoclonal antibody AP4-24H11 was shown previously to blunt quorum sensing-mediated changes in gene expression in vitro and protect mice from a lethal dose of S. aureus by sequestering the AIP signal. We have elucidated the crystal structure of the AP4-24H11 Fab in complex with AIP-4 at 2.5 {angstrom} resolution to determine its mechanism of ligand recognition. A key GluH95 provides much of the binding specificity through formation of hydrogen bonds with each of the four amide nitrogens in the AIP-4 macrocyclic ring. Importantly, these structural data give clues as to the interactions between the cognate staphylococcal AIP receptors AgrC and the AIPs, as AP4-24H11 {center_dot} AIP-4 binding recapitulates features that have been proposed for AgrC-AIP recognition. Additionally, these structural insights may enable the engineering of AIP cross-reactive antibodies or quorum quenching vaccines for use in active or passive immunotherapy for prevention or treatment of S. aureus infections.

  20. Structural basis for ligand recognition and discrimination of a quorum-quenching antibody.

    Science.gov (United States)

    Kirchdoerfer, Robert N; Garner, Amanda L; Flack, Caralyn E; Mee, Jenny M; Horswill, Alexander R; Janda, Kim D; Kaufmann, Gunnar F; Wilson, Ian A

    2011-05-13

    In the postantibiotic era, available treatment options for severe bacterial infections caused by methicillin-resistant Staphylococcus aureus have become limited. Therefore, new and innovative approaches are needed to combat such life-threatening infections. Virulence factor expression in S. aureus is regulated in a cell density-dependent manner using "quorum sensing," which involves generation and secretion of autoinducing peptides (AIPs) into the surrounding environment to activate a bacterial sensor kinase at a particular threshold concentration. Mouse monoclonal antibody AP4-24H11 was shown previously to blunt quorum sensing-mediated changes in gene expression in vitro and protect mice from a lethal dose of S. aureus by sequestering the AIP signal. We have elucidated the crystal structure of the AP4-24H11 Fab in complex with AIP-4 at 2.5 Å resolution to determine its mechanism of ligand recognition. A key Glu(H95) provides much of the binding specificity through formation of hydrogen bonds with each of the four amide nitrogens in the AIP-4 macrocyclic ring. Importantly, these structural data give clues as to the interactions between the cognate staphylococcal AIP receptors AgrC and the AIPs, as AP4-24H11·AIP-4 binding recapitulates features that have been proposed for AgrC-AIP recognition. Additionally, these structural insights may enable the engineering of AIP cross-reactive antibodies or quorum quenching vaccines for use in active or passive immunotherapy for prevention or treatment of S. aureus infections.

  1. Insights into specific DNA recognition during the assembly of a viral genome packaging machine.

    Science.gov (United States)

    de Beer, Tonny; Fang, Jenny; Ortega, Marcos; Yang, Qin; Maes, Levi; Duffy, Carol; Berton, Nancy; Sippy, Jean; Overduin, Michael; Feiss, Michael; Catalano, Carlos Enrique

    2002-05-01

    Terminase enzymes mediate genome "packaging" during the reproduction of DNA viruses. In lambda, the gpNu1 subunit guides site-specific assembly of terminase onto DNA. The structure of the dimeric DNA binding domain of gpNu1 was solved using nuclear magnetic resonance spectroscopy. Its fold contains a unique winged helix-turn-helix (wHTH) motif within a novel scaffold. Surprisingly, a predicted P loop ATP binding motif is in fact the wing of the DNA binding motif. Structural and genetic analysis has identified determinants of DNA recognition specificity within the wHTH motif and the DNA recognition sequence. The structure reveals an unexpected DNA binding mode and provides a mechanistic basis for the concerted action of gpNu1 and Escherichia coli integration host factor during assembly of the packaging machinery.

  2. Molecular recognition between glyconectins as an adhesion self-assembly pathway to multicellularity.

    Science.gov (United States)

    Misevic, Gradimir N; Guerardel, Yann; Sumanovski, Lazar T; Slomianny, Marie-Christine; Demarty, Maurice; Ripoll, Camille; Karamanos, Yannis; Maes, Emmanuel; Popescu, Octavian; Strecker, Gerard

    2004-04-01

    The appearance of multicellular forms of life has been tightly coupled to the ability of an organism to retain its own anatomical integrity and to distinguish self from non-self. Large glycoconjugates, which make up the outermost cell surface layer of all Metazoans, are the primary candidates for the primordial adhesion and recognition functions in biological self-assembly systems. Atomic force microscopy experiments demonstrated that the binding strength between a single pair of Porifera cell surface glyconectin 1 glycoconjugates from Microciona prolifera can hold the weight of 1600 cells, proving their adhesion functions. Here, measurement of molecular self-recognition of glyconectins (GNs) purified from three Porifera species was used as an experimental model for primordial xenogeneic self/non-self discrimination. Physicochemical and biochemical characterization of the three glyconectins, their glycans, and peptides using gel electrophoresis, ultracentrifugation, NMR, mass spectrometry, glycosaminoglycan-degrading enzyme treatment, amino acid and carbohydrate analyses, and peptide mapping showed that GNs define a new family of proteoglycan-like molecules exhibiting species-specific structures with complex and repetitive acidic carbohydrate motives different from the classical proteoglycans and mucins. In functional self-assembly color-coded bead, cell, and blotting assays, glyconectins displayed species-specific recognition and adhesion. Affinity-purified monospecific polyclonal antibodies prepared against GN1, -2, and -3 glycans selectively inhibited cell adhesion of the respective sponge species. These results together with species-specific coaggregation of GN carbohydrate-coated beads with cells showed that GN glycans are functional in cell recognition and adhesion. The specificity of carbohydrate-mediated homophilic GN interactions in Porifera approaches the binding selectivity of the evolutionarily advanced immunoglobulin superfamily. Xenoselectivity of

  3. Structure of the F-spondin Domain of Mindin an Integrin Ligand and Pattern Recognition Molecule

    Energy Technology Data Exchange (ETDEWEB)

    Y Li; C Cao; W Jia; L Yu; M Mo; Q Wang; Y Huang; J Lim; M Ishihara; et. al.

    2011-12-31

    Mindin (spondin-2) is an extracellular matrix protein of unknown structure that is required for efficient T-cell priming by dendritic cells. Additionally, mindin functions as a pattern recognition molecule for initiating innate immune responses. These dual functions are mediated by interactions with integrins and microbial pathogens, respectively. Mindin comprises an N-terminal F-spondin (FS) domain and C-terminal thrombospondin type 1 repeat (TSR). We determined the structure of the FS domain at 1.8-A resolution. The structure revealed an eight-stranded antiparallel beta-sandwich motif resembling that of membrane-targeting C2 domains, including a bound calcium ion. We demonstrated that the FS domain mediates integrin binding and identified the binding site by mutagenesis. The mindin FS domain therefore represents a new integrin ligand. We further showed that mindin recognizes lipopolysaccharide (LPS) through its TSR domain, and obtained evidence that C-mannosylation of the TSR influences LPS binding. Through these dual interactions, the FS and TSR domains of mindin promote activation of both adaptive and innate immune responses.

  4. Structure of the F-Spondin Domain of Mindin, an Integrin Ligand and Pattern Recognition Molecule

    Energy Technology Data Exchange (ETDEWEB)

    Li, Y.; Cao, C; Jia, W; Yu, L; Mo, M; Wang, Q; Huang, Y; Lim, J; Ishihara, M; et. al.

    2009-01-01

    Mindin (spondin-2) is an extracellular matrix protein of unknown structure that is required for efficient T-cell priming by dendritic cells. Additionally, mindin functions as a pattern recognition molecule for initiating innate immune responses. These dual functions are mediated by interactions with integrins and microbial pathogens, respectively. Mindin comprises an N-terminal F-spondin (FS) domain and C-terminal thrombospondin type 1 repeat (TSR). We determined the structure of the FS domain at 1.8-A resolution. The structure revealed an eight-stranded antiparallel ?-sandwich motif resembling that of membrane-targeting C2 domains, including a bound calcium ion. We demonstrated that the FS domain mediates integrin binding and identified the binding site by mutagenesis. The mindin FS domain therefore represents a new integrin ligand. We further showed that mindin recognizes lipopolysaccharide (LPS) through its TSR domain, and obtained evidence that C-mannosylation of the TSR influences LPS binding. Through these dual interactions, the FS and TSR domains of mindin promote activation of both adaptive and innate immune responses.

  5. Structural Insights into Ligand Recognition by a Sensing Domain of the Cooperative Glycine Riboswitch

    Energy Technology Data Exchange (ETDEWEB)

    L Huang; A Serganov; D Patel

    2011-12-31

    Glycine riboswitches regulate gene expression by feedback modulation in response to cooperative binding to glycine. Here, we report on crystal structures of the second glycine-sensing domain from the Vibrio cholerae riboswitch in the ligand-bound and unbound states. This domain adopts a three-helical fold that centers on a three-way junction and accommodates glycine within a bulge-containing binding pocket above the junction. Glycine recognition is facilitated by a pair of bound Mg{sup 2+} cations and governed by specific interactions and shape complementarity with the pocket. A conserved adenine extrudes from the binding pocket and intercalates into the junction implying that glycine binding in the context of the complete riboswitch could impact on gene expression by stabilizing the riboswitch junction and regulatory P1 helix. Analysis of riboswitch interactions in the crystal and footprinting experiments indicates that adjacent glycine-sensing modules of the riboswitch could form specific interdomain interactions, thereby potentially contributing to the cooperative response.

  6. Structure and behavior of human α-thrombin upon ligand recognition: thermodynamic and molecular dynamics studies.

    Directory of Open Access Journals (Sweden)

    Vivian de Almeira Silva

    Full Text Available Thrombin is a serine proteinase that plays a fundamental role in coagulation. In this study, we address the effects of ligand site recognition by alpha-thrombin on conformation and energetics in solution. Active site occupation induces large changes in secondary structure content in thrombin as shown by circular dichroism. Thrombin-D-Phe-Pro-Arg-chloromethyl ketone (PPACK exhibits enhanced equilibrium and kinetic stability compared to free thrombin, whose difference is rooted in the unfolding step. Small-angle X-ray scattering (SAXS measurements in solution reveal an overall similarity in the molecular envelope of thrombin and thrombin-PPACK, which differs from the crystal structure of thrombin. Molecular dynamics simulations performed with thrombin lead to different conformations than the one observed in the crystal structure. These data shed light on the diversity of thrombin conformers not previously observed in crystal structures with distinguished catalytic and conformational behaviors, which might have direct implications on novel strategies to design direct thrombin inhibitors.

  7. Cooperative assembly of Zn cross-linked artificial tripeptides with pendant hydroxyquinoline ligands.

    Science.gov (United States)

    Zhang, Meng; Gallagher, Joy A; Coppock, Matthew B; Pantzar, Lisa M; Williams, Mary Elizabeth

    2012-11-01

    An artificial peptide with three pendant hydroxyquinoline (hq) ligands on a palindromic backbone was designed and used to form multimetallic assemblies. Reaction of the tripeptide with zinc acetate led to a highly fluorescent tripeptide duplex with three Zn(II) coordinative cross-links. The binding process was monitored using spectrophotometric absorbance and emission titrations; NMR spectroscopy and mass spectrometry confirmed the identity and stoichiometry of the product structure. Titrations monitoring duplex formation of the zinc-tripeptide structure had a sigmoidal shape, equilibrium constant larger than the monomeric analogue, and a Hill coefficient >1, all of which indicate positive cooperativity. Photophysical characterization of the quantum yield, excited state lifetime, and polarization anisotropy are compared with the monometallic zinc-hq analogue. A higher than expected quantum yield for the trimetallic complex suggests a structure in which the central chromophore is shielded from solvent by π-stacking with neighboring Zn(II) complexes.

  8. Assembly of an allenylidene ligand, a terminal alkyne, and an acetonitrile molecule: formation of osmacyclopentapyrrole derivatives.

    Science.gov (United States)

    Bolaño, Tamara; Castarlenas, Ricardo; Esteruelas, Miguel A; Oñate, Enrique

    2006-03-29

    Treatment in acetonitrile at -30 C of the hydride-alkenylcarbyne complex [OsH([triple bond]CCH=CPh2)(CH3CN)2(P(i)Pr3)2][BF4]2 (1) with (t)BuOK produces the selective deprotonation of the alkenyl substituent of the carbyne and the formation of the bis-solvento hydride-allenylidene derivative [OsH(=C=C=CPh2)(CH3CN)2(P(i)Pr3)2]BF4 (2), which under carbon monoxide atmosphere is converted into [Os(CH=C=CPh2)(CO)(CH3CN)2(P(i)Pr3)2]BF4 (3). When the treatment of 1 with (t)BuOK is carried out in dichloromethane at room temperature, the fluoro-alkenylcarbyne [OsHF([triple bond]CCH=CPh2)(CH3CN)(P(i)Pr3)2]BF4 (4) is isolated. Complex 2 reacts with terminal alkynes. The reactions with phenylacetylene and cyclohexylacetylene afford [Os[(E)-CH=CHR](=C=C=CPh2)(CH3CN)2(P(i)Pr3)2]BF4 (R = Ph (5), Cy (6)), containing an alkenyl ligand beside the allenylidene, while the reaction with acetylene in dichloromethane at -20 degrees C gives the hydride-allenylidene-pi-alkyne [OsH(=C=C=CPh2)(eta2-HC[triple bond]CH)(P(i)Pr3)2]BF4 (7), with the alkyne acting as a four-electron donor ligand. In acetonitrile under reflux, complexes 5 and 6 are transformed into the osmacyclopentapyrrole compounds [Os[C=C(CPh2CR=CH)CMe=NH](CH3CN)2]BF4 (R = Ph (8), Cy (9)), as a result of the assembly of the allenylidene ligand, the alkenyl group, and an acetonitrile molecule. The X-ray structures of 2, 5, and 8 are also reported.

  9. Multicomponent assembly of fluorescent-tag functionalized ligands in metal-organic frameworks for sensing explosives.

    Science.gov (United States)

    Gole, Bappaditya; Bar, Arun Kumar; Mukherjee, Partha Sarathi

    2014-10-01

    Detection of trace amounts of explosive materials is significantly important for security concerns and pollution control. Four multicomponent metal-organic frameworks (MOFs-12, 13, 23, and 123) have been synthesized by employing ligands embedded with fluorescent tags. The multicomponent assembly of the ligands was utilized to acquire a diverse electronic behavior of the MOFs and the fluorescent tags were strategically chosen to enhance the electron density in the MOFs. The phase purity of the MOFs was established by PXRD, NMR spectroscopy, and finally by single-crystal XRD. Single-crystal structures of the MOFs-12 and 13 showed the formation of three-dimensional porous networks with the aromatic tags projecting inwardly into the pores. These electron-rich MOFs were utilized for detection of explosive nitroaromatic compounds (NACs) through fluorescence quenching with high selectivity and sensitivity. The rate of fluorescence quenching for all the MOFs follows the order of electron deficiency of the NACs. We also showed the detection of picric acid (PA) by luminescent MOFs is not always reliable and can be misleading. This attracts our attention to explore these MOFs for sensing picryl chloride (PC), which is as explosive as picric acid and used widely to prepare more stable explosives like 2,4,6-trinitroaniline from PA. Moreover, the recyclability and sensitivity studies indicated that these MOFs can be reused several times with parts per billion (ppb) levels of sensitivity towards PC and 2,4,6-trinitrotoluene (TNT).

  10. Structure of a glycomimetic ligand in the carbohydrate recognition domain of C-type lectin DC-SIGN. Structural requirements for selectivity and ligand design.

    Science.gov (United States)

    Thépaut, Michel; Guzzi, Cinzia; Sutkeviciute, Ieva; Sattin, Sara; Ribeiro-Viana, Renato; Varga, Norbert; Chabrol, Eric; Rojo, Javier; Bernardi, Anna; Angulo, Jesus; Nieto, Pedro M; Fieschi, Franck

    2013-02-20

    In genital mucosa, different fates are described for HIV according to the subtype of dendritic cells (DCs) involved in its recognition. This notably depends on the C-type lectin receptor, langerin or DC-SIGN, involved in gp120 interaction. Langerin blocks HIV transmission by its internalization in specific organelles of Langerhans cells. On the contrary, DC-SIGN enhances HIV trans-infection of T lymphocytes. Thus, approaches aiming to inhibit DC-SIGN, without blocking langerin, represent attractive anti-HIV strategies. We previously demonstrated that dendrons bearing multiple copies of glycomimetic compounds were able to block DC-SIGN-dependent HIV infection in cervical explant models. Optimization of such ligand requires detailed characterization of its binding mode. In the present work, we determined the first high-resolution structure of a glycomimetic/DC-SIGN complex by X-ray crystallography. This glycomimetic, pseudo-1,2-mannobioside, shares shape and conformational properties with Manα1-2Man, its natural counterpart. However, it uses the binding epitope previously described for Lewis X, a ligand specific for DC-SIGN among the C-type lectin family. Thus, selectivity gain for DC-SIGN versus langerin is observed with pseudo-1,2-mannobioside as shown by surface plasmon resonance analysis. In parallel, ligand binding was also analyzed by TR-NOESY and STD NMR experiments, combined with the CORCEMA-ST protocol. These studies demonstrate that the complex, defined by X-ray crystallography, represents the unique binding mode of this ligand as opposed to the several binding orientations described for the natural ligand. This exclusive binding mode and its selective interaction properties position this glycomimetic as a good lead compound for rational improvement based on a structurally driven approach.

  11. Self-assembly of metallosupramolecular rhombi from chiral concave 9,9’-spirobifluorene-derived bis(pyridine ligands

    Directory of Open Access Journals (Sweden)

    Rainer Hovorka

    2014-02-01

    Full Text Available Two new 9,9’-spirobifluorene-based bis(4-pyridines were synthesised in enantiopure and one also in racemic form. These ligands act as concave templates and form metallosupramolecular [(dppp2M2L2] rhombi with cis-protected [(dpppPd]2+ and [(dpppPt]2+ ions. The self-assembly process of the racemic ligand preferably occurs in a narcissistic self-recognising manner. Hence, a mixture of all three possible stereoisomers [(dppp2M2{(R-L}2](OTf4, [(dppp2M2{(S-L}2](OTf4, and [(dppp2M2{(R-L}{(S-L}](OTf4 was obtained in an approximate 1.5:1.5:1 ratio which corresponds to an amplification of the homochiral assemblies by a factor of approximately three as evidenced by NMR spectroscopy and mass spectrometry. The racemic homochiral assemblies could also be characterised by single crystal X-ray diffraction.

  12. Effect of ligand self-assembly on nanostructure and carrier transport behaviour in CdSe quantum dots

    Energy Technology Data Exchange (ETDEWEB)

    Li, Kuiying, E-mail: kuiyingli@ysu.edu.cn; Xue, Zhenjie

    2014-11-14

    Adjustment of the nanostructure and carrier behaviour of CdSe quantum dots (QDs) by varying the ligands used during QD synthesis enables the design of specific quantum devices via a self-assembly process of the QD core–shell structure without additional technologies. Surface photovoltaic (SPV) technology supplemented by X-ray diffractometry and infrared absorption spectroscopy were used to probe the characteristics of these QDs. Our study reveals that while CdSe QDs synthesized in the presence of and capped by thioglycolic acid, 3-mercaptopropionic acid, mercaptoethanol or α-thioglycerol ligands display zinc blende nanocrystalline structures, CdSe QDs modified by L-cysteine possess wurtzite nanocrystalline structures, because different end groups in these ligands induce distinctive nucleation and growth mechanisms. Carboxyl end groups in the ligand served to increase the SPV response of the QDs, when illuminated by hν ≥ E{sub g,nano-CdSe}. Increased length of the alkyl chains and side-chain radicals in the ligands partially inhibit photo-generated free charge carrier (FCC) transfer transitions of CdSe QDs illuminated by photon energy of 4.13 to 2.14 eV. The terminal hydroxyl group might better accommodate energy released in the non-radiative de-excitation process of photo-generated FCCs in the ligand's lowest unoccupied molecular orbital in the 300–580 nm wavelength region, when compared with other ligand end groups. - Highlights: • CdSe QDs modified by L-cysteine possess wurtzite nanocrystalline structures. • Carboxyl end groups in the ligand serve to increase the SPV response of CdSe QDs. • Terminal hydroxyl group in the ligand might accommodate non-radiative de-excitation process in CdSe QDs. • Increased length of the alkyl chains and side-chain radicals in the ligands partially inhibit carriers transport of CdSe QDs.

  13. Secondary ligand-directed assembly of Co(II) coordination polymers based on a pyridine carboxylate ligand

    Energy Technology Data Exchange (ETDEWEB)

    Cao, Ke-Li; Zhang, Yi-Ping; Cai, Yi-Ni; Xu, Xiao-Wei; Feng, Yun-Long, E-mail: sky37@zjnu.cn

    2014-07-01

    To investigate the influence of hydrogen bonds and secondary ligands on the structures and properties of the resulting frameworks, five new Co(II) compounds have been synthesized by the reactions of Co(II) salts and 3,5-bis(pyridin-4-ylmethoxy)benzoic acid (HL) with four rationally selected dicarboxylic acid ligands. Without secondary ligand, we got one compound [CoL{sub 2}(H{sub 2}O){sub 2}]{sub n}·2nH{sub 2}O (1), which possesses a 1D chain structure. In the presence of ancillary ligands, namely, 1,3-adamantanedicarboxylic acid (H{sub 2}adbc), terephthalic acid (H{sub 2}tpa), thiophene-2,5-dicarboxylic acid (H{sub 2}tdc) and 1,4-benzenedithioacetic acid (H{sub 2}bdtc), four 3D structures [Co{sub 2}L{sub 2}(adbc)]{sub n}·nH{sub 2}O (2), [Co{sub 2}L{sub 2}(tpa)]{sub n} (3), [Co{sub 2}L{sub 2}(tdc)]{sub n} (4), [Co{sub 2}L{sub 2}(bdtc)(H{sub 2}O)]{sub n} (5) were obtained, respectively. It can be observed from the architectures of 1–5 that hydrogen bonds and secondary ligands both have great effects on the spatial connective fashions, resulting in the formation of various dimensional compounds. The XRPD, TGA data of title polymers and the magnetic properties for 2 and 5 have also been investigated. - Graphical abstract: The structural differences show that the ancillary ligands have great effects on the spatial connective fashions, resulting in the formation of various dimensional compounds. - Highlights: • Five new Co(II) coordination polymers have been synthesized by solvothermal reactions based on 3,5-bis(pyridin-4-ylmethoxy)benzoic acid (HL). • The long-flexible ligand (HL) is a good candidate to produce interpenetrating architectures. • The secondary dicarboxylic acid ligands play important roles in the spatial connective fashions and the formation of various dimensional compounds. • The magnetism studies show that both 2 and 5 exhibit antiferromagnetic interactions.

  14. Recognition of Kinematic Joints of 3D Assembly Models Based on Reciprocal Screw Theory

    Directory of Open Access Journals (Sweden)

    Tao Xiong

    2016-01-01

    Full Text Available Reciprocal screw theory is used to recognize the kinematic joints of assemblies restricted by arbitrary combinations of geometry constraints. Kinematic analysis is common for reaching a satisfactory design. If a machine is large and the incidence of redesign frequent is high, then it becomes imperative to have fast analysis-redesign-reanalysis cycles. This work addresses this problem by providing recognition technology for converting a 3D assembly model into a kinematic joint model, which is represented by a graph of parts with kinematic joints among them. The three basic components of the geometric constraints are described in terms of wrench, and it is thus easy to model each common assembly constraint. At the same time, several different types of kinematic joints in practice are presented in terms of twist. For the reciprocal product of a twist and wrench, which is equal to zero, the geometry constraints can be converted into the corresponding kinematic joints as a result. To eliminate completely the redundant components of different geometry constraints that act upon the same part, the specific operation of a matrix space is applied. This ability is useful in supporting the kinematic design of properly constrained assemblies in CAD systems.

  15. Assembly of three novel metal (II) complexes based on polycarboxylate and 1,10-phenanthroline ligands

    Science.gov (United States)

    Chen, Xiaoli; Qiao, Yali; Gao, Loujun; Cui, Huali; Zhang, Meili; Lv, Junfang

    2013-04-01

    With the principles of crystal engineering, three novel metal(II) complexes, [Cu2(betd)(phen)4].15H2O (1), [Cd4(betd)2(phen)8]ṡ28H2O (2) and {[Co2(betd)(phen)2(H2O)2]·2H2O}n (3) (H4betd = bicyclo[2.2.2]oct-7-ene-2,3,5,6-tetracarboxylic acid, phen = 1,10-phenanthroline) were synthesized and structurally characterized by elemental analyses, IR spectroscopy, single-crystal X-ray diffraction analyses, TGA, powder XRD and fluorescent measurements. Complex 1 is a binuclear structure, novel water tapes are observed to be encapsulated in the 3D open supramolecular architecture by hydrogen bond interactions. In 2, two pairs of CdII ions joined with two (betd)4- ions to form a cyclic tetranuclear structure. The neighboring tetranuclear units are linked into 2D network through π⋯π stacking interactions. Interestingly, the lattice H2O molecules are joined by strong hydrogen bond interactions generating a wavy water layer, which contacts the 2D network to form 3D supramolecular structure. 3 shows a 2D (4, 4) grid network, which are assembled in an ABAB sequence to 3D supramolecular structures via π⋯π stacking interactions between two central phen ligands from two adjacent sheets and hydrogen bond interactions.

  16. Recognition of glycoprotein peroxidase via Con A-carrying self-assembly layer on gold.

    Science.gov (United States)

    Liu, Songqin; Wang, Kewei; Du, Dan; Sun, Yueming; He, Lin

    2007-07-01

    We have successfully fabricated a self-assembled layer of concanavalin A (Con A) on a gold surface for recognition of glycoproteins. The type IV Con A is covalently bound to 11-mercaptoundecanoic acid (MUA) on gold with a 2-(5-norbornene-2,3-dicarboximido)-1,1,3,3-tetramethyluronium tetrafluoroborate (TNTU) linkage. The binding interaction between glycoproteins and self-assembled Con A is studied using horseradish peroxidase (HRP) as a model glycoprotein. Voltammetric, electrochemical impedance studies, and photometric activity measurements show the presence of both specific and nonspecific bindings of HRP to the Con A interface. The specific binding is attributed to the Con A-sugar interaction where Con A selectively recognizes the glycosylation sites of HRP. The catalytic current of the HRP-loaded electrode, because of catalytic oxidation of thionine in the presence of hydrogen peroxide (H2O2), is found to be proportional to the HRP concentrations in the incubation solution. A linear correlation coefficient of 0.993 was obtained over a wide HRP concentration range of 12.5 microg/mL to 1 mg/mL. The approach described in this study provides a simple yet selective means to immobilize glycoproteins on a solid support. The specific binding achieved is desirable in biosensor fabrication, glycoprotein separation, recognition, and purification as well as in drug-releasing systems.

  17. Structure of a class II preQ1 riboswitch reveals ligand recognition by a new fold.

    Science.gov (United States)

    Liberman, Joseph A; Salim, Mohammad; Krucinska, Jolanta; Wedekind, Joseph E

    2013-06-01

    PreQ1 riboswitches regulate genes by binding the pyrrolopyrimidine intermediate preQ1 during the biosynthesis of the essential tRNA base queuosine. We report what is to our knowledge the first preQ1-II riboswitch structure at 2.3-Å resolution, which uses a previously uncharacterized fold to achieve effector recognition at the confluence of a three-way helical junction flanking a pseudoknotted ribosome-binding site. The results account for translational control mediated by the preQ1-II riboswitch class and expand the known repertoire of ligand-binding modes used by regulatory RNAs.

  18. Exploring the role of water in molecular recognition: predicting protein ligandability using a combinatorial search of surface hydration sites

    Science.gov (United States)

    Vukovic, Sinisa; Brennan, Paul E.; Huggins, David J.

    2016-09-01

    The interaction between any two biological molecules must compete with their interaction with water molecules. This makes water the most important molecule in medicine, as it controls the interactions of every therapeutic with its target. A small molecule binding to a protein is able to recognize a unique binding site on a protein by displacing bound water molecules from specific hydration sites. Quantifying the interactions of these water molecules allows us to estimate the potential of the protein to bind a small molecule. This is referred to as ligandability. In the study, we describe a method to predict ligandability by performing a search of all possible combinations of hydration sites on protein surfaces. We predict ligandability as the summed binding free energy for each of the constituent hydration sites, computed using inhomogeneous fluid solvation theory. We compared the predicted ligandability with the maximum observed binding affinity for 20 proteins in the human bromodomain family. Based on this comparison, it was determined that effective inhibitors have been developed for the majority of bromodomains, in the range from 10 to 100 nM. However, we predict that more potent inhibitors can be developed for the bromodomains BPTF and BRD7 with relative ease, but that further efforts to develop inhibitors for ATAD2 will be extremely challenging. We have also made predictions for the 14 bromodomains with no reported small molecule K d values by isothermal titration calorimetry. The calculations predict that PBRM1(1) will be a challenging target, while others such as TAF1L(2), PBRM1(4) and TAF1(2), should be highly ligandable. As an outcome of this work, we assembled a database of experimental maximal K d that can serve as a community resource assisting medicinal chemistry efforts focused on BRDs. Effective prediction of ligandability would be a very useful tool in the drug discovery process.

  19. Hand Gesture Modeling and Recognition for Human and Robot Interactive Assembly Using Hidden Markov Models

    Directory of Open Access Journals (Sweden)

    Fei Chen

    2015-04-01

    Full Text Available Gesture recognition is essential for human and robot collaboration. Within an industrial hybrid assembly cell, the performance of such a system significantly affects the safety of human workers. This work presents an approach to recognizing hand gestures accurately during an assembly task while in collaboration with a robot co-worker. We have designed and developed a sensor system for measuring natural human-robot interactions. The position and rotation information of a human worker’s hands and fingertips are tracked in 3D space while completing a task. A modified chain-code method is proposed to describe the motion trajectory of the measured hands and fingertips. The Hidden Markov Model (HMM method is adopted to recognize patterns via data streams and identify workers’ gesture patterns and assembly intentions. The effectiveness of the proposed system is verified by experimental results. The outcome demonstrates that the proposed system is able to automatically segment the data streams and recognize the gesture patterns thus represented with a reasonable accuracy ratio.

  20. Assembly of tetra, di and mononuclear molecular cadmium phosphonates using 2,4,6-triisopropylphenylphosponic acid and ancillary ligands.

    Science.gov (United States)

    Chandrasekhar, Vadapalli; Sasikumar, Palani; Boomishankar, Ramamoorthy

    2008-10-14

    The reaction of ArPO(3)H(2) (Ar = 2,4,6-iPr(3)-C(6)H(2)) with Cd(CH(3)COO)(2).2H(2)O using various co-ligands such as methanol, dimethylformamide (DMF) and 3,5-dimethylpyrazole (DMPZH) resulted in the formation of tetranuclear assemblies [Cd(4)(ArPO(3))(2)(ArPO(3)H)(4)(CH(3)OH)(4)].3(CH(3)OH) (1), [Cd(4)(ArPO(3))(2)(ArPO(3)H)(4)(DMF)(4)].3(DMF) (2) and [Cd(4)(ArPO(3))(2)(ArPO(3)H)(4)(DMF)(2)(DMPZH)(2)].2(DMF).2(H(2)O) (3). In all of these compounds the tetranuclear cadmium array, containing two five-coordinate and two six-coordinate cadmium atoms, is held together by two mu(4) capping [ArPO(3)](2-) and four anisobidentate mu(2) [ArPO(2)(OH)](-) ligands. Each cadmium atom is bound to an additional ancillary ligand. The reaction of ArPO(3)H(2) with Cd(CH(3)COO)(2).2H(2)O in the presence of the chelating ligand 2,2'-bipyridine (bipy) leads to the exclusive formation of the dinuclear assembly [Cd(2)(ArPO(3)H)(4)(bipy)(2)].(CH(3)OH)(H(2)O) (4). The latter contains an eight-membered Cd(2)P(2)O(4) inorganic ring formed as a result of the bridging coordination action of two anisobidentate mu(2) [ArPO(2)(OH)](-) ligands. Each cadmium atom is bound by one chelating bipy and one monodentate [ArPO(2)(OH)](-) ligands. Use of four equivalents of 3,5-dimethylpyrazole leads to the formation of the mononuclear derivative [Cd(ArPO(3)H)(2)(DMPZH)(4)] (5). The molecular structure of the latter comprises of a central cadmium atom surrounded by six monodentate ligands. Four of these are neutral pyrazole ligands that occupy the equatorial plane; the remaining two are anionic phosphinate ligands which are present trans to each other. The thermal analysis of 1 and 4 reveals that the char residue obtained at 600 degrees C consists predominantly of Cd(2)P(2)O(7).

  1. Graphene–cyclodextrin–cytochrome c layered assembly with improved electron transfer rate and high supramolecular recognition capability

    Energy Technology Data Exchange (ETDEWEB)

    Gong, Cheng-Bin; Guo, Cong-Cong; Jiang, Dan; Tang, Qian, E-mail: qiantang@swu.edu.cn; Liu, Chang-Hua; Ma, Xue-Bing

    2014-06-01

    This study aimed to develop a new graphene-based layered assembly, named graphene–cyclodextrin–cytochrome c with improved electron transfer rate. This assembly has combined high conductivity of graphene nanosheets (GNs), selectively binding properties and electronegativity of cyclodextrins (CDs), as well as electropositivity of cytochrome c (Cyt c). This assembly can also mimic the confined environments of the intermembrane space of mitochondria. A β-cyclodextrin (β-CD) functionalized GN (GN–CD) assembly was initially prepared by a simple wet-chemical strategy, i.e., in situ thermal reduction of graphene oxide with hydrazine hydrate in the presence of β-CD. Cyt c was then intercalated to the GN–CD assembly to form a layered self-assembled structure, GN–CD–Cyt c, through electrostatic interaction. Compared with GNs and GN–CD, GN–CD–Cyt c assembly displayed improved electron transfer rate and high supramolecular recognition capability toward six probe molecules. - Highlights: • A new tertiary layered assembly named GN–CD–Cyt c was prepared. • Compared with GNs and GN–CD, GN–CD–Cyt c shows improved electron transfer rate. • GN–CD–Cyt c displays high supramolecular recognition capability.

  2. Comparative analysis of species-specific ligand recognition in Toll-like receptor 8 signaling: a hypothesis.

    Directory of Open Access Journals (Sweden)

    Rajiv Gandhi Govindaraj

    Full Text Available Toll-like receptors (TLRs play a central role in the innate immune response by recognizing conserved structural patterns in a variety of microbes. TLRs are classified into six families, of which TLR7 family members include TLR7, 8, and 9, which are localized to endolysosomal compartments recognizing viral infection in the form of foreign nucleic acids. In our current study, we focused on TLR8, which has been shown to recognize different types of ligands such as viral or bacterial ssRNA as well as small synthetic molecules. The primary sequences of rodent and non-rodent TLR8s are similar, but the antiviral compound (R848 that activates the TLR8 pathway is species-specific. Moreover, the factors underlying the receptor's species-specificity remain unknown. To this end, comparative homology modeling, molecular dynamics simulations refinement, automated docking and computational mutagenesis studies were employed to probe the intermolecular interactions between this anti-viral compound and TLR8. Furthermore, comparative analyses of modeled TLR8 (rodent and non-rodent structures have shown that the variation mainly occurs at LRR14-15 (undefined region; hence, we hypothesized that this variation may be the primary reason for the exhibited species-specificity. Our hypothesis was further bolstered by our docking studies, which clearly showed that this undefined region was in close proximity to the ligand-binding site and thus may play a key role in ligand recognition. In addition, the interface between the ligand and TLR8s varied depending upon the amino acid charges, free energy of binding, and interaction surface. Therefore, our current work provides a hypothesis for previous in vivo studies in the context of TLR signaling.

  3. Cooperation between lateral ligand mobility and accessibility for receptor recognition in selectin-induced cell rolling

    NARCIS (Netherlands)

    Bakowsky, U; Schumacher, G; Gege, C; Schmidt, RR; Rothe, U; Bendas, G

    2002-01-01

    Selectin-induced leukocyte rolling along the endothelial surface is an essential step in the immune response. Several in vitro studies showed that this cell rolling is a highly regulated adhesion phenomenon, controlled by the kinetics and forces of selectin-ligand interactions. In the flow chamber s

  4. Understanding recognition and self-assembly in biology using the chemist's toolbox. Insight into medicinal chemistry.

    Science.gov (United States)

    Quirolo, Z B; Benedini, L A; Sequeira, M A; Herrera, M G; Veuthey, T V; Dodero, V I

    2014-01-01

    Medicinal chemistry is intimately connected with basic science such as organic synthesis, chemical biology and biophysical chemistry among other disciplines. The reason of such connections is due to the power of organic synthesis to provide designed molecules; chemical biology to give tools to discover biological and/or pathological pathways and biophysical chemistry which provides the techniques to characterize and the theoretical background to understand molecular behaviour. The present review provides some selective examples of these research areas. Initially, template dsDNA organic synthesis and the spatio-temporal control of transcription are presenting following by the supramolecular entities used in drug delivery, such as liposomes and liquid crystal among others. Finally, peptides and protein self-assembly is connected with biomaterials and as an important event in the balance between health and disease. The final aim of the present review is to show the power of chemical tools not only for the synthesis of new molecules but also to improve our understanding of recognition and self-assembly in the biological context.

  5. A solvent-controlled switch of manganese complex assemblies with a beta-diketonate-based ligand.

    Science.gov (United States)

    Aromí, Guillem; Gamez, Patrick; Roubeau, Olivier; Berzal, Paula Carrero; Kooijman, Huub; Spek, Anthony L; Driessen, Willem L; Reedijk, Jan

    2002-07-15

    The coordination properties of the new polynucleating ligand H(3)L1 (1,3-bis(3-oxo-3-phenylpropionyl)-2-hydroxy-5-methylbenzene) with Mn(II/III) are described. Depending on the solvent used, the reaction of H(3)L1 with Mn(OAc)(2) yields either of the two new multinuclear assemblies [Mn(2)(HL1)(2)(py)(4)] (1) and [Mn(3)(HL1)(3)] (2), as revealed by X-ray crystallography. The structure of 2 is remarkable in that it shows a unique asymmetric triple-stranded helicate. Complexes 1 and 2 can be interconverted by controlling the solvent of the reaction system, and therefore, this ensemble constitutes an interesting externally addressable switch. In the presence of Mn(III)/pyridine, partial degradation of H(3)L1 occurs via oxidative cleavage, and the new complex [Mn(2)(L2)(2)(py)(4)] (3) is formed. The crystal structure of this complex has shown the fully deprotonated form of the new donor H(3)L2 (3-(3-oxo-3-phenylpropionyl)-5-methylsalicylic acid). From the same reaction, the Mn(II) complex 1 is also obtained. A rational synthesis of H(3)L2 is reported, and this has been used to prepare 3 in high yields, directly from its components. Variable-temperature magnetic susceptibility (chi(m)) measurements were performed on complexes 1-3 under a magnetic field of 1 kG. The data for each complex were fit to the appropriate chi(m) vs T theoretical equation, respectively. In 1, the Mn(II) ions are uncoupled, with g = 2.01. The data from 2 were fit by assuming the presence of an exchange coupled Mn(II)...Mn(II) pair next to a magnetically isolated Mn(II) center. The fit gave J = -2.75 cm(-1), g(12) = 1.97, and g(3) = 1.92, respectively. In 3, two models fit the experimental data. In the most satisfactory, the Mn(III) ions are coupled antiferromagnetically with J = -1.48 cm(-1) and g = 1.98 and a term for weak ferromagnetic intermolecular exchange is included with zJ' = 0.39 cm(-1). The other model contemplates the presence of two uncoupled zero field split Mn(III) ions.

  6. Roles of mammalian structural units, ligand cluster and polyvalency in the Abrus precatorius agglutinin and glycoprotein recognition process.

    Science.gov (United States)

    Wu, Albert M; Wu, June H; Liu, Jia-Hau; Chen, Yuen-Yuen; Singha, Biswajit; Chow, Lu-Ping; Lin, Jung-Yaw

    2009-10-01

    Previous studies on one of the toxic type 2 ribosome inactivating proteins (RIP), Abrus precatorius agglutinin (APA), have shown that the recognition domains of APA are restricted to monomers of Galbeta1-3GalNAc (T, Thomsen-Friedenreich glycotope) and Galbeta1-3/4GlcNAc (blood group precursor type I/II sequences); which are essential but play a minor role in the recognition process. In this study, APA recognition factors were expanded to include ligand clusters and polyvalent glycotopes by enzyme-linked lectinosorbent binding and inhibition assays. Based on the results of molar relative potency, the essential mammalian structural units are Galbeta1-3GalNAcalpha/beta1- (T(alpha)/T(beta))>Galalpha1-4Gal (E)>Galbeta1-3/4GlcNAc (I/II) and avidity for tri-/di-antennary II(beta), T, E and II monomers was found to be 7.1 x 10(2), 4.0, 5.5, 3.7 and 2.4 times higher than monomeric Gal. Among natural polyvalent glycotopes or clusters, high-density polyvalent T(alpha) and complex multivalent I(beta)/II(beta) glycotopes greatly enhanced the affinity for APA over 10(4) times. Based on these results, it is concluded that contribution of monomeric T(alpha), II(beta), I(beta), E(beta) and their clusters and polyvalency play critical roles in this recognition process. The binding intensities of these factors in decreasing order are: polyvalent T(alpha), II(beta)/I(beta) and E(beta)>tri-antennary II(beta)>monomeric T(alpha), T(beta), I and II>Gal>GalNAc (weak). As one of type 2 RIP lectins, these recognition factors of the B chain are likely to be crucial for attachment and endocytosis. A comparison of the differential recognition factors and combining sites of APA with those of other lectins (Ricinus communis agglutinin, RCA(1) and ricin) is also illustrated.

  7. DMBT1 functions as pattern-recognition molecule for poly-sulfated and poly-phosphorylated ligands

    DEFF Research Database (Denmark)

    End, Caroline; Bikker, Floris; Renner, Marcus;

    2009-01-01

    Deleted in malignant brain tumors 1 (DMBT1) is a secreted glycoprotein displaying a broad bacterial-binding spectrum. Recent functional and genetic studies linked DMBT1 to the suppression of LPS-induced TLR4-mediated NF-kappaB activation and to the pathogenesis of Crohn's disease. Here, we aimed...... that DMBT1 functions as pattern-recognition molecule for poly-sulfated and poly-phosphorylated ligands providing a molecular basis for its broad bacterial-binding specificity and its inhibitory effects on LPS-induced TLR4-mediated NF-kappaB activation....... at unraveling the molecular basis of its function in mucosal protection and of its broad pathogen-binding specificity. We report that DMBT1 directly interacts with dextran sulfate sodium (DSS) and carrageenan, a structurally similar sulfated polysaccharide, which is used as a texturizer and thickener in human...

  8. The cell recognition model in chlorolichens involving a fungal lectin binding to an algal ligand can be extended to cyanolichens.

    Science.gov (United States)

    Vivas, M; Sacristán, M; Legaz, M E; Vicente, C

    2010-07-01

    Leptogium corniculatum, a cyanolichen containing Nostoc as photobiont, produces and secretes arginase to culture medium containing arginine. This secreted arginase was pre-purified by affinity chromatography on beads of activated agarose to which a polygalactosylated urease, purified from Evernia prunastri, was attached. Arginase was eluted from the beads with 50 mm alpha-d-galactose. The eluted arginase binds preferentially to the cell surface of Nostoc isolated from this lichen thallus, although it is also able to bind, to some extent, to the cell surface of the chlorobiont isolated from E. prunastri. Previous studies in chlorolichens have shown that a fungal lectin that develops subsidiary arginase activity can be a factor in recognition of compatible algal cells through binding to a polygalactosylated urease, which acts as a lectin ligand in the algal cell wall. Our experiments demonstrate that this model can now be extended to cyanolichens.

  9. Synthesis of Janus-like gold nanoparticles with hydrophilic/hydrophobic faces by surface ligand exchange and their self-assemblies in water.

    Science.gov (United States)

    Iida, Ryo; Kawamura, Hitoshi; Niikura, Kenichi; Kimura, Takashi; Sekiguchi, Shota; Joti, Yasumasa; Bessho, Yoshitaka; Mitomo, Hideyuki; Nishino, Yoshinori; Ijiro, Kuniharu

    2015-04-14

    This study aims at the synthesis of Janus gold nanoparticles (Janus GNPs) with hydrophilic/hydrophobic faces by a simple ligand exchange reaction in an homogeneous system and at the elucidation of the self-assembled structures of the Janus GNPs in water. As hydrophilic surface ligands, we synthesized hexaethylene glycol (E6)-terminated thiolate ligands with C3, C7, or C11 alkyl chains, referred to as E6C3, E6C7, and E6C11, respectively. As a hydrophobic ligand, a butyl-headed thiolate ligand C4-E6C11, in which a C4 alkyl was introduced on the E6C11 terminus, was synthesized. The degree of segregation between the two ligands on the GNPs (5 nm in diameter) was examined by matrix-assisted laser desorption/ionization time-of fright mass spectrometry (MALDI-TOF MS) analysis. We found that the choice of immobilization methods, one-step or two-step addition of the two ligands to the GNP solution, crucially affects the degree of segregation. The two-step addition of a hydrophilic ligand (E6C3) followed by a hydrophobic ligand (C4-E6C11) produced a large degree of segregation on the GNPs, providing Janus-like GNPs. When dispersed in water, these Janus-like GNPs formed assemblies of ∼160 nm in diameter, whereas Domain GNPs, in which the two ligands formed partial domains on the surface, were precipitated even when the molar ratio of the hydrophilic ligand and the hydrophobic ligand on the surface of the NPs was almost 1:1. The assembled structure of the Janus-like GNPs in water was directly observed by pulsed coherent X-ray solution scattering using an X-ray free-electron laser, revealing irregular spherical structures with uneven surfaces.

  10. Electronic structures of ruthenium complexes encircling non-innocent ligand assembly

    Indian Academy of Sciences (India)

    Amit Das; Dipanwita Das; Tanaya Kundu; Goutam Kumar Lahiri

    2012-11-01

    Electronic structural forms of selected mononuclear and dinuclear ruthenium complexes encompassing redox non-innocent terminal as well as bridging ligands have been addressed. The sensitive valence and spin situations of the complexes have been established in the native and accessible redox states via detailed analysis of their crystal structures, electrochemistry, UV/VIS/NIR spectroelectrochemistry, EPR signatures at the paramagnetic states and DFT calculations. Mononuclear complexes exhibit significant variations in valence and spin distribution processes based on the simple modification of the non-innocent ligand frameworks as well as electronic nature of the co-ligands, -donating or -accepting. Dinuclear complexes with modified pyrazine, -quinone and azo-derived redox-active bridging ligands show complex features including redoxinduced electron-transfer (RIET), remote metal to metal spin-interaction in a three-spin metal-bridge-metal arrangement as well as electron-transfer driven chemical transformation (EC).

  11. Modulation of neuronal serotonin uptake by a putative endogenous ligand of imipramine recognition sites.

    OpenAIRE

    Barbaccia, M. L.; Gandolfi, O; Chuang, D M; Costa, E

    1983-01-01

    Imipramine inhibits the serotonin uptake by binding with high affinity to regulatory sites of this uptake located on axons that release serotonin. The number of imipramine recognition sites located on crude synaptic membrane preparations is reduced by two daily injections of imipramine or desmethylimipramine for 3 weeks. When the binding sites for [3H]imipramine are down-regulated the Vmax of the neuronal uptake of serotonin is increased. Moreover, in minces prepared from the brain hippocampu...

  12. Exchanging ligand-binding specificity between a pair of mouse olfactory receptor paralogs reveals odorant recognition principles.

    Science.gov (United States)

    Baud, Olivia; Yuan, Shuguang; Veya, Luc; Filipek, Slawomir; Vogel, Horst; Pick, Horst

    2015-10-09

    A multi-gene family of ~1000 G protein-coupled olfactory receptors (ORs) constitutes the molecular basis of mammalian olfaction. Due to the lack of structural data its remarkable capacity to detect and discriminate thousands of odorants remains poorly understood on the structural level of the receptor. Using site-directed mutagenesis we transferred ligand specificity between two functionally related ORs and thereby revealed amino acid residues of central importance for odorant recognition and discrimination of the two receptors. By exchanging two of three residues, differing at equivalent positions of the putative odorant binding site between the mouse OR paralogs Olfr73 (mOR-EG) and Olfr74 (mOR-EV), we selectively changed ligand preference but remarkably also signaling activation strength in both ORs. Computer modeling proposed structural details at atomic resolution how the very same odorant molecule might interact with different contact residues to induce different functional responses in two related receptors. Our findings provide a mechanistic explanation of how the olfactory system distinguishes different molecular aspects of a given odorant molecule, and unravel important molecular details of the combinatorial encoding of odorant identity at the OR level.

  13. Binding Sites for Acylated Trehalose Analogs of Glycolipid Ligands on an Extended Carbohydrate Recognition Domain of the Macrophage Receptor Mincle*

    Science.gov (United States)

    Feinberg, Hadar; Rambaruth, Neela D. S.; Jégouzo, Sabine A. F.; Jacobsen, Kristian M.; Djurhuus, Rasmus; Poulsen, Thomas B.; Weis, William I.; Taylor, Maureen E.; Drickamer, Kurt

    2016-01-01

    The macrophage receptor mincle binds to trehalose dimycolate on the surface of Mycobacterium tuberculosis. Signaling initiated by this interaction leads to cytokine production, which underlies the ability of mycobacteria to evade the immune system and also to function as adjuvants. In previous work the mechanism for binding of the sugar headgroup of trehalose dimycolate to mincle has been elucidated, but the basis for enhanced binding to glycolipid ligands, in which hydrophobic substituents are attached to the 6-hydroxyl groups, has been the subject of speculation. In the work reported here, the interaction of trehalose derivatives with bovine mincle has been probed with a series of synthetic mimics of trehalose dimycolate in binding assays, in structural studies by x-ray crystallography, and by site-directed mutagenesis. Binding studies reveal that, rather than reflecting specific structural preference, the apparent affinity of mincle for ligands with hydrophobic substituents correlates with their overall size. Structural and mutagenesis analysis provides evidence for interaction of the hydrophobic substituents with multiple different portions of the surface of mincle and confirms the presence of three Ca2+-binding sites. The structure of an extended portion of the extracellular domain of mincle, beyond the minimal C-type carbohydrate recognition domain, also constrains the way the binding domains may interact on the surface of macrophages. PMID:27542410

  14. Comparative thermodynamic studies on substrate and product binding of O-Acetylserine Sulfhydrylase reveals two different ligand recognition modes†

    Directory of Open Access Journals (Sweden)

    Kumaran Sangaralingam

    2011-06-01

    Full Text Available Abstract Background The importance of understanding the detailed mechanism of cysteine biosynthesis in bacteria is underscored by the fact that cysteine is the only sulfur donor for all cellular components containing reduced sulfur. O-acetylserine sulfhydrylase (OASS catalyzes this crucial last step in the cysteine biosynthesis and has been recognized as an important gene for the survival and virulence of pathogenic bacteria. Structural and kinetic studies have contributed to the understanding of mechanistic aspects of OASS, but details of ligand recognition features of OASS are not available. In the absence of any detailed study on the energetics of ligand binding, we have studied the thermodynamics of OASS from Salmonella typhimurium (StOASS, Haemophilus influenzae (HiOASS, and Mycobacterium tuberculosis (MtOASS binding to their substrate O-acetylserine (OAS, substrate analogue (methionine, and product (cysteine. Results Ligand binding properties of three OASS enzymes are studied under defined solution conditions. Both substrate and product binding is an exothermic reaction, but their thermodynamic signatures are very different. Cysteine binding to OASS shows that both enthalpy and entropy contribute significantly to the binding free energy at all temperatures (10-30°C examined. The analyses of interaction between OASS with OAS (substrate or methionine (substrate analogue revealed a completely different mode of binding. Binding of both OAS and methionine to OASS is dominated by a favorable entropy change, with minor contribution from enthalpy change (ΔHSt-Met = -1.5 ± 0.1 kJ/mol; TΔSSt-Met = 8.2 kJ/mol at 20°C. Our salt dependent ligand binding studies indicate that methionine binding affinity is more sensitive to [NaCl] as compared to cysteine affinity. Conclusions We show that OASS from three different pathogenic bacteria bind substrate and product through two different mechanisms. Results indicate that predominantly entropy driven

  15. Layer-by-layer assembled carbon nanotube films with molecule recognition function and lower capacitive background current.

    Science.gov (United States)

    Kong, Bo; Zeng, Jinxiang; Luo, Guangming; Luo, Shenglian; Wei, Wanzhi; Li, Jun

    2009-02-01

    Multilayer films of multiwalled carbon nanotubes (MWCNTs) with molecule recognition function were assembled on glassy carbon (GC) electrode with lower capacitive background current by two steps: first, MWCNTs interacted with beta-cyclodextrin (beta-CD) with the aid of sonication to form beta-CD-MWCNTs nanocomposite, then the beta-CD-MWCNTs nanocomposite was assembled on GC electrode using layer-by-layer (LBL) method based on electrostatic interaction of positively charged biopolymer chitosan and negatively charged MWCNTs. The assembled beta-CD-MWCNTs multilayer films were characterized by scanning electron microscopy (SEM) and cyclic voltammetry. The SEM indicated that the MWCNTs multilayer films with beta-CD were somewhat more compact than that of the MWCNTs multilayer films without beta-CD. The cyclic voltammetric results indicated that the assembled MWCNTs with beta-CD on GC electrode exhibited lower capacitive background current than the assembled MWCNTs without beta-CD. The MWCNTs multilayer films with beta-CD were studied with respect to the electrocatalytic activity toward dopamine (DA). Compared with the MWCNTs multilayer films without beta-CD, the MWCNTs multilayer films with beta-CD possesses a much lower capacitive background current and higher electrocatalytic activity in phosphate buffer, which was ascribed to the relatively compact three-dimensional structure of the MWCNTs multilayer films with beta-CD and the excellent molecule recognition function of beta-CD.

  16. New Trends in Inspecting GPCR-ligand Recognition Process: the Contribution of the Molecular Modeling Section (MMS) at the University of Padova.

    Science.gov (United States)

    Ciancetta, Antonella; Cuzzolin, Alberto; Deganutti, Giuseppe; Sturlese, Mattia; Salmaso, Veronica; Cristiani, Andrea; Sabbadin, Davide; Moro, Stefano

    2016-09-01

    In this review, we present a survey of the recent advances carried out by our research groups in the field of ligand-GPCRs recognition process simulations recently implemented at the Molecular Modeling Section (MMS) of the University of Padova. We briefly describe a platform of tools we have tuned to aid the identification of novel GPCRs binders and the better understanding of their binding mechanisms, based on two extensively used computational techniques such as molecular docking and MD simulations. The developed methodologies encompass: (i) the selection of suitable protocols for docking studies, (ii) the exploration of the dynamical evolution of ligand-protein interaction networks, (iii) the detailed investigation of the role of water molecules upon ligand binding, and (iv) a glance at the way the ligand might go through prior reaching the binding site.

  17. Ligand recognition by the TPR domain of the import factor Toc64 from Arabidopsis thaliana.

    Science.gov (United States)

    Panigrahi, Rashmi; Adina-Zada, Abdussalam; Whelan, James; Vrielink, Alice

    2013-01-01

    The specific targeting of protein to organelles is achieved by targeting signals being recognised by their cognate receptors. Cytosolic chaperones, bound to precursor proteins, are recognized by specific receptors of the import machinery enabling transport into the specific organelle. The aim of this study was to gain greater insight into the mode of recognition of the C-termini of Hsp70 and Hsp90 chaperones by the Tetratricopeptide Repeat (TPR) domain of the chloroplast import receptor Toc64 from Arabidopsis thaliana (At). The monomeric TPR domain binds with 1∶1 stoichiometry in similar micromolar affinity to both Hsp70 and Hsp90 as determined by isothermal titration calorimetry (ITC). Mutations of the terminal EEVD motif caused a profound decrease in affinity. Additionally, this study considered the contributions of residues upstream as alanine scanning experiments of these residues showed reduced binding affinity. Molecular dynamics simulations of the TPR domain helices upon peptide binding predicted that two helices within the TPR domain move backwards, exposing the cradle surface for interaction with the peptide. Our findings from ITC and molecular dynamics studies suggest that AtToc64_TPR does not discriminate between C-termini peptides of Hsp70 and Hsp90.

  18. A fluorescent bis(benzoxazole) ligand: toward binuclear Zn(II)-Zn(II) assembly.

    Science.gov (United States)

    Chu, Qinghui; Medvetz, Doug A; Panzner, Matthew J; Pang, Yi

    2010-06-14

    A bis(benzoxazole) ligand (HL) has been synthesized, and its reaction with Zn(OAc)(2) has led to fluorescent complexes via formation of binuclear Zn(II)-Zn(II) cores. The ligand-to-metal ratio of the complexes varies from 1 : 1 to 2 : 1, depending on the reaction conditions. A large binding constant K = 8.3 x 10(20) [M(-3)] has been determined for the reaction L + Zn(2+)-->L(2):Zn(2)(2+). The result indicates that the bis(benzoxazole) ligand is a useful building block to construct a binuclear core. On the basis of X-ray analysis, the binuclear Zn(II)-Zn(II) distance in the complexes is determined to be approximately 3.22 A, which is quite comparable to that found in the enzymes (3.3 A). Absorption and fluorescence study shows that a subtle chemical environmental change within the binuclear core can induce a large optical response.

  19. Assembly of new polyoxometalate–templated metal–organic frameworks based on flexible ligands

    Energy Technology Data Exchange (ETDEWEB)

    Li, Na; Mu, Bao; Lv, Lei; Huang, Rudan, E-mail: huangrd@bit.edu.cn

    2015-03-15

    Four new polyoxometalate(POM)–templated metal–organic frameworks based on flexible ligands, namely, [Cu{sub 6}(bip){sub 12}(PMo{sup VI}{sub 12}O{sub 40}){sub 2}(PMo{sup V}Mo{sup VI}{sub 11}O{sub 40}O{sub 2})]·8H{sub 2}O(1), [Cu{sup I}{sub 3}Cu{sup II}{sub 3}(bip){sub 12}(PMo{sup VI}{sub 12}O{sub 40}){sub 2}(PMo{sup V}{sub 12}O{sub 34})]·8H{sub 2}O(2), [Ni{sub 6}(bip){sub 12}(PMo{sup VI}{sub 12}O{sub 40})(PMo{sup VI}{sub 11}Mo{sup V}O{sub 40}){sub 2}]Cl·6H{sub 2}O(3), [Co{sup II}{sub 3}Co{sup III}{sub 2}(H{sub 2}bib){sub 2}(Hbib){sub 2}(PW{sub 9}O{sub 34}){sub 2}(H{sub 2}O){sub 6}]·6H{sub 2}O(4) (bip=1,3-bis(imidazolyl)propane, bib=1,4-bis(imidazolyl)butane) have been obtained under hydrothermal condition and characterized by single-crystal X-ray diffraction analyses, elemental analyses, and thermogravimetric (TG) analyses. The studies of single crystal X-ray indicate that compounds 1–3 crystallize in the trigonal space group P-3, and compound 4 crystallizes in the triclinic space group P-1. Compounds 1 and 3 represent 3D frameworks, and POMs as the guest molecules are incorporated into the cages which are composed of the ligands and metals, while compounds 2 and 4 show 3D frameworks by hydrogen bonds. This compounds provide new examples of host–guest compounds based on flexible bis(imidazole) ligands. In addition, the electrochemical property and the catalytic property of compound 1 have also been investigated. - Graphical abstract: Four inorganic–organic hybrid compounds based polyoxometalates (POMs) and flexible ligands, namely, have been obtained under hydrothermal conditions and characterized by single-crystal X-ray diffraction analyses, elemental analyses, IR spectra, and thermogravimetric (TG) analyses. Compounds 1–3 are new examples of host–guest compounds based on flexible bis(imidazole) ligands and POMs as the guest molecules are incorporated into the cages which are composed of the ligands and metals. - Highlights: • Polyoxometalate

  20. Directional Carrier Transfer in Strongly Coupled Binary Nanocrystal Superlattice Films Formed by Assembly and in Situ Ligand Exchange at a Liquid–Air Interface

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Yaoting; Li, Siming; Gogotsi, Natalie; Zhao, Tianshuo; Fleury, Blaise; Kagan, Cherie R.; Murray, Christopher B.; Baxter, Jason B.

    2017-02-16

    Two species of monodisperse nanocrystals (NCs) can self-assemble into a variety of complex 2D and 3D periodic structures, or binary NC superlattice (BNSL) films, based on the relative number and size of the NCs. BNSL films offer great promise for both fundamental scientific studies and optoelectronic applications; however, the utility of as-assembled structures has been limited by the insulating ligands that originate from the synthesis of NCs. Here we report the application of an in situ ligand exchange strategy at a liquid–air interface to replace the long synthesis ligands with short ligands while preserving the long-range order of BNSL films. This approach is demonstrated for BNSL structures consisting of PbSe NCs of different size combinations and ligands of interest for photovoltaic devices, infrared detectors, and light-emitting diodes. To confirm enhanced coupling introduced by ligand exchange, we show ultrafast (~1 ps) directional carrier transfer across the type-I heterojunction formed by NCs of different sizes within ligand-exchanged BNSL films. In conclusion, this approach shows the potential promise of functional BNSL films, where the local and long-range energy landscape and electronic coupling can be adjusted by tuning NC composition, size, and interparticle spacing.

  1. Exploring ligand recognition, selectivity and dynamics of TPR domains of chloroplast Toc64 and mitochondria Om64 from Arabidopsis thaliana.

    Science.gov (United States)

    Panigrahi, Rashmi; Whelan, James; Vrielink, Alice

    2014-06-01

    The study aims to gain insight into the mode of ligand recognition by tetratricopeptide repeat (TPR) domains of chloroplast translocon at the outer envelope of chloroplast (Toc64) and mitochondrial Om64, two paralogous proteins that mediate import of proteins into chloroplast and mitochondria, respectively. Chaperone proteins associate with precursor proteins in the cytosol to maintain them in a translocation competent conformation and are recognized by Toc64 and Om64 that are located on the outer membrane of the target organelle. Heat shock proteins (Hsp70) and Hsp90 are two chaperones, which are known to play import roles in protein import. The C-termini of these chaperones are known to interact with the TPR domain of chloroplast Toc64 and mitochondrial Om64 in Arabidopsis thaliana (At). Using a molecular dynamics approach and binding energy calculations, we identify important residues involved in the interactions. Our findings suggest that the TPR domain from AtToc64 has higher affinity towards C-terminal residues of Hsp70. The interaction occurs as the terminal helices move towards each other enclosing the cradle on interaction of AtHsp70 with the TPR domain. In contrast, the TPR domain from AtOm64 does not discriminate between the C-termini of Hsp70 and Hsp90. These binding affinities are discussed with respect to our knowledge of protein targeting and specificity of protein import into endosymbiotic organelles in plant cells.

  2. Self-assembled silver polyhedra with embedded acetylide dianion stabilized by perfluorocarboxylate and 4-hydroxyquinoline ligands.

    Science.gov (United States)

    Zhao, Xiao-Li; Wang, Quan-Ming; Mak, Thomas C W

    2003-12-01

    Four new silver(I) double salts (L(2)H)(4)[Ag(10)(C(2))(CF(3)CO(2))(12)(L)(2)].5H(2)O (1), [Ag(8)(C(2))(CF(3)CO(2))(6)(L)(6)] (2), [(Ag(2)C(2))(AgC(2)F(5)CO(2))(6)(L)(3)(H(2)O)].H(2)O (3), and (L.H(3)O)(2)[Ag(11)(C(2))(2)(C(2)F(5)CO(2))(9)(H(2)O)(2)].H(2)O (4) incorporating the hitherto unexplored ligand 4-hydroxyquinoline (L) have been synthesized by the hydrothermal method. Compound 1 features an unprecedented bicapped square-antiprismatic Ag(10) silver cage with an embedded C(2)(2-) moiety, whereas the discrete supermolecule 2 bears a rhombohedral Ag(8) core similar to that previously found in Ag(2)C(2).6AgNO(3). Compound 3 contains a discrete supramolecular complex whose core is a (C(2))(2)@Ag(16) double cage constructed from the edge-sharing of two monocapped square antiprisms, which is completely surrounded by 12 pentafluoropropionate, 6 4-hydroxyquinoline, and 2 aqua ligands. The layer structure in 4 is constructed from a sinuous anionic silver column composed of fused irregular monocapped trigonal antiprisms each encapsulating a C(2)(2-) dianion, with L.H(3)O(+) species serving as hydrogen-bond connectors to adjacent columns.

  3. The characteristics of frequency distribution of KIR2DL1 alleles polymorphism and recognition HLA-C ligand in the Chinese Han population

    Institute of Scientific and Technical Information of China (English)

    王苗

    2014-01-01

    Objective To find out the distributed characteristics of KIR2DL1 alleles frequencies and the recognition HLAC ligand in the Chinese Han population.Methods The111 patients and 116 donors from CMDP were performed the KIR2DL1 high-resoluction typing and KIR genotyping using sequence-based testing(SBT)and PCR-SSP methods.Results A total of 224

  4. Resonant X-ray emission spectroscopy reveals d-d ligand-field states involved in the self-assembly of a square-planar platinum complex.

    Science.gov (United States)

    Garino, Claudio; Gallo, Erik; Smolentsev, Nikolay; Glatzel, Pieter; Gobetto, Roberto; Lamberti, Carlo; Sadler, Peter J; Salassa, Luca

    2012-11-28

    Resonant X-ray Emission Spectroscopy (RXES) is used to characterize the ligand field states of the prototypic self-assembled square-planar complex, [Pt(tpy)Cl]Cl (tpy=2,2':6',2''-terpyridine), and determine the effect of weak metal-metal and π-π interactions on their energy.

  5. Two Zn(II) coordination complexes assembled by trithiocyanuric acid and two different N-donor auxiliary ligands.

    Science.gov (United States)

    He, Xiao Xiao; Guo, Ya Mei

    2014-08-01

    The dipyridyl-type building blocks 4-amino-3,5-bis(pyridin-3-yl)-1,2,4-triazole (3-bpt) and 4,4'-bipyridine (bpy) have been used to assemble with Zn(II) in the presence of trithiocyanuric acid (ttcH3) to afford two coordination compounds, namely bis[4-amino-3,5-bis(pyridin-3-yl)-1,2,4-triazole-κN(3)]bis(trithiocyanurato-κ(2)N,S)zinc(II), [Zn(C3H2N3S3)2(C12H10N6)2]·2H2O, (1), and catena-poly[[[bis(trithiocyanurato-κ(2)N,S)zinc(II)]-μ-4,4'-bipyridine-κ(2)N:N'] 4,4'-bipyridine monosolvate], {[Zn2(C3H2N3S3)4(C10H8N2)3]·C10H8N2}n, (2). Single-crystal X-ray analysis indicates that complex (1) is a mononuclear structure, while complex (2) presents a one-dimensional chain coordination motif. In both complexes, the central Zn(II) cation adopts an octahedral geometry, coordinated by four N- and two S-donor atoms. Notably, trithiocyanurate (ttcH2(-)) adopts the same bidentate chelating coordination mode in each complex and exists in the thione tautomeric form. The 3-bpt co-ligand in (1) adopts a monodentate coordination mode and serves as a terminal pendant ligand, whereas the 4,4'-bipyridine (bpy) ligand in (2) adopts a bidentate-bridging coordination mode. The different coordination characters of the different N-donor auxiliary ligands lead to structural diversity for complexes (1) and (2). Further analysis indicates that the resultant three-dimensional supramolecular networks for (1) and (2) arise through intermolecular N-H...S and N-H...N hydrogen bonds. Both complexes have been further characterized by FT-IR spectroscopy and elemental analyses.

  6. EPSP synthase: binding studies using isothermal titration microcalorimetry and equilibrium dialysis and their implications for ligand recognition and kinetic mechanism.

    Science.gov (United States)

    Ream, J E; Yuen, H K; Frazier, R B; Sikorski, J A

    1992-06-23

    Isothermal titration calorimetry measurements are reported which give important new binding constant (Kd) information for various substrate and inhibitor complexes of Escherichia coli EPSP synthase (EPSPS). The validity of this technique was first verified by determining Kd's for the known binary complex with the substrate, shikimate 3-phosphate (S3P), as well as the herbicidal ternary complex with S3P and glyphosate (EPSPS.S3P.glyphosate). The observed Kd's agreed very well with those from previous independently determined kinetic and fluorescence binding measurements. Further applications unequivocally demonstrate for the first time a fairly tight interaction between phosphoenolpyruvate (PEP) and free enzyme (Kd = 390 microM) as well as a correspondingly weak affinity for glyphosate (Kd = 12 mM) alone with enzyme. The formation of the EPSPS.PEP binary complex was independently corroborated using equilibrium dialysis. These results strongly suggest that S3P synergizes glyphosate binding much more effectively than it does PEP binding. These observations add important new evidence to support the hypothesis that glyphosate acts as a transition-state analogue of PEP. However, the formation of a catalytically productive PEP binary complex is inconsistent with the previously reported compulsory binding order process required for catalysis and has led to new studies which completely revise the overall EPSPS kinetic mechanism. A previously postulated ternary complex between S3P and inorganic phosphate (EPSPS.S3P.Pi, Kd = 4 mM) was also detected for the first time. Quantitative binding enthalpies and entropies were also determined for each ligand complex from the microcalorimetry data. These values demonstrate a clear difference in thermodynamic parameters for recognition at the S3P site versus those observed for the PEP, Pi, and glyphosate sites.

  7. Multicomponent Self-assembly:Spontaneous Formation of a Metallomacrocycle from Two Quinoline Based Linear Ligands and Four Silver(Ⅰ) Nitrates

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    @@ Using metal ions to control the self-assembly of metallosupramolecules of varying architecture is one of the fascinating developments in supramolecular chemistry[1,2],particularly those concerned with the deliberate construction of molecular aggregates,like helices,rotaxanes,catenanes,knots,cages[3~6] and the crystal engineering of two or three dimensional networks with varied topology and interpenetration[7~10].Coordination bonds have proved themselves to be one of the most useful connectors in supramolecular self-assembly due to their versatile geometrical modes(e.g.linear,trigonal,square plane,tetrahedral,octahedral) in bond formations.By careful design of tailored ligands,various novel supramolecular architectures have been constructed.Recently,angular bi- or tridentate and other polydentate ligands have aroused a special interest,and a variety of molecular squares,boxes and cages[1~14] with internal cavity or void have been reported,in which many nanoscale structures are formed[6,15,16].We have been interested in the construction of metal based supramolecular structures with polydentate ligands[17~20] and herein report a new metallomacrocyclic complex assembled from two linear polydentate ligands and silver(Ⅰ) nitrate.

  8. Simple and rapid mercury ion selective electrode based on 1-undecanethiol assembled Au substrate and its recognition mechanism.

    Science.gov (United States)

    Li, Xian-Qing; Liang, Hai-Qing; Cao, Zhong; Xiao, Qing; Xiao, Zhong-Liang; Song, Liu-Bin; Chen, Dan; Wang, Fu-Liang

    2017-03-01

    A simple and rapid mercury ion selective electrode based on 1-undecanethiol (1-UDT) assembled Au substrate (Au/1-UDT) has been well constructed. 1-UDT was for the purpose of generating self-assembled monolayer on gold surface to recognize Hg(2+) in aqueous solution, which had a working concentration range of 1.0×10(-8)-1.0×10(-4)molL(-1), with a Nernst response slope of 28.83±0.4mV/-pC, a detection limit of 4.5×10(-9)molL(-1), and a good selectivity over the other tested cations. Also, the Au/1-UDT possessed good reproducibility, stability, and short response time. The recovery obtained for the determination of mercury ion in practical tremella samples was in the range of 99.8-103.4%. Combined electrochemical analysis and X-ray photoelectron spectroscopy (XPS) with quantum chemical computation, the probable recognition mechanism of the electrode for selective recognition of Hg(2+) has been investigated. The covalent bond formed between mercury and sulfur is stronger than the one between gold and sulfur and thus prevents the adsorption of 1-UDT molecules on the gold surface. The quantum chemical computation with density functional theory further demonstrates that the strong interaction between the mercury atom and the sulfur atom on the gold surface leads to the gold sulfur bond ruptured and the gold mercury metallophilic interaction.

  9. Structural Basis for Telomerase RNA Recognition and RNP Assembly by the Holoenzyme La Family Protein p65

    Energy Technology Data Exchange (ETDEWEB)

    Singh, Mahavir; Wang, Zhonghua; Koo, Bon-Kyung; Patel, Anooj; Cascio, Duilio; Collins, Kathleen; Feigon, Juli (UCLA); (UCB)

    2012-07-01

    Telomerase is a ribonucleoprotein complex essential for maintenance of telomere DNA at linear chromosome ends. The catalytic core of Tetrahymena telomerase comprises a ternary complex of telomerase RNA (TER), telomerase reverse transcriptase (TERT), and the essential La family protein p65. NMR and crystal structures of p65 C-terminal domain and its complex with stem IV of TER reveal that RNA recognition is achieved by a combination of single- and double-stranded RNA binding, which induces a 105{sup o} bend in TER. The domain is a cryptic, atypical RNA recognition motif with a disordered C-terminal extension that forms an {alpha} helix in the complex necessary for hierarchical assembly of TERT with p65-TER. This work provides the first structural insight into biogenesis and assembly of TER with a telomerase-specific protein. Additionally, our studies define a structurally homologous domain (xRRM) in genuine La and LARP7 proteins and suggest a general mode of RNA binding for biogenesis of their diverse RNA targets.

  10. STAT3 contributes to NK cell recognition by modulating expression of NKG2D ligands in adriamycin-resistant K562/AO2 cells.

    Science.gov (United States)

    Cai, Xiaohui; Lu, Xuzhang; Jia, Zhuxia; Zhang, Xiuwen; Han, Wenmin; Rong, Xiao; Ma, Lingdi; Zhou, Min; Chen, Baoan

    2015-11-01

    Leukemic cells can survive after chemotherapy by acquisition of multidrug resistance genes, but other phenotypes related to escape from immune recognition remain elusive. Adriamycin-resistant K562/AO2 cells are less susceptible to elimination by NK cells compared with wild type K562 cells due to lower expression of NKG2D ligands. Treatment of K562/AO2 cells with STAT3 inhibitor VII resulted in reduced expression of multidrug resistance gene P-glycoprotein, and up-regulation of NKG2D ligands on K562/AO2 cells. Meanwhile, K562/AO2 cells treated with STAT3 inhibitor proliferated less and were more susceptible to killing by NK cells than untreated K562/AO2 cells. The enhanced cytotoxicity of NK cells against K562/AO2 cells was partly blocked by treatment of NK cells with anti-NKG2D antibodies. These data suggest that STAT3 contributes to NK cell recognition by modulating NKG2D ligands in K562/AO2 cells, which may a mechanism by which cells survive and cause relapse of leukemia.

  11. An M12(L(1))12(L(2))12 cantellated tetrahedron: a case study on mixed-ligand self-assembly.

    Science.gov (United States)

    Sun, Qing-Fu; Sato, Sota; Fujita, Makoto

    2014-12-01

    In the self-assembly of Pd(II) ions and two different, but similarly shaped, ligands (1 and 2), neither random mixing nor self-sorting of the two ligands into two unmixed structures was observed. Instead a mixed, yet sorted, Pd12 (1)12 (2)12 cantellated tetrahedron (and its pseudoisomer) was selectively formed, thus revealing a fine example of intramolecular self-sorting. A case study showed that a homothetic ratio of >2 is necessary to observe cantellated tetrahedra.

  12. Lanthanide-directed synthesis of luminescent self-assembly supramolecular structures and mechanically bonded systems from acyclic coordinating organic ligands.

    Science.gov (United States)

    Barry, Dawn E; Caffrey, David F; Gunnlaugsson, Thorfinnur

    2016-06-01

    Herein some examples of the use of lanthanide ions (f-metal ions) to direct the synthesis of luminescent self-assembly systems (architectures) will be discussed. This area of lanthanide supramolecular chemistry is fast growing, thanks to the unique physical (magnetic and luminescent) and coordination properties of the lanthanides, which are often transferred to the resulting supermolecule. The emphasis herein will be on systems that are luminescent, and hence, generated by using either visibly emitting ions (such as Eu(III), Tb(III) and Sm(III)) or near infrared emitting ions (like Nd(III), Yb(III) and Er(III)), formed through the use of templating chemistry, by employing structurally simple ligands, possessing oxygen and nitrogen coordinating moieties. As the lanthanides have high coordination requirements, their use often allows for the formation of coordination compounds and supramolecular systems such as bundles, grids, helicates and interlocked molecules that are not synthetically accessible through the use of other commonly used templating ions such as transition metal ions. Hence, the use of the rare-earth metal ions can lead to the formation of unique and stable species in both solution and in the solid state, as well as functional and responsive structures.

  13. Ligand recognition and domain structure of Vps10p, a vacuolar protein sorting receptor in Saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Jørgensen, M U; Emr, S D; Winther, Jakob R.

    1999-01-01

    Vp10p is a receptor that sorts several different vacuolar proteins by cycling between a late Golgi compartment and the endosome. The cytoplasmic tail of Vps10p is necessary for the recycling, whereas the lumenal domain is predicted to interact with the soluble ligands. We have studied ligand bind...

  14. Anion-induced Ag(I) self-assemblies with electron deficient aromatic ligands: anion-π-system interactions as a driving force for templated coordination networks.

    Science.gov (United States)

    Safin, Damir A; Pialat, Amélie; Leitch, Alicea A; Tumanov, Nikolay A; Korobkov, Ilia; Filinchuk, Yaroslav; Brusso, Jaclyn L; Murugesu, Muralee

    2015-06-11

    Three novel 1D, 2D and 3D coordination polymers were successfully isolated using nitrogen based 3,6-bis(2'-pyrimidyl)-1,2,4,5-tetrazine (BPymTz) and 2,4,6-tris(2-pyrimidyl)-1,3,5-triazine (TPymT) ligands with Ag(I) ions. The formation of these supramolecular assemblies was templated through anion-π-system interactions.

  15. Selective recognition and stabilization of new ligands targeting the potassium form of the human telomeric G-quadruplex DNA

    Science.gov (United States)

    Lin, Yi-Hwa; Chuang, Show-Mei; Wu, Pei-Ching; Chen, Chun-Liang; Jeyachandran, Sivakamavalli; Lo, Shou-Chen; Huang, Hsu-Shan; Hou, Ming-Hon

    2016-08-01

    The development of a ligand that is capable of distinguishing among the wide variety of G-quadruplex structures and targeting telomeres to treat cancer is particularly challenging. In this study, the ability of two anthraquinone telomerase inhibitors (NSC749235 and NSC764638) to target telomeric G-quadruplex DNA was probed. We found that these ligands specifically target the potassium form of telomeric G-quadruplex DNA over the DNA counterpart. The characteristic interaction with the telomeric G-quadruplex DNA and the anticancer activities of these ligands were also explored. The results of this present work emphasize our understanding of the binding selectivity of anthraquinone derivatives to G-quadruplex DNA and assists in future drug development for G-quadruplex-specific ligands.

  16. Self-assembly synthesis,crystal structure and nonlinear optical properties of cluster compound containing PPh2Py ligand

    Institute of Scientific and Technical Information of China (English)

    ZHOU Jian-liang; WEI Chuan-jun; TONG Hai-xia; CHUN Xiao-gai; CHEN Qi-yuan

    2008-01-01

    Self-assembly cluster compound [WS4Cu3(PPh2Py)3Br]2·CH3OH (1) was synthesized by the reaction of (NH4)2WS4,CuBr and diphenyl-2-pyridyl-phosphine (PPh2Py) in CH3OH solution under a purified nitrogen atmosphere using standard Schlenk techniques.Its structure was determined by X-ray crystallography.It crystallizes in the triclinic crystal system P-1 space group with α=1.178 6(1)nm,b=1.302 6(1)nm,c=1.9917(2)nm,α=74.671(7)°,β=86.188(8)°,γ=64.141(6)°,V=2.649 5(5)nm',Z=1.The W center is slightly distorted from tetrahedral coordination geometry,and the structure is built up from three [Cu(PPh2Py)]+ units bridged by WS2-4 multifunctional ligand to form a tetranuclear symmetrical cube-like molecule.Measurement of the nonlinear optical (NLO) properties using the Z-scan technique with an 8 ns pulsed laser at 532 nm shows that the compound possesses NLO absorption and effective self-focusing effect at α2=6.7×10-11m/W and n2=5.64×10-18m2/W in a 1.5×10-4mol/L DMF solution.

  17. pH-responsive self-assembly by molecular recognition on a macroscopic scale.

    Science.gov (United States)

    Zheng, Yongtai; Hashidzume, Akihito; Harada, Akira

    2013-07-12

    Macroscopic pH-responsive self-assembly is successfully constructed by polyacrylamide(pAAm)-based gels carrying dansyl (Dns) and β-cyclodextrin (βCD) residues, which are represented as Dns-gel and βCD-gel, respectively. Dns-gel and βCD-gel assemble together at pH ≥ 4.0, but disassemble at pH ≤ 3.0. The adhesion strengths for pairs of Dns-gel/βCD-gel increase with increasing pH. The fluorescence study on the model system of pAAm modified with 1 mol% Dns moieties (pAAm/Dns) reveals that Dns residues are protonated at a lower pH, which results in the reduction in binding constant (K) for Dns residues and βCD.

  18. Recognition tunneling measurement of the conductance of DNA bases embedded in self-assembled monolayers.

    Science.gov (United States)

    Huang, Shuo; Chang, Shuai; He, Jin; Zhang, Peiming; Liang, Feng; Tuchband, Michael; Li, Shengqing; Lindsay, Stuart

    2010-12-09

    The DNA bases interact strongly with gold electrodes, complicating efforts to measure the tunneling conductance through hydrogen-bonded Watson Crick base pairs. When bases are embedded in a self-assembled alkane-thiol monolayer to minimize these interactions, new features appear in the tunneling data. These new features track the predictions of density-functional calculations quite well, suggesting that they reflect tunnel conductance through hydrogen-bonded base pairs.

  19. Small-molecule recognition for controlling molecular motion in hydrogen-bond-assembled rotaxanes.

    Science.gov (United States)

    Martinez-Cuezva, Alberto; Berna, Jose; Orenes, Raul-Angel; Pastor, Aurelia; Alajarin, Mateo

    2014-06-23

    Di(acylamino)pyridines successfully template the formation of hydrogen-bonded rotaxanes through five-component clipping reactions. A solid-state study showed the participation of the pyridine nitrogen atom in the stabilization of the mechanical bond between the thread and the benzylic amide macrocycle. The addition of external complementary binders to a series of interlocked bis(2,6-di(acylamino)pyridines) promoted restraint of the back and forward ring motion. The original translation can be restored through a competitive recognition event by the addition of a preorganized bis(di(acylamino)pyridine) that forms stronger ADA-DAD complexes with the external binders.

  20. Self-Assembly of Nano Hydroxyapatite or Aragonite Induced by Molecular Recognition to Soy Globulin 7S or 11S.

    Science.gov (United States)

    Liu, Dagang; Tian, Huafeng; Kumar, Rakesh; Zhang, Lina

    2009-09-01

    Molecular self-assembly is emerging as a viable 'bottom-up' approach to build stable organic/inorganic nanometer-scale blocks. Herein, under the conditions of appropriate pH and ionic strength, soy globulin 7S or 11S were coprecipitated with hydroxyapatite (HAp) or aragonite (Arag), respectively, to fabricate two organic/inorganic hybrids: 7S/HAp and 11S/Arag. Results from high-resolution transmission electron microscopy show that the hybrids exhibit a nanosized core-shell structure with globulin monomer 7S or 11S as core and HAp or Arag as shells. 7S/HAp and 11S/Arag present a disk and hexagon shape, respectively. After calcinations, monodispersed HAp without support from globulins existed as nanospheres. It was revealed that the globulin as host induces the self-assembly and growth layer by layer of HAp or Arag nanocrystals. The factors of molecular recognition and surface potential definitely affected the size and shape of the hierarchical blocks. This work provided a novel pathway to controllably synthesize a wide variety of precise plant protein/biomineral hybrid biomaterials.

  1. Urea-Functionalized M4L6 Cage Receptors: Self-Assembly, Dynamics, and Anion Recognition in Aqueous Solutions

    Energy Technology Data Exchange (ETDEWEB)

    Custelcean, Radu [ORNL; Bonnesen, Peter V [ORNL; Duncan, Nathan C [ORNL; Van Berkel, Gary J [ORNL; Hay, Benjamin [ORNL

    2012-01-01

    We present an extensive study of a novel class of de novo designed tetrahedral M{sub 4}L{sub 6} (M = Ni, Zn) cage receptors, wherein internal decoration of the cage cavities with urea anion-binding groups, via functionalization of the organic components L, led to selective encapsulation of tetrahedral oxoanions EO{sub 4}{sup -} (E = S, Se, Cr, Mo, W, n = 2; E = P, n = 3) from aqueous solutions, based on shape, size, and charge recognition. External functionalization with tBu groups led to enhanced solubility of the cages in aqueous methanol solutions, thereby allowing for their thorough characterization by multinuclear ({sup 1}H, {sup 13}C, {sup 77}Se) and diffusion NMR spectroscopies. Additional experimental characterization by electrospray ionization mass spectrometry, UV-vis spectroscopy, and single-crystal X-ray diffraction, as well as theoretical calculations, led to a detailed understanding of the cage structures, self-assembly, and anion encapsulation. We found that the cage self-assembly is templated by EO{sub 4}{sup -} oxoanions (n {ge} 2), and upon removal of the templating anion the tetrahedral M{sub 4}L{sub 6} cages rearrange into different coordination assemblies. The exchange selectivity among EO{sub 4}{sup -} oxoanions has been investigated with {sup 77}Se NMR spectroscopy using {sup 77}SeO{sub 4}{sup 2-} as an anionic probe, which found the following selectivity trend: PO{sub 4}{sup 3-} CrO{sub 4}{sup 2-} > SO{sub 4}{sup 2-} > SeO{sub 4}{sup 2-} > MoO{sub 4}{sup 2-} > WO{sub 4}{sup 2-}. In addition to the complementarity and flexibility of the cage receptor, a combination of factors have been found to contribute to the observed anion selectivity, including the anions charge, size, hydration, basicity, and hydrogen-bond acceptor abilities.

  2. Circular serendipity: in situ ligand transformation for the self-assembly of an hexadecametallic [Cu(II)16] wheel.

    Science.gov (United States)

    Kostopoulos, Andreas K; Katsenis, Athanassios D; Frost, Jamie M; Kessler, Vadim G; Brechin, Euan K; Papaefstathiou, Giannis S

    2014-12-11

    A [Cu(II)16] wheel was isolated serendipitously from the reaction of acetylacetone dioxime with copper(ii) chloride and lanthanide ions in a reaction initially designed to produce heterometallic 3d-4f cages. The ligand has been transformed in situ to three different forms, all found within the [Cu16] wheel, with the original ligand completely absent.

  3. Molecular recognition of naphthalene diimide ligands by telomeric quadruplex-DNA: the importance of the protonation state and mediated hydrogen bonds.

    Science.gov (United States)

    Spinello, A; Barone, G; Grunenberg, J

    2016-01-28

    In depth Monte Carlo conformational scans in combination with molecular dynamics (MD) simulations and electronic structure calculations were applied in order to study the molecular recognition process between tetrasubstituted naphthalene diimide (ND) guests and G-quadruplex (G4) DNA receptors. ND guests are a promising class of telomere stabilizers due to which they are used in novel anticancer therapeutics. Though several ND guests have been studied experimentally in the past, the protonation state under physiological conditions is still unclear. Based on chemical intuition, in the case of N-methyl-piperazine substitution, different protonation states are possible and might play a crucial role in the molecular recognition process by G4-DNA. Depending on the proton concentration, different nitrogen atoms of the N-methyl-piperazine might (or might not) be protonated. This fact was considered in our simulation in terms of a case by case analysis, since the process of molecular recognition is determined by possible donor or acceptor positions. The results of our simulations show that the electrostatic interactions between the ND ligands and the G4 receptor are maximized in the case of the protonation of the terminal nitrogen atoms, forming compact ND G4 complexes inside the grooves. The influence of different protonation states in terms of the ability to form hydrogen bonds with the sugar-phosphate backbone, as well as the importance of mediated vs. direct hydrogen bonding, was analyzed in detail by MD and relaxed force constant (compliance constant) simulations.

  4. Supramolecular assemblies and molecular recognition of amphiphilic schiff bases with barbituric acid in organized molecular films.

    Science.gov (United States)

    Jiao, Tifeng; Liu, Minghua

    2005-02-24

    A bolaform Schiff base, N,N'-bis(salicylidene)-1,10-decanediamine (BSC10), has been synthesized and its interfacial hydrogen bond formation or molecular recognition with barbituric acid was investigated in comparison with that of a single chain Schiff base, 2-hydroxybenzaldehyde-octadecylamine (HBOA). It has been found that while HBOA formed a monolayer at the air/water interface, the bolaform Schiff base formed a multilayer film with ordered layer structure on water surface. When the Schiff bases were spread on the subphase containing barbituric acid, both of the Schiff bases could form hydrogen bonds with barbituric acid in situ in the spreading films. As a result, an increase of the molecular areas in the isotherms was observed. The in situ H-bonded films could be transferred onto solid substrates, and the transferred multilayer films were characterized by various methods such as UV-vis and FT-IR spectrosopies. Spectral changes were observed for the films deposited from the barbituric acid subphase, which supported the hydrogen bond formation between the Schiff bases and barbituric acid. By measuring the MS-TOF of the deposited films dissolved in CHCl3 solution, it was concluded that a 2:1 complex of HBOA with barbituric acid and a 1:2 complex of BSC10 with barbituric acid were formed. On the other hand, when the multilayer films of both Schiff bases were immersed in an aqueous solution of barbituric acid, a similar molecular recognition through the hydrogen bond occurred. A clear conformational change of the alkyl spacer in the bolaform Schiff base was observed during the complex formation with the barbituric acid.

  5. Preparation of Core-Shell Coordination Molecular Assemblies via the Enrichment of Structure-Directing "Codes" of Bridging Ligands and Metathesis of Metal Units

    Energy Technology Data Exchange (ETDEWEB)

    Park, J; Chen, YP; Perry, Z; Li, JR; Zhou, HC

    2014-12-03

    A series of molybdenum- and copper-based MOPs were synthesized through coordination-driven process of a bridging ligand (3,3'-PDBAD, L-1) and dimetal paddlewheel clusters. Three conformers of the ligand exist with an ideal bridging angle between the two carboxylate groups of 0 degrees (H-2 zeta-L(1)), 120 degrees (H-2 beta-L-1), and of 90 degrees (H-2 beta-L-1), respectively. At ambient or lower temperature, (HL1)-L-2 and Mo-2(OAc)(4) or Cu-2(OAc)(4) were crystallized into a molecular square with ?-L-1 and Mo-2/Cu-2 units. With proper temperature elevation, not only the molecular square with ?-L-1 but also a lantern-shaped cage with a-L-1 formed simultaneously. Similar to how Watson-Crick pairs stabilize the helical structure of duplex DNA, the core-shell molecular assembly possesses favorable H-bonding interaction sites. This is dictated by the ligand conformation in the shell, coding for the formation and providing stabilization of the central lantern shaped core, which was not observed without this complementary interaction. On the basis of the crystallographic implications, a heterobimetallic cage was obtained through a postsynthetic metal ion metathesis, showing different reactivity of coordination bonds in the core and shell. As an innovative synthetic strategy, the site-selective metathesis broadens the structural diversity and properties of coordination assemblies.

  6. Conformational changes and ligand recognition of Escherichia coli D-xylose binding protein revealed

    DEFF Research Database (Denmark)

    Sooriyaarachchi, Sanjeewani; Ubhayasekera, Wimal; Park, Chankyu

    2010-01-01

    ATP binding cassette transport systems account for most import of necessary nutrients in bacteria. The periplasmic binding component (or an equivalent membrane-anchored protein) is critical to recognizing cognate ligand and directing it to the appropriate membrane permease. Here we report the X-r...

  7. Recognition of 3-D symmetric objects from range images in automated assembly tasks

    Science.gov (United States)

    Alvertos, Nicolas; Dcunha, Ivan

    1990-01-01

    A new technique is presented for the three dimensional recognition of symmetric objects from range images. Beginning from the implicit representation of quadrics, a set of ten coefficients is determined for symmetric objects like spheres, cones, cylinders, ellipsoids, and parallelepipeds. Instead of using these ten coefficients trying to fit them to smooth surfaces (patches) based on the traditional way of determining curvatures, a new approach based on two dimensional geometry is used. For each symmetric object, a unique set of two dimensional curves is obtained from the various angles at which the object is intersected with a plane. Using the same ten coefficients obtained earlier and based on the discriminant method, each of these curves is classified as a parabola, circle, ellipse, or hyperbola. Each symmetric object is found to possess a unique set of these two dimensional curves whereby it can be differentiated from the others. It is shown that instead of using the three dimensional discriminant which involves evaluation of the rank of its matrix, it is sufficient to use the two dimensional discriminant which only requires three arithmetic operations.

  8. Importance of the extracellular loops in G protein-coupled receptors for ligand recognition and receptor activation.

    Science.gov (United States)

    Peeters, M C; van Westen, G J P; Li, Q; IJzerman, A P

    2011-01-01

    G protein-coupled receptors (GPCRs) are the major drug target of medicines on the market today. Therefore, much research is and has been devoted to the elucidation of the function and three-dimensional structure of this large family of membrane proteins, which includes multiple conserved transmembrane domains connected by intra- and extracellular loops. In the last few years, the less conserved extracellular loops have garnered increasing interest, particularly after the publication of several GPCR crystal structures that clearly show the extracellular loops to be involved in ligand binding. This review will summarize the recent progress made in the clarification of the ligand binding and activation mechanism of class-A GPCRs and the role of extracellular loops in this process.

  9. Temperature-responsive self-assembled monolayers of oligo(ethylene glycol): control of biomolecular recognition.

    Science.gov (United States)

    Zareie, Hadi M; Boyer, Cyrille; Bulmus, Volga; Nateghi, Ebrahim; Davis, Thomas P

    2008-04-01

    Self-assembled monolayers (SAMs) of oligo(ethylene glycol) (OEG)-tethered molecules on gold are important for various biorelevant applications ranging from biomaterials to bioanalytical devices, where surface resistance to nonspecific protein adsorption is needed. Incorporation of a stimuli-responsive character to the OEG SAMs enables the creation of nonfouling surfaces with switchable functionality. Here we present an OEG-derived structure that is highly responsive to temperature changes in the vicinity of the physiological temperature, 37 degrees C. The temperature-responsive solution behavior of this new compound was demonstrated by UV-vis and nuclear magnetic resonance spectroscopy. Its chemisorption onto gold(111), and the retention of responsive behavior after chemisorption have been demonstrated by surface plasmon resonance (SPR), X-ray photoelectron spectroscopy (XPS), and atomic force and scanning tunneling microscopy. The OEG-derived SAMs have been shown to reversibly switch the wettability of the surface, as determined by contact angle measurements. More importantly, SPR and AFM studies showed that the OEG SAMs can be utilized to control the affinity binding of streptavidin to the biotin-tethered surface in a temperature-dependent manner while still offering the nonspecific protein-resistance to the surface.

  10. Near infrared (NIR) lanthanide emissive Langmuir-Blodgett monolayers formed using Nd(III) directed self-assembly synthesis of chiral amphiphilic ligands.

    Science.gov (United States)

    Barry, Dawn E; Kitchen, Jonathan A; Albrecht, Martin; Faulkner, Stephen; Gunnlaugsson, Thorfinnur

    2013-09-10

    The incorporation of chiral amphiphilic lanthanide-directed self-assembled Nd(III) complexes (Nd.13 and Nd.23) into stable Langmuir monolayers, and the subsequent Langmuir-Blodgett film formation of these, is described. The photophysical properties of the enantiomeric pair of ligands 1 and 2 in the presence of Nd(CF3SO3)3 were also investigated in CH3CN solutions using UV-vis, fluorescence, and lanthanide luminescence spectroscopies. Analysis of the resulting self-assembly processes revealed that two main species were formed in solution,1:1 and 1:3 Nd:L self-assembly complexes, with the latter being the dominant species upon the addition of 0.33 equivalents of Nd(III). Excited state lifetime measurements of Nd.13 and Nd.23 in CH3OH and CD3OD and CH3CN were also evaluated. The formation of the self-assembly in solution was also monitored by observing the changes in the circular dichroism (CD) spectra; and large differences were observed between the 1:3 and other stoichiometries in the spectra, allowing for correlation to be made with that seen in the emission studies of these systems. Surface pressure-area and surface pressure-time isotherms evidenced the formation of stable Langmuir monolayers of Nd.13 and Nd.23 at an air-water interface, and the deposition of these monolayers onto a quartz solid substrate (Langmuir-Blodgett films) gave rise to immobilized chiral monomolecular films which exhibited Nd(III) NIR luminescence upon excitation of the ligand chromophore, demonstrating efficient energy transfer to the Nd(III) excided state (sensitized) with concomitant emission centered at 800 and 1334 nm.

  11. Inhibition of cell-cell binding by lipid assemblies

    Energy Technology Data Exchange (ETDEWEB)

    Nagy, Jon O. (Rodeo, CA); Bargatze, Robert F. (Bozeman, MT)

    2001-05-22

    This invention relates generally to the field of therapeutic compounds designed to interfere between the binding of ligands and their receptors on cell surface. More specifically, it provides products and methods for inhibiting cell migration and activation using lipid assemblies with surface recognition elements that are specific for the receptors involved in cell migration and activation.

  12. Inhibition Of Call-Cell Binding By Kipid Assemblies

    Energy Technology Data Exchange (ETDEWEB)

    Nagy, Jon O. (Rodeo, CA), Bargatze, Robert F. (Bozeman, MT)

    2003-12-16

    This invention relates generally to the field of therapeutic compounds designed to interfere between the binding of ligands and their receptors on cell surface. More specifically, it provides products and methods for inhibiting cell migration and activation using lipid assemblies with surface recognition elements that are specific for the receptors involved in cell migration and activation.

  13. Hydrogen bonding discotic liquid crystals: Synthesis, self-assembly, and molecular recognition

    Science.gov (United States)

    Bushey, Mark Lawrence

    The triamides shown below form discotic liquid crystalline phases with intermolecular hydrogen bonding stabilizing the columnar structure, A and B. The mesomorphic orientations of the columns are dependent on the amide side chain. Three mesophasic orientations are described: columns aligned perpendicular to the surface, columns aligned parallel to the surface in a radial pattern, and columns aligned parallel to the surface in a parallel or aligned pattern. The aggregation of the tridodecyloxy-triamides show N-H shifting in the IR at elevated temperatures, an indication that hydrogen bonding is important in the association of liquid crystalline mesophases. Powder X-ray diffraction studies indicate packing of the columns into a hexagonal lattice.* Studies on triamides with chiral side chains result in molecules stacking into columns displaying a helical pitch. In concentrated solutions of dodecane, molecules with chiral side chains display behavior consistent with chiral nematic liquid crystals; a super helical packing of the chiral columns. These superhelical packed systems show temperature dependent selective reflection of visible light and fingerprint textures. Atomic force microscopy (AFM) confirms in sub-monolayer films, that molecules preferring an edge-on orientation form long columns on highly ordered pyrolytic graphite (HOPG), those that prefer a face-on orientation form large amorphous domains. Electrostatic force microscopy (EFM) images of the domains of molecules in the edge-on orientation provides no discernible polarity, imaging of the domains of molecules in the face-on orientation indicates a negative polar orientation. Scanning probe measurements (SPM) of the tridodecynyl-triamide have shown similar edge-on orientations of other tridodecyloxy-triamides. Powder X-ray diffraction of these liquid crystalline phases shows a hexagonal packing of the columnar assembly. Electro-optic switching studies indicate a piezoelectric switching mechanism, possibly

  14. Axial Ligand Effects on the Structures of Self-Assembled Gallium-Porphyrin Monolayers on Highly Oriented Pyrolytic Graphite.

    Science.gov (United States)

    Kamm, Judith M; Iverson, Cameron P; Lau, Wing-Yeung; Hopkins, Michael D

    2016-01-19

    Monolayers of five-coordinate gallium octaethylporphyrin complexes (Ga(OEP)X; X = Cl, Br, I, O3SCF3, CCPh) on highly oriented pyrolytic graphite were studied at the solid-liquid (1-phenyloctane) interface using scanning tunneling microscopy (STM) to probe the dependence of their properties on the nature of the axial X ligand. Density functional theory calculations of the gas-phase structures of the free molecules reveal that the gallium atom is positioned above the plane of the porphyrin macrocycle, with this pyramidal distortion increasing in magnitude according to X = O3SCF3 (displacement = 0.35 Å) monolayers are sensitive to the nature of the axial ligand: the monolayers of Ga(OEP)(O3SCF3) and Ga(OEP)(CCPh) exhibit damage during the STM experiment upon repeated scanning and upon toggling the sign of the bias potential, but monolayers of Ga(OEP)Cl, Ga(OEP)Br, and Ga(OEP)I do not. A second important ligand-influenced property is that Ga(OEP)I forms bilayer structures, whereas the other Ga(OEP)X compounds form monolayers exclusively under identical conditions. The top layer of the Ga(OEP)I bilayer is oriented with the iodo ligand directed away from the surface, like the bottom layer, but the molecules pack in a square, lower-density geometry. The comparatively large polarizability of the iodo ligand is suggested to be important in stabilizing the bilayer structure.

  15. Molecular recognition by cholesterol esterase of active site ligands: structure-reactivity effects for inhibition by aryl carbamates and subsequent carbamylenzyme turnover.

    Science.gov (United States)

    Feaster, S R; Lee, K; Baker, N; Hui, D Y; Quinn, D M

    1996-12-24

    Interactions of mammalian pancreatic cholesterol esterases from pig and rat with a family of aryl carbamates CnH2n+1NHCOOAr [n = 4-9; Ar = phenyl, p-X-phenyl (X = acetamido, bromo, fluoro, nitro, trifluoromethyl), 2-naphthyl, 2-tetrahydronaphthyl, estronyl] have been investigated, with an aim of delineating the ligand structural features which lead to effective molecular recognition by the active site of the enzyme. These carbamates inhibit the catalytic activity of CEase by rapid carbamylation of the active site, a process that shows saturation kinetics. Subsequent slow decarbamylation usually leads to full restoration of activity, and therefore aryl carbamates are transient inhibitors, or pseudo-substrates, of CEase. Structural variation of carbamate inhibitors allowed molecular recognition in the fatty acid binding and steroid binding loci of the extended active site to be probed, and the electronic nature of the carbamylation transition state to be characterized. Optimal inhibitory activity is observed when the length of the carbamyl function is n = 6 and n = 7 for porcine and rat cholesterol esterases, respectively, equivalent to eight- and nine-carbon fatty acyl chains. In contrast, inhibitory activity increases progressively as the partial molecular volume of the aromatic fragment increases. Hammett plots for p-substituted phenyl-N-hexyl carbamates indicate that the rate-determining step for carbamate inhibition is phenolate anion expulsion. Effects of the bile salt activator taurocholate on the kinetically resolved phases of the pseudo-substrate turnover of aryl carbamates were also studied. Taurocholate increases the affinity of the carbamate for the active site of cholesterol esterase in the reversible, noncovalent complex that precedes carbamylation and increases the rate constants of the serial carbamylation and decarbamylation steps. Structural variation of the N-alkyl chain and of the aryl fused-ring system provides an accounting of bile salt

  16. Self-Assembly of Discrete Metallocycles versus Coordination Polymers Based on Cu(I and Ag(I Ions and Flexible Ligands: Structural Diversification and Luminescent Properties

    Directory of Open Access Journals (Sweden)

    Javier Vallejos

    2016-02-01

    Full Text Available Three new Ag(I and one Cu(I coordination compounds with two different positional isomers, propane-1,3-diyl bis(pyridine-4-carboxylate (L1 and propane-1,3-diyl bis(pyridine-3-carboxylate (L2, of a bis-(pyridyl-carboxylate ligand have been synthesized. X-ray diffraction analysis revealed that the self-assembly of L1 with AgCF3SO3 and AgClO4 salts leads to the formation of discrete binuclear metallocycles {Ag(L1CF3SO3}2 (1 and {Ag(L1ClO4}2 (2, respectively. However, self-assembly of the other ligand, L2, with AgCF3SO3 and CuCl salts, results in a 1-D zig-zag chain {Ag(L2CF3SO3}∞ (3 and a 1-D double-stranded helical chain {Cu2Cl2(L22}∞ (4 coordination polymers, respectively. Solid emission spectra recorded at room temperature show interesting luminescence properties for all four compounds in the range from 438 to 550 nm, especially for compound 4 that was found to change its emission color when the wavelength of the excitation radiation is switched from 332 to 436 nm.

  17. Molecular recognition in a diverse set of protein-ligand interactions studied with molecular dynamics simulations and end-point free energy calculations.

    Science.gov (United States)

    Wang, Bo; Li, Liwei; Hurley, Thomas D; Meroueh, Samy O

    2013-10-28

    End-point free energy calculations using MM-GBSA and MM-PBSA provide a detailed understanding of molecular recognition in protein-ligand interactions. The binding free energy can be used to rank-order protein-ligand structures in virtual screening for compound or target identification. Here, we carry out free energy calculations for a diverse set of 11 proteins bound to 14 small molecules using extensive explicit-solvent MD simulations. The structure of these complexes was previously solved by crystallography and their binding studied with isothermal titration calorimetry (ITC) data enabling direct comparison to the MM-GBSA and MM-PBSA calculations. Four MM-GBSA and three MM-PBSA calculations reproduced the ITC free energy within 1 kcal·mol(-1) highlighting the challenges in reproducing the absolute free energy from end-point free energy calculations. MM-GBSA exhibited better rank-ordering with a Spearman ρ of 0.68 compared to 0.40 for MM-PBSA with dielectric constant (ε = 1). An increase in ε resulted in significantly better rank-ordering for MM-PBSA (ρ = 0.91 for ε = 10), but larger ε significantly reduced the contributions of electrostatics, suggesting that the improvement is due to the nonpolar and entropy components, rather than a better representation of the electrostatics. The SVRKB scoring function applied to MD snapshots resulted in excellent rank-ordering (ρ = 0.81). Calculations of the configurational entropy using normal-mode analysis led to free energies that correlated significantly better to the ITC free energy than the MD-based quasi-harmonic approach, but the computed entropies showed no correlation with the ITC entropy. When the adaptation energy is taken into consideration by running separate simulations for complex, apo, and ligand (MM-PBSAADAPT), there is less agreement with the ITC data for the individual free energies, but remarkably good rank-ordering is observed (ρ = 0.89). Interestingly, filtering MD snapshots by prescoring

  18. Syntheses, structures and photoluminescence of lanthanide-organic frameworks assembled from multifunctional N,O-donor ligand

    Energy Technology Data Exchange (ETDEWEB)

    Che, Guang-Bo, E-mail: guangboche@jlnu.edu.cn [Key Laboratory of Preparation and Applications of Environmental Friendly Materials, Jilin Normal University, Chinese Ministry of Education, Siping 136000 (China); Liu, Shu-Yu [Key Laboratory of Preparation and Applications of Environmental Friendly Materials, Jilin Normal University, Chinese Ministry of Education, Siping 136000 (China); Zhang, Qing [Institute of Functional Nano and Soft Materials (FUNSOM), Collaborative Innovation Center of Suzhou Nano Science and Technology, Soochow University, Suzhou 215123 (China); Liu, Chun-Bo, E-mail: liuchunbo431@gmail.com [School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang 212013 (China); Zhang, Xing-Jing [Key Laboratory of Preparation and Applications of Environmental Friendly Materials, Jilin Normal University, Chinese Ministry of Education, Siping 136000 (China)

    2015-05-15

    Four new lanthanide complexes [Ln(O–NCP){sub 2}(NO{sub 3})]{sub n} based on multifunctional N,O-donor ligand 2-(2-carboxyphenyl)imidazo(4,5-f)-(1,10)phenanthroline (O–HNCP) and Ln(NO{sub 3}){sub 3}·6H{sub 2}O (Ln=Nd(1), La(2), Sm(3), Eu(4)) have been achieved under hydrothermal conditions and characterized by elemental analyses, infrared spectra and single crystal X-ray diffraction. Structural analyses revealed that all of these four complexes possess similar two-dimensional layer structures. In addition, thermal stability and luminescent properties of these complexes were also investigated. - Graphical abstract: A series of lanthanide(III) coordination polymers with intriguing structures based on 2-(2-carboxyphenyl)imidazo(4,5-f)-(1,10)phenanthroline ligand have been hydrothermally synthesized. The thermal stabilities and photoluminescence properties of these complexes have been investigated. - Highlights: • Four lanthanide(III) complexes have been hydrothermally synthesized. • The N,O-donor O–HNCP was used as the ligand. • TGA and PL properties of complexes 1–4 have been investigated.

  19. Transgenic expression of the dicotyledonous pattern recognition receptor EFR in rice leads to ligand-dependent activation of defense responses.

    Directory of Open Access Journals (Sweden)

    Benjamin Schwessinger

    2015-03-01

    Full Text Available Plant plasma membrane localized pattern recognition receptors (PRRs detect extracellular pathogen-associated molecules. PRRs such as Arabidopsis EFR and rice XA21 are taxonomically restricted and are absent from most plant genomes. Here we show that rice plants expressing EFR or the chimeric receptor EFR::XA21, containing the EFR ectodomain and the XA21 intracellular domain, sense both Escherichia coli- and Xanthomonas oryzae pv. oryzae (Xoo-derived elf18 peptides at sub-nanomolar concentrations. Treatment of EFR and EFR::XA21 rice leaf tissue with elf18 leads to MAP kinase activation, reactive oxygen production and defense gene expression. Although expression of EFR does not lead to robust enhanced resistance to fully virulent Xoo isolates, it does lead to quantitatively enhanced resistance to weakly virulent Xoo isolates. EFR interacts with OsSERK2 and the XA21 binding protein 24 (XB24, two key components of the rice XA21-mediated immune response. Rice-EFR plants silenced for OsSERK2, or overexpressing rice XB24 are compromised in elf18-induced reactive oxygen production and defense gene expression indicating that these proteins are also important for EFR-mediated signaling in transgenic rice. Taken together, our results demonstrate the potential feasibility of enhancing disease resistance in rice and possibly other monocotyledonous crop species by expression of dicotyledonous PRRs. Our results also suggest that Arabidopsis EFR utilizes at least a subset of the known endogenous rice XA21 signaling components.

  20. Controlling the specificity of modularly assembled small molecules for RNA via ligand module spacing: targeting the RNAs that cause myotonic muscular dystrophy.

    Science.gov (United States)

    Lee, Melissa M; Childs-Disney, Jessica L; Pushechnikov, Alexei; French, Jonathan M; Sobczak, Krzysztof; Thornton, Charles A; Disney, Matthew D

    2009-12-02

    Myotonic muscular dystrophy types 1 and 2 (DM1 and DM2, respectively) are caused by expansions of repeating nucleotides in noncoding regions of RNA. In DM1, the expansion is an rCUG triplet repeat, whereas the DM2 expansion is an rCCUG quadruplet repeat. Both RNAs fold into hairpin structures with periodically repeating internal loops separated by two 5'GC/3'CG base pairs. The sizes of the loops, however, are different: the DM1 repeat forms 1 x 1 nucleotide UU loops while the DM2 repeat forms 2 x 2 nucleotide 5'CU/3'UC loops. DM is caused when the expanded repeats bind the RNA splicing regulator Muscleblind-like 1 protein (MBNL1), thus compromising its function. Therefore, one potential therapeutic strategy for these diseases is to prevent MBNL1 from binding the toxic RNA repeats. Previously, we designed nanomolar inhibitors of the DM2-MBNL1 interaction by modularly assembling 6'-N-5-hexyonate kanamycin A (K) onto a peptoid backbone. The K ligand binds the 2 x 2 pyrimidine-rich internal loops found in the DM2 RNA with high affinity. The best compound identified from that study contains three K modules separated by four propylamine spacing modules and is 20-fold selective for the DM2 RNA over the DM1 RNA. Because the modularly assembled K-containing compounds also bound the DM1 RNA, albeit with lower affinity, and because the loop size is different, we hypothesized that the optimal DM1 RNA binder may display K modules separated by a shorter distance. Indeed, here the ideal DM1 RNA binder has only two propylamine spacing modules separating the K ligands. Peptoids displaying three and four K modules on a peptoid scaffold bind the DM1 RNA with K(d)'s of 20 nM (3-fold selective for DM1 over DM2) and 4 nM (6-fold selective) and inhibit the RNA-protein interaction with IC(50)'s of 40 and 7 nM, respectively. Importantly, by coupling the two studies together, we have determined that appropriate spacing can affect binding selectivity by 60-fold (20- x 3-fold). The trimer and

  1. Linking ligand perception by PEPR pattern recognition receptors to cytosolic Ca2+ elevation and downstream immune signaling in plants.

    Science.gov (United States)

    Ma, Yi; Walker, Robin K; Zhao, Yichen; Berkowitz, Gerald A

    2012-11-27

    Little is known about molecular steps linking perception of pathogen invasion by cell surface sentry proteins acting as pattern recognition receptors (PRRs) to downstream cytosolic Ca(2+) elevation, a critical step in plant immune signaling cascades. Some PRRs recognize molecules (such as flagellin) associated with microbial pathogens (pathogen-associated molecular patterns, PAMPs), whereas others bind endogenous plant compounds (damage-associated molecular patterns, DAMPs) such as peptides released from cells upon attack. This work focuses on the Arabidopsis DAMPs plant elicitor peptides (Peps) and their receptors, PEPR1 and PEPR2. Pep application causes in vivo cGMP generation and downstream signaling that is lost when the predicted PEPR receptor guanylyl cyclase (GC) active site is mutated. Pep-induced Ca(2+) elevation is attributable to cGMP activation of a Ca(2+) channel. Some differences were identified between Pep/PEPR signaling and the Ca(2+)-dependent immune signaling initiated by the flagellin peptide flg22 and its cognate receptor Flagellin-sensing 2 (FLS2). FLS2 signaling may have a greater requirement for intracellular Ca(2+) stores and inositol phosphate signaling, whereas Pep/PEPR signaling requires extracellular Ca(2+). Maximal FLS2 signaling requires a functional Pep/PEPR system. This dependence was evidenced as a requirement for functional PEPR receptors for maximal flg22-dependent Ca(2+) elevation, H(2)O(2) generation, defense gene [WRKY33 and Plant Defensin 1.2 (PDF1.2)] expression, and flg22/FLS2-dependent impairment of pathogen growth. In a corresponding fashion, FLS2 loss of function impaired Pep signaling. In addition, a role for PAMP and DAMP perception in bolstering effector-triggered immunity (ETI) is reported; loss of function of either FLS2 or PEPR receptors impaired the hypersensitive response (HR) to an avirulent pathogen.

  2. Structural Basis of Differential Ligand Recognition by Two Classes of bis-(3-5)-cyclic Dimeric Guanosine Monophosphate-binding Riboswitches

    Energy Technology Data Exchange (ETDEWEB)

    K Smith; C Shanahan; E Moore; A Simon; S Strobel

    2011-12-31

    The bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) signaling pathway regulates biofilm formation, virulence, and other processes in many bacterial species and is critical for their survival. Two classes of c-di-GMP-binding riboswitches have been discovered that bind this second messenger with high affinity and regulate diverse downstream genes, underscoring the importance of RNA receptors in this pathway. We have solved the structure of a c-di-GMP-II riboswitch, which reveals that the ligand is bound as part of a triplex formed with a pseudoknot. The structure also shows that the guanine bases of c-di-GMP are recognized through noncanonical pairings and that the phosphodiester backbone is not contacted by the RNA. Recognition is quite different from that observed in the c-di-GMP-I riboswitch, demonstrating that at least two independent solutions for RNA second messenger binding have evolved. We exploited these differences to design a c-di-GMP analog that selectively binds the c-di-GMP-II aptamer over the c-di-GMP-I RNA. There are several bacterial species that contain both types of riboswitches, and this approach holds promise as an important tool for targeting one riboswitch, and thus one gene, over another in a selective fashion.

  3. Pattern recognition receptor signaling in human dendritic cells is enhanced by ICOS ligand and modulated by the Crohn's disease ICOSLG risk allele.

    Science.gov (United States)

    Hedl, Matija; Lahiri, Amit; Ning, Kaida; Cho, Judy H; Abraham, Clara

    2014-05-15

    Inflammatory bowel disease (IBD) is characterized by dysregulated intestinal immune homeostasis and cytokine secretion. Multiple loci are associated with IBD, but a functional explanation is missing for most. Here we found that pattern-recognition receptor (PRR)-induced cytokine secretion was diminished in human monocyte-derived dendritic cells (MDDC) from rs7282490 ICOSLG GG risk carriers. Homotypic interactions between the costimulatory molecule ICOS and the ICOS ligand on MDDCs amplified nucleotide-binding oligomerization domain 2 (NOD2)-initiated cytokine secretion. This amplification required arginine residues in the ICOSL cytoplasmic tail that recruited the adaptor protein RACK1 and the kinases PKC and JNK leading to PKC, MAPK, and NF-κB activation. MDDC from rs7282490 GG risk-carriers had reduced ICOSL expression and PRR-initiated signaling and this loss-of-function ICOSLG risk allele associated with an ileal Crohn's disease phenotype, similar to polymorphisms in NOD2. Taken together, ICOSL amplifies PRR-initiated outcomes, which might contribute to immune homeostasis.

  4. Synthesis of an S T = 7 [Mn 3 ] Mixed-Valence Complex Based on 1,3-Propanediol Ligand Derivatives and Its One-Dimensional Assemblies

    KAUST Repository

    Huang, Jian

    2013-10-07

    Controlled organization of high-spin complexes and single-molecule magnets is a great challenge in molecular magnetism in order to study the effect of the intercomplex magnetic interactions on the intrinsic properties of a given magnetic object. In this work, a new ST = 7 trinuclear mixed-valence Mn complex, [MnIIIMnII 2(LA) 2(Br)4(CH3OH)6] ·Br· (CH3OH)1.5·(H2O)0.5 (1), is reported using a pyridinium-functionalized 1,3-propanediol ligand (H 2LABr = 1-(3-bromo-2,2-bis(hydroxymethyl)propyl)pyridinium bromide). Using azido anions as bridging ligands and different pyridinium-functionalized 1,3-propanediol ligands (H2LBBr = 1-(3-bromo-2,2-bis(hydroxymethyl)propyl)-4-picolinium bromide; H 2LCBr = 1-(3-bromo-2,2-bis(hydroxymethyl)propyl)-3,5- lutidinium bromide), the linear [MnIIIMnII 2L2X4]+ building block has been assembled into one-dimensional coordination networks: [MnIIIMn II 2(LA)2(Br)4(CH 3OH)4(N3)]·((C2H 5)2O)1.25 (2∞), [MnIIIMn II 2(LB)2(Br)4(C 2H5OH)(CH3OH)(H2O) 2(N3)]·(H2O)0.25 (3∞), and [MnIIIMnII 2(LC) 2(Cl)3.8(Br)0.2(C2H 5OH)3(CH3OH)(N3)] (4∞). The syntheses, characterization, crystal structures, and magnetic properties of these new [Mn3]-based materials are reported. © 2013 American Chemical Society.

  5. Synthesis, properties and surface self-assembly of a pentanuclear cluster based on the new π-conjugated TTF-triazole ligand

    Science.gov (United States)

    Cui, Long; Geng, Yan-Fang; Leong, Chanel F.; Ma, Qian; D'Alessandro, Deanna M.; Deng, Ke; Zeng, Qing-Dao; Zuo, Jing-Lin

    2016-05-01

    The new π-extended redox-active ligand with both TTF and triazole units, 6-(4,5-bis(propylthio)-1,3-dithiol-2-ylidene)-1H-[1,3]dithiolo[4‧,5‧:4,5]benzo [1,2-d] [1-3]triazole, has been successfully prepared. Based on the versatile ligand and Cu(tta)2 precursors (tta- = 4,4,4-trifluoro-1-(thiophen-2-yl)butane-1,3-dione), a TTF-based pentanuclear CuII cluster (Cu5(tta)4(TTFN3)6) is synthesized and structurally characterized. Their absorption and electrochemical properties are investigated. Antiferromagnetic couplings are operative between metal ion centers bridged by triazoles in the complex. The self-assembled structure of the cluster complex on a highly oriented pyrolytic graphite (HOPG) surface was observed using scanning tunneling microscopy and density functional theory (DFT) calculations have been performed to provide insight into the formation mechanism. The introduction of the redox-active TTF unit into the cluster complexes with interesting magnetic properties renders them promising candidates for new multifunctional materials.

  6. Syntheses and Characterizations of Novel One-dimensional Coordination Polymers Self-assembled from Co(NCS)2 and Flexible Diester-bridged Pyridine-based Ligands

    Institute of Scientific and Technical Information of China (English)

    SONG,Li-Cheng(宋礼成); ZHANG,Wen-Xiong(张文雄); HU,Qing-Mei(胡青眉)

    2002-01-01

    The self-assembly reactions of Co(NCS)2 with diester-bridgedpyridine-based ligands pyCO2-(CH2),-O2Cpy (py= 4-pyridyl;m = 2, 3, 4) have been studied. Interestingly, while Co(NCS)2 reacted with pyCO2-(CH2)2-O2Cpy (La) in MeOH/H2Oor THF/MeCN to yield two coordination polymers [Co(NCS)2(La)2]n (1) and [Co(NCS)2(La)2@2THF]n (2), reactions of Co(NCS)2 with pyCO2-(CH2)3-O2Cpy (Lb) in MeOH/MeCN and Co(NCS)2 with pyCO2-( CH2)4-O2Cpy(Lc) in EtOH/H2O afforded [Co(NCS)2(Lb)2@0.5MeOH]n(3) and [Co(NCS)2(Lc)2@2H2O]n (4), respectively. The Xray diffraction analyses indicated that polymers 1-4 consist of a one-dimensional Co(H) chain in which each of the two adjacent Co(Ⅱ) ions is bridged by two pyCO2-(CH2)m-O2Cpy ligands to form a macrocycle, In addition, the structuress of polymers 1-4 were also characterized by infrared spectroscopy,thermogravimetry and elemental analysis.

  7. Low-Resolution Tactile Image Recognition for Automated Robotic Assembly Using Kernel PCA-Based Feature Fusion and Multiple Kernel Learning-Based Support Vector Machine

    Directory of Open Access Journals (Sweden)

    Yi-Hung Liu

    2014-01-01

    Full Text Available In this paper, we propose a robust tactile sensing image recognition scheme for automatic robotic assembly. First, an image reprocessing procedure is designed to enhance the contrast of the tactile image. In the second layer, geometric features and Fourier descriptors are extracted from the image. Then, kernel principal component analysis (kernel PCA is applied to transform the features into ones with better discriminating ability, which is the kernel PCA-based feature fusion. The transformed features are fed into the third layer for classification. In this paper, we design a classifier by combining the multiple kernel learning (MKL algorithm and support vector machine (SVM. We also design and implement a tactile sensing array consisting of 10-by-10 sensing elements. Experimental results, carried out on real tactile images acquired by the designed tactile sensing array, show that the kernel PCA-based feature fusion can significantly improve the discriminating performance of the geometric features and Fourier descriptors. Also, the designed MKL-SVM outperforms the regular SVM in terms of recognition accuracy. The proposed recognition scheme is able to achieve a high recognition rate of over 85% for the classification of 12 commonly used metal parts in industrial applications.

  8. Expression and purification of a natural N-terminal pre-ligand assembly domain of tumor necrosis factor receptor 1 (TNFR1 PLAD) and preliminary activity determination.

    Science.gov (United States)

    Cao, Jin; Meng, Fang; Gao, Xiangdong; Dong, Hongxia; Yao, Wenbing

    2011-04-01

    A domain at the NH(2) terminal (N-terminal) of tumor necrosis factor receptor (TNFR) termed the pre-ligand binding assembly domain (PLAD). The finding that PLAD can mediate a selective TNFR assembly in previously researches provides a novel target to the prevention of TNFR signaling in immune-mediated inflammatory diseases (IMID). In this study, a natural N-terminal TNFR1 PLAD was obtained for the first time through the methods of GST-tag fusion protein expression and enterokinase cleavage. After purification with a Q Sepharose Fast Flow column, a natural N-terminal TNFR1 PLAD which purity was up to 95%, was obtained and was identified using Nano LC-ECI-MS/MS. Secondary structure analysis of PLAD was carried out using circular dichroism spectra (CD). After that, the TNFR1 PLAD in vitro anti-TNFα activity and the specific TNFR1 affinity were determined. The results proved that the natural N-terminal TNFR1 PLAD can selectively inhibit TNFα bioactivity mainly through TNFR1. It infers an effective and safe strategy for treating variety of IMID with a low risk of side effects in future.

  9. Ligand and counterion control of Ag(I) architectures: assembly of a {Ag8} ring cluster mediated by hydrophobic and Ag...Ag interactions.

    Science.gov (United States)

    Fielden, John; Long, De-liang; Slawin, Alexandra M Z; Kögerler, Paul; Cronin, Leroy

    2007-10-29

    A strategy combining ligand design and counterion variation has been used to investigate the assembly of silver(I) complexes. As a result, dinuclear, octanuclear, and polymeric silver(I) species have been synthesized by complexation of the rigid aliphatic amino ligands cis-3,5-diamino-trans-hydroxycyclohexane (DAHC), cis-3,5-diamino-trans-methoxycyclohexane (DAMC), and cis-3,5-diamino-trans-tert-butyldimethylsilylanyloxycyclohexane (DATC) with silver(I) triflate, nitrate, and perchlorate. The compositions of these aggregates, established by X-ray crystallography and elemental analysis, are [{Ag(DAHC)}2](CF3SO3)2 (1), [{Ag(DAMC)}2](CF3SO3)2 (2), [{Ag(DAMC)}2](NO3)2 (3), [{Ag(DATC)}6{Ag(DAHC)}2](NO3)8 (4), and [{Ag(DATC}n](NO3)n (5), where the DAHC present in 4 is formed by in situ hydrolysis of the acid labile silyl ether group. The type of aggregate formed depends both upon the noncoordinating O-substituent of the ligand and the (also noncoordinating) counterion, with the normal preference of the ligand topology for forming Ag2L2 structures being broken by introduction of the bulky, lipophilic O-tert-butyldimethylsilyl (TBDMS) group. Of particular note is the octanuclear silver ring structure 4, which is isolated only when both the O-TBDMS group and the nitrate counteranion are present and is formed from four Ag2L2 dimers connected by Ag...Ag and hydrogen-bonding interactions. Diffusion rate measurement of this {Ag8} complex by 1H NMR (DOSY) indicates dissociation in CD3OD and CD3CN, showing that this supramolecular ring structure is formed upon crystallization, and establishing a qualitative limit to the strength of Ag...Ag interactions in solution. When solutions of the {Ag8} cluster in methanol are kept for several days though, a new UV-vis absorption is observed at around 430 nm, consistent with the formation of silver nanoparticles.

  10. Predicting the right spacing between protein immobilization sites on self-assembled monolayers to optimize ligand binding.

    Science.gov (United States)

    Perez, Javier Batista; Tyagi, Deependra; Yang, Mo; Calvo, Loany; Perez, Rolando; Moreno, Ernesto; Zhu, Jinsong

    2015-09-01

    Self-assembled monolayers designed to immobilize capture antibodies are usually prepared using a mixture of functional and inactive linkers. Here, using low molar ratios (1:1 to 1:100) of the two linkers resulted in loss of binding capability of the anti-EGFR (epidermal growth factor receptor) antibody nimotuzumab, as assessed by surface plasmon resonance imaging. We then developed a simple theoretical model to predict the optimal surface density of the functional linker, taking into account the antibody size and linker diameter. A high (1:1000) dilution of the functional linker yielded the best results. As an advantage, this approach does not require chemical modification of the protein.

  11. Recognition of interaction interface residues in low-resolution structures of protein assemblies solely from the positions of C(alpha atoms.

    Directory of Open Access Journals (Sweden)

    Rupali A Gadkari

    Full Text Available BACKGROUND: The number of available structures of large multi-protein assemblies is quite small. Such structures provide phenomenal insights on the organization, mechanism of formation and functional properties of the assembly. Hence detailed analysis of such structures is highly rewarding. However, the common problem in such analyses is the low resolution of these structures. In the recent times a number of attempts that combine low resolution cryo-EM data with higher resolution structures determined using X-ray analysis or NMR or generated using comparative modeling have been reported. Even in such attempts the best result one arrives at is the very course idea about the assembly structure in terms of trace of the C(alpha atoms which are modeled with modest accuracy. METHODOLOGY/PRINCIPAL FINDINGS: In this paper first we present an objective approach to identify potentially solvent exposed and buried residues solely from the position of C(alpha atoms and amino acid sequence using residue type-dependent thresholds for accessible surface areas of C(alpha. We extend the method further to recognize potential protein-protein interface residues. CONCLUSION/ SIGNIFICANCE: Our approach to identify buried and exposed residues solely from the positions of C(alpha atoms resulted in an accuracy of 84%, sensitivity of 83-89% and specificity of 67-94% while recognition of interfacial residues corresponded to an accuracy of 94%, sensitivity of 70-96% and specificity of 58-94%. Interestingly, detailed analysis of cases of mismatch between recognition of interface residues from C(alpha positions and all-atom models suggested that, recognition of interfacial residues using C(alpha atoms only correspond better with intuitive notion of what is an interfacial residue. Our method should be useful in the objective analysis of structures of protein assemblies when positions of only (alpha positions are available as, for example, in the cases of integration of cryo

  12. Effects of Connecting Ligands on Photoinduced Electron Transfer Properties of Functionalized Self-assembled Solid Films%配体对功能自组装薄膜的光致电子转移特性的影响

    Institute of Scientific and Technical Information of China (English)

    韦天新; 史环环; 黄春辉; 于小峰; 黄慧忠; 吴念祖

    2006-01-01

    A strategy for fabricating the functionalized self-assembled films is proposed. Through the comparison of three self-assembled films of 3,4,9,10-perylene tetracarboxylic acid (PTA) with different connecting ligands, i.e.oxalic acid (Ox), succinic acid (Su), or terephthalic acid (Tp), it was found that the optimal system was composed of oxalic acid, Ce4+ and 3,4,9,10-perylene tetracarboxylic acid,which was much better than simple covalent connecting PTA films and the connecting ligands played an important role for the properties of self-assembled (SA)films. All these films were characterized by contact angle, UV spectra, cyclic voltammetry and XPS. The phoof dye-sensitized indium tin oxide (ITO) systems. The effects of light intensity, bias voltage, and electron donor on photoinduced electron transfer properties were also studied. The possible mechanism of electron transfer is proposed.

  13. Self-assembly of iron coordination polymer of bowl-shaped N-ligand and dodecamolybdosilicate anion

    Science.gov (United States)

    Tang, Qun; Chen, Ya-Guang

    2014-06-01

    [FeII2(ttmb)2(H2O)6][SiMo12O40]·4H2O (1) (ttmb = 1,3,5-tris(triazol-1-ylmethyl) benzene) was synthesized under hydrothermal conditions and characterized by IR spectroscopy, TG analysis and X-ray diffraction method. In 1 the bowl-like tridentate ligand, ttmb, bridges Fe2+ ions forming a coordination polymeric layer, [FeII2(ttmb)2(H2O)6]n4n+, with a large dimensional grid of 7.00 × 7.11 Å, in the presence of Keggin-type polyoxoanion as a template. The coordination polymeric layers and the polyoxoanions are fused into an inorganic-organic hybrid by hydrogen bonds. The photoluminescent spectrum of 1 in solid state at room temperature shows that the coordination of ttmb to Fe2+ ion results in a quench of the ttmb intramolecular fluorescence and a weak O-Mo LMCT fluorescent emission was observed at 520 nm.

  14. Water participation in molecular recognition and protein-ligand association: Probing the drug binding site "Sudlow I" in human serum albumin

    Science.gov (United States)

    Al-Lawatia, Najla; Steinbrecher, Thomas; Abou-Zied, Osama K.

    2012-03-01

    Human serum albumin (HSA) plays an important role in the transport and disposition of endogenous and exogenous ligands present in blood. Its capacity to reversibly bind a large variety of drugs results in its prevailing role in drug pharmacokinetics and pharmacodynamics. In this work, we used 7-hydroxyquinoline (7HQ) as a probe to study the binding nature of one of the major drug binding sites of HSA (Sudlow I) and to reveal the local environment around the probe in the binding site. The interaction between 7HQ and HSA at a physiological pH of 7.2 was investigated using steady-state and lifetime spectroscopic measurements, molecular docking and molecular dynamics (MD) simulations methods. The fluorescence results indicate a selective interaction between 7HQ and the Trp214 residue. The reduction in both the intensity and lifetime of the Trp214 fluorescence upon probe binding indicates the dominant role of static quenching. Molecular docking and MD simulations show that 7HQ binds in Sudlow site I close to Trp214, confirming the experimental results, and pinpoint the dominant role of hydrophobic interaction in the binding site. Electrostatic interactions were also found to be important in which two water molecules form strong hydrogen bonds with the polar groups of 7HQ. Detection of water in the binding site agrees with the absorption and fluorescence results that show the formation of a zwitterion tautomer of 7HQ. The unique spectral signatures of 7HQ in water make this molecule a potential probe for detecting the presence of water in nanocavities of proteins. Interaction of 7HQ with water in the binding site shows that water molecules can be crucial for molecular recognition and association in protein binding sites.

  15. Self-assembled M2L4 coordination cages : Synthesis and potential applications

    NARCIS (Netherlands)

    Schmidt, Andrea; Casini, Angela; Kuehn, Fritz E.

    2014-01-01

    Metal-mediated self-assemblies of the general formula MxLy (M = metal ion, L = ligand) have emerged as a promising research area of supramolecular chemistry because of their applicability in various fields such as molecular recognition, catalysis and drug delivery. The focus of this review is on dis

  16. Synthesis of grafted phosphorylcholine polymer layers as specific recognition ligands for C-reactive protein focused on grafting density and thickness to achieve highly sensitive detection.

    Science.gov (United States)

    Kamon, Yuri; Kitayama, Yukiya; Itakura, Akiko N; Fukazawa, Kyoko; Ishihara, Kazuhiko; Takeuchi, Toshifumi

    2015-04-21

    We studied the effects of layer thickness and grafting density of poly(2-methacryloyloxyethyl phosphorylcholine) (PMPC) thin layers as specific ligands for the highly sensitive binding of C-reactive protein (CRP). PMPC layer thickness was controlled by surface-initiated activators generated by electron transfer for atom transfer radical polymerization (AGET ATRP). PMPC grafting density was controlled by utilizing mixed self-assembled monolayers with different incorporation ratios of the bis[2-(2-bromoisobutyryloxy)undecyl] disulfide ATRP initiator, as modulated by altering the feed molar ratio with (11-mercaptoundecyl)tetra(ethylene glycol). X-ray photoelectron spectroscopy and ellipsometry measurements were used to characterize the modified surfaces. PMPC grafting densities were estimated from polymer thickness and the molecular weight obtained from sacrificial initiator during surface-initiated AGET ATRP. The effects of thickness and grafting density of the obtained PMPC layers on CRP binding performance were investigated using surface plasmon resonance employing a 10 mM Tris-HCl running buffer containing 140 mM NaCl and 2 mM CaCl2 (pH 7.4). Furthermore, the non-specific binding properties of the obtained layers were investigated using human serum albumin (HSA) as a reference protein. The PMPC layer which has 4.6 nm of thickness and 1.27 chains per nm(2) of grafting density showed highly sensitive CRP detection (limit of detection: 4.4 ng mL(-1)) with low non-specific HSA adsorption, which was improved 10 times than our previous report of 50 ng mL(-1).

  17. Quenched Assembly of NIR-Active Gold Nanoclusters Capped with Strongly Bound Ligands by Tuning Particle Charge via pH and Salinity.

    Science.gov (United States)

    Stover, Robert J; Murthy, Avinash K; Nie, Golay D; Gourisankar, Sai; Dear, Barton J; Truskett, Thomas M; Sokolov, Konstantin V; Johnston, Keith P

    2014-07-03

    Gold nanospheres coated with a binary monolayer of bound citrate and cysteine ligands were assembled into nanoclusters, in which the size and near-infrared (NIR) extinction were tuned by varying the pH and concentration of added NaCl. During full evaporation of an aqueous dispersion of 4.5 ± 1.8 nm Au primary particles, the nanoclusters were formed and quenched by the triblock copolymer polylactic acid (PLA)(1K)-b-poly(ethylene glycol) (PEG)(10K)-b-PLA(1K), which also provided steric stabilization. The short-ranged depletion and van der Waals attractive forces were balanced against longer ranged electrostatic repulsion to tune the nanocluster diameter and NIR extinction. Upon lowering the pH from 7 to 5 at a given salinity, the magnitude of the charge on the primary particles decreased, such that the weaker electrostatic repulsion increased the hydrodynamic diameter and, consequently, NIR extinction of the clusters. At a given pH, as the concentration of NaCl was increased, the NIR extinction decreased monotonically. Furthermore, the greater screening of the charges on the nanoclusters weakened the interactions with PLA(1K)-b-PEG(10K)-b-PLA(1K) and thus lowered the amount of adsorbed polymer on the nanocluster surface. The generalization of the concept of self-assembly of small NIR-active nanoclusters to include a strongly bound thiol and the manipulation of the morphologies and NIR extinction by variation of pH and salinity not only is of fundamental interest but also is important for optical biomedical imaging and therapy.

  18. G protein-coupled receptor 30 ligand G-1 increases aryl hydrocarbon receptor signalling by inhibition of tubulin assembly and cell cycle arrest in human MCF-7 cells.

    Science.gov (United States)

    Tarnow, Patrick; Tralau, Tewes; Luch, Andreas

    2016-08-01

    Regulatory crosstalk between the aryl hydrocarbon receptor (AHR) and oestrogen receptor α (ERα) is well established. Apart from the nuclear receptors ERα and ERβ, oestrogen signalling further involves an unrelated G protein-coupled receptor termed GPR30. In order to investigate potential regulatory crosstalk, this study investigated the influence of G-1 as one of the few GPR30-specific ligands on the AHR regulon in MCF-7 cells. As a well-characterised model system, these human mammary carcinoma cells co-express all three receptors (AHR, ERα and GPR30) and are thus ideally suited to study corresponding regulatory pathway interactions on transcript level. Indeed, treatment with micromolar concentrations of the GPR30-specific agonist G-1 resulted in up-regulation of AHR as well as the transcripts for cytochromes P450 1A1 and 1B1, two well-known targets of the AHR regulon. While this was partly attributable to G-1-mediated inhibition of tubulin assembly and subsequent cell cycle arrest in the G2/M phase, the effects nevertheless required functional AHR. However, G-1-induced up-regulation of CYP 1A1 was not mediated by GPR30, as G15 antagonist treatment as well as a knockdown of GPR30 and AHR failed to inhibit this effect.

  19. Molecular recognition and self-assembly special feature: Self-assembled biomimetic [2Fe2S]-hydrogenase-based photocatalyst for molecular hydrogen evolution.

    Science.gov (United States)

    Kluwer, A M; Kapre, R; Hartl, F; Lutz, M; Spek, A L; Brouwer, A M; van Leeuwen, P W N M; Reek, J N H

    2009-06-30

    The large-scale production of clean energy is one of the major challenges society is currently facing. Molecular hydrogen is envisaged as a key green fuel for the future, but it becomes a sustainable alternative for classical fuels only if it is also produced in a clean fashion. Here, we report a supramolecular biomimetic approach to form a catalyst that produces molecular hydrogen using light as the energy source. It is composed of an assembly of chromophores to a bis(thiolate)-bridged diiron ([2Fe2S]) based hydrogenase catalyst. The supramolecular building block approach introduced in this article enabled the easy formation of a series of complexes, which are all thoroughly characterized, revealing that the photoactivity of the catalyst assembly strongly depends on its nature. The active species, formed from different complexes, appears to be the [Fe(2)(micro-pdt)(CO)(4){PPh(2)(4-py)}(2)] (3) with 2 different types of porphyrins (5a and 5b) coordinated to it. The modular supramolecular approach was important in this study as with a limited number of building blocks several different complexes were generated.

  20. Ion-pair triple helicates and mesocates self-assembled from ditopic 2,2 -bipyridine-bis(urea) ligands and Ni(II) and Fe(II) sulfate salts

    Energy Technology Data Exchange (ETDEWEB)

    Custelcean, Radu [ORNL; Bonnesen, Peter V [ORNL; Roach, Benjamin D [ORNL; Duncan, Nathan C [ORNL

    2012-01-01

    NiSO{sub 4} and FeSO{sub 4} self-assemble with heteroditopic ligands (L) comprising 2,2{prime}-bipyridine and o-phenylene-(bis)urea cation- and anion-binding sites, respectively, into [ML{sub 3}SO{sub 4}] (M = Ni{sup 2+}, Fe{sup 2+}) triple-stranded ion-pair helicates and mesocates.

  1. Self-assembly of novel supramolecular silver(I) compound based on mixed ligands bipy/TST3- H3TST=2,4,6-tris (4-sulfophenylamino)-1,3,5-triazine

    NARCIS (Netherlands)

    Yu, Yunfang; Wei, Yongqin; Broer, Ria; Wu, Kechen

    2007-01-01

    The novel supramolecular silver(I) compound with formula [Ag-6(TST)(2)(bipy)(6)(H2O)(2)](n) center dot 3nH(2)O (1) based on assembly of Ag(I) and mixed ligand bipy/TST3-, bipy = 2,2'-bipyridine, H3TST = 2,4,6-tris(4-sulfophenylamino)-1,3,5-triazine, has been prepared by hydrothermal method. In the s

  2. Fluorescence turn-on recognition of chiral amino acids using dye incorporated β-CD functionalized AuNPs assembly

    Energy Technology Data Exchange (ETDEWEB)

    Aswathy, B., E-mail: aswathybv@gmail.com; Sony, G., E-mail: emailtosony@gmail.com

    2014-10-15

    An assembly of dye incorporated β-cyclodextrin (βCD) functionalized AuNPs for the fluorescent probing of chiral amino acids is presented. Gold nanoparticles (AuNPs) possessing a high extinction coefficient function can be used as excellent fluorescent quenchers in AuNP–fluorophore system. Inclusion of fluorescein (FL) into β-cyclodextrin (βCD) makes energy transfer to occur through the donor and quencher nearby. This energy transfer switches off by virtue of the analyte induced release of FL from β-CD cavity, which results in the fluorescence recovery of the quenched dye. Analysis suggests that the assembly of AuNPs–βCDs–FL is effective as a turn-on fluorescent probe for the chiroselective optical discrimination between D,L-tryptophan, D,L-phenyl alanine and D,L-tyrosine. The detection limits for analyzing L-tryptophan, L-phenyl alanine and L-tyrosine were found to be 0.59, 1.2 and 1.5 μM respectively. - Highlights: • Fluorescence quenching AuNP–βCD–dye assembly via energy transfer. • Energy transfer from dye to AuNPs is a SET process. • Fluorescence turn-on detection of amino acids by the competitive binding method. • Chiroselective discrimination between enantiomeric amino acids.

  3. Orc1 Binding to Mitotic Chromosomes Precedes Spatial Patterning during G1 Phase and Assembly of the Origin Recognition Complex in Human Cells.

    Science.gov (United States)

    Kara, Nihan; Hossain, Manzar; Prasanth, Supriya G; Stillman, Bruce

    2015-05-08

    Replication of eukaryotic chromosomes occurs once every cell division cycle in normal cells and is a tightly controlled process that ensures complete genome duplication. The origin recognition complex (ORC) plays a key role during the initiation of DNA replication. In human cells, the level of Orc1, the largest subunit of ORC, is regulated during the cell division cycle, and thus ORC is a dynamic complex. Upon S phase entry, Orc1 is ubiquitinated and targeted for destruction, with subsequent dissociation of ORC from chromosomes. Time lapse and live cell images of human cells expressing fluorescently tagged Orc1 show that Orc1 re-localizes to condensing chromatin during early mitosis and then displays different nuclear localization patterns at different times during G1 phase, remaining associated with late replicating regions of the genome in late G1 phase. The initial binding of Orc1 to mitotic chromosomes requires C-terminal amino acid sequences that are similar to mitotic chromosome-binding sequences in the transcriptional pioneer protein FOXA1. Depletion of Orc1 causes concomitant loss of the mini-chromosome maintenance (Mcm2-7) helicase proteins on chromatin. The data suggest that Orc1 acts as a nucleating center for ORC assembly and then pre-replication complex assembly by binding to mitotic chromosomes, followed by gradual removal from chromatin during the G1 phase.

  4. Examining the critical roles of human CB2 receptor residues Valine 3.32 (113) and Leucine 5.41 (192) in ligand recognition and downstream signaling activities.

    Science.gov (United States)

    Alqarni, Mohammed; Myint, Kyaw Zeyar; Tong, Qin; Yang, Peng; Bartlow, Patrick; Wang, Lirong; Feng, Rentian; Xie, Xiang-Qun

    2014-09-26

    We performed molecular modeling and docking to predict a putative binding pocket and associated ligand-receptor interactions for human cannabinoid receptor 2 (CB2). Our data showed that two hydrophobic residues came in close contact with three structurally distinct CB2 ligands: CP-55,940, SR144528 and XIE95-26. Site-directed mutagenesis experiments and subsequent functional assays implicated the roles of Valine residue at position 3.32 (V113) and Leucine residue at position 5.41 (L192) in the ligand binding function and downstream signaling activities of the CB2 receptor. Four different point mutations were introduced to the wild type CB2 receptor: V113E, V113L, L192S and L192A. Our results showed that mutation of Val113 with a Glutamic acid and Leu192 with a Serine led to the complete loss of CB2 ligand binding as well as downstream signaling activities. Substitution of these residues with those that have similar hydrophobic side chains such as Leucine (V113L) and Alanine (L192A), however, allowed CB2 to retain both its ligand binding and signaling functions. Our modeling results validated by competition binding and site-directed mutagenesis experiments suggest that residues V113 and L192 play important roles in ligand binding and downstream signaling transduction of the CB2 receptor.

  5. Self-recognition mechanism of MamA, a magnetosome-associated TPR-containing protein, promotes complex assembly.

    Science.gov (United States)

    Zeytuni, Natalie; Ozyamak, Ertan; Ben-Harush, Kfir; Davidov, Geula; Levin, Maxim; Gat, Yair; Moyal, Tal; Brik, Ashraf; Komeili, Arash; Zarivach, Raz

    2011-08-16

    The magnetosome, a biomineralizing organelle within magnetotactic bacteria, allows their navigation along geomagnetic fields. Magnetosomes are membrane-bound compartments containing magnetic nanoparticles and organized into a chain within the cell, the assembly and biomineralization of magnetosomes are controlled by magnetosome-associated proteins. Here, we describe the crystal structures of the magnetosome-associated protein, MamA, from Magnetospirillum magneticum AMB-1 and Magnetospirillum gryphiswaldense MSR-1. MamA folds as a sequential tetra-trico-peptide repeat (TPR) protein with a unique hook-like shape. Analysis of the MamA structures indicates two distinct domains that can undergo conformational changes. Furthermore, structural analysis of seven crystal forms verified that the core of MamA is not affected by crystallization conditions and identified three protein-protein interaction sites, namely a concave site, a convex site, and a putative TPR repeat. Additionally, relying on transmission electron microscopy and size exclusion chromatography, we show that highly stable complexes form upon MamA homooligomerization. Disruption of the MamA putative TPR motif or N-terminal domain led to protein mislocalization in vivo and prevented MamA oligomerization in vitro. We, therefore, propose that MamA self-assembles through its putative TPR motif and its concave site to create a large homooligomeric scaffold which can interact with other magnetosome-associated proteins via the MamA convex site. We discuss the structural basis for TPR homooligomerization that allows the proper function of a prokaryotic organelle.

  6. Molecular Recognition of the Catalytic Zinc(II) Ion in MMP-13: Structure-Based Evolution of an Allosteric Inhibitor to Dual Binding Mode Inhibitors with Improved Lipophilic Ligand Efficiencies.

    Science.gov (United States)

    Fischer, Thomas; Riedl, Rainer

    2016-03-01

    Matrix metalloproteinases (MMPs) are a class of zinc dependent endopeptidases which play a crucial role in a multitude of severe diseases such as cancer and osteoarthritis. We employed MMP-13 as the target enzyme for the structure-based design and synthesis of inhibitors able to recognize the catalytic zinc ion in addition to an allosteric binding site in order to increase the affinity of the ligand. Guided by molecular modeling, we optimized an initial allosteric inhibitor by addition of linker fragments and weak zinc binders for recognition of the catalytic center. Furthermore we improved the lipophilic ligand efficiency (LLE) of the initial inhibitor by adding appropriate zinc binding fragments to lower the clogP values of the inhibitors, while maintaining their potency. All synthesized inhibitors showed elevated affinity compared to the initial hit, also most of the novel inhibitors displayed better LLE. Derivatives with carboxylic acids as the zinc binding fragments turned out to be the most potent inhibitors (compound 3 (ZHAWOC5077): IC50 = 134 nM) whereas acyl sulfonamides showed the best lipophilic ligand efficiencies (compound 18 (ZHAWOC5135): LLE = 2.91).

  7. Collision-induced dissociation of noncovalent complexes between vancomycin antibiotics and peptide ligand stereoisomers: evidence for molecular recognition in the gas phase

    DEFF Research Database (Denmark)

    Jørgensen, Thomas J. D.; Delforge, D; Remacle, J;

    1999-01-01

    In solution, the antibiotics of the vancomycin group bind stereospecifically to peptides with the C-terminal sequence: -L-Lys-D-Ala-D-Ala, Substitution by a L-Ala at either of the two C-terminal residues causes a dramatic decrease in the binding affinity to the antibiotics. This solution behavior...... complexes formed between vancomycin and tripeptide stereoisomers. In negative ion mode the CID results show that a complex formed between vancomycin and a -L-Ala-L-Ala ligand fragments more readily than a complex formed between vancomycin and a -D-Ala-D-Ala ligand. This difference in gas phase stability...

  8. Rational design for cooperative recognition of specific nucleobases using β-cyclodextrin-modified DNAs and fluorescent ligands on DNA and RNA scaffolds.

    Science.gov (United States)

    Futamura, Akika; Uemura, Asuka; Imoto, Takeshi; Kitamura, Yusuke; Matsuura, Hirotaka; Wang, Chun-Xia; Ichihashi, Toshiki; Sato, Yusuke; Teramae, Norio; Nishizawa, Seiichi; Ihara, Toshihiro

    2013-08-05

    We propose a binary fluorimetric method for DNA and RNA analysis by the combined use of two probes rationally designed to work cooperatively. One probe is an oligonucleotide (ODN) conjugate bearing a β-cyclodextrin (β-CyD). The other probe is a small reporter ligand, which comprises linked molecules of a nucleobase-specific heterocycle and an environment-sensitive fluorophore. The heterocycle of the reporter ligand recognizes a single nucleobase displayed in a gap on the target labeled with the conjugate and, at the same time, the fluorophore moiety forms a luminous inclusion complex with nearby β-CyD. Three reporter ligands, MNDS (naphthyridine-dansyl linked ligand), MNDB (naphthyridine-DBD), and DPDB (pyridine-DBD), were used for DNA and RNA probing with 3'-end or 5'-end modified β-CyD-ODN conjugates. For the DNA target, the β-CyD tethered to the 3'-end of the ODN facing into the gap interacted with the fluorophore sticking out into the major groove of the gap site (MNDS and DPDB). Meanwhile the β-CyD on the 5'-end of the ODN interacted with the fluorophore in the minor groove (MNDB and DPDB). The results obtained by this study could be a guideline for the design of binary DNA/RNA probe systems based on controlling the proximity of functional molecules.

  9. Non-equivalence of Key Positively Charged Residues of the Free Fatty Acid 2 Receptor in the Recognition and Function of Agonist Versus Antagonist Ligands*

    Science.gov (United States)

    Sergeev, Eugenia; Hansen, Anders Højgaard; Pandey, Sunil K.; MacKenzie, Amanda E.; Hudson, Brian D.; Ulven, Trond; Milligan, Graeme

    2016-01-01

    Short chain fatty acids (SCFAs) are produced in the gut by bacterial fermentation of poorly digested carbohydrates. A key mediator of their actions is the G protein-coupled free fatty acid 2 (FFA2) receptor, and this has been suggested as a therapeutic target for the treatment of both metabolic and inflammatory diseases. However, a lack of understanding of the molecular determinants dictating how ligands bind to this receptor has hindered development. We have developed a novel radiolabeled FFA2 antagonist to probe ligand binding to FFA2, and in combination with mutagenesis and molecular modeling studies, we define how agonist and antagonist ligands interact with the receptor. Although both agonist and antagonist ligands contain negatively charged carboxylates that interact with two key positively charged arginine residues in transmembrane domains V and VII of FFA2, there are clear differences in how these interactions occur. Specifically, although agonists require interaction with both arginine residues to bind the receptor, antagonists require an interaction with only one of the two. Moreover, different chemical series of antagonist interact preferentially with different arginine residues. A homology model capable of rationalizing these observations was developed and provides a tool that will be invaluable for identifying improved FFA2 agonists and antagonists to further define function and therapeutic opportunities of this receptor. PMID:26518871

  10. A Stimuli-Responsive Biosensor of Glucose on Layer-by-Layer Films Assembled through Specific Lectin-Glycoenzyme Recognition

    Directory of Open Access Journals (Sweden)

    Huiqin Yao

    2016-04-01

    Full Text Available The research on intelligent bioelectrocatalysis based on stimuli-responsive materials or interfaces is of great significance for biosensors and other bioelectronic devices. In the present work, lectin protein concanavalin A (Con A and glycoenzyme glucose oxidase (GOD were assembled into {Con A/GOD}n layer-by-layer (LbL films by taking advantage of the biospecific lectin-glycoenzyme affinity between them. These film electrodes possess stimuli-responsive properties toward electroactive probes such as ferrocenedicarboxylic acid (Fc(COOH2 by modulating the surrounding pH. The CV peak currents of Fc(COOH2 were quite large at pH 4.0 but significantly suppressed at pH 8.0, demonstrating reversible stimuli-responsive on-off behavior. The mechanism of stimuli-responsive property of the films was explored by comparative experiments and attributed to the different electrostatic interaction between the films and the probes at different pH. This stimuli-responsive films could be used to realize active/inactive electrocatalytic oxidation of glucose by GOD in the films and mediated by Fc(COOH2 in solution, which may establish a foundation for fabricating novel stimuli-responsive electrochemical biosensors based on bioelectrocatalysis with immobilized enzymes.

  11. Impedimetric biosensor based on self-assembled hybrid cystein-gold nanoparticles and CramoLL lectin for bacterial lipopolysaccharide recognition.

    Science.gov (United States)

    Oliveira, Maria D L; Andrade, Cesar A S; Correia, Maria T S; Coelho, Luana C B B; Singh, Pankaj R; Zeng, Xiangqun

    2011-10-01

    We report the development of a new selective and specific electrochemical biosensor for bacterial lipolysaccharide (LPS). An electrode interface was constructed using a l-cysteine-gold nanoparticle (AuNpCys) composite to be immobilized by electrostatic interaction in the network of a poly(vinyl chloride-vinyl acetate maleic acid) (PVM) layer on a gold bare electrode. The impedimetric biosensor is fabricated by self-assembled CramoLL lectin on the PVM-AuNpCys-modified gold electrode through electrostatic interaction. CramoLL is used as the recognition interface. AFM images showed that LPS was specifically recognized on the PVM-AuNpCys-CramoLL system surface. The measurements of cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) showed that the electrochemical response of a redox probe system (K(4)[Fe(CN)(6)](4-)/K(3)[Fe(CN)(6)](3-)) were blocked, due to the procedures of modified electrode with PVM-AuNpCys-CramoLL. In the majority of the experiments the lectin retained its activity as observed through its interaction with LPS from Escherichia coli, Serratia marcescens, Salmonella enterica and Klebsiella pneumoniae. The results are expressed in terms of the charge transfer resistance and current peak anodic using the EIS and CV techniques for the development of a biosensor for contamination by endotoxins. A new type of sensor for selective discrimination of LPS types with a high sensitivity has been obtained.

  12. Anion-directed assembly and crystal transformation of Ag(I) coordination polymers with a versatile tripyridyltriazole ligand 3,4-bis(2-pyridyl)-5-(4-pyridyl)-1,2,4-triazole

    Science.gov (United States)

    Li, Cheng-Peng; Chen, Jing; Guo, Wei; Du, Miao

    2015-03-01

    A series of distinct Ag(I) coordination polymers, namely {[Ag2(L224)(H2O)3](SiF6)(H2O)4}n (1), {[Ag2(L224)2(NO3)](NO3)(H2O)}n (3), {[Ag2(L224)(OOCC6H5)(H2O)](NO3)(H2O)2}n (4), and {[Ag(L224)2](CF3SO3)(H2O)0.25}n (5) have been synthesized by assembling a versatile ligand 3,4-bis(2-pyridyl)-5-(4-pyridyl)-1,2,4-triazole (L224) with different Ag(I) salts. Their diverse 1D and 2D coordination arrays indicate the critical role of counterions in structural assemblies. Interestingly, single-crystal-to-single-crystal (SC-SC) transformation from 1 to {[Ag2(L224)(CF3COO)2(H2O)](H2O)}n (2) will occur in the water solution of Ag(CF3COO). Structural comparison and mechanism of SC-SC transformation are discussed. These Ag(I) coordination polymers show enhanced ligand-based solid-state fluorescent emissions.

  13. Self-assembly synthesis, structural features, and photophysical properties of dilanthanide complexes derived from a novel amide type ligand: energy transfer from Tb(III) to Eu(III) in a heterodinuclear derivative.

    Science.gov (United States)

    Gao, Cunji; Kirillov, Alexander M; Dou, Wei; Tang, Xiaoliang; Liu, Liangliang; Yan, Xuhuan; Xie, Yujie; Zang, Peixian; Liu, Weisheng; Tang, Yu

    2014-01-21

    A novel amide type ligand benzyl-N,N-bis[(2'-furfurylaminoformyl)phenoxyl)ethyl]-amine (L) has been designed and applied for the self-assembly generation of homodinuclear lanthanide coordination compounds [Ln2(μ2-L)2(NO3)6(EtOH)2] [Ln = Eu (1), Tb (2), and Gd (3)] and a heterodinuclear derivative [EuTb(μ2-L)2(NO3)6(EtOH)2] (4). All the complexes have been characterized by the X-ray single-crystal diffraction analyses. They are isostructural, crystallize in a monoclinic space group P21/c, and form [2 + 2] rectangular macrocycle structures. Compound 4 is the first example of a [2 + 2] rectangular macrocycle heterodinuclear EuTb complex assembled from an amide type ligand. In 4, the discrete 0D dimeric [EuTb(μ2-L)2(NO3)6(EtOH)2] units are extended, via the multiple N-H···O hydrogen bonds, into a 2D supramolecular network that has been topologically classified as a uninodal 4-connected underlying net with the sql [Shubnikov tetragonal plane net] topology. The triplet state ((3)ππ*) of L studied by the Gd(III) complex 3 demonstrated that the ligand beautifully populates Tb(III) emission (Φ = 52%), whereas the corresponding Eu(III) derivative 1 shows weak luminescence efficiency (Φ = 0.7%) because the triplet state of L has a poor match with (5)D1 energy level of Eu(III). Furthermore, the photoluminescent properties of heterodinuclear complex 4 have been compared with those of the analogous homodinuclear compounds. The quantum yield and lifetime measurements prove that energy transfer from Tb(III) to Eu(III) is being achieved, namely, that the Tb(III) center is also acting to sensitize the Eu(III) and enhancing Eu(III) emission in 4.

  14. Novel 3-D Supramolecular Architectures Constructed from Zn2+ ions, Oxybis(4-benzoate) and Di(2-pyridyl)amine Ligands

    Institute of Scientific and Technical Information of China (English)

    TANG Long; LI Dong-Sheng; FU Feng; WANG Ji-Jiang; HU Huai-Ming; WANG Yao-Yu

    2007-01-01

    Using the V-shaped oba dianions as bridging ligands and dpa molecules as terminal ligands, a new 1D helical coordination-polymeric chain, [Zn(oba)(dpa)]n [oba=oxybis(4-benzoate), dpa=di(2-pyridyl)amine], was synthesized and characterized by single-crystal X-ray diffraction, elemental analyses, UV-Vis and IR spectra, and TGA analysis. X-ray structural analysis revealed that, oba and dpa ligands played an important role in the self-assembly of the helical chains by providing potential supramolecular recognition sites for π-π aromatic stacking and hydrogen-bond interactions, resulting in the self-assembly of the (4,4) networks to give a 3-D supramolecular framework.The photoluminescence properties of the title compound were also investigated, showing intense blue photoluminescence properties at room temperature.

  15. Self-assembled copper(II) metallacycles derived from asymmetric Schiff base ligands: efficient hosts for ADP/ATP in phosphate buffer.

    Science.gov (United States)

    Kumar, Amit; Pandey, Rampal; Kumar, Ashish; Gupta, Rakesh Kumar; Dubey, Mrigendra; Mohammed, Akbar; Mobin, Shaikh M; Pandey, Daya Shankar

    2015-10-21

    Novel asymmetric Schiff base ligands 2-{[3-(3-hydroxy-1-methyl-but-2-enylideneamino)-2,4,6-trimethylphenylimino]-methyl}-phenol (H2L(1)) and 1-{[3-(3-hydroxy-1-methyl-but-2-enylideneamino)-2,4,6-trimethylphenylimino]-methyl}-naphthalen-2-ol (H2L(2)) possessing dissimilar N,O-chelating sites and copper(ii) metallacycles (CuL(1))4 (1) and (CuL(2))4 (2) based on these ligands have been described. The ligands and complexes have been thoroughly characterized by satisfactory elemental analyses, and spectral (IR, (1)H, (13)C NMR, ESI-MS, UV/vis) and electrochemical studies. Structures of H2L(2) and 1 have been unambiguously determined by X-ray single crystal analyses. The crystal structure of H2L(2) revealed the presence of two distinct N,O-chelating sites on dissimilar cores (naphthalene and β-ketoaminato groups) offering a diverse coordination environment. Metallacycles 1 and 2 having a cavity created by four Cu(ii) centres coordinated in a homo- and heteroleptic fashion with respective ligands act as efficient hosts for adenosine-5'-diphosphate (ADP) and adenosine-5'-triphosphate (ATP) respectively, over other nucleoside polyphosphates (NPPs). The disparate sensitivity of these metallacycles toward ADP and ATP has been attributed to the size of the ligands assuming diverse dimensions and spatial orientations. These are attuned for π-π stacking and electrostatic interactions suitable for different guest molecules under analogous conditions, metallacycle 1 offers better orientation for ADP, while 2 for ATP. The mechanism of the host-guest interaction has been investigated by spectral and electrochemical studies and supported by molecular docking studies.

  16. A multi-resolution model to capture both global fluctuations of an enzyme and molecular recognition in the ligand-binding site

    CERN Document Server

    Fogarty, Aoife C; Kremer, Kurt

    2016-01-01

    In multi-resolution simulations, different system components are simultaneously modelled at different levels of resolution, these being smoothly coupled together. In the case of enzyme systems, computationally expensive atomistic detail is needed in the active site to capture the chemistry of substrate binding. Global properties of the rest of the protein also play an essential role, determining the structure and fluctuations of the binding site; however, these can be modelled on a coarser level. Similarly, in the most computationally efficient scheme only the solvent hydrating the active site requires atomistic detail. We present a methodology to couple atomistic and coarse-grained protein models, while solvating the atomistic part of the protein in atomistic water. This allows a free choice of which protein and solvent degrees of freedom to include atomistically, without loss of accuracy in the atomistic description. This multi-resolution methodology can successfully model stable ligand binding, and we furt...

  17. Solvent-dependent assembly of discrete and continuous CoCl₂ adamantane-based ligand complexes: observations by CSI-mass spectrometry and X-ray crystallography.

    Science.gov (United States)

    Ohara, Kazuaki; Tominaga, Masahide; Azumaya, Isao; Yamaguchi, Kentaro

    2013-01-01

    Discrete and continuous coordination structures were obtained in single crystals of CoCl₂ and an adamantane-based bidentate ligand bearing imidazolyl groups, depending on the methanol concentration in a methanol-chloroform mixture. Single-crystal X-ray structure analysis revealed that the metal centers exhibited a tetrahedral geometry in the discrete complex and an octahedral geometry in the continuous metal complex. Conventional analytical methods, including UV-vis and NMR spectroscopy, could not identify those two complexes in solution. In contrast, cold-spray ionization mass spectrometry could detect differences between the discrete complex and the continuous metal complex, and ion peaks due to continuous ligand adducts were found only in the spectrum of the continuous metal complex.

  18. Solvent-Controlled Assembly of ionic Metal-Organic Frameworks Based on Indium and Tetracarboxylate Ligand: Topology Variety and Gas Sorption Properties

    KAUST Repository

    Zheng, Bing

    2016-07-15

    Four Metal-Organic Frameworks (MOFs) based on Indium and tetracarboxylate ligand have been synthesized through regulation of the solvent conditions, the resulted compounds not only exhibited rich structural topologies (pts, soc and unique topologies), but also interesting charge reversal framework features. By regulating the solvent, different building units (indium monomer, trimer) have been generated in situ, and they are connected with the ligand to form ionic frameworks 1-4, respectively. Among the synthesized four ionic frameworks, compounds 3 and 4 could keep their crystallinity upon heating temperature up to 300oC after fully removal of solvent guest molecules, they also exhibit the charge reversal framework features (3 adopts an overall cationic framework, while 4 has an anionic framework). Both compounds 3 and 4 exhibit significant uptake capacity for CO2 and H2, besides that, compounds 3 and 4 also present excellent selective adsorption of CO2 over N2 and CH4.

  19. The IntFOLD server: an integrated web resource for protein fold recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction.

    Science.gov (United States)

    Roche, Daniel B; Buenavista, Maria T; Tetchner, Stuart J; McGuffin, Liam J

    2011-07-01

    The IntFOLD server is a novel independent server that integrates several cutting edge methods for the prediction of structure and function from sequence. Our guiding principles behind the server development were as follows: (i) to provide a simple unified resource that makes our prediction software accessible to all and (ii) to produce integrated output for predictions that can be easily interpreted. The output for predictions is presented as a simple table that summarizes all results graphically via plots and annotated 3D models. The raw machine readable data files for each set of predictions are also provided for developers, which comply with the Critical Assessment of Methods for Protein Structure Prediction (CASP) data standards. The server comprises an integrated suite of five novel methods: nFOLD4, for tertiary structure prediction; ModFOLD 3.0, for model quality assessment; DISOclust 2.0, for disorder prediction; DomFOLD 2.0 for domain prediction; and FunFOLD 1.0, for ligand binding site prediction. Predictions from the IntFOLD server were found to be competitive in several categories in the recent CASP9 experiment. The IntFOLD server is available at the following web site: http://www.reading.ac.uk/bioinf/IntFOLD/.

  20. Assemblies of a new flexible multicarboxylate ligand and d10 metal centers toward the construction of homochiral helical coordination polymers: structures, luminescence, and NLO-active properties.

    Science.gov (United States)

    Zang, Shuangquan; Su, Yang; Li, Yizhi; Ni, Zhaoping; Meng, Qingjin

    2006-01-01

    Hydro(solvo)thermal reactions between a new flexible multicarboxylate ligand of 2,2',3,3'-oxydiphthalic acid (2,2',3,3'-H(4)ODPA) and M(NO(3))(2).xH(2)O (M = Zn, x = 6; M = Cd, x = 4) in the presence of 4,4'-bipyridine (bpy) afford two novel homochiral helical coordination polymers [[Zn(2)(2,2',3,3'-ODPA)(bpy)(H(2)O)(3)].(H(2)O)(2) for 1 and [Cd(2)(2,2',3,3'-ODPA)(bpy)(H(2)O)(3)].(H(2)O)(2) for 2]. Though having almost the same chemical formula, they have different space groups (P2(1)2(1)2(1) for 1 and P2(1) for 2) and different bridging modes of the 2,2',3,3'-ODPA ligand. Two kinds of homochiral helices (right-handed) are found in both 1 and 2, each of which discriminates only one kind of crystallographical nonequivalent metal atom. 1 has a 2D metal-organic framework and can be seen as the unity of two parallel homochiral Zn1 and Zn2 helices, in which the nodes are etheric oxygen atoms. In contrast, 2 has a 3D metal-organic framework and consists of two partially overlapped homochiral Cd1 and Cd2 helices in the two dimensions. Moreover, metal-ODPA helices give a 2D chiral herringbone structural motif in both 1 and 2 in the two dimensions, which are further strengthened by the second ligand of bpy. Bulk materials for 1 and 2 all have good second-harmonic generation activity, approximately 1 and 0.8 times that of urea.

  1. Rational assembly of Pb(II)/Cd(II)/Mn(II) coordination polymers based on flexible V-shaped dicarboxylate ligand: Syntheses, helical structures and properties

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Gao-Shan [School of Environment and Chemical Engineering, Nanchang Hangkong University, Nanchang 330063 (China); Liu, Chong-Bo, E-mail: cbliu@nchu.edu.cn [School of Environment and Chemical Engineering, Nanchang Hangkong University, Nanchang 330063 (China); School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332 (United States); Liu, Hong [School of Environment and Chemical Engineering, Nanchang Hangkong University, Nanchang 330063 (China); Robbins, Julianne; Zhang, Z. John [School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332 (United States); Yin, Hong-Shan [School of Environment and Chemical Engineering, Nanchang Hangkong University, Nanchang 330063 (China); Wen, Hui-Liang [State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047 (China); Wang, Yu-Hua [School of Environment and Chemical Engineering, Nanchang Hangkong University, Nanchang 330063 (China)

    2015-05-15

    Six new coordination polymers, namely, [Pb(L)(H{sub 2}O)] (1), [Pb(L)(phen)] (2), [Pb{sub 2}(L){sub 2}(4,4′-bipy){sub 0.5}] (3), [Cd(L)(phen)] (4), [Cd(L)(4,4′-bipy)]·H{sub 2}O (5) and [Mn(L)(4,4′-bipy)]·H{sub 2}O (6) have been synthesized by the hydrothermal reaction of 2,2′-[hexafluoroisopropylidenebis(p-phenyleneoxy)]diacetic acid (H{sub 2}L) with Pb(II)/Cd(II)/Mn(II) in the presence of ancillary ligands 4,4′-bipyridine (4,4′-bipy) or 1,10-phenanthroline (phen). Complexes 1 and 4–6 exhibit 2-D structures, and complexes 2–3 display 3-D frameworks, of which L{sup 2−} ligands join metal ions to single-stranded helical chains of 1, 3–6 and double-stranded helical chains of 2. Complexes 2 and 3 also contain double-stranded Metal–O helices. Topology analysis reveals that complexes 1 and 4 both represent 4-connected sql net, 2 represents 6-connected pcu net, 3 exhibits a novel (3,12)-connected net, while 5 and 6 display (3,5)-connected gek1 net. The six complexes exhibit two kinds of inorganic–organic connectivities: I{sup 0}O{sup 2} for 1, 4–6, and I{sup 1}O{sup 2} for 2–3. The photoluminescent properties of 4–5 and the magnetic properties of 6 have been investigated. - Graphical abstract: Six new Pb(II)/Cd(II)/Mn(II) coordination polymers with helical structures based on flexible V-shaped dicarboxylate ligand have been synthesized and structurally characterized. Photoluminescent and magnetic properties have been investigated. - Highlights: • Six novel M(II) coordination polymers with 2,2′-[hexafluoroisopropylidenebis(p-phenyleneoxy)]diacetic acid and N-donor ligands. • Complexes 1–6 show diverse intriguing helical characters. • The luminescent properties of complexes 1–5 were investigated. • Complex 6 shows antiferromagnetic coupling.

  2. Spacer-Controlled Supramolecular Assemblies of Cu(II with Bis(2-Hydroxyphenylimine Ligands. from Monoligand Complexes to Double-Stranded Helicates and Metallomacrocycles

    Directory of Open Access Journals (Sweden)

    Norman Kelly

    2016-09-01

    Full Text Available Reaction of Cu(NO32·3H2O or Cu(CH3COO2·H2O with the bis(2-hydroxyphenylimine ligands H2L1-H2L4 gave four Cu(II complexes of composition [Cu2(L1(NO32(H2O]·MeOH, [Cu2(L22], [Cu2(L32] and [Cu2(L42]·2MeOH. Depending on the spacer unit, the structures are characterized by a dinuclear arrangement of Cu(II within one ligand (H2L1, by a double-stranded [2+2] helical binding mode (H2L2 and H2L3 and a [2 + 2] metallomacrocycle formation (H2L4. In these complexes, the Cu(II coordination geometries are quite different, varying between common square planar or square pyramidal arrangements, and rather rare pentagonal bipyramidal and tetrahedral geometries. In addition, solution studies of the complex formation using UV/Vis and ESI-MS as well as solvent extraction are reported.

  3. Cyclo- and carbophosphazene-supported ligands for the assembly of heterometallic (Cu2+/Ca2+, Cu2+/Dy3+, Cu2+/Tb3+) complexes: synthesis, structure, and magnetism.

    Science.gov (United States)

    Chandrasekhar, Vadapalli; Senapati, Tapas; Dey, Atanu; Das, Sourav; Kalisz, Marguerite; Clérac, Rodolphe

    2012-02-20

    The carbophosphazene and cyclophosphazene hydrazides, [{NC(N(CH(3))(2))}(2){NP{N(CH(3))NH(2)}(2)}] (1) and [N(3)P(3)(O(2)C(12)H(8))(2){N(CH(3))NH(2)}(2)] were condensed with o-vanillin to afford the multisite coordination ligands [{NC(N(CH(3))(2))}(2){NP{N(CH(3))N═CH-C(6)H(3)-(o-OH)(m-OCH(3))}(2)}] (2) and [{N(2)P(2)(O(2)C(12)H(8))(2)}{NP{N(CH(3))N═CH-C (6)H(3)-(o-OH)(m-OCH(3))}(2)}] (3), respectively. These ligands were used for the preparation of heterometallic complexes [{NC(N(CH(3))(2))}(2){NP{N(CH(3))N═CH-C(6)H(3)-(o-O)(m-OCH(3))}(2)}{CuCa(NO(3))(2)}] (4), [{NC(N(CH(3))(2))}(2){NP{N(CH(3))N═CH-C(6)H(3)-(o-O)(m-OCH(3))}(2)}{Cu(2)Ca(2)(NO(3))(4)}]·4H(2)O (5), [{NC(N(CH(3))(2))}(2){NP{N(CH(3))N═CH-C(6)H(3)-(o-O)(m-OCH(3))}(2)}{CuDy(NO(3))(4)}]·CH(3)COCH(3) (6), [{NP(O(2)C(12)H(8))}(2){NP{N(CH(3))N═CH-C(6)H(3)-(o-O)(m-OCH(3))}(2)}{CuDy(NO(3))(3)}] (7), and [{NP(O(2)C(12)H(8))}(2){NP{N(CH(3))N═CH-C(6)H(3)-(o-O)(m-OCH(3))}(2)}{CuTb(NO(3))(3)}] (8). The molecular structures of these compounds reveals that the ligands 2 and 3 possess dual coordination pockets which are used to specifically bind the transition metal ion and the alkaline earth/lanthanide metal ion; the Cu(2+)/Ca(2+), Cu(2+)/Tb(3+), and Cu(2+)/Dy(3+) pairs in these compounds are brought together by phenoxide and methoxy oxygen atoms. While 4, 6, 7, and 8 are dinuclear complexes, 5 is a tetranuclear complex. Detailed magnetic properties on 6-8 reveal that these compounds show weak couplings between the magnetic centers and magnetic anisotropy. However, the ac susceptibility experiments did not reveal any out of phase signal suggesting that in these compounds slow relaxation of magnetization is absent above 1.8 K.

  4. Metal ions directed assembly of two coordination polymers based on an organic phosphonate anion and a multidentate N-donor ligand

    Science.gov (United States)

    Kan, Wei-Qiu; Xu, Ji-Ming; Wen, Shi-Zheng; Yang, Lin

    2017-01-01

    Two new coordination polymers [Cd(4,4‧-tmbpt)(HL)(H2O)] (1) and [Cu(4,4‧-tmbpt)(HL)]·H2O (2) (H3L = 2‧-carboxybiphenyl-4-ylmethylphosphonic and 4,4‧-tmbpt = 1-((1H-1,2,4-triazol-1-yl)methyl)-3,5-bis(4-pyridyl)-1,2,4-triazole) have been synthesized hydrothermally. The two compounds have the same metal to ligand ratio, but different metal ions. As a result, the two compounds display different 2D layer structures, which is mainly caused by the different coordination numbers of the different metal ions. The effects of the metal ions on the structures, the optical band gaps and photoluminescent and photocatalytic properties of the compounds have been studied.

  5. Synthesis, structures and magnetic properties of a series of polynuclear copper(II)-lanthanide(III) complexes assembled with carboxylate and hydroxide ligands

    Institute of Scientific and Technical Information of China (English)

    CHEN, Xiao-Ming; YANG, Yang-Yi

    2000-01-01

    Heteromnetallic copper(I)-lanthanide(Ⅲ) complexes have been made with a variety of exclusively O-donor ligands in cluding betaines (zwitterionic carboxylates) and chloroac etate, which are dinuclear CuLn, tetranuclear Cu2Ln2, pen tanuclear Cu3Ln2, and octadecanuclear Cu12 Ln3 complexes. Tne results show that subtle changes in both the carboxylates and acidity of the reaction solution can cause drastic changoes in the structures of the products. Magnetic studies exhibit that shieldirng of the Ln3+ 4f electrons by the outer shell electrons is very effective to preclude significant coutpling interaction be tween the Ln3+ 4f electrons and Cu2+ 3d electrons in either a mono-atomic hydroxide-bridged, or a carboxylate-bridged system.

  6. Direct C-N Coupling in an in Situ Ligand Transformation and the Self-Assembly of a Tetrametallic [Ni(II)4] Staircase.

    Science.gov (United States)

    Ghosh, Aloke Kumar; Singha Mahapatra, Tufan; Clérac, Rodolphe; Mathonière, Corine; Bertolasi, Valerio; Ray, Debashis

    2015-06-01

    A [Ni(II)4] staircase complex was serendipitously prepared from the reaction of the binucleating Schiff base proligand 2,6-bis[[(3-hydroxypropyl)imino]methyl]-4-methylphenol (H3L2) and 3,5-dimethylpyrazole (Me2pzH) with nickel(II) nitrate in a reaction at room temperature, initially aimed to yield a dinuclear complex. From a room temperature metal ion/ligand reaction, the proligand H3L2 in situ transformed to modified forms HL3(2-) and HL4(2-), allowing the [Ni4] formation. Variable-temperature magnetic behavior of a [Ni4] complex reveals antiferromagnetic interactions with stabilization of a diamagnetic ground state (ST = 0).

  7. Cubane-type Cu(II)4 and Mn(II)2Mn(III)2 complexes based on pyridoxine: a versatile ligand for metal assembling.

    Science.gov (United States)

    Marino, Nadia; Armentano, Donatella; Mastropietro, Teresa F; Julve, Miguel; De Munno, Giovanni; Martínez-Lillo, José

    2013-10-21

    By using Vitamin B6 in its monodeprotonated pyridoxine form (PN-H) [PN = 3-hydroxy-4,5-bis(hydroxymethyl)-2-methylpyridine], two tetranuclear compounds of formula [Mn4(PN-H)4(CH3CO2)3Cl2]Cl·2CH3OH·2H2O (1) and [Cu4(PN-H)4Cl2(H2O)2]Cl2 (2) have been synthesized and magneto-structurally characterized. 1 crystallizes in the triclinic system with space group P1 whereas 2 crystallizes in the orthorhombic system with Fdd2 as space group. They exhibit Mn(II)2Mn(III)2 (1) and Cu(II)4 (2) cubane cores containing four monodeprotonated pyridoxine groups simultaneously acting as chelating and bridging ligands (1 and 2), three bridging acetate ligands in the syn-syn conformation (1), and two terminally bound chloride anions (1 and 2) plus two coordinated water molecules (2). The electroneutrality is achieved by the presence of chloride counterions in both compounds. Tri- [Mn(1) and Mn(3)] and divalent [Mn(2) and Mn(4)] manganese centers coexist in 1, all being six-coordinate with distorted Mn(1/3)O6 and Mn(2/4)O5Cl octahedral surroundings, respectively, the equatorial Mn-O bonds being about 0.2 Å shorter at the former ones. The two crystallographically independent copper(II) ions in 2 are five-coordinate in somewhat distorted CuO5 [Cu(1)] and CuO4Cl [Cu(2)] square pyramidal geometries. The values of the intracore metal-metal separation cover the ranges 3.144(1)-3.535(1) (1) and 2.922(6)-3.376(1) Å (2). The magnetic properties of 1 and 2 were investigated in the temperature range 1.9-300 K, and they correspond to an overall antiferromagnetic behavior with susceptibility maxima at 5.0 (1) and 65.0 K (2). The analysis of the magnetic susceptibility data showed the coexistence of intracore antiferro- and ferromagnetic interactions in the two compounds. Their values compare well with those existing in the literature for the parent systems.

  8. Tetrameric Self-Assembly of a Cu(II) Complex Containing Schiff-Base Ligand and Its Unusually High Catecholase-like Activity

    Energy Technology Data Exchange (ETDEWEB)

    Sarkar, Shuranjan; Lee, Hongin [Kyungpook National Univ., Daegu (Korea, Republic of); Lee, Woo Ram; Hong, Chang Seop [Korea Univ., Seoul (Korea, Republic of)

    2013-09-15

    We report a new tetrameric supramolecular Cu(II) complex (Cu{sub 4}L{sub 4} = tetrakis(N,N'-bis(salicylidene)-2,2'-ethylenedianiline) Copper(II)) with a Schiff-base ligand (H{sub 2}L = N,N'-bis (salicylaldimine)-1,2-ethylenediamine) containing two N,O-bidentate chelate groups. Though the copper sites of Cu{sub 4}L{sub 4} are non-coupled, the complex exhibits a unusually high catecholase-like activity (k{sub cat} = 935 h{sup -1}) when the Cu{sub 4}L{sub 4} solution is treated with 3,5-di-tert-butylcatechol (3,5-DTBC) at basic condition in the presence of air. Combined information obtained from UV-VIS and EPR measurements could lead the suggestion of the reaction pathway in which the substrate may bind to Cu(II) ions by anti-anti didentate bridging mode.

  9. Assembly of lipophilic tetranuclear (Cu4 and Zn4) molecular metallophosphonates from 2,4,6-triisopropylphenylphosponic acid and pyrazole ligands.

    Science.gov (United States)

    Chandrasekhar, Vadapalli; Sasikumar, Palani; Boomishankar, Ramamoorthy; Anantharaman, Ganapathi

    2006-04-17

    A sterically hindered aryl phosphonic acid ArP(O)(OH)2 (2) (Ar = 2,4,6-isopropylphenyl) was synthesized and structurally characterized. ArP(O)(OH)2 forms an interesting hydrogen-bonded corrugated sheet-type supramolecular structure in the solid-state. A three-component reaction involving ArP(O)(OH)2, 3,5-dimethylpyrazole(DMPZH), and Cu(CH3COO)2.H2O produces the tetranuclear Cu(II) compound [Cu4(mu3-OH)2{ArPO2(OH)}2(CH3CO2)2(DMPZH)4][CH3COO]2.CH2Cl2 (3). A similar three-component reaction involving ArP(O)(OH)2, 3,5-dimethylpyrazole, and Zn(CH3COO)2.2H2O yields the tetranuclear Zn(II) compound [Zn4{ArPO3}2{ArPO2(OH)}2{DMPZH}4(DMPZ)2].5MeOH (4). While 3 has been found to have an asymmetric cage structure where two dinuclear copper cores are bridged by bidentate [ArPO2(OH)]- ligands, 4 possesses an open-book tricyclic structure composed of three fused metallophosphonate rings. Magnetic studies on 3 revealed antiferromagnetic behavior.

  10. Ancillary ligand-assisted assembly of C{sub 3}-symmetric 4,4′,4″-nitrilotribenzoic acid with divalent Zn{sup 2+} ions: Syntheses, topological structures, and photoluminescence properties

    Energy Technology Data Exchange (ETDEWEB)

    Cui, Li-Ting; Niu, Yan-Fei [Shanghai Key Laboratory of Green Chemistry and Chemical Processes, Department of Chemistry, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062 (China); Han, Jie, E-mail: chan@ouhk.edu.hk [School of Science & Technology, The Open University of Hong Kong, Kowloon, Hong Kong SAR (China); Zhao, Xiao-Li, E-mail: xlzhao@chem.ecnu.edu.cn [Shanghai Key Laboratory of Green Chemistry and Chemical Processes, Department of Chemistry, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062 (China)

    2015-07-15

    4,4′,4″-nitrilotribenzoic acid (H{sub 3}L), a C{sub 3}-symmetric ligand, was found to self-assemble into two polymorphs driven by intermolecular hydrogen-bonding interactions. Reactions of this ligand with Zn{sup 2+} under solvothermal conditions resulted in four new coordination polymers bearing interesting structural motifs: [Zn{sub 2}(L){sub 2}(py){sub 2}]·2(H{sub 2}NMe{sub 2}){sup +}·DMF·2H{sub 2}O (1), [Zn{sub 2}(L)(H{sub 2}L)(bipy)]·1.5H{sub 2}O·Guest (2), [Zn{sub 2}(L){sub 2}(bipy)]·2(H{sub 2}NMe{sub 2}){sup +}·2DMF (3), and [Zn{sub 3}(L){sub 2}(bpa)]·2H{sub 2}O·Guest (4) (H{sub 3}L=4,4′,4′′-nitrilotribenzoic acid, DMF=dimethylformamide, py=pyridine, bipy=4,4′-bipyridine, bpa=1,2-bis(4-pyridyl)diazene). Single-crystal structural analysis revealed that compound 1 exhibits a rare example of twofold interpenetrating anionic 3D (3,3)-net framework containing helical channels, whereas in 2, the 3D pillar-layer structure generated from bipy-pillared Zn{sub 2}(L)(H{sub 2}L) layer is further reinforced by intermolecular hydrogen bonding among pairs of free –COOH units. Compound 3 shows an interesting entangled architecture of 2D→3D parallel polycatenation consisting five-coordinated Zn{sup 2+} ions. Compound 4 displays a 3D pillar-layer framework with trimeric Zn{sub 3}(CO{sub 2}){sub 6} serving as secondary building unit (SBU). The syntheses, structures, thermal stabilities, powder X-ray diffractions and solid-state photoluminescence properties for these crystalline materials have been carried out. In addition, supramolecular assembly of H{sub 3}L under solvothermal conditions will also be addressed. - Graphical abstract: Supramolecular assembly of 4,4′,4′′-nitrilotribenzoic acid and its ligand behavior toward Zn{sup 2+} were investigated, which exhibit two polymorphs of the free acid and four metal coordination polymers bearing interesting structural motifs. - Highlights: • Two polymorphs of H{sub 3}L showing different hydrogen

  11. Computational understanding and experimental characterization of twice-as-smart quadruplex ligands as chemical sensors of bacterial nucleotide second messengers

    Science.gov (United States)

    Zhou, Jie; Roembke, Benjamin T.; Paragi, Gabor; Laguerre, Aurélien; Sintim, Herman O.; Fonseca Guerra, Célia; Monchaud, David

    2016-01-01

    A twice-as-smart ligand is a small molecule that experiences a structural switch upon interaction with its target (i.e., smart ligand) that concomitantly triggers its fluorescence (i.e., smart probe). Prototypes of twice-as-smart ligands were recently developed to track and label G-quadruplexes: these higher-order nucleic acid structures originate in the assembly of four guanine(G)-rich DNA or RNA strands, whose stability is imparted by the formation and the self-assembly of G-quartets. The first prototypes of twice-as-smart quadruplex ligands were designed to exploit the self-association of quartets, being themselves synthetic G-quartets. While their quadruplex recognition capability has been thoroughly documented, some doubts remain about the precise photophysical mechanism that underlies their peculiar spectroscopic properties. Here, we uncovered this mechanism via complete theoretical calculations. Collected information was then used to develop a novel application of twice-as-smart ligands, as efficient chemical sensors of bacterial signaling pathways via the fluorescent detection of naturally occurring extracellular quadruplexes formed by cyclic dimeric guanosine monophosphate (c-di-GMP). PMID:27667717

  12. Co-assembly of CdTe and Fe{sub 3}O{sub 4} with molecularly imprinted polymer for recognition and separation of endocrine disrupting chemicals

    Energy Technology Data Exchange (ETDEWEB)

    Chang, Limin, E-mail: aaaa2139@163.com [School of Chemistry, Jilin Normal University, Siping 136000 (China); Chen, Shaona [State Key Lab of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090 (China); Department of Chemistry, Harbin Institute of Technology, Harbin 150090 (China); Chu, Jia [College of Chemistry and Chemical Engineering, Xi’an University of Science and Technology, Xi’an 710054 (China); Li, Xin, E-mail: lixin@hit.edu.cn [State Key Lab of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090 (China); Department of Chemistry, Harbin Institute of Technology, Harbin 150090 (China)

    2013-11-01

    In this study, we present a general protocol to fabricate imprinting matrix co-loaded with CdTe quantum dots and Fe{sub 3}O{sub 4} nanoparticles for the recognition of endocrine disrupting chemicals (EDCs). The resultant composites were characterized by transmission electron microscopy, fluorescence spectroscopy, and energy dispersive spectroscopy. The materials have been demonstrated to be characterized with spherical shape with a saturation magnetization value of 1.7 emu g{sup −1}. Furthermore, the rebinding experiments show that the resultant materials have greater affinity and selectivity towards p-nitrophenol (model EDCs) over structurally related compounds. We believe that the effective method proposed in this work might provide a platform to prepare magnetic and fluorescent molecularly imprinted polymers for the recognition and separation of EDCs.

  13. Co-assembly of CdTe and Fe3O4 with molecularly imprinted polymer for recognition and separation of endocrine disrupting chemicals

    Science.gov (United States)

    Chang, Limin; Chen, Shaona; Chu, Jia; Li, Xin

    2013-11-01

    In this study, we present a general protocol to fabricate imprinting matrix co-loaded with CdTe quantum dots and Fe3O4 nanoparticles for the recognition of endocrine disrupting chemicals (EDCs). The resultant composites were characterized by transmission electron microscopy, fluorescence spectroscopy, and energy dispersive spectroscopy. The materials have been demonstrated to be characterized with spherical shape with a saturation magnetization value of 1.7 emu g-1. Furthermore, the rebinding experiments show that the resultant materials have greater affinity and selectivity towards p-nitrophenol (model EDCs) over structurally related compounds. We believe that the effective method proposed in this work might provide a platform to prepare magnetic and fluorescent molecularly imprinted polymers for the recognition and separation of EDCs.

  14. Construction and Ion Exchange Properties of Supramolecular Complexes with Organic Ligands and Metal Ions

    Institute of Scientific and Technical Information of China (English)

    SUN; WeiYin

    2001-01-01

    Supramolecular architectures with specific topologies such as closed threedimensional molecular cages present a large range of applications in material science, medicine and chemical technology.1,2 In the past decades, a number of such frameworks, e.g. M6L4, M12L8 and M18L6, have been synthesized by assembly of organic ligands with transitional metal salts.3-5 However, the M3L2 type cage-like complexes are not well known up to now.6,7 We report herein the generation of M3L2 type cages by tripodal ligands and various metal salts, and the anion exchange, molecular recognition properties of these metallosupramolecular cages.  ……

  15. Construction and Ion Exchange Properties of Supramolecular Complexes with Organic Ligands and Metal Ions

    Institute of Scientific and Technical Information of China (English)

    SUN WeiYin; FAN Jian

    2001-01-01

    @@ Supramolecular architectures with specific topologies such as closed threedimensional molecular cages present a large range of applications in material science, medicine and chemical technology.1,2 In the past decades, a number of such frameworks, e.g. M6L4, M12L8 and M18L6, have been synthesized by assembly of organic ligands with transitional metal salts.3-5 However, the M3L2 type cage-like complexes are not well known up to now.6,7 We report herein the generation of M3L2 type cages by tripodal ligands and various metal salts, and the anion exchange, molecular recognition properties of these metallosupramolecular cages.

  16. Aptamer-assembled nanomaterials for fluorescent sensing and imaging

    Science.gov (United States)

    Lu, Danqing; He, Lei; Zhang, Ge; Lv, Aiping; Wang, Ruowen; Zhang, Xiaobing; Tan, Weihong

    2017-01-01

    Aptamers, which are selected in vitro by a technology known as the systematic evolution of ligands by exponential enrichment (SELEX), represent a crucial recognition element in molecular sensing. With advantages such as good biocompatibility, facile functionalization, and special optical and physical properties, various nanomaterials can protect aptamers from enzymatic degradation and nonspecific binding in living systems and thus provide a preeminent platform for biochemical applications. Coupling aptamers with various nanomaterials offers many opportunities for developing highly sensitive and selective sensing systems. Here, we focus on the recent applications of aptamer-assembled nanomaterials in fluorescent sensing and imaging. Different types of nanomaterials are examined along with their advantages and disadvantages. Finally, we look toward the future of aptamer-assembled nanomaterials.

  17. Pattern recognition

    CERN Document Server

    Theodoridis, Sergios

    2003-01-01

    Pattern recognition is a scientific discipline that is becoming increasingly important in the age of automation and information handling and retrieval. Patter Recognition, 2e covers the entire spectrum of pattern recognition applications, from image analysis to speech recognition and communications. This book presents cutting-edge material on neural networks, - a set of linked microprocessors that can form associations and uses pattern recognition to ""learn"" -and enhances student motivation by approaching pattern recognition from the designer's point of view. A direct result of more than 10

  18. Stimuli-Responsive Metal?Ligand Assemblies

    OpenAIRE

    McConnell, Anna J.; Wood, Christopher S.; Neelakandan, Prakash P.; Nitschke, Jonathan R.

    2015-01-01

    This is the accepted manuscript of a paper published in Chemical Reviews (McConnell AJ, Wood CS, Neelakandan PP, Nitschke JR, Chemical Reviews (2015) 115(15):7729-7793. doi:10.1021/cr500632f). The final version is available at http://dx.doi.org/10.1021/cr500632f The Engineering and Physical Sciences Research Council and the European Research Council are acknowledged for financial support.

  19. Selective and visual Ca(2+) ion recognition in solution and in a self-assembly organogel of the terpyridine-based derivative triggered by ultrasound.

    Science.gov (United States)

    Geng, Lijun; Li, Yajuan; Wang, Zengyao; Wang, Yanqiu; Feng, Guoliang; Pang, Xuelei; Yu, Xudong

    2015-11-07

    A new kind of terpyridine-based Ca(2+) sensor TS was designed and studied based on the internal charge transfer (ICT). In the diluted solution state, TS sensed Ca(2+) and Mg(2+) ions among test ions via an "off-on" approach as seen from fluorescence spectra of test ions. Moreover, TS was able to form stable fluorescent gels in organic solvents accelerated by ultrasound, indicating the ultrasound responsive properties of TS molecules. The S-gel of TS could be successfully used to selectively recognize Ca(2+) through fluorescent emission color and morphological changes, which was different from that of the solution state. It was predicated that the competition between the self-assembly of TS molecules and the host–guest interaction of TS with Ca(2+) or Mg(2+) was responsible for the sensing properties. To the best of our knowledge, this is the first example that organogels could selectively sense Ca2+ ions.

  20. Anion Recognition Triggered Nanoribbon-Like Self-Assembly: A Fluorescent Chemosensor for Nitrate in Acidic Aqueous Solution and Living Cells.

    Science.gov (United States)

    Yang, Yaping; Chen, Shiyan; Ni, Xin-Long

    2015-07-21

    A water-soluble π-conjugated bispyridinium phenylenevinylene-based fluorogenic probe has been developed as a novel fluorescent chemosensor for highly selective, sensitive, and rapid detection of NO3(-) anion in acidic aqueous media. This system self-assembles to a nanoribbon as a result of ionic interaction. The positively charged chemosensor generates a nearly instantaneous significant fluorescence signal (475 vs 605 nm) in response to NO3(-) in the green/yellow spectral region, with a large Stokes shift (130 nm). The fluorescence changes can be attributed to the self-aggregation of the sensor triggered by ionic interaction, which occurs as a consequence of the subtle cooperation of electrostatic ionic bonding, van der Waals forces, and π-stacking of the π-conjugated aromatic moieties. Importantly, this chemosensor has been employed for the first time for the fluorescence detection of intracellular NO3(-) anion in cultured cells.

  1. Atomic interactions of neonicotinoid agonists with AChBP: Molecular recognition of the distinctive electronegative pharmacophore

    Energy Technology Data Exchange (ETDEWEB)

    Talley, Todd T.; Harel, Michal; Hibbs, Ryan E.; Radi, Zoran; Tomizawa, Motohiro; Casida, John E.; Taylor, Palmer (UCB); (UCSD)

    2008-07-28

    Acetylcholine-binding proteins (AChBPs) from mollusks are suitable structural and functional surrogates of the nicotinic acetylcholine receptors when combined with transmembrane spans of the nicotinic receptor. These proteins assemble as a pentamer with identical ACh binding sites at the subunit interfaces and show ligand specificities resembling those of the nicotinic receptor for agonists and antagonists. A subset of ligands, termed the neonicotinoids, exhibit specificity for insect nicotinic receptors and selective toxicity as insecticides. AChBPs are of neither mammalian nor insect origin and exhibit a distinctive pattern of selectivity for the neonicotinoid ligands. We define here the binding orientation and determinants of differential molecular recognition for the neonicotinoids and classical nicotinoids by estimates of kinetic and equilibrium binding parameters and crystallographic analysis. Neonicotinoid complex formation is rapid and accompanied by quenching of the AChBP tryptophan fluorescence. Comparisons of the neonicotinoids imidacloprid and thiacloprid in the binding site from Aplysia californica AChBP at 2.48 and 1.94 {angstrom} in resolution reveal a single conformation of the bound ligands with four of the five sites occupied in the pentameric crystal structure. The neonicotinoid electronegative pharmacophore is nestled in an inverted direction compared with the nicotinoid cationic functionality at the subunit interfacial binding pocket. Characteristic of several agonists, loop C largely envelops the ligand, positioning aromatic side chains to interact optimally with conjugated and hydrophobic regions of the neonicotinoid. This template defines the association of interacting amino acids and their energetic contributions to the distinctive interactions of neonicotinoids.

  2. Macromolecular recognition: Recognition of polymer side chains by cyclodextrin

    Science.gov (United States)

    Hashidzume, Akihito; Harada, Akira

    2015-12-01

    The interaction of cyclodextrins (CD) with water soluble polymers possessing guest residues has been investigated as model systems in biological molecular recognition. The selectivity of interaction of CD with polymer-carrying guest residues is controlled by polymer chains, i.e., the steric effect of polymer main chain, the conformational effect of polymer main chain, and multi-site interaction. Macroscopic assemblies have been also realized based on molecular recognition using polyacrylamide-based gels possessing CD and guest residues.

  3. Multiple ligand simultaneous docking: orchestrated dancing of ligands in binding sites of protein.

    Science.gov (United States)

    Li, Huameng; Li, Chenglong

    2010-07-30

    Present docking methodologies simulate only one single ligand at a time during docking process. In reality, the molecular recognition process always involves multiple molecular species. Typical protein-ligand interactions are, for example, substrate and cofactor in catalytic cycle; metal ion coordination together with ligand(s); and ligand binding with water molecules. To simulate the real molecular binding processes, we propose a novel multiple ligand simultaneous docking (MLSD) strategy, which can deal with all the above processes, vastly improving docking sampling and binding free energy scoring. The work also compares two search strategies: Lamarckian genetic algorithm and particle swarm optimization, which have respective advantages depending on the specific systems. The methodology proves robust through systematic testing against several diverse model systems: E. coli purine nucleoside phosphorylase (PNP) complex with two substrates, SHP2NSH2 complex with two peptides and Bcl-xL complex with ABT-737 fragments. In all cases, the final correct docking poses and relative binding free energies were obtained. In PNP case, the simulations also capture the binding intermediates and reveal the binding dynamics during the recognition processes, which are consistent with the proposed enzymatic mechanism. In the other two cases, conventional single-ligand docking fails due to energetic and dynamic coupling among ligands, whereas MLSD results in the correct binding modes. These three cases also represent potential applications in the areas of exploring enzymatic mechanism, interpreting noisy X-ray crystallographic maps, and aiding fragment-based drug design, respectively.

  4. Assembling novel Cd(II) complexes with multidentate nitrogen donor ligands obtained in situ from the system: zerovalent copper, cadmium oxide, 1-hydroxymethyl-3,5-dimethylpyrazole and ammonium thiocyanate.

    Science.gov (United States)

    Barszcz, Barbara; Masternak, Joanna; Sawka-Dobrowolska, Wanda

    2013-05-07

    A novel 3D coordination polymer [Cd2(L(1))(2)(SCN)(4)(MeOH)(2)](n) (1) and monomeric [Cd(NCS)(2)L(2)] (2) (L(1) = urotropine, L(2) = tris(1-(3,5-dimethylpyrazolylmethyl))amine) have been prepared in a one-pot synthesis using 1-hydroxymethyl-3,5-dimethylpyrazole as the starting ligand. The most prominent feature is the formation in situ of the organic compounds: urotropine and scorpionate-tripodal ligands.

  5. Rational design of ligands targeting triplet repeating transcripts that cause RNA dominant disease: application to myotonic muscular dystrophy type 1 and spinocerebellar ataxia type 3.

    Science.gov (United States)

    Pushechnikov, Alexei; Lee, Melissa M; Childs-Disney, Jessica L; Sobczak, Krzysztof; French, Jonathan M; Thornton, Charles A; Disney, Matthew D

    2009-07-22

    Herein, we describe the design of high affinity ligands that bind expanded rCUG and rCAG repeat RNAs expressed in myotonic dystrophy type 1 (DM1) and spinocerebellar ataxia type 3. These ligands also inhibit, with nanomolar IC(50) values, the formation of RNA-protein complexes that are implicated in both disorders. The expanded rCUG and rCAG repeats form stable RNA hairpins with regularly repeating internal loops in the stem and have deleterious effects on cell function. The ligands that bind the repeats display a derivative of the bisbenzimidazole Hoechst 33258, which was identified by searching known RNA-ligand interactions for ligands that bind the internal loop displayed in these hairpins. A series of 13 modularly assembled ligands with defined valencies and distances between ligand modules was synthesized to target multiple motifs in these RNAs simultaneously. The most avid binder, a pentamer, binds the rCUG repeat hairpin with a K(d) of 13 nM. When compared to a series of related RNAs, the pentamer binds to rCUG repeats with 4.4- to >200-fold specificity. Furthermore, the affinity of binding to rCUG repeats shows incremental gains with increasing valency, while the background binding to genomic DNA is correspondingly reduced. Then, it was determined whether the modularly assembled ligands inhibit the recognition of RNA repeats by Muscleblind-like 1 (MBNL1) protein, the expanded-rCUG binding protein whose sequestration leads to splicing defects in DM1. Among several compounds with nanomolar IC(50) values, the most potent inhibitor is the pentamer, which also inhibits the formation of rCAG repeat-MBNL1 complexes. Comparison of the binding data for the designed synthetic ligands and MBNL1 to repeating RNAs shows that the synthetic ligand is 23-fold higher affinity and more specific to DM1 RNAs than MBNL1. Further studies show that the designed ligands are cell permeable to mouse myoblasts. Thus, cell permeable ligands that bind repetitive RNAs have been designed

  6. Molecular recognition between ligands and nucleic acids: Novel pyridine- and benzoxazole-containing agents related to Hoechst 33258 that exhibit altered DNA sequence specificity deduced from footprinting analysis and spectroscopic studies

    Energy Technology Data Exchange (ETDEWEB)

    Bathini, Y.; Rao, K.E.; Shea, R.G.; Lown, J.W. (Univ. of Alberta, Edmonton (Canada))

    The syntheses of certain analogues of the DNA minor groove binding agent Hoechst 33258 designed to exhibit altered sequence recognition are described. The structural modifications include the following: substitution of pyridine for the benzene ring of the benzimidazole moiety, replacement of one benzimidazole unit by a benzoxazole in the two possible orientations with respect to the DNA receptor, and a synthesis of 2,2{prime}-m-phenylenebis(6-(4-methyl-1-piperazinyl)benzimidazole). Sequence recognition of these agents on a HindIII/EcoRI fragment of pBR322 DNA was determined by MPE footprinting procedures. Some of the analogues exhibited altered DNA sequence preference compared with Hoechst 33258. In particular, a structure bearing a benzoxazole moiety with the oxygen oriented inward to the minor groove together with an inward-directed pyridine nitrogen appears to confer the property of recognition of a GC base pair within the binding sequence. The possible factors, structural, stereochemical, and electrostatic, contributing to the altered DNA sequence recognition properties are discussed.

  7. A Dynamic Combinatorial Approach for Identifying Side Groups that Stabilize DNA-Templated Supramolecular Self-Assemblies

    Directory of Open Access Journals (Sweden)

    Delphine Paolantoni

    2015-02-01

    Full Text Available DNA-templated self-assembly is an emerging strategy for generating functional supramolecular systems, which requires the identification of potent multi-point binding ligands. In this line, we recently showed that bis-functionalized guanidinium compounds can interact with ssDNA and generate a supramolecular complex through the recognition of the phosphodiester backbone of DNA. In order to probe the importance of secondary interactions and to identify side groups that stabilize these DNA-templated self-assemblies, we report herein the implementation of a dynamic combinatorial approach. We used an in situ fragment assembly process based on reductive amination and tested various side groups, including amino acids. The results reveal that aromatic and cationic side groups participate in secondary supramolecular interactions that stabilize the complexes formed with ssDNA.

  8. Controlling Nanocrystal Superlattice Symmetry and Shape-Anisotropic Interactions through Variable Ligand Surface Coverage

    KAUST Repository

    Choi, Joshua J.

    2011-03-09

    The assembly of colloidal nanocrystals (NCs) into superstructures with long-range translational and orientational order is sensitive to the molecular interactions between ligands bound to the NC surface. We illustrate how ligand coverage on colloidal PbS NCs can be exploited as a tunable parameter to direct the self-assembly of superlattices with predefined symmetry. We show that PbS NCs with dense ligand coverage assemble into face-centered cubic (fcc) superlattices whereas NCs with sparse ligand coverage assemble into body-centered cubic (bcc) superlattices which also exhibit orientational ordering of NCs in their lattice sites. Surface chemistry characterization combined with density functional theory calculations suggest that the loss of ligands occurs preferentially on {100} than on reconstructed {111} NC facets. The resulting anisotropic ligand distribution amplifies the role of NC shape in the assembly and leads to the formation of superlattices with translational and orientational order. © 2011 American Chemical Society.

  9. Liquid-liquid interfacial nanoparticle assemblies

    Science.gov (United States)

    Emrick, Todd S.; Russell, Thomas P.; Dinsmore, Anthony; Skaff, Habib; Lin, Yao

    2008-12-30

    Self-assembly of nanoparticles at the interface between two fluids, and methods to control such self-assembly process, e.g., the surface density of particles assembling at the interface; to utilize the assembled nanoparticles and their ligands in fabrication of capsules, where the elastic properties of the capsules can be varied from soft to tough; to develop capsules with well-defined porosities for ultimate use as delivery systems; and to develop chemistries whereby multiple ligands or ligands with multiple functionalities can be attached to the nanoparticles to promote the interfacial segregation and assembly of the nanoparticles. Certain embodiments use cadmium selenide (CdSe) nanoparticles, since the photoluminescence of the particles provides a convenient means by which the spatial location and organization of the particles can be probed. However, the systems and methodologies presented here are general and can, with suitable modification of the chemistries, be adapted to any type of nanoparticle.

  10. Fingerprint recognition

    OpenAIRE

    Diefenderfer, Graig T.

    2006-01-01

    The use of biometrics is an evolving component in today's society. Fingerprint recognition continues to be one of the most widely used biometric systems. This thesis explores the various steps present in a fingerprint recognition system. The study develops a working algorithm to extract fingerprint minutiae from an input fingerprint image. This stage incorporates a variety of image pre-processing steps necessary for accurate minutiae extraction and includes two different methods of ridge thin...

  11. Realization Techniques of Virtual Assembly Process Planning System

    Institute of Scientific and Technical Information of China (English)

    LIU Jian-hua; NING Ru-xin; TANG Cheng-tong

    2005-01-01

    The key realization techniques of virtual assembly process planning (VAPP) system are analyzed,including virtual assembly model, real-time collision detection, automatic constraint recognition algorithm, cable harness assembly process planning and visual assembly process plan at the workshop. A virtual assembly model based on hierarchical assembly task list (HATL) is put forward, in which assembly tasks are defined to express component assembling operations and are sequentially and hierarchically organized according to different subassemblies, which can perfectly model the construction process of product. And a multi-layer automatic geometry constraint recognition algorithm of how to identify assembly constraint relations in the virtual environment is proposed, then a four-layer collision detection algorithm is discussed. A VAPP system is built and some simple mechanical assemblies are used to illustrate the feasibility of the proposed method and algorithms.

  12. Assembly of Organosilver(I) Networks with Multinuclear Supramolecular Synthons Containing All-carbon and Carbon-rich Anionic Ligands%含全碳和多炔阴离子配体的银簇化合物的超分子组装及其结构研究

    Institute of Scientific and Technical Information of China (English)

    侯俊傑; 胡婷; 譚耀新; 麥松威

    2015-01-01

    This review summarizes recent advances conducted by our group on related silver complexes of ( a) all-carbon ligands C2-6 and C2-8 , (b) 1,5-hexadiyne-1,6-diide C6H2-4 , (c) ethynediide C2-2 and ethynide R—C-2 assembled with phosphonic acids, ( d) aryl, alicyclic and heteroaromatic ethynides, and ( e) ethynides that are sta-bilized by different types of silver…carbon binding interactions in the crystalline state, which are further consolidated by weak intra/intermolecular forces. The effects of the solvent, bulkiness of ligands and ancillary ligands on the construction of coordination networks are also discussed.%总结了我们在新型炔银簇化合物研究方面的最新进展。这些化合物分为以下几种类型:(a)1,3,5-己三炔基和1,3,5,7-辛四炔基;(b)1,5-己二炔基;(c)经膦酸配体组装的乙炔基和烷基乙炔基;(d)苯乙炔基、环烷基乙炔基和含氮杂环基乙炔基结构单元的银簇化合物;( e)经不同类型的银-碳配位键连接,并进一步通过分子内/分子间作用力稳固其配位网络的炔银化合物。我们还进一步讨论了溶剂、配体的位阻大小和辅助配体类型对于多维配位网络结构的影响。

  13. Syntheses, spectral, electrochemical and thermal studies of mononuclear manganese(III) complexes with ligands derived from 1,2-propanediamine and 2-hydroxy-3 or 5-methoxybenzaldehyde: Self-assembled monolayer formation on nanostructure zinc oxide thin film

    Science.gov (United States)

    Habibi, Mohammad Hossein; Askari, Elham; Amirnasr, Mehdi; Amiri, Ahmad; Yamane, Yuki; Suzuki, Takayoshi

    2011-08-01

    Mononuclear Mn(III) complexes have been prepared via the Mn(II) reaction of an equimolar of Schiff-bases derived from reaction of 2-hydroxy-3-methoxybenzaldehyde or 2-hydroxy-5-methoxybenzaldehyde with 1,2-diaminopropane. Axial ligands L include: pyridine (py) and H 2O. The resulting complexes have been characterized by FT-IR and UV-vis spectroscopy. The crystal structures of the complexes were determined and indicate that in the solid state the complex adopts a slightly distorted octahedral environment of the imine N and hydroxo O with the two axial ligands. The electrochemical reduction of these complexes at a glassy carbon electrode in acetonitrile solution indicates that the first reduction process corresponding to Mn III-Mn II is electrochemically quasi-reversible. Thermal stability of these complexes was determined by TG and DTG. Layers of these complexes were formed on nanostructure zinc oxide thin film and a red shift was observed when zinc oxide thin film is modified by complex.

  14. Structural Basis of Cooperative Ligand Binding by the Glycine Riboswitch

    OpenAIRE

    Butler, Ethan B.; Xiong, Yong; Wang, Jimin; Strobel, Scott A.

    2011-01-01

    The glycine riboswitch regulates gene expression through the cooperative recognition of its amino acid ligand by a tandem pair of aptamers. A 3.6Å crystal structure of the tandem riboswitch from the glycine permease operon of Fusobacterium nucleatum reveals the glycine binding sites and an extensive network of interactions, largely mediated by asymmetric A-minor contacts, that serve to communicate ligand binding status between the aptamers. These interactions provide a structural basis for ho...

  15. Landscape of protein-small ligand binding modes.

    Science.gov (United States)

    Kasahara, Kota; Kinoshita, Kengo

    2016-09-01

    Elucidating the mechanisms of specific small-molecule (ligand) recognition by proteins is a long-standing conundrum. While the structures of these molecules, proteins and ligands, have been extensively studied, protein-ligand interactions, or binding modes, have not been comprehensively analyzed. Although methods for assessing similarities of binding site structures have been extensively developed, the methods for the computational treatment of binding modes have not been well established. Here, we developed a computational method for encoding the information about binding modes as graphs, and assessing their similarities. An all-against-all comparison of 20,040 protein-ligand complexes provided the landscape of the protein-ligand binding modes and its relationships with protein- and chemical spaces. While similar proteins in the same SCOP Family tend to bind relatively similar ligands with similar binding modes, the correlation between ligand and binding similarities was not very high (R(2)  = 0.443). We found many pairs with novel relationships, in which two evolutionally distant proteins recognize dissimilar ligands by similar binding modes (757,474 pairs out of 200,790,780 pairs were categorized into this relationship, in our dataset). In addition, there were an abundance of pairs of homologous proteins binding to similar ligands with different binding modes (68,217 pairs). Our results showed that many interesting relationships between protein-ligand complexes are still hidden in the structure database, and our new method for assessing binding mode similarities is effective to find them.

  16. Dynamic nanoparticle assemblies.

    Science.gov (United States)

    Wang, Libing; Xu, Liguang; Kuang, Hua; Xu, Chuanlai; Kotov, Nicholas A

    2012-11-20

    a molecule from atoms. Finer classification of NP assemblies in accord with established conventions in the field may include different size dimensionalities: discrete assemblies (artificial molecules) and one-dimensional (spaced chains), two-dimensional (sheets), and three-dimensional (superlattices, twisted structures) assemblies. Notably, these dimensional attributes must be regarded as primarily topological in nature because all of these superstructures can acquire complex three-dimensional shapes. We discuss three primary strategies used to prepare NP superstructures: (1) anisotropy-based assemblies utilizing either intrinsic force field anisotropy around NPs or external anisotropy associated with templates or applied fields, (2) assembly methods utilizing uniform NPs with isotropic interactions, and (3) methods based on mutual recognition of biomolecules, such as DNA and antigen-antibody interactions. We consider optical, electronic, and magnetic properties of dynamic superstructures, focusing primarily on multiparticle effects in NP superstructures as represented by surface plasmon resonance, NP-NP charge transport, and multibody magnetization. Unique properties of NP superstructures are being applied to biosensing, drug delivery, and nanoelectronics. For both Class 1 and Class 2 dynamic assemblies, biosensing is the most dominant and well-developed area of dynamic nanostructures being successfully transitioned into practice. We can foresee the rapid development of dynamic NP assemblies toward applications in harvesting of dissipated energy, photonics, and electronics. The final part of this Account is devoted to the fundamental questions facing dynamic assemblies of NPs in the future.

  17. Designer TGFβ superfamily ligands with diversified functionality.

    Directory of Open Access Journals (Sweden)

    George P Allendorph

    Full Text Available Transforming Growth Factor--beta (TGFβ superfamily ligands, including Activins, Growth and Differentiation Factors (GDFs, and Bone Morphogenetic Proteins (BMPs, are excellent targets for protein-based therapeutics because of their pervasiveness in numerous developmental and cellular processes. We developed a strategy termed RASCH (Random Assembly of Segmental Chimera and Heteromer, to engineer chemically-refoldable TGFβ superfamily ligands with unique signaling properties. One of these engineered ligands, AB208, created from Activin-βA and BMP-2 sequences, exhibits the refolding characteristics of BMP-2 while possessing Activin-like signaling attributes. Further, we find several additional ligands, AB204, AB211, and AB215, which initiate the intracellular Smad1-mediated signaling pathways more strongly than BMP-2 but show no sensitivity to the natural BMP antagonist Noggin unlike natural BMP-2. In another design, incorporation of a short N-terminal segment from BMP-2 was sufficient to enable chemical refolding of BMP-9, without which was never produced nor refolded. Our studies show that the RASCH strategy enables us to expand the functional repertoire of TGFβ superfamily ligands through development of novel chimeric TGFβ ligands with diverse biological and clinical values.

  18. Sequence assembly

    DEFF Research Database (Denmark)

    Scheibye-Alsing, Karsten; Hoffmann, S.; Frankel, Annett Maria

    2009-01-01

    Despite the rapidly increasing number of sequenced and re-sequenced genomes, many issues regarding the computational assembly of large-scale sequencing data have remain unresolved. Computational assembly is crucial in large genome projects as well for the evolving high-throughput technologies and...... in genomic DNA, highly expressed genes and alternative transcripts in EST sequences. We summarize existing comparisons of different assemblers and provide a detailed descriptions and directions for download of assembly programs at: http://genome.ku.dk/resources/assembly/methods.html....

  19. Facial Recognition

    Directory of Open Access Journals (Sweden)

    Mihalache Sergiu

    2014-05-01

    Full Text Available During their lifetime, people learn to recognize thousands of faces that they interact with. Face perception refers to an individual's understanding and interpretation of the face, particularly the human face, especially in relation to the associated information processing in the brain. The proportions and expressions of the human face are important to identify origin, emotional tendencies, health qualities, and some social information. From birth, faces are important in the individual's social interaction. Face perceptions are very complex as the recognition of facial expressions involves extensive and diverse areas in the brain. Our main goal is to put emphasis on presenting human faces specialized studies, and also to highlight the importance of attractiviness in their retention. We will see that there are many factors that influence face recognition.

  20. Autonomous Environment Recognition by Robotic Manipulators

    OpenAIRE

    Senda, Kei; Okano, Yuzo

    2001-01-01

    This paper discusses methods of autonomus environment recognition and action by a robotic manipulator working with dynamic interaction to the enviroment, e.g., assembling. A method automatically recognizes the contacting situation with the work site from the sensor outputs and the robotic manipulator motion. The autonomous recognition then discriminates the constraint conditions at manopulator hand using the self-organizing map that is a kind of unsupervisedlearning of neural networks. The di...

  1. Metal Vector Manipulated Molecular Self-Assembly from Werner System to Cotton System

    Institute of Scientific and Technical Information of China (English)

    YU Shu-Yan; ZHANG Zhong-Xing; HUANG Hui; LI Sheng-Hui; HUANG Hai-Ping

    2004-01-01

    A definition of metal vector was given to coordinatively unsaturated metals or asymmetrically coordinated metal complexes in which the metal center is partly blocked by inert chelating ligand(s), thus possess specific reactivity and directionality, such as cis-coordinated square Pd(Ⅱ) or Pt(Ⅱ) complexes. Metal vectors have been extensively used in coordination catalysis and molecular assembly. In 1990, Fujita [ 1 ] first demonstrated the utility of cis-coordinated square Pd(Ⅱ)or Pt(Ⅱ) complexes as a right angular 2D metal vector in the formation of molecular square, a cyclic tetramer with nano-cavity and unique molecular recognition. So far, much attention has been paid to the use of the mononuclear coordination centers (Werner-type metal vectors) in molecular assembly.As late as 1999, Cotton et al. [2] reported the use of cis-coordinated metal-metal bonded dimetal units (Cotton-type metal vectors) to direct assembly of molecular squares.This presentation includes two parts: 1) Werner-type metal vector directed molecular assembly; [3]2) Cotton-type metal vector directed molecular assembly.[4]Firstly, the Werner-type metal vector, cis-coordinated Pd(Ⅱ) nitrate, was used to direct a 6-component self-assembly. This leads to the formation of a molecular bowl or crown with syn,syn,syn conformation. These structures are analogues of calix[3]arenes and can function as anion receptors. Interestingly, an nitrate is found to distort from a trigonal plane into a trigonal pyramid when binding to the bottom of the molecular bowl.Secondly, the Cotton-type metal vector, cis-diRh(Ⅱ, Ⅱ), was used to assemble di- or poly-carboxylate anions into neutral supermolecules. Most interestingly, a calixarene-based carceplex with four cis-diRh(Ⅱ, Ⅱ) fastners was obtained[5].All self-assembling entities were studied by both X-ray crystallographic analysis and solution NMR spectra, which are consistent with the presence of assembling structures even in solution.

  2. Selective oxoanion separation using a tripodal ligand

    Energy Technology Data Exchange (ETDEWEB)

    Custelcean, Radu; Moyer, Bruce A.; Rajbanshi, Arbin

    2016-02-16

    The present invention relates to urea-functionalized crystalline capsules self-assembled by sodium or potassium cation coordination and by hydrogen-bonding water bridges to selectively encapsulate tetrahedral divalent oxoanions from highly competitive aqueous alkaline solutions and methods using this system for selective anion separations from industrial solutions. The method involves competitive crystallizations using a tripodal tris(urea) functionalized ligand and, in particular, provides a viable approach to sulfate separation from nuclear wastes.

  3. Stereochemistry in subcomponent self-assembly.

    Science.gov (United States)

    Castilla, Ana M; Ramsay, William J; Nitschke, Jonathan R

    2014-07-15

    CONSPECTUS: As Pasteur noted more than 150 years ago, asymmetry exists in matter at all organization levels. Biopolymers such as proteins or DNA adopt one-handed conformations, as a result of the chirality of their constituent building blocks. Even at the level of elementary particles, asymmetry exists due to parity violation in the weak nuclear force. While the origin of homochirality in living systems remains obscure, as does the possibility of its connection with broken symmetries at larger or smaller length scales, its centrality to biomolecular structure is clear: the single-handed forms of bio(macro)molecules interlock in ways that depend upon their handednesses. Dynamic artificial systems, such as helical polymers and other supramolecular structures, have provided a means to study the mechanisms of transmission and amplification of stereochemical information, which are key processes to understand in the context of the origins and functions of biological homochirality. Control over stereochemical information transfer in self-assembled systems will also be crucial for the development of new applications in chiral recognition and separation, asymmetric catalysis, and molecular devices. In this Account, we explore different aspects of stereochemistry encountered during the use of subcomponent self-assembly, whereby complex structures are prepared through the simultaneous formation of dynamic coordinative (N → metal) and covalent (N═C) bonds. This technique provides a useful method to study stereochemical information transfer processes within metal-organic assemblies, which may contain different combinations of fixed (carbon) and labile (metal) stereocenters. We start by discussing how simple subcomponents with fixed stereogenic centers can be incorporated in the organic ligands of mononuclear coordination complexes and communicate stereochemical information to the metal center, resulting in diastereomeric enrichment. Enantiopure subcomponents were then

  4. Speaker Recognition

    DEFF Research Database (Denmark)

    Mølgaard, Lasse Lohilahti; Jørgensen, Kasper Winther

    2005-01-01

    Speaker recognition is basically divided into speaker identification and speaker verification. Verification is the task of automatically determining if a person really is the person he or she claims to be. This technology can be used as a biometric feature for verifying the identity of a person...... in applications like banking by telephone and voice mail. The focus of this project is speaker identification, which consists of mapping a speech signal from an unknown speaker to a database of known speakers, i.e. the system has been trained with a number of speakers which the system can recognize....

  5. The recognition of work

    OpenAIRE

    Nierling, Linda

    2007-01-01

    The following article argues that recognition structures in work relations differ significantly in the sphere of paid work in contrast to unpaid work in private spheres. According to the systematic approach on recognition of Axel Honneth three different levels of recognition are identified: the interpersonal recognition, organisational recognition and societal recognition. Based on this framework it can be stated that recognition structures in the sphere of paid work and in private spheres di...

  6. A Novel Binding Pattern Unique in Two Ligands for One Carbohydrate Recognition Domain in Galectins%半乳糖凝集素糖结合的新模式:一个糖结合域的双重配体结合

    Institute of Scientific and Technical Information of China (English)

    卞乘凤; 张英; 李德峰; 王大成

    2011-01-01

    半乳糖凝集素家族通过糖识别结构域(CRD)可以专一性识别和结合含β-半乳糖的多糖配体来发挥其生物学功能.到目前发现的CRD对β-半乳糖的识别模式是非常保守的,在结构已知的半乳糖凝集素结构中,一个CRD只能结合一个多糖配体分子.最近,通过对人源半乳糖凝聚素-3 CRD与对硝基TF二糖(TFN)复合物的晶体结构解析首次发现,一个CRD可以同时结合2个TFN分子.与这2个TFN分子有双向结合的残基突变体E165A结构分析显示,一个残基的突变引起的结构上的微小变化会使结合位点2丧失结合糖底物的能力,而位点1的配体结合却不受影响.这表明,结合位点1对糖底物保守的识别和结合是基本的、主要的,而结合位点2对于糖有条件的结合,是额外的、次要的.序列比对和立体化学分析显示,参与新位点2结合的关键残基在其他半乳糖凝集素分子中都是保守的,而它们参与糖配体结合并不常见,表明它们作用的发挥是有条件的.可能在复杂寡聚结构的情况下,如有多重分支结构,双重结合位点将有利于对这类配体分子的辨识和结合,已有一系列研究报道,具有分支结构的寡糖与半乳糖分子的亲和势明显高于单价糖配体,与上述分析相一致.对这类双重位点糖结合的可能生物学意义进行了讨论.%Galectins are a protein family with diverse biological functions,which are unique in specifically recognition and binding with β-galactosides as the primary structural basis for its functional performance.So far,all structurally characterized galectins display a conservative binding mode for the β-galactoside-containing carbohydrate ligands,in which one carbohydrate recognition domain (CRD) binds only one ligand.Here a novel binding pattern unique in two carbohydrate ligands for one CRD was reported,which is observed from the structure of Gal-3 CRD complexed with glycan TFN.In this doublet binding

  7. Ligand-controlled assembly of Cd(II) coordination polymers based on mixed ligands of naphthalene-dicarboxylate and dipyrido[3,2-d:2‧,3‧-f]quinoxaline: From 0D+1D cocrystal, 2D rectangular network (4,4), to 3D PtS-type architecture

    Science.gov (United States)

    Liu, Guocheng; Chen, Yongqiang; Wang, Xiuli; Chen, Baokuan; Lin, Hongyan

    2009-03-01

    Three novel Cd(II) coordination polymers, namely, [Cd(Dpq)(1,8-NDC)(H 2O) 2][Cd(Dpq)(1,8-NDC)]·2H 2O ( 1), [Cd(Dpq)(1,4-NDC)(H 2O)] ( 2), and [Cd(Dpq)(2,6-NDC)] ( 3) have been obtained from hydrothermal reactions of cadmium(II) nitrate with the mixed ligands dipyrido [3,2-d:2',3'-f]quinoxaline (Dpq) and three structurally related naphthalene-dicarboxylate ligands [1,8-naphthalene-dicarboxylic acid (1,8-H 2NDC), 1,4-naphthalene-dicarboxylic acid (1,4-H 2NDC), and 2,6-naphthalene-dicarboxylic acid (2,6-H 2NDC)]. Single-crystal X-ray diffraction analysis reveals that the three polymers exhibit novel structures due to different naphthalene-dicarboxylic acid. Compound 1 is a novel cocrystal of left- and right-handed helical chains and binuclear complexes and ultimately packed into a 3D supramolecular structure through hydrogen bonds and π- π stacking interactions. Compound 2 shows a 2D rectangular network (4,4) bridged by 1,4-NDC with two kinds of coordination modes and ultimately packed into a 3D supramolecular structure through inter-layer π- π stacking interactions. Compound 3 is a new 3D coordination polymer with distorted PtS-type network. In addition, the title compounds exhibit blue/green emission in solid state at room temperature.

  8. Nanoparticle decoration with surfactants: Molecular interactions, assembly, and applications

    Science.gov (United States)

    Heinz, Hendrik; Pramanik, Chandrani; Heinz, Ozge; Ding, Yifu; Mishra, Ratan K.; Marchon, Delphine; Flatt, Robert J.; Estrela-Lopis, Irina; Llop, Jordi; Moya, Sergio; Ziolo, Ronald F.

    2017-02-01

    Nanostructures of diverse chemical nature are used as biomarkers, therapeutics, catalysts, and structural reinforcements. The decoration with surfactants has a long history and is essential to introduce specific functions. The definition of surfactants in this review is very broad, following its lexical meaning ;surface active agents;, and therefore includes traditional alkyl modifiers, biological ligands, polymers, and other surface active molecules. The review systematically covers covalent and non-covalent interactions of such surfactants with various types of nanomaterials, including metals, oxides, layered materials, and polymers as well as their applications. The major themes are (i) molecular recognition and noncovalent assembly mechanisms of surfactants on the nanoparticle and nanocrystal surfaces, (ii) covalent grafting techniques and multi-step surface modification, (iii) dispersion properties and surface reactions, (iv) the use of surfactants to influence crystal growth, as well as (v) the incorporation of biorecognition and other material-targeting functionality. For the diverse materials classes, similarities and differences in surfactant assembly, function, as well as materials performance in specific applications are described in a comparative way. Major factors that lead to differentiation are the surface energy, surface chemistry and pH sensitivity, as well as the degree of surface regularity and defects in the nanoparticle cores and in the surfactant shell. The review covers a broad range of surface modifications and applications in biological recognition and therapeutics, sensors, nanomaterials for catalysis, energy conversion and storage, the dispersion properties of nanoparticles in structural composites and cement, as well as purification systems and classical detergents. Design principles for surfactants to optimize the performance of specific nanostructures are discussed. The review concludes with challenges and opportunities.

  9. Recognition & Reconstruction

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    AS Libya rolls on toward its new destiny without former leader Muammar Gaddafi,the legitimacy of the National Transitional Council(NTC) is no longer in doubt. The United Nations has put its full force behind Libya’s former rebels,with the news that the NTC has occupied their nation’s seat at the world body and that certain sanctions imposed on the previous government will be lifted. The UN General Assembly vote of 114 nations to 17,with 15 abstentions,is a clear indication that the world is eager to get Libya’s economy moving and

  10. Ligand modeling and design

    Energy Technology Data Exchange (ETDEWEB)

    Hay, B.P. [Pacific Northwest National Lab., Richland, WA (United States)

    1997-10-01

    The purpose of this work is to develop and implement a molecular design basis for selecting organic ligands that would be used in the cost-effective removal of specific radionuclides from nuclear waste streams. Organic ligands with metal ion specificity are critical components in the development of solvent extraction and ion exchange processes that are highly selective for targeted radionuclides. The traditional approach to the development of such ligands involves lengthy programs of organic synthesis and testing, which in the absence of reliable methods for screening compounds before synthesis, results in wasted research effort. The author`s approach breaks down and simplifies this costly process with the aid of computer-based molecular modeling techniques. Commercial software for organic molecular modeling is being configured to examine the interactions between organic ligands and metal ions, yielding an inexpensive, commercially or readily available computational tool that can be used to predict the structures and energies of ligand-metal complexes. Users will be able to correlate the large body of existing experimental data on structure, solution binding affinity, and metal ion selectivity to develop structural design criteria. These criteria will provide a basis for selecting ligands that can be implemented in separations technologies through collaboration with other DOE national laboratories and private industry. The initial focus will be to select ether-based ligands that can be applied to the recovery and concentration of the alkali and alkaline earth metal ions including cesium, strontium, and radium.

  11. Three luminescent d{sup 10} metal coordination polymers assembled from a semirigid V-shaped ligand with high selective detecting of Cu{sup 2+} ion and nitrobenzene

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Wei-Ping [Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education, Shaanxi Key Laboratory of Physico-Inorg. Chem., College of Chemistry & Materials Science, Northwest University, Xi’an 710069 (China); Institute of Functional Materials, College of Chemistry and Pharmaceutical Engineering, Sichuan University of Science & Engineering, Zigong 643000 (China); Liu, Ping; Liang, Yu-Tong; Cui, Lin; Xi, Zheng-Ping [Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education, Shaanxi Key Laboratory of Physico-Inorg. Chem., College of Chemistry & Materials Science, Northwest University, Xi’an 710069 (China); Wang, Yao-Yu, E-mail: wyaoyu@nwu.edu.cn [Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education, Shaanxi Key Laboratory of Physico-Inorg. Chem., College of Chemistry & Materials Science, Northwest University, Xi’an 710069 (China)

    2015-08-15

    Three 2D luminescent coordination polymers with helical frameworks, [ZnL{sub 2}]{sub n} (1) and ([ML{sub 2}]·(H{sub 2}O)){sub n} (M=Zn (2), Cd (3)) (HL=4-((2-methyl-1 H-imidazol-1-yl)methyl)benzoic acid), have been assembled under hydro(solvo)thermal conditions. Complex 1 is in chiral space group and displays a rare 2D→2D 2-fold parallel interpenetrated layer network with two types of chiral double helixes. Interestingly, the single crystal structure analyses indicate the coexistence of enantiomers la and 1b in one pot, while the bulk crystallization of 1 are racemic mixtures based on the CD measurement. 2 and 3 are isostructural, in the structure, there are two kinds of 2D chiral helical-layers which stack in an -ABAB- sequence leading to the overall structure are mesomer and achiral. All compounds display intense luminescence in solid state at room temperature with high chemical and thermal stability. More importantly, 1 has been successfully applied in the detection of Cu{sup 2+} ions in aqueous media and nitrobenzene and the probable detecting mechanism was also discussed. - Graphical abstract: Three luminescent d{sup 10} metal coordination polymers with helical-layer based on 4-((2-methyl-1H-imidazol-1-yl)methyl)benzoic acid have been obtained. Compound 1 shows high selective detecting for Cu{sup 2+} ion in aqueous and nitrobenzene. - Highlights: • Three coordination polymers with chiral helical-layer have been obtained. • 1 Can luminescent detect Cu{sup 2+} ion in aqueous media and nitrobenzene. • Racemic mixture or mesomer compounds can be obtained by controlling the reaction conditions.

  12. Chemometric analysis of ligand receptor complementarity: identifying Complementary Ligands Based on Receptor Information (CoLiBRI).

    Science.gov (United States)

    Oloff, Scott; Zhang, Shuxing; Sukumar, Nagamani; Breneman, Curt; Tropsha, Alexander

    2006-01-01

    We have developed a novel structure-based chemoinformatics approach to search for Complimentary Ligands Based on Receptor Information (CoLiBRI). CoLiBRI is based on the representation of both receptor binding sites and their respective ligands in a space of universal chemical descriptors. The binding site atoms involved in the interaction with ligands are identified by the means of a computational geometry technique known as Delaunay tessellation as applied to X-ray characterized ligand-receptor complexes. TAE/RECON multiple chemical descriptors are calculated independently for each ligand as well as for its active site atoms. The representation of both ligands and active sites using chemical descriptors allows the application of well-known chemometric techniques in order to correlate chemical similarities between active sites and their respective ligands. We have established a protocol to map patterns of nearest neighbor active site vectors in a multidimensional TAE/RECON space onto those of their complementary ligands and vice versa. This protocol affords the prediction of a virtual complementary ligand vector in the ligand chemical space from the position of a known active site vector. This prediction is followed by chemical similarity calculations between this virtual ligand vector and those calculated for molecules in a chemical database to identify real compounds most similar to the virtual ligand. Consequently, the knowledge of the receptor active site structure affords straightforward and efficient identification of its complementary ligands in large databases of chemical compounds using rapid chemical similarity searches. Conversely, starting from the ligand chemical structure, one may identify possible complementary receptor cavities as well. We have applied the CoLiBRI approach to a data set of 800 X-ray characterized ligand-receptor complexes in the PDBbind database. Using a k nearest neighbor (kNN) pattern recognition approach and variable selection

  13. Surfactant Ligand Removal and Rational Fabrication of Inorganically Connected Quantum Dots

    KAUST Repository

    Zhang, Haitao

    2011-12-14

    A novel method is reported to create inorganically connected nanocrystal (NC) assemblies for both II-VI and IV-VI semiconductors by removing surfactant ligands using (NH 4) 2S. This surface modification process differs from ligand exchange methods in that no new surfactant ligands are introduced and the post-treated NC surfaces are nearly bare. The detailed mechanism study shows that the high reactivity between (NH 4) 2S and metal-surfactant ligand complexes enables the complete removal of surfactant ligands in seconds and converts the NC metal-rich shells into metal sulfides. The post-treated NCs are connected through metal-sulfide bonding and form a larger NCs film assembly, while still maintaining quantum confinement. Such "connected but confined" NC assemblies are promising new materials for electronic and optoelectronic devices. © 2011 American Chemical Society.

  14. Ligand modeling and design

    Energy Technology Data Exchange (ETDEWEB)

    Hay, B. [Pacific Northwest Lab., Richland, WA (United States)

    1996-10-01

    The purpose of this work is to develop and implement a molecular design basis for selecting organic ligands that would be used tin applications for the cost-effective removal of specific radionuclides from nuclear waste streams.

  15. Investigation of efficient features for image recognition by neural networks.

    Science.gov (United States)

    Goltsev, Alexander; Gritsenko, Vladimir

    2012-04-01

    In the paper, effective and simple features for image recognition (named LiRA-features) are investigated in the task of handwritten digit recognition. Two neural network classifiers are considered-a modified 3-layer perceptron LiRA and a modular assembly neural network. A method of feature selection is proposed that analyses connection weights formed in the preliminary learning process of a neural network classifier. In the experiments using the MNIST database of handwritten digits, the feature selection procedure allows reduction of feature number (from 60 000 to 7000) preserving comparable recognition capability while accelerating computations. Experimental comparison between the LiRA perceptron and the modular assembly neural network is accomplished, which shows that recognition capability of the modular assembly neural network is somewhat better.

  16. Fluorescent BINOL-based sensor for thorium recognition and a density functional theory investigation.

    Science.gov (United States)

    Wen, Jun; Dong, Liang; Tian, Jie; Jiang, Tao; Yang, Yan-Qiu; Huang, Zeng; Yu, Xiao-Qi; Hu, Chang-Wei; Hu, Sheng; Yang, Tong-Zai; Wang, Xiao-Lin

    2013-12-15

    A novel 1,1'-bi-2-naphthol (BINOL) derivative fluorescence sensor L-1 for the recognition of thorium ion with a fluorescence quench response. This ligand showed high selectivity and sensitivity for thorium ion recognition. Coordination effects were investigated by DFT calculations, and the coordination modes and sites were confirmed. Moreover, the coordination abilities of the L-1 ligand with Th(4+) and UO2(2+) were evaluated.

  17. Identification of VDR Antagonists among Nuclear Receptor Ligands Using Virtual Screening

    Directory of Open Access Journals (Sweden)

    Kelly Teske

    2014-04-01

    Full Text Available Herein, we described the development of two virtual screens to identify new vitamin D receptor (VDR antagonists among nuclear receptor (NR ligands. Therefore, a database of 14330 nuclear receptor ligands and their NR affinities was assembled using the online available “Binding Database.” Two different virtual screens were carried out in conjunction with a reported VDR crystal structure applying a stringent and less stringent pharmacophore model to filter docked NR ligand conformations. The pharmacophore models were based on the spatial orientation of the hydroxyl functionalities of VDR's natural ligands 1,25(OH2D3 and 25(OH2D3. The first virtual screen identified 32 NR ligands with a calculated free energy of VDR binding of more than -6.0 kJ/mol. All but nordihydroguaiaretic acid (NDGA are VDR ligands, which inhibited the interaction between VDR and coactivator peptide SRC2-3 with an IC50 value of 15.8 μM. The second screen identified 162 NR ligands with a calculated free energy of VDR binding of more than -6.0 kJ/mol. More than half of these ligands were developed to bind VDR followed by ERα/β ligands (26%, TRα/β ligands (7%, and LxRα/β ligands (7%. The binding between VDR and ERα ligand H6036 as well as TRα/β ligand triiodothyronine and a homoserine analog thereof was confirmed by fluorescence polarization.

  18. Recognition of self-assembled water-nitrate cluster in a Co(III)-2,2'-bipyridine host: Synthesis, X-ray structure, DNA cleavage, molecular docking and anticancer activity

    Indian Academy of Sciences (India)

    SUBRATA DAS; ANANDAN RANJANI; LOGANATHAN GAYATHRI; SUBHASISH SAHA; JORGE PASAN; DHARUMADURAI DHANASEKARAN; MOHAMMAD ABDULKADER AKBARSHA; MILAN MAJI; BHASKAR BISWAS

    2016-11-01

    A mononuclear cobalt(III) complex [Co(bpy)₂Cl₂]NO₃·2H₂O (1) (bpy = 2,2'-bipyridine) has been synthesized and crystallographically characterized. Self-assembly of the lattice water molecules from rectangular tetrameric water cluster interacts with nitrate anion along the c-axis forming a six membered hexagonal water-nitrate cluster. It presents a new mode of association of water molecules with nitrate molecules which is not predicted theoretically or found experimentally. The molecule effectively cleaves bacterial genomic DNA and shows important cytotoxicity against human hepatocarcinoma cell (HepG2).

  19. Sabot assembly

    Energy Technology Data Exchange (ETDEWEB)

    Bzorgi, Fariborz

    2016-11-08

    A sabot assembly includes a projectile and a housing dimensioned and configured for receiving the projectile. An air pressure cavity having a cavity diameter is disposed between a front end and a rear end of the housing. Air intake nozzles are in fluid communication with the air pressure cavity and each has a nozzle diameter less than the cavity diameter. In operation, air flows through the plurality of air intake nozzles and into the air pressure cavity upon firing of the projectile from a gun barrel to pressurize the air pressure cavity for assisting in separation of the housing from the projectile upon the sabot assembly exiting the gun barrel.

  20. Gesture Recognition Summarization

    Institute of Scientific and Technical Information of China (English)

    ZHANG Ting-fang; FENG Zhi-quan; SU Yuan-yuan; JIANG Yan

    2014-01-01

    Gesture recognition is an important research in the field of human-computer interaction. Hand Gestures are strong variable and flexible, so the gesture recognition has always been an important challenge for the researchers. In this paper, we first outlined the development of gestures recognition, and different classification of gestures based on different purposes. Then we respectively introduced common methods used in the process of gesture segmentation, feature extraction and recognition. Finally, the gesture recognition was summarized and the studying prospects were given.

  1. Iris Recognition Technique

    Institute of Scientific and Technical Information of China (English)

    XIE Mei

    2006-01-01

    The demand on security is increasing greatly in these years and biometric recognition gradually becomes a hot field of research. Iris recognition is a new branch of biometric recognition, which is regarded as the most stable, safe and accurate biometric recognition method. In these years, much progress in this field has been made by scholars and experts of different countries. In this paper, some successful iris recognition methods are listed and their performance are compared. Furthermore, the existing problems and challenges are discussed.

  2. Molecular Mechanisms of Cell-cell Recognition

    Institute of Scientific and Technical Information of China (English)

    WANG Jia-Huai

    2004-01-01

    Cell-cell recognition is the key for multicellular organisms to survive. This recognition critically depends on protein-protein interactions from opposing cell surfaces. Recent structural investigations reveal unique features of these cell surface receptors and how they interact. These interactions are specific, but usually relatively weak, with more hydrophilic forces involved in binding. The receptors appear to have specialized ways to present their key interacting elements for ligand-binding from the cell surface. Cell-cell contacts are multivalent. A large group of cell surface molecules are engaged in interactions. Characteristic weak interactions make possible for each individual molecule pair within the group to constantly associate-dissociate-reassociate, such that the cell-cell recognition becomes a dynamic process. The immunological synapse is a good example for immune receptors to be orchestrated in performing immunological function in a collective fashion.

  3. Insights into Protein–Ligand Interactions: Mechanisms, Models, and Methods

    Directory of Open Access Journals (Sweden)

    Xing Du

    2016-01-01

    Full Text Available Molecular recognition, which is the process of biological macromolecules interacting with each other or various small molecules with a high specificity and affinity to form a specific complex, constitutes the basis of all processes in living organisms. Proteins, an important class of biological macromolecules, realize their functions through binding to themselves or other molecules. A detailed understanding of the protein–ligand interactions is therefore central to understanding biology at the molecular level. Moreover, knowledge of the mechanisms responsible for the protein-ligand recognition and binding will also facilitate the discovery, design, and development of drugs. In the present review, first, the physicochemical mechanisms underlying protein–ligand binding, including the binding kinetics, thermodynamic concepts and relationships, and binding driving forces, are introduced and rationalized. Next, three currently existing protein-ligand binding models—the “lock-and-key”, “induced fit”, and “conformational selection”—are described and their underlying thermodynamic mechanisms are discussed. Finally, the methods available for investigating protein–ligand binding affinity, including experimental and theoretical/computational approaches, are introduced, and their advantages, disadvantages, and challenges are discussed.

  4. Macromolecular recognition in the Protein Data Bank

    Energy Technology Data Exchange (ETDEWEB)

    Janin, Joël, E-mail: joel.janin@ibbmc.u-psud.fr [Laboratoire d’Enzymologie et de Biochimie Structurales, UPR9063, CNRS, 91198 Gif-sur-Yvette (France); Institut de Biochimie et Biologie Moléculaire et Cellulaire, UMR8619, Bâtiment 430, Université Paris-Sud, 91405 Orsay (France); Rodier, Francis [Laboratoire d’Enzymologie et de Biochimie Structurales, UPR9063, CNRS, 91198 Gif-sur-Yvette (France); Chakrabarti, Pinak [Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Calcutta 700 054 (India); Bahadur, Ranjit P. [Institut de Biochimie et Biologie Moléculaire et Cellulaire, UMR8619, Bâtiment 430, Université Paris-Sud, 91405 Orsay (France); Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Calcutta 700 054 (India); Laboratoire d’Enzymologie et de Biochimie Structurales, UPR9063, CNRS, 91198 Gif-sur-Yvette (France)

    2007-01-01

    X-ray structures in the PDB illustrate both the specific recognition of two polypeptide chains in protein–protein complexes and dimeric proteins and their nonspecific interaction at crystal contacts. Crystal structures deposited in the Protein Data Bank illustrate the diversity of biological macromolecular recognition: transient interactions in protein–protein and protein–DNA complexes and permanent assemblies in homodimeric proteins. The geometric and physical chemical properties of the macromolecular interfaces that may govern the stability and specificity of recognition are explored in complexes and homodimers compared with crystal-packing interactions. It is found that crystal-packing interfaces are usually much smaller; they bury fewer atoms and are less tightly packed than in specific assemblies. Standard-size interfaces burying 1200–2000 Å{sup 2} of protein surface occur in protease–inhibitor and antigen–antibody complexes that assemble with little or no conformation changes. Short-lived electron-transfer complexes have small interfaces; the larger size of the interfaces observed in complexes involved in signal transduction and homodimers correlates with the presence of conformation changes, often implicated in biological function. Results of the CAPRI (critical assessment of predicted interactions) blind prediction experiment show that docking algorithms efficiently and accurately predict the mode of assembly of proteins that do not change conformation when they associate. They perform less well in the presence of large conformation changes and the experiment stimulates the development of novel procedures that can handle such changes.

  5. Sequence-specific recognition of DNA nanostructures.

    Science.gov (United States)

    Rusling, David A; Fox, Keith R

    2014-05-15

    DNA is the most exploited biopolymer for the programmed self-assembly of objects and devices that exhibit nanoscale-sized features. One of the most useful properties of DNA nanostructures is their ability to be functionalized with additional non-nucleic acid components. The introduction of such a component is often achieved by attaching it to an oligonucleotide that is part of the nanostructure, or hybridizing it to single-stranded overhangs that extend beyond or above the nanostructure surface. However, restrictions in nanostructure design and/or the self-assembly process can limit the suitability of these procedures. An alternative strategy is to couple the component to a DNA recognition agent that is capable of binding to duplex sequences within the nanostructure. This offers the advantage that it requires little, if any, alteration to the nanostructure and can be achieved after structure assembly. In addition, since the molecular recognition of DNA can be controlled by varying pH and ionic conditions, such systems offer tunable properties that are distinct from simple Watson-Crick hybridization. Here, we describe methodology that has been used to exploit and characterize the sequence-specific recognition of DNA nanostructures, with the aim of generating functional assemblies for bionanotechnology and synthetic biology applications.

  6. Attenuation of pattern recognition receptor signaling is mediated by a MAP kinase kinase kinase

    NARCIS (Netherlands)

    Mithoe, S.C.; Ludwig, C.; Pel, M.J.C.; Cucinotta, M.; Casartelli, A.; Mbengue, M.; Sklenar, J.; Derbyshire, P.; Robatzek, S.; Pieterse, C.M.J.; Aebersold, R.; Menke, F.L.H.

    2016-01-01

    Pattern recognition receptors (PRRs) play a key role in plant and animal innate immunity. PRR binding of their cognate ligand triggers a signaling network and activates an immune response. Activation of PRR signaling must be controlled prior to ligand binding to prevent spurious signaling and immune

  7. Molecule Recognition Imaging and Highly Ordered Gold Nanoparticle Templating of Functional Bacterial S-Layer Nanoarrays

    Institute of Scientific and Technical Information of China (English)

    Jilin TANG; Andreas Ebner; Helga Badelt-Lichtblau; Christian Rankl; Michael Leitner; Hermann J.Gruber; Uwe B.Sleytr; Nicola Ilk; Peter Hinterdorfer

    2009-01-01

    @@ Molecular recognition between receptors and their cognate ligands plays an important role in life sciences.Such specific interactions include those between complementary strands of DNA,enzyme and substrate,antigen and antibody,lectin and carbohydrate,ligands and cell surface receptors as well as between cell adhesion proteins.

  8. Photolabile plasmonic vesicles assembled from amphiphilic gold nanoparticles for remote-controlled traceable drug delivery

    Science.gov (United States)

    Song, Jibin; Fang, Zheng; Wang, Chenxu; Zhou, Jiajing; Duan, Bo; Pu, Lu; Duan, Hongwei

    2013-06-01

    We have developed a new type of photo-responsive plasmonic vesicles that allow for active delivery of anticancer payloads to specific cancer cells and personalized drug release regulated by external photo-irradiation. Our results show that amphiphilic gold nanoparticles carrying hydrophilic poly(ethylene glycol) (PEG) and photo-responsive hydrophobic poly(2-nitrobenzyl acrylate) (PNBA) can assemble into plasmonic vesicles with gold nanoparticles embedded in the hydrophobic shell of PNBA, which can be converted into hydrophilic poly(acrylic acid) upon photo exposure. Benefiting from the interparticle plasmonic coupling of gold nanoparticles in close proximity, the plasmonic vesicles assembled from amphiphilic gold nanoparticles exhibit distinctively different optical properties from single nanoparticle units, which offer the opportunity to track the photo-triggered disassembly of the vesicles and the associated cargo release by plasmonic imaging. We have shown the dense layer of PEG grafts on the vesicles not only endow plasmonic vesicles with excellent colloidal stability, but also serve as flexible spacers for bioconjugation of targeting ligands to facilitate the specific recognition of cancer cells. The targeted delivery of model anticancer drug doxorubicin, investigated by dual-modality plasmonic and fluorescence imaging and toxicity studies, clearly demonstrated the potential of photolabile plasmonic vesicles as multi-functional drug carriers.We have developed a new type of photo-responsive plasmonic vesicles that allow for active delivery of anticancer payloads to specific cancer cells and personalized drug release regulated by external photo-irradiation. Our results show that amphiphilic gold nanoparticles carrying hydrophilic poly(ethylene glycol) (PEG) and photo-responsive hydrophobic poly(2-nitrobenzyl acrylate) (PNBA) can assemble into plasmonic vesicles with gold nanoparticles embedded in the hydrophobic shell of PNBA, which can be converted into

  9. Structural Basis of Cooperative Ligand Binding by the Glycine Riboswitch

    Energy Technology Data Exchange (ETDEWEB)

    E Butler; J Wang; Y Xiong; S Strobel

    2011-12-31

    The glycine riboswitch regulates gene expression through the cooperative recognition of its amino acid ligand by a tandem pair of aptamers. A 3.6 {angstrom} crystal structure of the tandem riboswitch from the glycine permease operon of Fusobacterium nucleatum reveals the glycine binding sites and an extensive network of interactions, largely mediated by asymmetric A-minor contacts, that serve to communicate ligand binding status between the aptamers. These interactions provide a structural basis for how the glycine riboswitch cooperatively regulates gene expression.

  10. Templated Formation of Discrete RNA and DNA:RNA Hybrid G-Quadruplexes and Their Interactions with Targeting Ligands.

    Science.gov (United States)

    Bonnat, Laureen; Dejeu, Jérôme; Bonnet, Hugues; Génnaro, Béatrice; Jarjayes, Olivier; Thomas, Fabrice; Lavergne, Thomas; Defrancq, Eric

    2016-02-24

    G-rich RNA and DNA oligonucleotides derived from the human telomeric sequence were assembled onto addressable cyclopeptide platforms through oxime ligations and copper-catalyzed azide-alkyne cycloaddition (CuAAc) reactions. The resulting conjugates were able to fold into highly stable RNA and DNA:RNA hybrid G-quadruplex (G4) architectures as demonstrated by UV, circular dichroism (CD), and NMR spectroscopic analysis. Whereas rationally designed parallel RNA and DNA:RNA hybrid G4 topologies could be obtained, we could not force the formation of an antiparallel RNA G4 structure, thus supporting the idea that this topology is strongly disfavored. The binding affinities of four representative G4 ligands toward the discrete RNA and DNA:RNA hybrid G4 topologies were compared to the one obtained with the corresponding DNA G4 structure. Surface plasmon resonance (SPR) binding analysis suggests that the accessibility to G4 recognition elements is different among the three structures and supports the idea that G4 ligands might be shaped to achieve structure selectivity in a biological context.

  11. Integrated Virtual Assembly Process Planning System

    Institute of Scientific and Technical Information of China (English)

    LIU Jianhua; HOU Weiwei; HOU Weiwei; SHANG Wei; SHANG Wei; NING Ruxin; NING Ruxin

    2009-01-01

    Assembly process planning(APP) for complicated products is a time-consuming and difficult work with conventional method. Virtual assembly process planning(VAPP) provides engineers a new and efficiency way. Previous studies in VAPP are almost isolated and dispersive, and have not established a whole understanding and discussed key realization techniques of VAPP from a systemic and integrated view. The integrated virtual assembly process planning(IVAPP) system is a new virtual reality based engineering application, which offers engineers an efficient, intuitive, immersive and integrated method for assembly process planning in a virtual environment. Based on analysis the information integration requirement of VAPP, the architecture of IVAPP is proposed. Through the integrated structure, IVAPP system can realize information integration and workflow controlling. In order to model the assembly process in IVAPP, a hierarchical assembly task list(HATL) is presented, in which different assembly tasks for assembling different components are organized into a hierarchical list. A process-oriented automatic geometrical constraint recognition algorithm(AGCR) is proposed, so that geometrical constraints between components can be automatically recognized during the process of interactive assembling. At the same time, a progressive hierarchical reasoning(PHR) model is discussed. AGCR and PHR will greatly reduce the interactive workload. A discrete control node model(DCNM) for cable harness assembly planning in IVAPP is detailed. DCNM converts a cable harness into continuous flexed line segments connected by a series of section center points, and designs can realize cable harness planning through controlling those control nodes. Mechanical assemblies (such as transmission case and engine of automobile) are used to illustrate the feasibility of the proposed method and algorithms. The application of IVAPP system reveals advantages over the traditional assembly process planning method

  12. Ficolins and FIBCD1: Soluble and membrane bound pattern recognition molecules with acetyl group selectivity

    DEFF Research Database (Denmark)

    Thomsen, Theresa; Schlosser, Anders; Holmskov, Uffe

    2011-01-01

    as pattern recognition molecules. Ficolins are soluble oligomeric proteins composed of trimeric collagen-like regions linked to fibrinogen-related domains (FReDs) that have the ability to sense molecular patterns on both pathogens and apoptotic cell surfaces and activate the complement system. The ficolins......D-containing molecules, and discusses structural resemblance but also diversity in recognition of acetylated ligands....

  13. Ligand fitting with CCP4

    Science.gov (United States)

    2017-01-01

    Crystal structures of protein–ligand complexes are often used to infer biology and inform structure-based drug discovery. Hence, it is important to build accurate, reliable models of ligands that give confidence in the interpretation of the respective protein–ligand complex. This paper discusses key stages in the ligand-fitting process, including ligand binding-site identification, ligand description and conformer generation, ligand fitting, refinement and subsequent validation. The CCP4 suite contains a number of software tools that facilitate this task: AceDRG for the creation of ligand descriptions and conformers, Lidia and JLigand for two-dimensional and three-dimensional ligand editing and visual analysis, Coot for density interpretation, ligand fitting, analysis and validation, and REFMAC5 for macromolecular refinement. In addition to recent advancements in automatic carbohydrate building in Coot (LO/Carb) and ligand-validation tools (FLEV), the release of the CCP4i2 GUI provides an integrated solution that streamlines the ligand-fitting workflow, seamlessly passing results from one program to the next. The ligand-fitting process is illustrated using instructive practical examples, including problematic cases such as post-translational modifications, highlighting the need for careful analysis and rigorous validation. PMID:28177312

  14. Object reading: text recognition for object recognition

    NARCIS (Netherlands)

    Karaoglu, S.; van Gemert, J.C.; Gevers, T.

    2012-01-01

    We propose to use text recognition to aid in visual object class recognition. To this end we first propose a new algorithm for text detection in natural images. The proposed text detection is based on saliency cues and a context fusion step. The algorithm does not need any parameter tuning and can d

  15. Dump assembly

    Science.gov (United States)

    Goldmann, Louis H.

    1986-01-01

    A dump assembly having a fixed conduit and a rotatable conduit provided with overlapping plates, respectively, at their adjacent ends. The plates are formed with openings, respectively, normally offset from each other to block flow. The other end of the rotatable conduit is provided with means for securing the open end of a filled container thereto. Rotation of the rotatable conduit raises and inverts the container to empty the contents while concurrently aligning the conduit openings to permit flow of material therethrough.

  16. General Assembly

    CERN Multimedia

    Staff Association

    2016-01-01

    5th April, 2016 – Ordinary General Assembly of the Staff Association! In the first semester of each year, the Staff Association (SA) invites its members to attend and participate in the Ordinary General Assembly (OGA). This year the OGA will be held on Tuesday, April 5th 2016 from 11:00 to 12:00 in BE Auditorium, Meyrin (6-2-024). During the Ordinary General Assembly, the activity and financial reports of the SA are presented and submitted for approval to the members. This is the occasion to get a global view on the activities of the SA, its financial management, and an opportunity to express one’s opinion, including taking part in the votes. Other points are listed on the agenda, as proposed by the Staff Council. Who can vote? Only “ordinary” members (MPE) of the SA can vote. Associated members (MPA) of the SA and/or affiliated pensioners have a right to vote on those topics that are of direct interest to them. Who can give his/her opinion? The Ordinary General Asse...

  17. Synthesis and Chiral Recognition of a New Type of Chiral Calix[4]arene Derivatives

    Institute of Scientific and Technical Information of China (English)

    HE,Yong-Bing; LI,Jian-Feng; XIAO,Yuan-Jing; WEI,Lan-Hua; WU,Xiao-Jun; MENG,Ling-Zhi

    2003-01-01

    Two new chiral calix[4] arenes bearing chiral pendants, which were from by-product of the antibiotic industry, were synthesized and characterized by 1H NMR, MS-FAB and elemental analysis. Studies of 1H NMR of the two calix [4] arene derivatives indicate that they exist in cone conformation in solution. Results of chiral recognition of the two chiral ligands 2a and 2b towards the tartaric acid derivative 3 show that ligand 2a exhibited good chiral recognition abilities compared to ligand 2b.

  18. Quantitative Analysis of Multivalent Ligand Presentation on Gold Glyconanoparticles and Their Effects on Protein Binding

    Science.gov (United States)

    Wang, Xin; Ramström, Olof; Yan, Mingdi

    2010-03-01

    Bio-functionalized nanomaterials, which combine functions of biological ligands and unique properties of nano-sized building blocks, have exhibited increased potential applications in biosensing, therapeutics, and diagnostics. Glyconanoparitcles carrying a monolayer of carbohydrate ligands on nanoparticles provide an excellent platform for sensitive protein recognitions. Using Au nanoparticles as the scaffold, multivalent interactions between glycan ligands and proteins have been demonstrated. However, quantitative analysis especially the binding affinity of the resulting glyconanoparticles is challenging to determine. Here we present a new characterization technique, based on fluorescent competition binding assays, for measuring dissociation constants for glyconanoparticles-protein interactions. Au nanoparticles coupled with a series of un-derivatized carbohydrates were prepared by a photocoupling chemistry. Dramatic binding affinity enhancement was observed due to the high ligand density on nanoparticles, which was highly relevant to ligand display, controlled by the linker type, chain length, ligand size and density.

  19. Molecular Component Structures Mediated Formation of Self-assemblies

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Molecular recognition directed self-assemblies from complementary molecular components, melamine and barbituric acid derivatives were studied by means of NMR, fluorescence, and TEM. It was found that both the process of the self-assembly and the morphologies of the result ed self-assemblies could be mediated by modifying the structures of the molecular components used. The effect of the structures of the molecular components on the formation of the self-as semblies was discussed in terms of intermolecular interactions.

  20. Riboswitch structure in the ligand-free state.

    Science.gov (United States)

    Liberman, Joseph A; Wedekind, Joseph E

    2012-01-01

    Molecular investigations of riboswitches bound to small-molecule effectors have produced a wealth of information on how these molecules achieve high affinity and specificity for a target ligand. X-ray crystal structures have been determined for the ligand-free state for representatives of the preQ₁-I, S-adenosylmethionine I, lysine, and glycine aptamer classes. These structures in conjunction with complimentary techniques, such as in-line probing, NMR spectroscopy, Förster resonance energy transfer, small-angle scattering, and computational simulations, have demonstrated that riboswitches adopt multiple conformations in the absence of ligand. Despite a number of investigations that support ligand-dependent folding, mounting evidence suggests that free-state riboswitches interact with their effectors in the sub-populations of largely prefolded states as embodied by the principle of conformational selection, which has been documented extensively for protein-mediated ligand interactions. Fundamental riboswitch investigations of the bound and free states have advanced our understanding of RNA folding, ligand recognition, and how these factors culminate in communication between an aptamer and its expression platform. An understanding of these topics is essential to comprehend riboswitch gene regulation at the molecular level, which has already provided a basis to understand the mechanism of action of natural antimicrobials.

  1. LigandRNA: computational predictor of RNA-ligand interactions.

    Science.gov (United States)

    Philips, Anna; Milanowska, Kaja; Lach, Grzegorz; Bujnicki, Janusz M

    2013-12-01

    RNA molecules have recently become attractive as potential drug targets due to the increased awareness of their importance in key biological processes. The increase of the number of experimentally determined RNA 3D structures enabled structure-based searches for small molecules that can specifically bind to defined sites in RNA molecules, thereby blocking or otherwise modulating their function. However, as of yet, computational methods for structure-based docking of small molecule ligands to RNA molecules are not as well established as analogous methods for protein-ligand docking. This motivated us to create LigandRNA, a scoring function for the prediction of RNA-small molecule interactions. Our method employs a grid-based algorithm and a knowledge-based potential derived from ligand-binding sites in the experimentally solved RNA-ligand complexes. As an input, LigandRNA takes an RNA receptor file and a file with ligand poses. As an output, it returns a ranking of the poses according to their score. The predictive power of LigandRNA favorably compares to five other publicly available methods. We found that the combination of LigandRNA and Dock6 into a "meta-predictor" leads to further improvement in the identification of near-native ligand poses. The LigandRNA program is available free of charge as a web server at http://ligandrna.genesilico.pl.

  2. Vesicular Stomatitis Virus Infection Promotes Immune Evasion by Preventing NKG2D-Ligand Surface Expression

    DEFF Research Database (Denmark)

    Jensen, Helle; Andresen, Lars; Nielsen, Jens;

    2011-01-01

    Vesicular stomatitis virus (VSV) has recently gained attention for its oncolytic ability in cancer treatment. Initially, we hypothesized that VSV infection could increase immune recognition of cancer cells through induction of the immune stimulatory NKG2D-ligands. Here we show that VSV infection...... mutant strain, VSV DM51, which possess a defective M protein, prevented MICA surface expression similarly to wild-type VSV. The VSV mediated down modulation of NKG2D-ligand expression did not involve apoptosis. Constitutive expression of MICA bypassed the escape mechanism, suggesting that VSV affect NKG2......D-ligand expression at an early post-transcriptional level. Our results show that VSV possess an escape mechanism, which could affect the immune recognition of VSV infected cancer cells. This may also have implications for immune recognition of cancer cells after combined treatment with VSV...

  3. Natural Cytotoxicity Receptors: Pattern Recognition and Involvement of Carbohydrates

    Directory of Open Access Journals (Sweden)

    Angel Porgador

    2005-01-01

    Full Text Available Natural cytotoxicity receptors (NCRs, expressed by natural killer (NK cells, trigger NK lysis of tumor and virus-infected cells on interaction with cell-surface ligands of these target cells. We have determined that viral hemagglutinins expressed on the surface of virus-infected cells are involved in the recognition by the NCRs, NKp44 and NKp46. Recognition of tumor cells by the NCRs NKp30 and NKp46 involves heparan sulfate epitopes expressed on the tumor cell membrane. Our studies provide new evidence for the identity of the ligands for NCRs and indicate that a broader definition should be applied to pathological patterns recognized by innate immune receptors. Since nonmicrobial endogenous carbohydrate structures contribute significantly to this recognition, there is an imperative need to develop appropriate tools for the facile sequencing of carbohydrate moieties.

  4. Ligand-Receptor Interactions

    CERN Document Server

    Bongrand, Pierre

    2008-01-01

    The formation and dissociation of specific noncovalent interactions between a variety of macromolecules play a crucial role in the function of biological systems. During the last few years, three main lines of research led to a dramatic improvement of our understanding of these important phenomena. First, combination of genetic engineering and X ray cristallography made available a simultaneous knowledg of the precise structure and affinity of series or related ligand-receptor systems differing by a few well-defined atoms. Second, improvement of computer power and simulation techniques allowed extended exploration of the interaction of realistic macromolecules. Third, simultaneous development of a variety of techniques based on atomic force microscopy, hydrodynamic flow, biomembrane probes, optical tweezers, magnetic fields or flexible transducers yielded direct experimental information of the behavior of single ligand receptor bonds. At the same time, investigation of well defined cellular models raised the ...

  5. Assembling consumption

    DEFF Research Database (Denmark)

    Assembling Consumption marks a definitive step in the institutionalisation of qualitative business research. By gathering leading scholars and educators who study markets, marketing and consumption through the lenses of philosophy, sociology and anthropology, this book clarifies and applies...... the investigative tools offered by assemblage theory, actor-network theory and non-representational theory. Clear theoretical explanation and methodological innovation, alongside empirical applications of these emerging frameworks will offer readers new and refreshing perspectives on consumer culture and market...... societies. This is an essential reading for both seasoned scholars and advanced students of markets, economies and social forms of consumption....

  6. Gold nanoparticles having dipicolinic acid imprinted nanoshell for Bacillus cereus spores recognition

    Energy Technology Data Exchange (ETDEWEB)

    Gueltekin, Aytac [Department of Chemistry, Trakya University, Edirne (Turkey); Ersoez, Arzu; Huer, Deniz [Department of Chemistry, Anadolu University, Eskisehir (Turkey); Sarioezlue, Nalan Yilmaz [Department of Biology, Anadolu University, Eskisehir (Turkey); Denizli, Adil [Department of Chemistry, Hacettepe University, Ankara (Turkey); Say, Ridvan, E-mail: rsay@anadolu.edu.tr [Department of Chemistry, Anadolu University, Eskisehir (Turkey); BIBAM (Plant, Drug and Scientific Research Center) Anadolu University (Turkey)

    2009-10-15

    Taking into account the recognition element for sensors linked to molecular imprinted polymers (MIPs), a proliferation of interest has been witnessed by those who are interested in this subject. Indeed, MIP nanoparticles are theme which recently has come to light in the literature. In this study, we have proposed a novel thiol ligand-capping method with polymerizable methacryloylamidocysteine (MAC) attached to gold nanoparticles, reminiscent of a self-assembled monolayer. Furthermore, a surface shell by synthetic host polymers based on molecular imprinting method for recognition has been reconstructed. In this method, methacryloyl iminodiacetic acid-chrome (MAIDA-Cr(III)) has been used as a new metal-chelating monomer via metal coordination-chelation interactions and dipicolinic acid (DPA) which is the main participant of Bacillus cereus spores has been used as a template. Nanoshell sensors with templates produce a cavity that is selective for DPA. The DPA can simultaneously chelate to Cr(III) metal ion and fit into the shape-selective cavity. Thus, the interaction between Cr(III) ion and free coordination spheres has an effect on the binding ability of the gold nanoparticles nanosensor. The interactions between DPA and MIP particles were studied observing fluorescence measurements. DPA addition caused significant decreases in fluorescence intensity because they induced photoluminescence emission from Au nanoparticles through the specific binding to the recognition sites of the crosslinked nanoshell polymer matrix. The binding affinity of the DPA imprinted nanoparticles has been explored by using the Langmuir and Scatchard methods and the analysis of the quenching results has been performed in terms of the Stern-Volmer equation.

  7. Recognition and Toleration

    DEFF Research Database (Denmark)

    Lægaard, Sune

    2010-01-01

    Recognition and toleration are ways of relating to the diversity characteristic of multicultural societies. The article concerns the possible meanings of toleration and recognition, and the conflict that is often claimed to exist between these two approaches to diversity. Different forms...... or interpretations of recognition and toleration are considered, confusing and problematic uses of the terms are noted, and the compatibility of toleration and recognition is discussed. The article argues that there is a range of legitimate and importantly different conceptions of both toleration and recognition...

  8. Indirect readout in protein-peptide recognition: a different story from classical biomolecular recognition.

    Science.gov (United States)

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

    2014-07-28

    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.

  9. Structural Analysis Uncovers Lipid-Binding Properties of Notch Ligands

    Directory of Open Access Journals (Sweden)

    Chandramouli R. Chillakuri

    2013-11-01

    Full Text Available The Notch pathway is a core cell-cell signaling system in metazoan organisms with key roles in cell-fate determination, stem cell maintenance, immune system activation, and angiogenesis. Signals are initiated by extracellular interactions of the Notch receptor with Delta/Serrate/Lag-2 (DSL ligands, whose structure is highly conserved throughout evolution. To date, no structure or activity has been associated with the extreme N termini of the ligands, even though numerous mutations in this region of Jagged-1 ligand lead to human disease. Here, we demonstrate that the N terminus of human Jagged-1 is a C2 phospholipid recognition domain that binds phospholipid bilayers in a calcium-dependent fashion. Furthermore, we show that this activity is shared by a member of the other class of Notch ligands, human Delta-like-1, and the evolutionary distant Drosophila Serrate. Targeted mutagenesis of Jagged-1 C2 domain residues implicated in calcium-dependent phospholipid binding leaves Notch interactions intact but can reduce Notch activation. These results reveal an important and previously unsuspected role for phospholipid recognition in control of this key signaling system.

  10. The use of a versatile o-vanilloyl hydrazone ligand to prepare SMM-like Dy3 molecular cluster pair.

    Science.gov (United States)

    Xue, Shufang; Zhao, Lang; Guo, Yun-Nan; Zhang, Peng; Tang, Jinkui

    2012-09-14

    A novel lanthanide molecular cluster pair (MCP), displaying single molecule magnet behaviour, was assembled using the novel o-vanilloyl hydrazone ligand, versatile in terms of denticity, tautomerism and the rotatable C-C bond.

  11. 2D and 3D Supramolecular Assemblies from Bis(dipyridylamine) Ligands: Syntheses and Crystal Structures%双(二吡啶胺)配体的二维和三维超分子配位聚合物的合成与晶体结构

    Institute of Scientific and Technical Information of China (English)

    丁彩霞; 曾凡花; 汪成; 倪佳; 伍锡荣; 解永树

    2011-01-01

    从含4,4′-二吡啶胺结构单元的双(二吡啶胺)桥联配体出发,采用溶剂热法合成了2个结构新颖的配位聚合物:[CdL1 Br2]n·7.5nH2O[L1=N,N,N′,N′-四(4-吡啶)-1,4-苯二胺](1)和[Cu2L2(μ1.1,3-SCN)2]n·nMeOH[L2=N,N-二 (2-吡啶)-N′,N′-二(4-吡啶)-1,4-苯二胺](2),对它们进行了元素分析、红外光谱、1H NMR和紫外-可见光谱等表征,并用X射线单晶衍射测定了其晶体结构.单晶测试结果表明,配合物1中配体L1的4个吡啶N原子均参与配位,桥联了4个Cd原子,每个Cd原子与4个吡啶N原子和2个溴配位,形成六配位的八面体构型.通过这些配位作用,最终形成包含Kagome结构的三维超分子网络.配合物2是由一维柱状[Cu(SCN)]n链通过L2桥联生成的二维结构.有趣的是,L2中具有螯合能力的2,2′-二吡啶胺单元并未参与配位,只有4,4′-二吡啶胺单元中的2个吡啶N原子分别与1个Cu(Ⅰ)配位,连接了相邻2条平行的{Cu(SCN)}n链,形成二维结构.%Starting from two bis(dipyridylamine) ligands containing 4,4'-dipyridylamine moieties, two novel coordination polymers, [ CdL1 Br2 ]n ? 7. 5nH2O [ L1 = N, N, N', W-tetrakis (4-pyridyl) -1,4-phenylenedia-mine](l) and [Cu2L2(μ1,13-SCN)2]n ? rcMeOH[L2 = N,N-di(2-pyridyl)-N',N'-di(4-pyridyl-l ,4-pheny-lenediamine ] (2) , were prepared under solvothermal conditions. Their structures were characterized by elemental analyses, IR spectrum and X-ray single-crystal diffraction measurements. In complex 1, L1 utilizes all its pyridyl nitrogens to coordinate with four Cd( II ) centers to afford a three-dimensional(3D) supramolecular assembly containing Kagome structures. Complex 2 has a 2D sheet structure composed of [ CuSCN]∞ columns and bridging L2 ligands with SCN- coordinated in a rare μ1,1,3-bridging mode. It is noteworthy that the 2,2'-dipyridylamine unit of L2 is unexpectedly left noncoordinated.

  12. General Assembly

    CERN Multimedia

    Staff Association

    2015-01-01

    Mardi 5 mai à 11 h 00 Salle 13-2-005 Conformément aux statuts de l’Association du personnel, une Assemblée générale ordinaire est organisée une fois par année (article IV.2.1). Projet d’ordre du jour : 1- Adoption de l’ordre du jour. 2- Approbation du procès-verbal de l’Assemblée générale ordinaire du 22 mai 2014. 3- Présentation et approbation du rapport d’activités 2014. 4- Présentation et approbation du rapport financier 2014. 5- Présentation et approbation du rapport des vérificateurs aux comptes pour 2014. 6- Programme 2015. 7- Présentation et approbation du projet de budget 2015 et taux de cotisation pour 2015. 8- Pas de modifications aux Statuts de l'Association du personnel proposée. 9- Élections des membres de la Commission é...

  13. General Assembly

    CERN Multimedia

    Staff Association

    2016-01-01

    Mardi 5 avril à 11 h 00 BE Auditorium Meyrin (6-2-024) Conformément aux statuts de l’Association du personnel, une Assemblée générale ordinaire est organisée une fois par année (article IV.2.1). Projet d’ordre du jour : Adoption de l’ordre du jour. Approbation du procès-verbal de l’Assemblée générale ordinaire du 5 mai 2015. Présentation et approbation du rapport d’activités 2015. Présentation et approbation du rapport financier 2015. Présentation et approbation du rapport des vérificateurs aux comptes pour 2015. Programme de travail 2016. Présentation et approbation du projet de budget 2016 Approbation du taux de cotisation pour 2017. Modifications aux Statuts de l'Association du personnel proposée. Élections des membres de la Commissio...

  14. General assembly

    CERN Multimedia

    Staff Association

    2015-01-01

    Mardi 5 mai à 11 h 00 Salle 13-2-005 Conformément aux statuts de l’Association du personnel, une Assemblée générale ordinaire est organisée une fois par année (article IV.2.1). Projet d’ordre du jour : Adoption de l’ordre du jour. Approbation du procès-verbal de l’Assemblée générale ordinaire du 22 mai 2014. Présentation et approbation du rapport d’activités 2014. Présentation et approbation du rapport financier 2014. Présentation et approbation du rapport des vérificateurs aux comptes pour 2014. Programme 2015. Présentation et approbation du projet de budget 2015 et taux de cotisation pour 2015. Pas de modifications aux Statuts de l'Association du personnel proposée. Élections des membres de la Commission électorale. &am...

  15. Supramolecular Lego assembly towards three-dimensional multi-responsive hydrogels.

    Science.gov (United States)

    Ma, Chunxin; Li, Tiefeng; Zhao, Qian; Yang, Xuxu; Wu, Jingjun; Luo, Yingwu; Xie, Tao

    2014-08-27

    Inspired by the assembly of Lego toys, hydrogel building blocks with heterogeneous responsiveness are assembled utilizing macroscopic supramolecular recognition as the adhesion force. The Lego hydrogel provides 3D transformation upon pH variation. After disassembly of the building blocks by changing the oxidation state, they can be re-assembled into a completely new shape.

  16. Conformational diversity of flexible ligand in metal-organic frameworks controlled by size-matching mixed ligands

    Energy Technology Data Exchange (ETDEWEB)

    Hua, Xiu-Ni; Qin, Lan; Yan, Xiao-Zhi; Yu, Lei; Xie, Yi-Xin; Han, Lei, E-mail: hanlei@nbu.edu.cn

    2015-12-15

    Hydrothermal reactions of N-auxiliary flexible exo-bidentate ligand 1,3-bis(4-pyridyl)propane (bpp) and carboxylates ligands naphthalene-2,6-dicarboxylic acid (2,6-H{sub 2}ndc) or 4,4′-(hydroxymethylene)dibenzoic acid (H{sub 2}hmdb), in the presence of cadmium(II) salts have given rise to two novel metal-organic frameworks based on flexible ligands (FL-MOFs), namely, [Cd{sub 2}(2,6-ndc){sub 2}(bpp)(DMF)]·2DMF (1) and [Cd{sub 3}(hmdb){sub 3}(bpp)]·2DMF·2EtOH (2) (DMF=N,N-Dimethylformamide). Single-crystal X-ray diffraction analyses revealed that compound 1 exhibits a three-dimensional self-penetrating 6-connected framework based on dinuclear cluster second building unit. Compound 2 displays an infinite three-dimensional ‘Lucky Clover’ shape (2,10)-connected network based on the trinuclear cluster and V-shaped organic linkers. The flexible bpp ligand displays different conformations in 1 and 2, which are successfully controlled by size-matching mixed ligands during the self-assembly process. - Graphical abstract: Compound 1 exhibits a 3D self-penetrating 6-connected framework based on dinuclear cluster, and 2 displays an infinite 3D ‘Lucky Clover’ shape (2,10)-connected network based on the trinuclear cluster. The flexible 1,3-bis(4-pyridyl)propane ligand displays different conformations in 1 and 2, which successfully controlled by size-matching mixed ligands during the self-assembly process.

  17. Gold Nanoparticle Monolayers from Sequential Interfacial Ligand Exchange and Migration in a Three-Phase System

    Science.gov (United States)

    Yang, Guang; Hallinan, Daniel T.

    2016-10-01

    Using a three-phase system, centimeter-scale monolayer gold nanoparticle (Au NP) films have been prepared that have long-range order and hydrophobic ligands. The system contains an interface between an aqueous phase containing Au NPs and an oil phase containing one of various types of amine ligands, and a water/air interface. As the Au NPs diffuse to the water/oil interface, ligand exchange takes place which temporarily traps them at the water/oil interface. The ligand-exchanged particles then spontaneously migrate to the air/water interface, where they self-assemble, forming a monolayer under certain conditions. The spontaneous formation of the NP film at the air/water interface was due to the minimization of the system Helmholtz free energy. However, the extent of surface functionalization was dictated by kinetics. This decouples interfacial ligand exchange from interfacial self-assembly, while maintaining the simplicity of a single system. The interparticle center-to-center distance was dictated by the amine ligand length. The Au NP monolayers exhibit tunable surface plasma resonance and excellent spatial homogeneity, which is useful for surface-enhanced Raman scattering. The “air/water/oil” self-assembly method developed here not only benefits the fundamental understanding of NP ligand conformations, but is also applicable to the manufacture of plasmonic nanoparticle devices with precisely designed optical properties.

  18. Gold Nanoparticle Monolayers from Sequential Interfacial Ligand Exchange and Migration in a Three-Phase System

    Science.gov (United States)

    Yang, Guang; Hallinan, Daniel T.

    2016-01-01

    Using a three-phase system, centimeter-scale monolayer gold nanoparticle (Au NP) films have been prepared that have long-range order and hydrophobic ligands. The system contains an interface between an aqueous phase containing Au NPs and an oil phase containing one of various types of amine ligands, and a water/air interface. As the Au NPs diffuse to the water/oil interface, ligand exchange takes place which temporarily traps them at the water/oil interface. The ligand-exchanged particles then spontaneously migrate to the air/water interface, where they self-assemble, forming a monolayer under certain conditions. The spontaneous formation of the NP film at the air/water interface was due to the minimization of the system Helmholtz free energy. However, the extent of surface functionalization was dictated by kinetics. This decouples interfacial ligand exchange from interfacial self-assembly, while maintaining the simplicity of a single system. The interparticle center-to-center distance was dictated by the amine ligand length. The Au NP monolayers exhibit tunable surface plasma resonance and excellent spatial homogeneity, which is useful for surface-enhanced Raman scattering. The “air/water/oil” self-assembly method developed here not only benefits the fundamental understanding of NP ligand conformations, but is also applicable to the manufacture of plasmonic nanoparticle devices with precisely designed optical properties. PMID:27762394

  19. Bexarotene ligand pharmaceuticals.

    Science.gov (United States)

    Hurst, R E

    2000-12-01

    Bexarotene (LGD-1069), from Ligand, was the first retinoid X receptor (RXR)-selective, antitumor retinoid to enter clinical trials. The company launched the drug for the treatment of cutaneous T-cell lymphoma (CTCL), as Targretin capsules, in the US in January 2000 [359023]. The company filed an NDA for Targretin capsules in June 1999, and for topical gel in December 1999 [329011], [349982] specifically for once-daily oral administration for the treatment of patients with early-stage CTCL who have not tolerated other therapies, patients with refractory or persistent early stage CTCL and patients with refractory advanced stage CTCL. The FDA approved Targretin capsules at the end of December 1999 for once-daily oral treatment of all stages of CTCL in patients refractory to at least one prior systemic therapy, at an initial dose of 300 mg/m2/day. After an NDA was submitted in December 1999 for Targretin gel, the drug received Priority Review status for use as a treatment of cutaneous lesions in patients with stage IA, IB or IIA CTCL [354836]. The FDA issued an approvable letter in June 2000, and granted marketing clearance for CTCL in the same month [370687], [372768], [372769], [373279]. Ligand had received Orphan Drug designation for this indication [329011]. At the request of the FDA, Ligand agreed to carry out certain post-approval phase IV and pharmacokinetic studies [351604]. The company filed an MAA with the EMEA for Targretin Capsules to treat lymphoma in November 1999 [348944]. The NDA for Targretin gel is based on a multicenter phase III trial that was conducted in the US, Canada, Europe and Australia involving 50 patients and a multicenter phase I/II clinical program involving 67 patients. Targretin gel was evaluated for the treatment of patients with early stage CTCL (IA-IIA) who were refractory to, intolerant to, or reached a response plateau for at least 6 months on at least two prior therapies. Efficacy results exceeded the protocol-defined response

  20. Tunable longitudinal modes in extended silver nanoparticle assemblies

    Directory of Open Access Journals (Sweden)

    Serene S. Bayram

    2016-08-01

    Full Text Available Nanostructured materials with tunable properties are of great interest for a wide range of applications. The self-assembly of simple nanoparticle building blocks could provide an inexpensive means to achieve this goal. Here, we generate extended anisotropic silver nanoparticle assemblies in solution using controlled amounts of one of three inexpensive, widely available, and environmentally benign short ditopic ligands: cysteamine, dithiothreitol and cysteine in aqueous solution. The self-assembly of our extended structures is enforced by hydrogen bonding. Varying the ligand concentration modulates the extent and density of these unprecedented anisotropic structures. Our results show a correlation between the chain nature of the assembly and the generation of spectral anisotropy. Deuterating the ligand further enhances the anisotropic signal by triggering more compact aggregates and reveals the importance of solvent interactions in assembly size and morphology. Spectral and morphological evolutions of the AgNPs assemblies are followed via UV–visible spectroscopy and transmission electron microscopy (TEM. Spectroscopic measurements are compared to calculations of the absorption spectra of randomly assembled silver chains and aggregates based on the discrete dipole approximation. The models support the experimental findings and reveal the importance of aggregate size and shape as well as particle polarizability in the plasmon coupling between nanoparticles.

  1. Pattern recognition and massively distributed computing.

    Science.gov (United States)

    Davies, E Keith; Glick, Meir; Harrison, Karl N; Richards, W Graham

    2002-12-01

    A feature of Peter Kollman's research was his exploitation of the latest computational techniques to devise novel applications of the free energy perturbation method. He would certainly have seized upon the opportunities offered by massively distributed computing. Here we describe the use of over a million personal computers to perform virtual screening of 3.5 billion druglike molecules against protein targets by pharmacophore pattern matching, together with other applications of pattern recognition such as docking ligands without any a priori knowledge about the binding site location.

  2. A conserved juxtacrine signal regulates synaptic partner recognition in Caenorhabditis elegans

    Directory of Open Access Journals (Sweden)

    Mock Natalyn

    2011-06-01

    Full Text Available Abstract Background An essential stage of neural development involves the assembly of neural circuits via formation of inter-neuronal connections. Early steps in neural circuit formation, including cell migration, axon guidance, and the localization of synaptic components, are well described. However, upon reaching their target region, most neurites still contact many potential partners. In order to assemble functional circuits, it is critical that within this group of cells, neurons identify and form connections only with their appropriate partners, a process we call synaptic partner recognition (SPR. To understand how SPR is mediated, we previously developed a genetically encoded fluorescent trans-synaptic marker called NLG-1 GRASP, which labels synaptic contacts between individual neurons of interest in dense cellular environments in the genetic model organism Caenorhabditis elegans. Results Here, we describe the first use of NLG-1 GRASP technology, to identify SPR genes that function in this critical process. The NLG-1 GRASP system allows us to assess synaptogenesis between PHB sensory neurons and AVA interneurons instantly in live animals, making genetic analysis feasible. Additionally, we employ a behavioral assay to specifically test PHB sensory circuit function. Utilizing this approach, we reveal a new role for the secreted UNC-6/Netrin ligand and its transmembrane receptor UNC-40/Deleted in colorectal cancer (DCC in SPR. Synapses between PHB and AVA are severely reduced in unc-6 and unc-40 animals despite normal axon guidance and subcellular localization of synaptic components. Additionally, behavioral defects indicate a complete disruption of PHB circuit function in unc-40 mutants. Our data indicate that UNC-40 and UNC-6 function in PHB and AVA, respectively, to specify SPR. Strikingly, overexpression of UNC-6 in postsynaptic neurons is sufficient to promote increased PHB-AVA synaptogenesis and to potentiate the behavioral response

  3. Multimodal eye recognition

    Science.gov (United States)

    Zhou, Zhi; Du, Yingzi; Thomas, N. L.; Delp, Edward J., III

    2010-04-01

    Multimodal biometrics use more than one means of biometric identification to achieve higher recognition accuracy, since sometimes a unimodal biometric is not good enough used to do identification and classification. In this paper, we proposed a multimodal eye recognition system, which can obtain both iris and sclera patterns from one color eye image. Gabor filter and 1-D Log-Gabor filter algorithms have been applied as the iris recognition algorithms. In sclera recognition, we introduced automatic sclera segmentation, sclera pattern enhancement, sclera pattern template generation, and sclera pattern matching. We applied kernelbased matching score fusion to improve the performance of the eye recognition system. The experimental results show that the proposed eye recognition method can achieve better performance compared to unimodal biometric identification, and the accuracy of our proposed kernel-based matching score fusion method is higher than two classic linear matching score fusion methods: Principal Component Analysis (PCA) and Linear Discriminant Analysis (LDA).

  4. Pattern recognition & machine learning

    CERN Document Server

    Anzai, Y

    1992-01-01

    This is the first text to provide a unified and self-contained introduction to visual pattern recognition and machine learning. It is useful as a general introduction to artifical intelligence and knowledge engineering, and no previous knowledge of pattern recognition or machine learning is necessary. Basic for various pattern recognition and machine learning methods. Translated from Japanese, the book also features chapter exercises, keywords, and summaries.

  5. Solution assembly of cytokine receptor ectodomain complexes

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Zining; Ciardelli, T.L. [Dartmouth Medical School, Hanover, NH (United States). Dept. of Pharmacology and Toxicology; Johnson, K.W. [Chiron Corp., Emeryville, CA (United States)] [and others

    1995-09-01

    For the majority of single transmembrane-spanning cell surface receptors, signal transmission across the lipid bilayer barrier involves several discrete components of molecular recognition. The interaction between ligand and the extracellular segment of its cognate receptor (ectodomain) initiates either homomeric or heteromeric association of receptor subunits. Specific recognition among these subunits may then occur between ectodomain regions, within the membrane by interhelical contact or inside the cell between cytoplasmic domains. Any or all of these interactions may contribute to the stability of the signaling complex. It is the characteristics of ligand binding by the ectodomains of these receptors that controls the heteromeric or homomeric nature and the stoichiometry of the complex. Cytokines and their receptors belong to a growing family of macromolecular systems that exhibit these functional features and share many structural similarities as well. Interleukin-2 is a multifunctional cytokine that represents, perhaps, the most complex example to date of ligand recognition among the hematopoietin receptor family. It is the cooperative binding of IL-2 by all three proteins on the surface of activated T-lymphocytes, however, that ultimately results in crosslinking of the {beta}- and {gamma}-subunits and signaling via association of their cytoplasmic domains. Although the high-affinity IL-2R functions as a heterotrimer, heterodimers of the receptor subunits are also physiologically important. The {alpha}/{beta} heterodimer or {open_quotes}pseudo-high affinity{close_quotes} receptor captures IL-2 as a preformed cell surface complex while the {beta}/{gamma} intermediate affinity site exists, in the absence of the {alpha} subunit, on the majority of natural killer cells. We have begun to study stable complexes of cytokine receptor ectodomains of defined composition and that mimic the ligand binding characteristics of the equivalent cell surface receptor sites.

  6. Programmed Nanomaterial Assemblies in Large Scales: Applications of Synthetic and Genetically- Engineered Peptides to Bridge Nano-Assemblies and Macro-Assemblies

    Energy Technology Data Exchange (ETDEWEB)

    Matsui, Hiroshi

    2014-09-09

    Work is reported in these areas: Large-scale & reconfigurable 3D structures of precise nanoparticle assemblies in self-assembled collagen peptide grids; Binary QD-Au NP 3D superlattices assembled with collagen-like peptides and energy transfer between QD and Au NP in 3D peptide frameworks; Catalytic peptides discovered by new hydrogel-based combinatorial phage display approach and their enzyme-mimicking 2D assembly; New autonomous motors of metal-organic frameworks (MOFs) powered by reorganization of self-assembled peptides at interfaces; Biomimetic assembly of proteins into microcapsules on oil-in-water droplets with structural reinforcement via biomolecular recognition-based cross-linking of surface peptides; and Biomimetic fabrication of strong freestanding genetically-engineered collagen peptide films reinforced by quantum dot joints. We gained the broad knowledge about biomimetic material assembly from nanoscale to microscale ranges by coassembling peptides and NPs via biomolecular recognition. We discovered: Genetically-engineered collagen-like peptides can be self-assembled with Au NPs to generate 3D superlattices in large volumes (> μm{sup 3}); The assembly of the 3D peptide-Au NP superstructures is dynamic and the interparticle distance changes with assembly time as the reconfiguration of structure is triggered by pH change; QDs/NPs can be assembled with the peptide frameworks to generate 3D superlattices and these QDs/NPs can be electronically coupled for the efficient energy transfer; The controlled assembly of catalytic peptides mimicking the catalytic pocket of enzymes can catalyze chemical reactions with high selectivity; and, For the bacteria-mimicking swimmer fabrication, peptide-MOF superlattices can power translational and propellant motions by the reconfiguration of peptide assembly at the MOF-liquid interface.

  7. RESEARCH OF GUIDANCE TECHNOLOGY FOR ASSEMBLY MODELING IN VIRTUAL ENVIRONMENT

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Technology of movement and knowledge guidance in virtual assembly is presented. The designer can move the mechanical part precisely under the movement guidance. The movement guidance is implemented based on constraint recognition and assembly degree of freedom analysis. A multi-hierarchy knowledge base is built to represent the assembly knowledge and information. The virtual assembly system judges the requirement of the designer based on the context of design task and searches for the useful knowledge and information, which can be provided to the designer in a natural way.

  8. Synthesis and enzymatic cleavage of dual-ligand quantum dots

    Energy Technology Data Exchange (ETDEWEB)

    Sewell, Sarah L. [Department of Biomedical Engineering, Vanderbilt University, Nashville, TN (United States); Giorgio, Todd D., E-mail: todd.d.giorgio@vanderbilt.edu [Department of Biomedical Engineering, Vanderbilt University, Nashville, TN (United States); Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN (United States)

    2009-05-05

    Site directed therapy promises to minimize treatment-limiting systemic effects associated with cytotoxic agents that have no specificity for pathologic tissues. One general strategy is to target cell surface receptors uniquely presented on particular tissues. Highly specific in vivo targeting of an emerging neoplasm through a single molecular recognition mechanism has not generally been successful. Nonspecific binding and specific binding to non-target cells compromise the therapeutic index of small molecule, ubiquitous cancer targeting ligands. In this work, we have designed and fabricated a nanoparticle (NP) construct that could potentially overcome the current limitations of targeted in vivo delivery. Quantum dots (QDs) were functionalized with a poly(ethylene glycol) (PEG) modified to enable specific cleavage by matrix metalloprotease-7 (MMP-7). The QDs were further functionalized with folic acid, a ligand for a cell surface receptor that is overexpressed in many tumors, but also expressed in some normal tissues. The nanomolecular construct is designed so that the PEG initially conceals the folate ligand and construct binding to cells is inhibited. MMP-7 activated peptide cleavage and subsequent unmasking of the folate ligand occurs only near tumor tissue, resulting in a proximity activated (PA) targeting system. QDs functionalized with both the MMP-7 cleavable substrate and folic acid were successfully synthesized and characterized. The proteolytic capability of the dual ligand QD construct was quantitatively assessed by fluorometric analysis and compared to a QD construct functionalized with only the PA ligand. The dual ligand PA nanoparticles studied here exhibit significant susceptibility to cleavage by MMP-7 at physiologically relevant conditions. The capacity to autonomously convert a biopassivated nanostructure to a tissue-specific targeted delivery agent in vivo represents a paradigm change for site-directed therapies.

  9. Comparison of associative recognition versus source recognition.

    Science.gov (United States)

    Park, Heekyeong; Abellanoza, Cheryl; Schaeffer, James D

    2014-10-03

    The importance of the medial temporal lobe (MTL) for memory of arbitrary associations has been well established. However, the contribution of the MTL in concurrent retrieval of different classes of associations remains unclear. The present fMRI study investigated neural correlates of concurrent retrieval of associative and source memories. Participants studied a list of object pairs with two study tasks and judged the status and context of the pair during test. Associative retrieval was supported by neural activity in bilateral prefrontal cortex and left ventral occipito-temporal cortex, while source recognition was linked to activity in the right caudate. Both the hippocampus and MTL cortex showed retrieval activity for associative and source memory. Importantly, greater brain activity for successful associative recognition accompanied with successful source recognition was evident in left perirhinal and anterior hippocampal regions. These results indicate that the MTL is critical in the retrieval of different classes of associations.

  10. Macrocyclic Assembly: A Dive into the Pecking Order and Applied Aspects of Multitalented Metallomacrocycles

    Directory of Open Access Journals (Sweden)

    Ashu Chaudhary

    2014-01-01

    Full Text Available To aid in knowledge of macrocyclic complexes and biomedical scientists, we are presenting here a review article with compilation of work done so far along in relation to macrocyclic ligands and their metal complexes. The metal ion chemistry of macrocyclic ligands has now become a major subdivision of coordination chemistry. This overview focuses on developments in design, synthesis, and self-assembly of metal-based architectures and ligands related to macrocyclic chemistry.

  11. Multimodal recognition of emotions

    NARCIS (Netherlands)

    Datcu, D.

    2009-01-01

    This thesis proposes algorithms and techniques to be used for automatic recognition of six prototypic emotion categories by computer programs, based on the recognition of facial expressions and emotion patterns in voice. Considering the applicability in real-life conditions, the research is carried

  12. Recognition measured values

    OpenAIRE

    LEITKEP, Zdeněk

    2012-01-01

    This work deals recognition measured values. The main task is to find suitable method for preprocessing images and create interface to software performing recognition. Created application will be used primarily to analyze the photos on site acquisition. Application is developed in Java and properly documented on javadoc level.

  13. Handwritten Digits Recognition

    OpenAIRE

    Grand, Eric

    2000-01-01

    My work of diploma consisted in developing a Windows application for the recognition of the handwritten digits. The source images come from a pen-scanner. The user can also draw the digits directly with the mouse and do the recognition of it. In this software, I integrated the SVM Light reconizer.

  14. Melatonin: functions and ligands.

    Science.gov (United States)

    Singh, Mahaveer; Jadhav, Hemant R

    2014-09-01

    Melatonin is a chronobiotic substance that acts as synchronizer by stabilizing bodily rhythms. Its synthesis occurs in various locations throughout the body, including the pineal gland, skin, lymphocytes and gastrointestinal tract (GIT). Its synthesis and secretion is controlled by light and dark conditions, whereby light decreases and darkness increases its production. Thus, melatonin is also known as the 'hormone of darkness'. Melatonin and analogs that bind to the melatonin receptors are important because of their role in the management of depression, insomnia, epilepsy, Alzheimer's disease (AD), diabetes, obesity, alopecia, migraine, cancer, and immune and cardiac disorders. In this review, we discuss the mechanism of action of melatonin in these disorders, which could aid in the design of novel melatonin receptor ligands.

  15. Macrocyclic G-quadruplex ligands

    DEFF Research Database (Denmark)

    Nielsen, M C; Ulven, Trond

    2010-01-01

    G-quadruplex stabilizing compounds have recently received increased interest due to their potential application as anticancer therapeutics. A significant number of structurally diverse G-quadruplex ligands have been developed. Some of the most potent and selective ligands currently known are macr...

  16. Vesicular stomatitis virus infection promotes immune evasion by preventing NKG2D-ligand surface expression.

    Directory of Open Access Journals (Sweden)

    Helle Jensen

    Full Text Available Vesicular stomatitis virus (VSV has recently gained attention for its oncolytic ability in cancer treatment. Initially, we hypothesized that VSV infection could increase immune recognition of cancer cells through induction of the immune stimulatory NKG2D-ligands. Here we show that VSV infection leads to a robust induction of MICA mRNA expression, however the subsequent surface expression is potently hindered. Thus, VSV lines up with human cytomegalovirus (HCMV and adenovirus, which actively subvert the immune system by negatively affecting NKG2D-ligand surface expression. VSV infection caused an active suppression of NKG2D-ligand surface expression, affecting both endogenous and histone deacetylase (HDAC-inhibitor induced MICA, MICB and ULBP-2 expression. The classical immune escape mechanism of VSV (i.e., the M protein blockade of nucleocytoplasmic mRNA transport was not involved, as the VSV mutant strain, VSV(ΔM51, which possess a defective M protein, prevented MICA surface expression similarly to wild-type VSV. The VSV mediated down modulation of NKG2D-ligand expression did not involve apoptosis. Constitutive expression of MICA bypassed the escape mechanism, suggesting that VSV affect NKG2D-ligand expression at an early post-transcriptional level. Our results show that VSV possess an escape mechanism, which could affect the immune recognition of VSV infected cancer cells. This may also have implications for immune recognition of cancer cells after combined treatment with VSV and chemotherapeutic drugs.

  17. Tailoring self-assembled monolayers at the electrochemical interface

    Indian Academy of Sciences (India)

    S Varatharajan; Sheela Berchmans; V Yegnaraman

    2009-09-01

    The main focus of this review is to illustrate the amenability of self-assembled monolayers (SAMs) for functionalisation with different receptors, catalytic materials, biomolecules, enzymes, antigen-antibody, etc for various applications. The review discusses initially about the preparation and characterization of SAMs and tailoring of SAMs by incorporation of suitable recognition elements. A description of how the molecular recognition is achieved through forces like electrostatic, covalent and host-guest interactions is included in the review.

  18. Molecular Recognition Directed Self-Assembly of Supramolecular Architectures

    Science.gov (United States)

    1994-06-30

    experiments have demonstrated that various substituted gallic acid derivatives can be used to construct exo-receptors with a tapered shape. 1.2...om , No .O.𔃺J04-0 * • . .. . •. *. " ..s *.-aI*mdl ,•t, ,t,.lmageg t..4o4etqr S b~lr~Ptqld O l- ’ .,JS 4t *V 41N~q #l• .W4 *W E~ uS n I.reCt.On .’ ,e...le*,.1,’*f 2 I:I %C.*, t.AGENCY USE ONLY (L~eive b;ank) ~2. REPORT DATE I1"REPORT TYPE AND DATES COVERED IJune 30, 1994 I Abstract Report #11 4

  19. Handbook of Face Recognition

    CERN Document Server

    Li, Stan Z

    2011-01-01

    This highly anticipated new edition provides a comprehensive account of face recognition research and technology, spanning the full range of topics needed for designing operational face recognition systems. After a thorough introductory chapter, each of the following chapters focus on a specific topic, reviewing background information, up-to-date techniques, and recent results, as well as offering challenges and future directions. Features: fully updated, revised and expanded, covering the entire spectrum of concepts, methods, and algorithms for automated face detection and recognition systems

  20. Mobile intention recognition

    CERN Document Server

    Kiefer, Peter

    2011-01-01

    Mobile Intention Recognition addresses problems of practical relevance for mobile system engineers: how can we make mobile assistance systems more intelligent? How can we model and recognize patterns of human behavior which span more than a limited spatial context? This text provides an overview on plan and intention recognition, ranging from the late 1970s to very recent approaches. This overview is unique as it discusses approaches with respect to the specificities of mobile intention recognition. This book covers problems from research on mobile assistance systems using methods from artific

  1. PCA facial expression recognition

    Science.gov (United States)

    El-Hori, Inas H.; El-Momen, Zahraa K.; Ganoun, Ali

    2013-12-01

    This paper explores and compares techniques for automatically recognizing facial actions in sequences of images. The comparative study of Facial Expression Recognition (FER) techniques namely Principal Component's analysis (PCA) and PCA with Gabor filters (GF) is done. The objective of this research is to show that PCA with Gabor filters is superior to the first technique in terms of recognition rate. To test and evaluates their performance, experiments are performed using real database by both techniques. The universally accepted five principal emotions to be recognized are: Happy, Sad, Disgust and Angry along with Neutral. The recognition rates are obtained on all the facial expressions.

  2. Synthesis of metal-hydrazone complexes and vapochromic behavior of their hydrogen-bonded proton-transfer assemblies.

    Science.gov (United States)

    Kobayashi, Atsushi; Dosen, Masa-aki; Chang, Mee; Nakajima, Kiyohiko; Noro, Shin-ichiro; Kato, Masako

    2010-11-03

    We synthesized and investigated a new series of metal-hydrazone complexes, including deprotonated [MX(mtbhp)] and protonated forms [MX(Hmtbhp)](ClO(4)) (M = Pd(2+), Pt(2+); X = Cl(-), Br(-); Hmtbhp = 2-(2-(2-(methylthio)benzylidene)hydrazinyl)pyridine) and hydrogen-bonded proton-transfer (HBPT) assemblies containing [PdBr(mtbhp)] and bromanilic acid (H(2)BA). The mtbhp hydrazone ligand acts as a tridentate SNN ligand and provides a high proton affinity. UV-vis spectroscopy revealed that these metal-hydrazone complexes follow a reversible protonation-deprotonation reaction ([MX(mtbhp)] + H(+) ⇋ [MX(Hmtbhp)](+)), resulting in a remarkable color change from red to yellow. Reactions between proton acceptor [PdBr(mtbhp)] (A) and proton donor H(2)BA (D) afforded four types of HBPT assemblies with different D/A ratios: for D/A = 1:1, {[PdBr(Hmtbhp)](HBA)·Acetone} and {[PdBr(Hmtbhp)](HBA)·2(1,4-dioxane)}; for D/A = 1:2, [PdBr(Hmtbhp)](2)(BA); and for D/A = 3:2, {[PdBr(Hmtbhp)](2)(HBA)(2)(H(2)BA)·2Acetonitrile}. The proton donor gave at least one proton to the acceptor to form the hydrogen bonded A···D pair of [PdBr(Hmtbhp)](+)···HBA(-). The strength of the hydrogen bond in the pair depends on the kind of molecule bound to the free monoanionic bromanilate OH group. Low-temperature IR spectra (T < 150 K) showed that the hydrogen bond distance between [PdBr(Hmtbhp)](+) and bromanilate was short enough (ca. 2.58 Å) to induce proton migration in the [PdBr(Hmtbhp)](2)(BA) assembly in the solid state. The hydrogen bonds formed not only between [PdBr(Hmtbhp)](+) and HBA(-) but also between HBA(-) and neutral H(2)BA molecules in the {[PdBr(Hmtbhp)](2)(HBA)(2)(H(2)BA)·2Acetonitrile} assembly. The H(2)BA-based flexible hydrogen bond network and strong acidic host structure result in an interesting vapor adsorption ability and vapochromic behavior in this assembly because the vapor-induced rearrangement of the hydrogen bond network, accompanied by changes in

  3. Probe tip heating assembly

    Science.gov (United States)

    Schmitz, Roger William; Oh, Yunje

    2016-10-25

    A heating assembly configured for use in mechanical testing at a scale of microns or less. The heating assembly includes a probe tip assembly configured for coupling with a transducer of the mechanical testing system. The probe tip assembly includes a probe tip heater system having a heating element, a probe tip coupled with the probe tip heater system, and a heater socket assembly. The heater socket assembly, in one example, includes a yoke and a heater interface that form a socket within the heater socket assembly. The probe tip heater system, coupled with the probe tip, is slidably received and clamped within the socket.

  4. Glutamate receptor ligands

    DEFF Research Database (Denmark)

    Guldbrandt, Mette; Johansen, Tommy N; Frydenvang, Karla Andrea;

    2002-01-01

    Homologation and substitution on the carbon backbone of (S)-glutamic acid [(S)-Glu, 1], as well as absolute stereochemistry, are structural parameters of key importance for the pharmacological profile of (S)-Glu receptor ligands. We describe a series of methyl-substituted 2-aminoadipic acid (AA......-ray crystallographic analyses, chemical correlation, and CD spectral analyses. The effects of the individual stereoisomers at ionotropic and metabotropic (S)-Glu receptors (iGluRs and mGluRs) were characterized. Compounds with S-configuration at the alpha-carbon generally showed mGluR2 agonist activity of similar...... limited effect on pharmacology. Structure-activity relationships at iGluRs in the rat cortical wedge preparation showed a complex pattern, some compounds being NMDA receptor agonists [e.g., EC(50) =110 microM for (2S,5RS)-5-methyl-AA (6a,b)] and some compounds showing NMDA receptor antagonist effects [e...

  5. Composite organization of the cobalamin binding and cubilin recognition sites of intrinsic factor.

    Science.gov (United States)

    Fedosov, Sergey N; Fedosova, Natalya U; Berglund, Lars; Moestrup, Søren K; Nexø, Ebba; Petersen, Torben E

    2005-03-08

    Intrinsic factor (IF(50)) is a cobalamin (Cbl)-transporting protein of 50 kDa, which can be cleaved into two fragments: the 30 kDa N-terminal peptide IF(30) and the 20 kDa C-terminal glycopeptide IF(20). Experiments on binding of Cbl to IF(30), IF(20), and IF(50) revealed comparable association rate constants (k(+)(Cbl) = 4 x 10(6), 14 x 10(6), and 26 x 10(6) M(-1) s(-1), respectively), but the equilibrium dissociation constants were essentially different (K(Cbl) = 200 microM, 0.2 microM, and cubilin in the presence or absence of Cbl. Neither apo nor holo forms of IF(20) and IF(30) were recognized by the receptor. When two fragments were mixed and incubated with Cbl, they associated into a stable complex, IF(30+20).Cbl, which bound to cubilin as well as the noncleaved IF(50).Cbl complex. We suggest that formation of the cubilin recognition site on IF is caused by assembly of two distant domains, which allows the saturated protein to be recognized by the receptor. The obtained parameters for ligand and receptor binding indicate that both full-length IF(50) and the fragments may be involved in Cbl assimilation.

  6. Newnes electronics assembly handbook

    CERN Document Server

    Brindley, Keith

    2013-01-01

    Newnes Electronics Assembly Handbook: Techniques, Standards and Quality Assurance focuses on the aspects of electronic assembling. The handbook first looks at the printed circuit board (PCB). Base materials, basic mechanical properties, cleaning of assemblies, design, and PCB manufacturing processes are then explained. The text also discusses surface mounted assemblies and packaging of electromechanical assemblies, as well as the soldering process. Requirements for the soldering process; solderability and protective coatings; cleaning of PCBs; and mass solder/component reflow soldering are des

  7. Metal nanoparticle - block copolymer composite assembly and disassembly

    NARCIS (Netherlands)

    Li, Z.H.; Sai, H.; Warren, S.C.; Kamperman, M.M.G.; Arora, H.; Gruner, S.M.; Wiesner, U.

    2009-01-01

    Ligand-stabilized platinum nanoparticles (Pt NPs) were self-assembled with poly(isoprene-block-dimethylaminoethyl methacrylate) (PI-b-PDMAEMA) block copolymers to generate organic-inorganic hybrid materials. High loadings of NPs in hybrids were achieved through usage of N,N-di-(2-(allyloxy)ethyl)-N-

  8. Construction of Supramolecular Architectures via Self-assembly

    Institute of Scientific and Technical Information of China (English)

    Takeharu; Haino

    2007-01-01

    1 Results In this paper we report supramolecular polymeric nano networks formed by the molecular-recognition-directed self-assembly between a calix[5]arene and C60[1]. Covalently-linked double-calix[5]arenes take up C60 into their cavities[2]. This complementary interaction creates a strong non-covalent bonding; thus,the iterative self-assembly between dumbbell fullerene 1 and ditopic host 2 can produce the supramolecular polymer networks (See Fig.1).

  9. Fluorescent naphthalene-based benzene tripod for selective recognition of fluoride in physiological condition

    Indian Academy of Sciences (India)

    Barun kumar Datta; Chirantan Kar; Gopal Das

    2015-02-01

    Aluminium complex of a naphthalene-based benzene tripod ligand system has been reported for the selective recognition of fluoride in aqueous medium in physiological condition. The ligand can selectively recognize Al3+ through enhancement in the fluorescence intensity and this in situ formed aluminium complex recognizes fluoride through quenching of fluorescence. The receptor system detects fluoride in nanomolar range. The sensing property was extended for practical utility to sense fluoride in tap water, pond water and river water.

  10. A Novel Benzimidazolyl based Receptor for the recognition of Fluoride and Cyanide Anion

    Indian Academy of Sciences (India)

    ERAMONI SAIKIA; PANKAJ DUTTA; BOLIN CHETIA

    2017-01-01

    A novel benzimidazole based ligand (1) has been synthesized and studied its anion recognition properties. The binding of anion with 1 was studied using UV-Visible spectroscopy, fluorescence spectroscopy and ¹H-NMR techniques at very low concentrations. The results obtained from the spectroscopic studies indicatethat ligand 1 is an efficient anion receptor providing changes in chemical shift and optical signals for the detection of two most environmentally important anions, fluoride and cyanide.

  11. Synthesis, characterization and self-assembly of Co3+ complexes appended with phenol and catechol groups

    Indian Academy of Sciences (India)

    Afsar Ali; Deepak Bansal; Rajeev Gupt

    2014-09-01

    This work presents the syntheses, characterization and hydrogen bonding based self-assembly of Co3+ complexes of pyridine-amide based bidentate ligands containing appended phenol and catechol groups. Placement of multiple hydrogen bond donors (phenolic OH and amidic NH groups) and acceptors (Oamide groups) in these molecules results in interesting self-assembled architectures.

  12. Dual recognition of the human telomeric G-quadruplex by a neomycin-anthraquinone conjugate.

    Science.gov (United States)

    Ranjan, Nihar; Davis, Erik; Xue, Liang; Arya, Dev P

    2013-06-28

    The authors report the recognition of a G-quadruplex formed by four repeat human telomeric DNA with aminosugar intercalator conjugates. The recognition of the G-quadruplex through dual binding mode ligands significantly increased the affinity of ligands for the G-quadruplex. One such example is a neomycin-anthraquinone conjugate (2) which exhibited nanomolar affinity for the quadruplex, and the affinity of (2) is nearly 1000 fold higher for the human telomeric G-quadruplex DNA than its constituent units, neomycin and anthraquinone.

  13. Local Innate Responses to TLR Ligands in the Chicken Trachea

    Directory of Open Access Journals (Sweden)

    Neda Barjesteh

    2016-07-01

    Full Text Available The chicken upper respiratory tract is the portal of entry for respiratory pathogens, such as avian influenza virus (AIV. The presence of microorganisms is sensed by pathogen recognition receptors (such as Toll-like receptors (TLRs of the innate immune defenses. Innate responses are essential for subsequent induction of potent adaptive immune responses, but little information is available about innate antiviral responses of the chicken trachea. We hypothesized that TLR ligands induce innate antiviral responses in the chicken trachea. Tracheal organ cultures (TOC were used to investigate localized innate responses to TLR ligands. Expression of candidate genes, which play a role in antiviral responses, was quantified. To confirm the antiviral responses of stimulated TOC, chicken macrophages were treated with supernatants from stimulated TOC, prior to infection with AIV. The results demonstrated that TLR ligands induced the expression of pro-inflammatory cytokines, type I interferons and interferon stimulated genes in the chicken trachea. In conclusion, TLR ligands induce functional antiviral responses in the chicken trachea, which may act against some pathogens, such as AIV.

  14. Forensic speaker recognition

    NARCIS (Netherlands)

    Meuwly, Didier

    2009-01-01

    The aim of forensic speaker recognition is to establish links between individuals and criminal activities, through audio speech recordings. This field is multidisciplinary, combining predominantly phonetics, linguistics, speech signal processing, and forensic statistics. On these bases, expert-based

  15. Work and Recognition

    DEFF Research Database (Denmark)

    Willig, Rasmus

    2004-01-01

    individual and collective identity formation and has led to an increase in social pathological illnesses such as stress and depression. By juxtaposing these analyses with Honneth’s theory on recognition, we conclude that the contemporary logic of work is unable to provide adequate forms of recognition......The article deals with the relationship between work and recognition, taking Axel Honneth’s social-philosophical theory of the struggle for recognition as its point of departure. In order to give sociological substance to Honneth’s theory, we turn to three contemporary social theorists - Jean......-Pierre Le Goff, Christophe Dejours and Emmanuel Renault. In spite of many differences, their work is united by a critical description of the logic of work and its consequences for individual individuation. These theorists agree that the growth of autonomy, flexibility and mobility has destabilised...

  16. Human Emotion Recognition System

    Directory of Open Access Journals (Sweden)

    Dilbag Singh

    2012-08-01

    Full Text Available This paper discusses the application of feature extraction of facial expressions with combination of neural network for the recognition of different facial emotions (happy, sad, angry, fear, surprised, neutral etc... Humans are capable of producing thousands of facial actions during communication that vary in complexity, intensity, and meaning. This paper analyses the limitations with existing system Emotion recognition using brain activity. In this paper by using an existing simulator I have achieved 97 percent accurate results and it is easy and simplest way than Emotion recognition using brain activity system. Purposed system depends upon human face as we know face also reflects the human brain activities or emotions. In this paper neural network has been used for better results. In the end of paper comparisons of existing Human Emotion Recognition System has been made with new one.

  17. Genetics, genomics, and evolutionary biology of NKG2D ligands.

    Science.gov (United States)

    Carapito, Raphael; Bahram, Seiamak

    2015-09-01

    Human and mouse NKG2D ligands (NKG2DLs) are absent or only poorly expressed by most normal cells but are upregulated by cell stress, hence, alerting the immune system in case of malignancy or infection. Although these ligands are numerous and highly variable (at genetic, genomic, structural, and biochemical levels), they all belong to the major histocompatibility complex class I gene superfamily and bind to a single, invariant, receptor: NKG2D. NKG2D (CD314) is an activating receptor expressed on NK cells and subsets of T cells that have a key role in the recognition and lysis of infected and tumor cells. Here, we review the molecular diversity of NKG2DLs, discuss the increasing appreciation of their roles in a variety of medical conditions, and propose several explanations for the evolutionary force(s) that seem to drive the multiplicity and diversity of NKG2DLs while maintaining their interaction with a single invariant receptor.

  18. Conformational proofreading: the impact of conformational changes on the specificity of molecular recognition.

    Directory of Open Access Journals (Sweden)

    Yonatan Savir

    Full Text Available To perform recognition, molecules must locate and specifically bind their targets within a noisy biochemical environment with many look-alikes. Molecular recognition processes, especially the induced-fit mechanism, are known to involve conformational changes. This raises a basic question: Does molecular recognition gain any advantage by such conformational changes? By introducing a simple statistical-mechanics approach, we study the effect of conformation and flexibility on the quality of recognition processes. Our model relates specificity to the conformation of the participant molecules and thus suggests a possible answer: Optimal specificity is achieved when the ligand is slightly off target; that is, a conformational mismatch between the ligand and its main target improves the selectivity of the process. This indicates that deformations upon binding serve as a conformational proofreading mechanism, which may be selected for via evolution.

  19. The Recognition Of Fatigue

    DEFF Research Database (Denmark)

    Elsass, Peter; Jensen, Bodil; Mørup, Rikke;

    2007-01-01

    Elsass P., Jensen B., Morup R., Thogersen M.H. (2007). The Recognition Of Fatigue: A qualitative study of life-stories from rehabilitation clients. International Journal of Psychosocial Rehabilitation. 11 (2), 75-87......Elsass P., Jensen B., Morup R., Thogersen M.H. (2007). The Recognition Of Fatigue: A qualitative study of life-stories from rehabilitation clients. International Journal of Psychosocial Rehabilitation. 11 (2), 75-87...

  20. Evaluating music emotion recognition

    DEFF Research Database (Denmark)

    Sturm, Bob L.

    2013-01-01

    A fundamental problem with nearly all work in music genre recognition (MGR)is that evaluation lacks validity with respect to the principal goals of MGR. This problem also occurs in the evaluation of music emotion recognition (MER). Standard approaches to evaluation, though easy to implement, do...... not reliably differentiate between recognizing genre or emotion from music, or by virtue of confounding factors in signals (e.g., equalization). We demonstrate such problems for evaluating an MER system, and conclude with recommendations....

  1. Why recognition is rational

    Directory of Open Access Journals (Sweden)

    Clintin P. Davis-Stober

    2010-07-01

    Full Text Available The Recognition Heuristic (Gigerenzer and Goldstein, 1996; Goldstein and Gigerenzer, 2002 makes the counter-intuitive prediction that a decision maker utilizing less information may do as well as, or outperform, an idealized decision maker utilizing more information. We lay a theoretical foundation for the use of single-variable heuristics such as the Recognition Heuristic as an optimal decision strategy within a linear modeling framework. We identify conditions under which over-weighting a single predictor is a mini-max strategy among a class of a priori chosen weights based on decision heuristics with respect to a measure of statistical lack of fit we call ``risk''. These strategies, in turn, outperform standard multiple regression as long as the amount of data available is limited. We also show that, under related conditions, weighting only one variable and ignoring all others produces the same risk as ignoring the single variable and weighting all others. This approach has the advantage of generalizing beyond the original environment of the Recognition Heuristic to situations with more than two choice options, binary or continuous representations of recognition, and to other single variable heuristics. We analyze the structure of data used in some prior recognition tasks and find that it matches the sufficient conditions for optimality in our results. Rather than being a poor or adequate substitute for a compensatory model, the Recognition Heuristic closely approximates an optimal strategy when a decision maker has finite data about the world.

  2. The Molecular Recognition Paradigm of Environmental Chemicals with Biomacromolecules.

    Science.gov (United States)

    Zhang, Wenjing; Pan, Liumeng; Wang, Haifei; Lv, Xuan; Ding, Keke

    2017-01-01

    The interactions of ligands with biomacromolecules play a fundamental role in almost all bioprocesses occuring in living organisms. The binding of ligands can cause the conformational changes of biomacromolecules, possibly affecting their physiological functions. The interactions of ligands with biomacromolecules are thus becoming a research hotspot. However, till now, there still lacks a systematic compilation of review with the focus on the interactions between environmental chemicals and biomacromolecules. In this review, we focus on the molecular recognition paradigm of environmental chemicals with biomacromolecules and chemical basis for driving the complex formation. The state-of-the-art review on in vitro and in silico studies on interaction of organic chemicals with transport proteins, nuclear receptors and CYP450 enzymes was provided, and the enantioselective interactions of chiral environmental chemicals was also mentioned.

  3. Tuning the size of a redox-active tetrathiafulvalene-based self-assembled ring

    Directory of Open Access Journals (Sweden)

    Sébastien Bivaud

    2015-06-01

    Full Text Available The synthesis of a new Pd coordination-driven self-assembled ring M6L3 constructed from a concave tetrapyridyl π-extended tetrathiafulvalene ligand (exTTF is described. The same ligand is also able to self-assemble in a M4L2 mode as previously described. Herein, we demonstrate that the bulkiness of the ancillary groups in the Pd complex allows for modulating the size and the shape of the resulting discrete self-assembly, which therefore incorporate two (M4L2 or three (M6L3 electroactive exTTF sidewalls.

  4. Evolutionarily conserved paired immunoglobulin-like receptor α (PILRα) domain mediates its interaction with diverse sialylated ligands.

    Science.gov (United States)

    Sun, Yonglian; Senger, Kate; Baginski, Tomasz K; Mazloom, Anita; Chinn, Yvonne; Pantua, Homer; Hamidzadeh, Kajal; Ramani, Sree Ranjani; Luis, Elizabeth; Tom, Irene; Sebrell, Andrew; Quinones, Gabriel; Ma, Yan; Mukhyala, Kiran; Sai, Tao; Ding, Jiabing; Haley, Benjamin; Shadnia, Hooman; Kapadia, Sharookh B; Gonzalez, Lino C; Hass, Philip E; Zarrin, Ali A

    2012-05-04

    Paired immunoglobulin-like receptor (PILR) α is an inhibitory receptor that recognizes several ligands, including mouse CD99, PILR-associating neural protein, and Herpes simplex virus-1 glycoprotein B. The physiological function(s) of interactions between PILRα and its cellular ligands are not well understood, as are the molecular determinants of PILRα/ligand interactions. To address these uncertainties, we sought to identify additional PILRα ligands and further define the molecular basis for PILRα/ligand interactions. Here, we identify two novel PILRα binding partners, neuronal differentiation and proliferation factor-1 (NPDC1), and collectin-12 (COLEC12). We find that sialylated O-glycans on these novel PILRα ligands, and on known PILRα ligands, are compulsory for PILRα binding. Sialylation-dependent ligand recognition is also a property of SIGLEC1, a member of the sialic acid-binding Ig-like lectins. SIGLEC1 Ig domain shares ∼22% sequence identity with PILRα, an identity that includes a conserved arginine localized to position 97 in mouse and human SIGLEC1, position 133 in mouse PILRα and position 126 in human PILRα. We observe that PILRα/ligand interactions require conserved PILRα Arg-133 (mouse) and Arg-126 (human), in correspondence with a previously reported requirement for SIGLEC1 Arg-197 in SIGLEC1/ligand interactions. Homology modeling identifies striking similarities between PILRα and SIGLEC1 ligand binding pockets as well as at least one set of distinctive interactions in the galactoxyl-binding site. Binding studies suggest that PILRα recognizes a complex ligand domain involving both sialic acid and protein motif(s). Thus, PILRα is evolved to engage multiple ligands with common molecular determinants to modulate myeloid cell functions in anatomical settings where PILRα ligands are expressed.

  5. Fellows Celebrated at Joint Assembly

    Science.gov (United States)

    2009-06-01

    The 2009 AGU Fellows were presented at the recent Joint Assembly in Toronto, Ontario, Canada. At a formal ceremony on 26 May 2009, AGU President Timothy L. Grove introduced each Fellow and read a brief statement of the achievements for which each had been selected. The presentations were followed by a reception for meeting attendees and a banquet at which family members and close colleagues further feted the honorees. AGU Fellows are scientists who have attained “acknowledged eminence in the geophysical sciences.” Election to AGU Fellowship is a very high recognition by one's peers. The number of Fellows elected may not exceed 0.1% of the membership in any given year.

  6. Emergence of hierarchical structural complexities in nanoparticles and their assembly

    Science.gov (United States)

    Zeng, Chenjie; Chen, Yuxiang; Kirschbaum, Kristin; Lambright, Kelly J.; Jin, Rongchao

    2016-12-01

    We demonstrate that nanoparticle self-assembly can reach the same level of hierarchy, complexity, and accuracy as biomolecules. The precise assembly structures of gold nanoparticles (246 gold core atoms with 80 p-methylbenzenethiolate surface ligands) at the atomic, molecular, and nanoscale levels were determined from x-ray diffraction studies. We identified the driving forces and rules that guide the multiscale assembly behavior. The protecting ligands self-organize into rotational and parallel patterns on the nanoparticle surface via C-Hṡṡṡπ interaction, and the symmetry and density of surface patterns dictate directional packing of nanoparticles into crystals with orientational, rotational, and translational orders. Through hierarchical interactions and symmetry matching, the simple building blocks evolve into complex structures, representing an emergent phenomenon in the nanoparticle system.

  7. Assembly of MHC class I molecules within the endoplasmic reticulum.

    Science.gov (United States)

    Zhang, Yinan; Williams, David B

    2006-01-01

    MHC class I molecules bind cytosolically derived peptides within the endoplasmic reticulum (ER) and present them at the cell surface to cytotoxic T cells. A major focus of our laboratory has been to understand the functions of the diverse proteins involved in the intracellular assembly of MHC class I molecules. These include the molecular chaperones calnexin and calreticulin, which enhance the proper folding and subunit assembly of class I molecules and also retain assembly intermediates within the ER; ERp57, a thiol oxidoreductase that promotes heavy chain disulfide formation and proper assembly of the peptide loading complex; tapasin, which recruits class I molecules to the TAP peptide transporter and enhances the loading of high affinity peptide ligands; and Bap31, which is involved in clustering assembled class I molecules at ER exit sites for export along the secretory pathway. This review describes our contributions to elucidating the functions of these proteins; the combined effort of many dedicated students and postdoctoral fellows.

  8. ABS-Scan: In silico alanine scanning mutagenesis for binding site residues in protein-ligand complex.

    Science.gov (United States)

    Anand, Praveen; Nagarajan, Deepesh; Mukherjee, Sumanta; Chandra, Nagasuma

    2014-01-01

    Most physiological processes in living systems are fundamentally regulated by protein-ligand interactions. Understanding the process of ligand recognition by proteins is a vital activity in molecular biology and biochemistry. It is well known that the residues present at the binding site of the protein form pockets that provide a conducive environment for recognition of specific ligands. In many cases, the boundaries of these sites are not well defined. Here, we provide a web-server to systematically evaluate important residues in the binding site of the protein that contribute towards the ligand recognition through in silico alanine-scanning mutagenesis experiments. Each of the residues present at the binding site is computationally mutated to alanine. The ligand interaction energy is computed for each mutant and the corresponding ΔΔG values are calculated by comparing it to the wild type protein, thus evaluating individual residue contributions towards ligand interaction. The server will thus provide a ranked list of residues to the user in order to obtain loss-of-function mutations. This web-tool can be freely accessed through the following address: http://proline.biochem.iisc.ernet.in/abscan/.

  9. Nanoparticle Assemblies at Fluid Interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Russell, Thomas P. [Univ. of Massachusetts, Amherst, MA (United States). Dept. of Polymer Science and Engineering

    2015-03-10

    A systematic study of the structure and dynamics of nanoparticles (NP) and NP-surfactants was performed. The ligands attached to both the NPs and NP-surfactants dictate the manner in which the nanoscopic materials assemble at fluid interfaces. Studies have shown that a single layer of the nanoscpic materials form at the interface to reduce the interactions between the two immiscible fluids. The shape of the NP is, also, important, where for spherical particles, a disordered, liquid-like monolayer forms, and, for nanorods, ordered domains at the interface is found and, if the monolayers are compressed, the orientation of the nanorods with respect to the interface can change. By associating end-functionalized polymers to the NPs assembled at the interface, NP-surfactants are formed that increase the energetic gain in segregating each NP at the interface which allows the NP-surfactants to jam at the interface when compressed. This has opened the possibility of structuring the two liquids by freezing in shape changes of the liquids.

  10. Contrasting roles for TLR ligands in HIV-1 pathogenesis.

    Directory of Open Access Journals (Sweden)

    Beda Brichacek

    Full Text Available The first line of a host's response to various pathogens is triggered by their engagement of cellular pattern recognition receptors (PRRs. Binding of microbial ligands to these receptors leads to the induction of a variety of cellular factors that alter intracellular and extracellular environment and interfere directly or indirectly with the life cycle of the triggering pathogen. Such changes may also affect any coinfecting microbe. Using ligands to Toll-like receptors (TLRs 5 and 9, we examined their effect on human immunodeficiency virus (HIV-1 replication in lymphoid tissue ex vivo. We found marked differences in the outcomes of such treatment. While flagellin (TLR5 agonist treatment enhanced replication of CC chemokine receptor 5 (CCR 5-tropic and CXC chemokine receptor 4 (CXCR4-tropic HIV-1, treatment with oligodeoxynucleotide (ODN M362 (TLR9 agonist suppressed both viral variants. The differential effects of these TLR ligands on HIV-1 replication correlated with changes in production of CC chemokines CCL3, CCL4, CCL5, and of CXC chemokines CXCL10, and CXCL12 in the ligand-treated HIV-1-infected tissues. The nature and/or magnitude of these changes were dependent on the ligand as well as on the HIV-1 viral strain. Moreover, the tested ligands differed in their ability to induce cellular activation as evaluated by the expression of the cluster of differentiation markers (CD 25, CD38, CD39, CD69, CD154, and human leukocyte antigen D related (HLA-DR as well as of a cell proliferation marker, Ki67, and of CCR5. No significant effect of the ligand treatment was observed on apoptosis and cell death/loss in the treated lymphoid tissue ex vivo. Our results suggest that binding of microbial ligands to TLRs is one of the mechanisms that mediate interactions between coinfected microbes and HIV-1 in human tissues. Thus, the engagement of appropriate TLRs by microbial molecules or their mimetic might become a new strategy for HIV therapy or prevention.

  11. Programming biomolecular self-assembly pathways.

    Science.gov (United States)

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

    2008-01-17

    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.

  12. A multistep continuous-flow system for rapid on-demand synthesis of receptor ligands

    DEFF Research Database (Denmark)

    Petersen, Trine P; Ritzén, Andreas; Ulven, Trond

    2009-01-01

    A multistep continuous-flow system for synthesis of receptor ligands by assembly of three variable building blocks in a single unbroken flow is described. The sequence consists of three reactions and two scavenger steps, where a Cbz-protected diamine is reacted with an isocyanate, deprotected, an...

  13. Metal-Metal Interactions in Heterobimetallic Complexes with Dinucleating Redox-Active Ligands

    NARCIS (Netherlands)

    Broere, D.L.J.; Modder, D.K.; Blokker, E.; Siegler, M.A.; van der Vlugt, J.I.

    2016-01-01

    The tuning of metal-metal interactions in multinuclear assemblies is a challenge. Selective P coordination of a redox-active PNO ligand to AuI followed by homoleptic metalation of the NO pocket with NiII affords a unique trinuclear Au-Ni-Au complex. This species features two antiferromagnetically co

  14. Antibody-ligand interactions for hydrophobic charge-induction chromatography: a surface plasmon resonance study.

    Science.gov (United States)

    Cheng, Fang; Li, Ming-Yang; Wang, Han-Qi; Lin, Dong-Qiang; Qu, Jing-Ping

    2015-03-24

    This article describes the use of surface plasmon resonance (SPR) spectroscopy to study antibody-ligand interactions for hydrophobic charge-induction chromatography (HCIC) and its versatility in investigating the surface and solution factors affecting the interactions. Two density model surfaces presenting the HCIC ligand (mercapto-ethyl-pyridine, MEP) were prepared on Au using a self-assembly technique. The surface chemistry and structure, ionization, and protein binding of such model surfaces were characterized by X-ray photoelectron spectroscopy (XPS), near-edge X-ray absorption fine structure (NEXAFS), contact-angle titration, and SPR, respectively. The influences of the surface and solution factors, e.g., ligand density, salt concentration, and solution pH, on protein adsorption were determined by SPR. Our results showed that ligand density affects both equilibrium and dynamic aspects of the interactions. Specifically, a dense ligand leads to an increase in binding strength, rapid adsorption, slow desorption, and low specificity. In addition, both hydrophobic interactions and hydrogen bonding contribute significantly to the protein adsorption at neutral pH, while the electrostatic repulsion is overwhelmed under acidic conditions. The hydrophobic interaction at a high concentration of lyotropic salt would cause drastic conformational changes in the adsorbed protein. Combined with the self-assembly technique, SPR proves to be a powerful tool for studying the interactions between an antibody and a chromatographic ligand.

  15. Heterobifunctional crosslinkers for tethering single ligand molecules to scanning probes

    Energy Technology Data Exchange (ETDEWEB)

    Riener, Christian K.; Kienberger, Ferry; Hahn, Christoph D.; Buchinger, Gerhard M.; Egwim, Innocent O.C.; Haselgruebler, Thomas; Ebner, Andreas; Romanin, Christoph; Klampfl, Christian; Lackner, Bernd; Prinz, Heino; Blaas, Dieter; Hinterdorfer, Peter; Gruber, Hermann J

    2003-11-14

    Single molecule recognition force microscopy (SMRFM) is a versatile atomic force microscopy (AFM) method to probe specific interactions of cognitive molecules on the single molecule level. It allows insights to be gained into interaction potentials and kinetic barriers and is capable of mapping interaction sites with nm positional accuracy. These applications require a ligand to be attached to the AFM tip, preferably by a distensible poly(ethylene glycol) (PEG) chain between the measuring tip and the ligand molecule. The PEG chain greatly facilitates specific binding of the ligand to immobile receptor sites on the sample surface. The present study contributes to tip-PEG-ligand tethering in three ways: (i) a convenient synthetic route was found to prepare NH{sub 2}-PEG-COOH which is the key intermediate for long heterobifunctional crosslinkers; (ii) a variety of heterobifunctional PEG derivatives for tip-PEG-ligand linking were prepared from NH{sub 2}-PEG-COOH; (iii) in particular, a new PEG crosslinker with one thiol-reactive end and one terminal nitrilotriacetic acid (NTA) group was synthesized and successfully used to tether His{sub 6}-tagged protein molecules to AFM tips via noncovalent NTA-Ni{sup 2+}-His{sub 6} bridges. The new crosslinker was applied to link a recombinant His{sub 6}-tagged fragment of the very-low density lipoprotein receptor to the AFM tip whereupon specific docking to the capsid of human rhinovirus particles was observed by force microscopy. In a parallel study, the specific interaction of the small GTPase Ran with the nuclear import receptor importin {beta}1 was studied in detail by SMRFM, using the new crosslinker to link His{sub 6}-tagged Ran to the measuring tip [Nat. Struct. Biol. (2003), 10, 553-557].

  16. Polymer Directed Protein Assemblies

    NARCIS (Netherlands)

    van Rijn, Patrick

    2013-01-01

    Protein aggregation and protein self-assembly is an important occurrence in natural systems, and is in some form or other dictated by biopolymers. Very obvious influences of biopolymers on protein assemblies are, e. g., virus particles. Viruses are a multi-protein assembly of which the morphology is

  17. Visualization of Metal-to-Ligand and Ligand-to-Ligand Charge Transfer in Metal-Ligand Complexes

    Institute of Scientific and Technical Information of China (English)

    Yong Ding; Jian-xiu Guo; Xiang-si Wang; Sha-sha Liu; Feng-cai Ma

    2009-01-01

    Three methods including the atomic resolved density of state, charge difference density, and the transition density matrix are used to visualize metal to ligand charge transfer (MLCT) in ruthenium(Ⅱ) ammine complex. The atomic resolved density of state shows that there is density of Ru on the HOMOs. All the density is localized on the ammine, which reveals that the excited electrons in the Ru complex are delocalized over the ammine ligand. The charge difference density shows that all the holes are localized on the Ru and the electrons on the ammine. The localization explains the MLCT on excitation. The transition density matrix shows that there is electron-hole coherence between Ru and ammine. These methods are also used to examine the MLCT in Os(bpy)(p0p)Cl ("Osp0p"; bpy=2,2'-bipyridyl; p0p=4,4'-bipyridyl) and the ligand-to-ligand charge transfer (LLCT) in Alq3. The calculated results show that these methods are powerful to examine MLCT and LLCT in the metal-ligand system.

  18. Touchless palmprint recognition systems

    CERN Document Server

    Genovese, Angelo; Scotti, Fabio

    2014-01-01

    This book examines the context, motivation and current status of biometric systems based on the palmprint, with a specific focus on touchless and less-constrained systems. It covers new technologies in this rapidly evolving field and is one of the first comprehensive books on palmprint recognition systems.It discusses the research literature and the most relevant industrial applications of palmprint biometrics, including the low-cost solutions based on webcams. The steps of biometric recognition are described in detail, including acquisition setups, algorithms, and evaluation procedures. Const

  19. Recognition as care

    DEFF Research Database (Denmark)

    Ahlmark, Nanna; Whyte, Susan Reynolds; Harting, Janneke

    2014-01-01

    This longitudinal study provides critical insight into the social processes of municipal diabetes training for Arabic-speaking immigrants in Denmark focusing on participants’ experiences. Our study builds on observations of three diabetes courses and 36 interviews with participants at the start of......-based and solidarity-based recognition to analyse what was at stake in these experiences, and we engage Annemarie Mol’s concept of a logic of care to show how recognition unfolded practically during the training. We propose that participants’ wider social context and experiences of misrecognition situated the training...

  20. Sensor mount assemblies and sensor assemblies

    Science.gov (United States)

    Miller, David H [Redondo Beach, CA

    2012-04-10

    Sensor mount assemblies and sensor assemblies are provided. In an embodiment, by way of example only, a sensor mount assembly includes a busbar, a main body, a backing surface, and a first finger. The busbar has a first end and a second end. The main body is overmolded onto the busbar. The backing surface extends radially outwardly relative to the main body. The first finger extends axially from the backing surface, and the first finger has a first end, a second end, and a tooth. The first end of the first finger is disposed on the backing surface, and the tooth is formed on the second end of the first finger.

  1. Structural and mechanistic insights into cooperative assembly of dimeric Notch transcription complexes

    Energy Technology Data Exchange (ETDEWEB)

    Arnett, Kelly L.; Hass, Matthew; McArthur, Debbie G.; Ilagan, Ma Xenia G.; Aster, Jon C.; Kopan, Raphael; Blacklow, Stephen C. (WU); (BWH); (DFCI)

    2010-11-12

    Ligand-induced proteolysis of Notch produces an intracellular effector domain that transduces essential signals by regulating the transcription of target genes. This function relies on the formation of transcriptional activation complexes that include intracellular Notch, a Mastermind co-activator and the transcription factor CSL bound to cognate DNA. These complexes form higher-order assemblies on paired, head-to-head CSL recognition sites. Here we report the X-ray structure of a dimeric human Notch1 transcription complex loaded on the paired site from the human HES1 promoter. The small interface between the Notch ankyrin domains could accommodate DNA bending and untwisting to allow a range of spacer lengths between the two sites. Cooperative dimerization occurred on the human and mouse Hes5 promoters at a sequence that diverged from the CSL-binding consensus at one of the sites. These studies reveal how promoter organizational features control cooperativity and, thus, the responsiveness of different promoters to Notch signaling.

  2. Collagen fibril surface displays a constellation of sites capable of promoting fibril assembly, stability, and hemostasis

    Energy Technology Data Exchange (ETDEWEB)

    Orgel, J.P.; Antipova, O.; Sagi, I.; Bitler, A.; Qiu, D.; Wang, R.; Xu, Y.; San Antonio, J.D. (IIT)

    2011-12-14

    Fibrillar collagens form the structural basis of organs and tissues including the vasculature, bone, and tendon. They are also dynamic, organizational scaffolds that present binding and recognition sites for ligands, cells, and platelets. We interpret recently published X-ray diffraction findings and use atomic force microscopy data to illustrate the significance of new insights into the functional organization of the collagen fibril. These data indicate that collagen's most crucial functional domains localize primarily to the overlap region, comprising a constellation of sites we call the 'master control region.' Moreover, the collagen's most exposed aspect contains its most stable part - the C-terminal region that controls collagen assembly, cross-linking, and blood clotting. Hidden beneath the fibril surface exists a constellation of 'cryptic' sequences poised to promote hemostasis and cell - collagen interactions in tissue injury and regeneration. These findings begin to address several important, and previously unresolved, questions: How functional domains are organized in the fibril, which domains are accessible, and which require proteolysis or structural trauma to become exposed? Here we speculate as to how collagen fibrillar organization impacts molecular processes relating to tissue growth, development, and repair.

  3. 3D vision assisted flexible robotic assembly of machine components

    Science.gov (United States)

    Ogun, Philips S.; Usman, Zahid; Dharmaraj, Karthick; Jackson, Michael R.

    2015-12-01

    Robotic assembly systems either make use of expensive fixtures to hold components in predefined locations, or the poses of the components are determined using various machine vision techniques. Vision-guided assembly robots can handle subtle variations in geometries and poses of parts. Therefore, they provide greater flexibility than the use of fixtures. However, the currently established vision-guided assembly systems use 2D vision, which is limited to three degrees of freedom. The work reported in this paper is focused on flexible automated assembly of clearance fit machine components using 3D vision. The recognition and the estimation of the poses of the components are achieved by matching their CAD models with the acquired point cloud data of the scene. Experimental results obtained from a robot demonstrating the assembly of a set of rings on a shaft show that the developed system is not only reliable and accurate, but also fast enough for industrial deployment.

  4. [Prosopagnosia and facial expression recognition].

    Science.gov (United States)

    Koyama, Shinichi

    2014-04-01

    This paper reviews clinical neuropsychological studies that have indicated that the recognition of a person's identity and the recognition of facial expressions are processed by different cortical and subcortical areas of the brain. The fusiform gyrus, especially the right fusiform gyrus, plays an important role in the recognition of identity. The superior temporal sulcus, amygdala, and medial frontal cortex play important roles in facial-expression recognition. Both facial recognition and facial-expression recognition are highly intellectual processes that involve several regions of the brain.

  5. Soldering in electronics assembly

    CERN Document Server

    Judd, Mike

    2013-01-01

    Soldering in Electronics Assembly discusses several concerns in soldering of electronic assemblies. The book is comprised of nine chapters that tackle different areas in electronic assembly soldering. Chapter 1 discusses the soldering process itself, while Chapter 2 covers the electronic assemblies. Chapter 3 talks about solders and Chapter 4 deals with flux. The text also tackles the CS and SC soldering process. The cleaning of soldered assemblies, solder quality, and standards and specifications are also discussed. The book will be of great use to professionals who deal with electronic assem

  6. Why mercury prefers soft ligands

    Energy Technology Data Exchange (ETDEWEB)

    Riccardi, Demian M [ORNL; Guo, Hao-Bo [ORNL; Gu, Baohua [ORNL; Parks, Jerry M [ORNL; Summers, Anne [University of Georgia, Athens, GA; Miller, S [University of California, San Francisco; Liang, Liyuan [ORNL; Smith, Jeremy C [ORNL

    2013-01-01

    Mercury (Hg) is a major global pollutant arising from both natural and anthropogenic sources. Defining the factors that determine the relative affinities of different ligands for the mercuric ion, Hg2+, is critical to understanding its speciation, transformation, and bioaccumulation in the environment. Here, we use quantum chemistry to dissect the relative binding free energies for a series of inorganic anion complexes of Hg2+. Comparison of Hg2+ ligand interactions in the gaseous and aqueous phases shows that differences in interactions with a few, local water molecules led to a clear periodic trend within the chalcogenide and halide groups and resulted in the well-known experimentally observed preference of Hg2+ for soft ligands such as thiols. Our approach establishes a basis for understanding Hg speciation in the biosphere.

  7. Reverse depletion effects and the determination of ligand density on some spherical bioparticles

    Science.gov (United States)

    Wang, Chunxiang; Liu, Yanhui; Fan, Yangtao; Liu, Yijun; Li, Qiancheng; Xu, Houqiang

    2016-06-01

    In cell environments crowded with macromolecules, the depletion effects act and assist in the assembly of a wide range of cellular structures, from the cytoskeleton to the chromatin loop, which are well accepted. But a recent quantum dot experiment indicated that the dimensions of the receptor-ligand complex have strong effects on the size-dependent exclusion of proteins in cell environments. In this article, a continuum elastic model is constructed to resolve the competition between the dimension of the receptor-ligand complex and depletion effects in the endocytosis of a spherical virus-like bioparticle. Our results show that the depletion effects do not always assist endocytosis of a spherical virus-like bioparticle; while the dimension of the ligand-receptor complex is larger than the size of a small bioparticle in cell environments, the depletion effects do not work and reverse effects appear. The ligand density covered on the virus can be identified quantitatively.

  8. Phenanthroline-2,9-bistriazoles as selective G-quadruplex ligands

    DEFF Research Database (Denmark)

    Nielsen, Mads Corvinius; Larsen, Anders Foller; Abdikadir, Faisal Hussein

    2014-01-01

    G-quadruplex (G4) ligands are currently receiving considerable attention as potential anticancer therapeutics. A series of phenanthroline-2,9-bistriazoles carrying tethered positive end groups has been synthesized and evaluated as G4 stabilizers. The compounds were efficiently assembled by copper......(I)-catalyzed azide-alkyne cycloaddition (CuAAC) in CH2Cl2 and water in the presence of a complexing agent. Characterization of the target compounds on telomeric and c-KIT G4 sequences led to the identification of guanidinium-substituted compounds as potent G4 DNA ligands with high selectivity over duplex DNA....... The diisopropylguanidium ligands exhibited high selectivity for the proto-oncogenic sequence c-KIT over the human telomeric sequence in the surface plasmon resonance (SPR) assay, whereas the compounds appeared potent on both G4 structures in the FRET melting temperature assay. The phenanthroline-2,9-bistriazole ligands...

  9. Automatic aircraft recognition

    Science.gov (United States)

    Hmam, Hatem; Kim, Jijoong

    2002-08-01

    Automatic aircraft recognition is very complex because of clutter, shadows, clouds, self-occlusion and degraded imaging conditions. This paper presents an aircraft recognition system, which assumes from the start that the image is possibly degraded, and implements a number of strategies to overcome edge fragmentation and distortion. The current vision system employs a bottom up approach, where recognition begins by locating image primitives (e.g., lines and corners), which are then combined in an incremental fashion into larger sets of line groupings using knowledge about aircraft, as viewed from a generic viewpoint. Knowledge about aircraft is represented in the form of whole/part shape description and the connectedness property, and is embedded in production rules, which primarily aim at finding instances of the aircraft parts in the image and checking the connectedness property between the parts. Once a match is found, a confidence score is assigned and as evidence in support of an aircraft interpretation is accumulated, the score is increased proportionally. Finally a selection of the resulting image interpretations with the highest scores, is subjected to competition tests, and only non-ambiguous interpretations are allowed to survive. Experimental results demonstrating the effectiveness of the current recognition system are given.

  10. Recognition of fractal graphs

    NARCIS (Netherlands)

    Perepelitsa, VA; Sergienko, [No Value; Kochkarov, AM

    1999-01-01

    Definitions of prefractal and fractal graphs are introduced, and they are used to formulate mathematical models in different fields of knowledge. The topicality of fractal-graph recognition from the point of view, of fundamental improvement in the efficiency of the solution of algorithmic problems i

  11. Tolerance and recognition

    Directory of Open Access Journals (Sweden)

    Hans Marius Hansteen

    2014-12-01

    Full Text Available Even though “toleration” and “recognition” designate opposing attitudes (to tolerate something, implies a negative stance towards it, whereas recognition seems to imply a positive one, the concepts do not constitute mutually exclusive alternatives. However, “toleration” is often associated with liberal universalism, focusing on individual rights, whereas “recognition” often connotes communitarian perspectives, focusing on relations and identity. This paper argues that toleration may be founded on recognition, and that recognition may imply toleration. In outlining a differentiated understanding of the relationship between toleration and recognition, it seems apt to avoid an all-to-general dichotomy between universalism and particularism or, in other words, to reach beyond the debate between liberalism and communitarianism in political philosophy.The paper takes as its starting point the view that the discussion on toleration and diversity in intercultural communication is one of the contexts where it seems important to get beyond the liberal/communitarian dichotomy. Some basic features of Rainer Forst’s theory of toleration and Axel Honneth’s theory of the struggle for recognition are presented, in order to develop a more substantial understanding of the relationship between the concepts of toleration and recognition. One lesson from Forst is that toleration is a normatively dependent concept, i.e., that it is impossible to deduce principles for toleration and its limits from a theory of toleration as such. A central lesson from Honneth is that recognition – understood as a basic human need – is always conflictual and therefore dynamic.Accordingly, a main point in the paper is that the theory of struggles for and about recognition (where struggles for designates struggles within an established order of recognition, and struggles about designates struggles that challenge established orders of recognition may clarify what

  12. Automatic object recognition

    Science.gov (United States)

    Ranganath, H. S.; Mcingvale, Pat; Sage, Heinz

    1988-01-01

    Geometric and intensity features are very useful in object recognition. An intensity feature is a measure of contrast between object pixels and background pixels. Geometric features provide shape and size information. A model based approach is presented for computing geometric features. Knowledge about objects and imaging system is used to estimate orientation of objects with respect to the line of sight.

  13. Pattern recognition in bioinformatics.

    Science.gov (United States)

    de Ridder, Dick; de Ridder, Jeroen; Reinders, Marcel J T

    2013-09-01

    Pattern recognition is concerned with the development of systems that learn to solve a given problem using a set of example instances, each represented by a number of features. These problems include clustering, the grouping of similar instances; classification, the task of assigning a discrete label to a given instance; and dimensionality reduction, combining or selecting features to arrive at a more useful representation. The use of statistical pattern recognition algorithms in bioinformatics is pervasive. Classification and clustering are often applied to high-throughput measurement data arising from microarray, mass spectrometry and next-generation sequencing experiments for selecting markers, predicting phenotype and grouping objects or genes. Less explicitly, classification is at the core of a wide range of tools such as predictors of genes, protein function, functional or genetic interactions, etc., and used extensively in systems biology. A course on pattern recognition (or machine learning) should therefore be at the core of any bioinformatics education program. In this review, we discuss the main elements of a pattern recognition course, based on material developed for courses taught at the BSc, MSc and PhD levels to an audience of bioinformaticians, computer scientists and life scientists. We pay attention to common problems and pitfalls encountered in applications and in interpretation of the results obtained.

  14. Implicit ligand theory: rigorous binding free energies and thermodynamic expectations from molecular docking.

    Science.gov (United States)

    Minh, David D L

    2012-09-14

    A rigorous formalism for estimating noncovalent binding free energies and thermodynamic expectations from calculations in which receptor configurations are sampled independently from the ligand is derived. Due to this separation, receptor configurations only need to be sampled once, facilitating the use of binding free energy calculations in virtual screening. Demonstrative calculations on a host-guest system yield good agreement with previous free energy calculations and isothermal titration calorimetry measurements. Implicit ligand theory provides guidance on how to improve existing molecular docking algorithms and insight into the concepts of induced fit and conformational selection in noncovalent macromolecular recognition.

  15. Functional interactions between polypyrimidine tract binding protein and PRI peptide ligand containing proteins.

    Science.gov (United States)

    Coelho, Miguel B; Ascher, David B; Gooding, Clare; Lang, Emma; Maude, Hannah; Turner, David; Llorian, Miriam; Pires, Douglas E V; Attig, Jan; Smith, Christopher W J

    2016-08-15

    Polypyrimidine tract binding protein (PTBP1) is a heterogeneous nuclear ribonucleoprotein (hnRNP) that plays roles in most stages of the life-cycle of pre-mRNA and mRNAs in the nucleus and cytoplasm. PTBP1 has four RNA binding domains of the RNA recognition motif (RRM) family, each of which can bind to pyrimidine motifs. In addition, RRM2 can interact via its dorsal surface with proteins containing short peptide ligands known as PTB RRM2 interacting (PRI) motifs, originally found in the protein Raver1. Here we review our recent progress in understanding the interactions of PTB with RNA and with various proteins containing PRI ligands.

  16. Molecular insight in the purification of immunoglobulin by pseudobiospecific ligand l-histidine and histidyl moieties in histidine ligand affinity chromatography (HLAC) by molecular docking.

    Science.gov (United States)

    Savane, Tushar S; Kumar, Sanjit; Janakiraman, Vignesh Narasimhan; Kamalanathan, Agamudi S; Vijayalakshmi, Mookambeswaran A

    2016-05-15

    Pseudobiospecific ligand l-histidine is an inexpensive, highly stable, non-toxic ligand explored successfully over the last twenty years for the purification of immunoglobulins in immobilised histidine ligand affinity chromatography. It is of great interest to know the molecular recognition sites of IgG to immobilized l-histidine. Here, we have used an in silico approach to explore the molecular recognition of l-histidine by IgG. We have assessed the feasible binding modes of histidine and its moieties at different sites of IgG and considered only those binding conformations which are exhibited via the imidazole ring NH group or any other OH donating group apart from the ones which are terminally conjugated with the support matrix. We categorised binding site into two categories; category I: inner binding groove and category II: surface binding groove and observed that the hinge region of IgG has most favourable binding pocket for l-histidine and histidyl moieties. Ser and Tyr residues on the hinge region make several significant interactions with l-histidine and histidyl moieties. In case of Fc region of IgG, l-histidine and histidyl moieties closely resemble the binding modes of Protein A, biomimetic ligand 22/8 and B domain of SpA to IgG. In addition to these we have also observed a significant binding site for l-histidine and histidyl moieties at Fab region of IgG.

  17. Confined-but-Connected Quantum Solids via Controlled Ligand Displacement

    KAUST Repository

    Baumgardner, William J.

    2013-07-10

    Confined-but-connected quantum dot solids (QDS) combine the advantages of tunable, quantum-confined energy levels with efficient charge transport through enhanced electronic interdot coupling. We report the fabrication of QDS by treating self-assembled films of colloidal PbSe quantum dots with polar nonsolvents. Treatment with dimethylformamide balances the rates of self-assembly and ligand displacement to yield confined-but-connected QDS structures with cubic ordering and quasi-epitaxial interdot connections through facets of neighboring dots. The QDS structure was analyzed by a combination of transmission electron microscopy and wide-angle and small-angle X-ray scattering. Excitonic absorption signatures in optical spectroscopy confirm that quantum confinement is preserved. Transport measurements show significantly enhanced conductivity in treated films. © 2013 American Chemical Society.

  18. Autonomy and Recognition

    Directory of Open Access Journals (Sweden)

    Miguel Giusti

    2007-04-01

    Full Text Available Resumen:El presente ensayo contiene dos partes. En la primera se hace una breve descripción de las carencias de la reflexión moral a las que parece venir al encuentro el concepto de reconocimiento. Charles Taylor y Axel Honneth, protagonistas en estos debates, dan buenas razones para dirigir la discusión hacia el tema del reconocimiento, pero no coinciden ni en su definición, ni en el modo de recuperar la tesis de Hegel, ni tampoco en la forma de tratar la relación entre autonomía y reconocimiento. En la segunda parte se analiza la concepción propiamente hegeliana, con la intención de destacar el nexo esencial, no la ruptura, que existe entre la noción de reconocimiento y el modelo conceptual de la voluntad libre o del espíritu. Abstract:This essay is divided into two parts. The first one is a short description of the deficiencies of moral reflection, which seem to lead the discussion towards the concept of recognition. Charles Taylor and Axel Honneth, two of the protagonists of these debates, give very good reasons for turning the argument towards the issue of recognition, but they do not agree on its definition, on the way to recover the Hegelian thesis, or on how to approach the relationship between autonomy and recognition. The second part constitutes an analysis of the Hegelian conception of recognition, in order to highlight the essential link –rather than the rupture– between the notion of recognition and the conceptual model of free will or spirit.

  19. Galeotti on recognition as inclusion

    DEFF Research Database (Denmark)

    Lægaard, Sune

    2008-01-01

    Anna Elisabetta Galeotti's theory of 'toleration as recognition' has been criticised by Peter Jones for being conceptually incoherent, since liberal toleration presupposes a negative attitude to differences, whereas multicultural recognition requires positive affirmation hereof. The paper spells ...

  20. Explicit all-atom modeling of realistically sized ligand-capped nanocrystals.

    Science.gov (United States)

    Kaushik, Ananth P; Clancy, Paulette

    2012-03-21

    We present a study of an explicit all-atom representation of nanocrystals of experimentally relevant sizes (up to 6 nm), "capped" with alkyl chain ligands, in vacuum. We employ all-atom molecular dynamics simulation methods in concert with a well-tested intermolecular potential model, MM3 (molecular mechanics 3), for the studies presented here. These studies include determining the preferred conformation of an isolated single nanocrystal (NC), pairs of isolated NCs, and (presaging studies of superlattice arrays) unit cells of NC superlattices. We observe that very small NCs (3 nm) behave differently in a superlattice as compared to larger NCs (6 nm and above) due to the conformations adopted by the capping ligands on the NC surface. Short ligands adopt a uniform distribution of orientational preferences, including some that lie against the face of the nanocrystal. In contrast, longer ligands prefer to interdigitate. We also study the effect of changing ligand length and ligand coverage on the NCs on the preferred ligand configurations. Since explicit all-atom modeling constrains the maximum system size that can be studied, we discuss issues related to coarse-graining the representation of the ligands, including a comparison of two commonly used coarse-grained models. We find that care has to be exercised in the choice of coarse-grained model. The data provided by these realistically sized ligand-capped NCs, determined using explicit all-atom models, should serve as a reference standard for future models of coarse-graining ligands using united atom models, especially for self-assembly processes.

  1. Explicit all-atom modeling of realistically sized ligand-capped nanocrystals

    KAUST Repository

    Kaushik, Ananth P.

    2012-01-01

    We present a study of an explicit all-atom representation of nanocrystals of experimentally relevant sizes (up to 6 nm), capped with alkyl chain ligands, in vacuum. We employ all-atom molecular dynamics simulation methods in concert with a well-tested intermolecular potential model, MM3 (molecular mechanics 3), for the studies presented here. These studies include determining the preferred conformation of an isolated single nanocrystal (NC), pairs of isolated NCs, and (presaging studies of superlattice arrays) unit cells of NC superlattices. We observe that very small NCs (3 nm) behave differently in a superlattice as compared to larger NCs (6 nm and above) due to the conformations adopted by the capping ligands on the NC surface. Short ligands adopt a uniform distribution of orientational preferences, including some that lie against the face of the nanocrystal. In contrast, longer ligands prefer to interdigitate. We also study the effect of changing ligand length and ligand coverage on the NCs on the preferred ligand configurations. Since explicit all-atom modeling constrains the maximum system size that can be studied, we discuss issues related to coarse-graining the representation of the ligands, including a comparison of two commonly used coarse-grained models. We find that care has to be exercised in the choice of coarse-grained model. The data provided by these realistically sized ligand-capped NCs, determined using explicit all-atom models, should serve as a reference standard for future models of coarse-graining ligands using united atom models, especially for self-assembly processes. © 2012 American Institute of Physics.

  2. Probing riboswitch-ligand interactions using thiamine pyrophosphate analogues.

    Science.gov (United States)

    Chen, Liuhong; Cressina, Elena; Dixon, Neil; Erixon, Karl; Agyei-Owusu, Kwasi; Micklefield, Jason; Smith, Alison G; Abell, Chris; Leeper, Finian J

    2012-08-14

    The Escherichia coli thiM riboswitch forms specific contacts with its natural ligand, thiamine pyrophosphate (TPP or thiamine diphosphate), allowing it to generate not only nanomolar binding affinity, but also a high degree of discrimination against similar small molecules. A range of synthetic TPP analogues have been used to probe each of the riboswitch-ligand interactions. The results show that the pyrimidine-sensing helix of thiM is exquisitely tuned to select for TPP by recognising the H-bonding donor and acceptors around its aminopyrimidine ring and also by forming π-stacking interactions that may be sensitive to the electronics of the ring. The central thiazolium ring of TPP appears to be more important for ligand recognition than previously thought. It may contribute to binding via long-range electrostatic interactions and/or by exerting an electron withdrawing effect on the pyrimidine ring, allowing its presence to be sensed indirectly and thereby allowing discrimination between thiamine (and its phosphate esters) and other aminopyrimidines found in vivo. The pyrophosphate moiety is essential for submicromolar binding affinity, but unexpectedly, it does not appear to be strictly necessary for modulation of gene expression.

  3. RECOGNITION AND ASSESSMENT IN ACCOUNTANCY

    Directory of Open Access Journals (Sweden)

    DIMA FLORIN CONSTANTIN

    2012-11-01

    Full Text Available The recognition and assessment of the component elements of the annual financial statements’ structures is crucial in order that the information released by them fulfils the qualitative characteristics and the reflected image is a “true and fair view”. Therefore, our approach takes into consideration the recognition and assessment methods for the component elements of the financial statements’ structures, as well as certain possible risks arising from the erroneous recognition or non-recognition of some of these elements.

  4. Determinants of cyanuric acid and melamine assembly in water.

    Science.gov (United States)

    Ma, Mingming; Bong, Dennis

    2011-07-19

    While the recognition of cyanuric acid (CA) by melamine (M) and their derivatives has been known to occur in both water and organic solvents for some time, analysis of CA/M assembly in water has not been reported (Ranganathan, A.; Pedireddi, V. R.; Rao, C. N. R. J. Am. Chem. Soc.1999, 121, 1752-1753; Mathias, J. P.; Simanek, E. E.; Seto, C. T.; Whitesides, G. M. Macromol. Symp.1994, 77, 157-166; Zerkowski, J. A.; MacDonald, J. C.; Seto, C. T.; Wierda, D. A.; Whitesides, G. M. J. Am. Chem. Soc.1994, 116, 2382-2391; Mathias, J. P.; Seto, C. T.; Whitesides, G. M. Polym. Prepr.1993, 34, 92-93; Seto, C. T.; Whitesides, G. M. J. Am. Chem. Soc.1993, 115, 905-916; Zerkowski, J. A.; Seto, C. T.; Whitesides, G. M. J. Am. Chem. Soc.1992, 114, 5473-5475; Seto, C. T.; Whitesides, G. M. J. Am. Chem. Soc.1990, 112, 6409-6411; Wang, Y.; Wei, B.; Wang, Q. J. Chem. Cryst.1990, 20, 79-84; ten Cate, M. G. J.; Huskens, J.; Crego-Calama, M.; Reinhoudt, D. N. Chem.-Eur. J.2004, 10, 3632-3639). We have examined assembly of CA/M, as well as assembly of soluble trivalent CA and M derivatives (TCA/TM), in aqueous solvent, using a combination of solution phase NMR, isothermal titration and differential scanning calorimetry (ITC/DSC), cryo-transmission electron microscopy (cryo-TEM), and synthetic chemistry. While the parent heterocycles coprecipitate in water, the trivalent system displays more controlled and cooperative assembly that occurs at lower concentrations than the parent and yields a stable nanoparticle suspension. The assembly of both parent and trivalent systems is rigorously 1:1 and proceeds as an exothermic, proton-transfer coupled process in neutral pH water. Though CA and M are considered canonical hydrogen-bonding motifs in organic solvents, we find that their assembly in water is driven in large part by enthalpically favorable surface-area burial, similar to what is observed with nucleic acid recognition. There are currently few synthetic systems capable of robust molecular

  5. Supporting Quality Teachers with Recognition

    Science.gov (United States)

    Andrews, Hans A.

    2011-01-01

    Value has been found in providing recognition and awards programs for excellent teachers. Research has also found a major lack of these programs in both the USA and in Australia. Teachers receiving recognition and awards for their teaching have praised recognition programs as providing motivation for them to continue high-level instruction.…

  6. Superficial Priming in Episodic Recognition

    Science.gov (United States)

    Dopkins, Stephen; Sargent, Jesse; Ngo, Catherine T.

    2010-01-01

    We explored the effect of superficial priming in episodic recognition and found it to be different from the effect of semantic priming in episodic recognition. Participants made recognition judgments to pairs of items, with each pair consisting of a prime item and a test item. Correct positive responses to the test item were impeded if the prime…

  7. Word Recognition in Auditory Cortex

    Science.gov (United States)

    DeWitt, Iain D. J.

    2013-01-01

    Although spoken word recognition is more fundamental to human communication than text recognition, knowledge of word-processing in auditory cortex is comparatively impoverished. This dissertation synthesizes current models of auditory cortex, models of cortical pattern recognition, models of single-word reading, results in phonetics and results in…

  8. Six Regularities of Source Recognition

    Science.gov (United States)

    Glanzer, Murray; Hilford, Andy; Kim, Kisok

    2004-01-01

    In recent work, researchers have shown that source-recognition memory can be incorporated in an extended signal detection model that covers both it and item-recognition memory (A. Hilford, M. Glanzer, K. Kim, & L. T. DeCarlo, 2002). In 5 experiments, using learning variables that have an established effect on item recognition, the authors tested…

  9. Forensic Face Recognition: A Survey

    NARCIS (Netherlands)

    Ali, Tauseef; Spreeuwers, Luuk; Veldhuis, Raymond; Quaglia, Adamo; Epifano, Calogera M.

    2012-01-01

    The improvements of automatic face recognition during the last 2 decades have disclosed new applications like border control and camera surveillance. A new application field is forensic face recognition. Traditionally, face recognition by human experts has been used in forensics, but now there is a

  10. A race for RAGE ligands.

    Science.gov (United States)

    Schleicher, Erwin D

    2010-08-01

    In experimental animals a causal involvement of the multiligand receptor for advanced glycation end products (RAGE) in the development of diabetic vascular complications has been demonstrated. However, the nature of RAGE ligands present in patients with diabetic nephropathy has not yet been defined; this leaves open the relevance of the RAGE system to the human disease.

  11. A strategy for the incorporation of water molecules present in a ligand binding site into a three-dimensional quantitative structure--activity relationship analysis.

    Science.gov (United States)

    Pastor, M; Cruciani, G; Watson, K A

    1997-12-05

    Water present in a ligand binding site of a protein has been recognized to play a major role in ligand-protein interactions. To date, rational drug design techniques do not usually incorporate the effect of these water molecules into the design strategy. This work represents a new strategy for including water molecules into a three-dimensional quantitative structure-activity relationship analysis using a set of glucose analogue inhibitors of glycogen phosphorylase (GP). In this series, the structures of the ligand-enzyme complexes have been solved by X-ray crystallography, and the positions of the ligands and the water molecules at the ligand binding site are known. For the structure-activity analysis, some water molecules adjacent to the ligands were included into an assembly which encompasses both the inhibitor and the water involved in the ligand-enzyme interaction. The mobility of some water molecules at the ligand binding site of GP gives rise to differences in the ligand-water assembly which have been accounted for using a simulation study involving force-field energy calculations. The assembly of ligand plus water was used in a GRID/GOLPE analysis, and the models obtained compare favorably with equivalent models when water was excluded. Both models were analyzed in detail and compared with the crystallographic structures of the ligand-enzyme complexes in order to evaluate their ability to reproduce the experimental observations. The results demonstrate that incorporation of water molecules into the analysis improves the predictive ability of the models and makes them easier to interpret. The information obtained from interpretation of the models is in good agreement with the conclusions derived from the structural analysis of the complexes and offers valuable insights into new characteristics of the ligands which may be exploited for the design of more potent inhibitors.

  12. Molecular cloning of porcine chemokine CXC motif ligand 2 (CXCL2) and mapping to the SSC8

    Science.gov (United States)

    Maternal recognition of pregnancy is accompanied by inflammatory responses with leukocytosis and increased levels of cytokines and chemokines. Human trophoblast cells secrete chemokine CXC motif ligand 1 (CXCL1)/Gro-a and other chemotactic proteins, while monocytes co-cultured with trophoblast cells...

  13. Vehicle License Plate Recognition Syst

    Directory of Open Access Journals (Sweden)

    Meenakshi,R. B. Dubey

    2012-12-01

    Full Text Available The vehicle license plate recognition system has greater efficiency for vehicle monitoring in automatic zone access control. This Plate recognition system will avoid special tags, since all vehicles possess a unique registration number plate. A number of techniques have been used for car plate characters recognition. This system uses neural network character recognition and pattern matching of characters as two character recognition techniques. In this approach multilayer feed-forward back-propagation algorithm is used. The performance of the proposed algorithm has been tested on several car plates and provides very satisfactory results.

  14. Silk: molecular organization and control of assembly.

    Science.gov (United States)

    Valluzzi, Regina; Winkler, Stefan; Wilson, Donna; Kaplan, David L

    2002-02-28

    The interface between the science and engineering of biology and materials is an area of growing interest. One of the goals of this field is to utilize biological synthesis and processing of polymers as a route to gain insight into topics such as molecular recognition, self-assembly and the formation of materials with well-defined architectures. The biological processes involved in polymer synthesis and assembly can offer important information on fundamental interactions involved in the formation of complex material architectures, as well as practical knowledge into new and important materials related to biomaterial uses and tissue engineering needs. Classic approaches in biology, including genetic engineering, controlled microbial physiology and enzymatic synthesis, are prototypical methods used to control polymer structure and chemistry, including stereoselectivity and regioselectivity, to degrees unattainable using traditional synthetic chemistry. This type of control can lead to detailed and systematic studies of the formation of the structural hierarchy in materials and the subsequent biological responses to these materials.

  15. ex vivo DNA assembly

    Directory of Open Access Journals (Sweden)

    Adam B Fisher

    2013-10-01

    Full Text Available Even with decreasing DNA synthesis costs there remains a need for inexpensive, rapid and reliable methods for assembling synthetic DNA into larger constructs or combinatorial libraries. Advances in cloning techniques have resulted in powerful in vitro and in vivo assembly of DNA. However, monetary and time costs have limited these approaches. Here, we report an ex vivo DNA assembly method that uses cellular lysates derived from a commonly used laboratory strain of Escherichia coli for joining double-stranded DNA with short end homologies embedded within inexpensive primers. This method concurrently shortens the time and decreases costs associated with current DNA assembly methods.

  16. Target Assembly Facility

    Data.gov (United States)

    Federal Laboratory Consortium — The Target Assembly Facility integrates new armor concepts into actual armored vehicles. Featuring the capability ofmachining and cutting radioactive materials, it...

  17. Nanoparticle Array Assembly Using Chemical Templates

    Science.gov (United States)

    Adams, Sarah Marie

    This dissertation demonstrates chemically-driven self-assembly techniques to produce assemblies of closely-spaced metal nanoparticles from colloidal nanoparticle solution in order to engineer enhanced optical fields. Planar nanoparticle assemblies provide a platform for a multitude of applications and material architectures. With nanoscale inter-particle spacing, metallic nanoparticles enable increased efficiency of photovoltaic devices due to light focusing and enhancement of electromagnetic fields useful for optical sensing of molecules due to coupling of the plasmon resonance in nanoparticle gaps. For molecular sensors, development of self-assembled two-dimensional assemblies of closely-spaced nanoparticles is useful for producing surface plasmon resonance sensors and surface-enhanced Raman spectroscopy (SERS) based sensing. Using chemical self-assembly, monodisperse, colloidal gold nanoparticles were attached on self-organized polymer templates in order to pattern assemblies of nanoparticle clusters with sub-10 nanometer inter-particle spacing. First citrate-stabilized Au nanoparticles were functionalized with thioctic acid ligands in solution. Then poly(methyl methacrylate) domains in phase-separated poly(styrene-block-methyl methacrylate) (PS-b-PMMA) thin films were chemically modified with surface amine functional groups. Au nanoparticles were preferentially attached to the functionalized PMMA surface domains using cross-linking chemistry. This method allows for versatility of size, shape, and composition. In this dissertation, we demonstrated attachment of 5, 10, and 20 nm Au and 20 nm Ag nanoparticles. PS-b-PMMA thin films also exhibit versatility of domain size and morphology by varying polymer molecular weights. The nanoparticle diameter to PMMA domain size ratio influenced the cluster size. As the ratio decreased, larger clusters were observed on PMMA domains with increased frequency. SERS measurement of nanoparticle assemblies showed uniform signal

  18. Crystal-Structure-Guided Design of Self-Assembling RNA Nanotriangles.

    Science.gov (United States)

    Boerneke, Mark A; Dibrov, Sergey M; Hermann, Thomas

    2016-03-14

    RNA nanotechnology uses RNA structural motifs to build nanosized architectures that assemble through selective base-pair interactions. Herein, we report the crystal-structure-guided design of highly stable RNA nanotriangles that self-assemble cooperatively from short oligonucleotides. The crystal structure of an 81 nucleotide nanotriangle determined at 2.6 Å resolution reveals the so-far smallest circularly closed nanoobject made entirely of double-stranded RNA. The assembly of the nanotriangle architecture involved RNA corner motifs that were derived from ligand-responsive RNA switches, which offer the opportunity to control self-assembly and dissociation.

  19. Toxoplasma gondii peptide ligands open the gate of the HLA class I binding groove.

    Science.gov (United States)

    McMurtrey, Curtis; Trolle, Thomas; Sansom, Tiffany; Remesh, Soumya G; Kaever, Thomas; Bardet, Wilfried; Jackson, Kenneth; McLeod, Rima; Sette, Alessandro; Nielsen, Morten; Zajonc, Dirk M; Blader, Ira J; Peters, Bjoern; Hildebrand, William

    2016-01-29

    HLA class I presentation of pathogen-derived peptide ligands is essential for CD8+ T-cell recognition of Toxoplasma gondii infected cells. Currently, little data exist pertaining to peptides that are presented after T. gondii infection. Herein we purify HLA-A*02:01 complexes from T. gondii infected cells and characterize the peptide ligands using LCMS. We identify 195 T. gondii encoded ligands originating from both secreted and cytoplasmic proteins. Surprisingly, T. gondii ligands are significantly longer than uninfected host ligands, and these longer pathogen-derived peptides maintain a canonical N-terminal binding core yet exhibit a C-terminal extension of 1-30 amino acids. Structural analysis demonstrates that binding of extended peptides opens the HLA class I F' pocket, allowing the C-terminal extension to protrude through one end of the binding groove. In summary, we demonstrate that unrealized structural flexibility makes MHC class I receptive to parasite-derived ligands that exhibit unique C-terminal peptide extensions.

  20. A Vitamin D Receptor Selectively Activated by Gemini Analogs Reveals Ligand Dependent and Independent Effects

    Directory of Open Access Journals (Sweden)

    Tiphaine Huet

    2015-02-01

    Full Text Available The bioactive form of vitamin D [1,25(OH2D3] regulates mineral and bone homeostasis and exerts potent anti-inflammatory and antiproliferative properties through binding to the vitamin D receptor (VDR. The 3D structures of the VDR ligand-binding domain with 1,25(OH2D3 or gemini analogs unveiled the molecular mechanism underlying ligand recognition. On the basis of structure-function correlations, we generated a point-mutated VDR (VDRgem that is unresponsive to 1,25(OH2D3, but the activity of which is efficiently induced by the gemini ligands. Moreover, we show that many VDR target genes are repressed by unliganded VDRgem and that mineral ion and bone homeostasis are more impaired in VDRgem mice than in VDR null mice, demonstrating that mutations abolishing VDR ligand binding result in more severe skeletal defects than VDR null mutations. As gemini ligands induce VDRgem transcriptional activity in mice and normalize their serum calcium levels, VDRgem is a powerful tool to further unravel both liganded and unliganded VDR signaling.

  1. Electrophilic Metal Alkyl Chemistry in New Ligand Environments

    Energy Technology Data Exchange (ETDEWEB)

    Jordan, Richard F. [University of Chicago

    2013-06-30

    The goals of this project were to design new electrophilic metal alkyl complexes and to exploit these systems in fundamental studies of olefin polymerization and other important and new catalytic reactions. A key target reaction is insertion copolymerization of olefins and polar CH2=CHX vinyl monomers such as vinyl halides and vinyl ethers. During the period covered by this report we (i) investigated the properties of ortho-alkoxy-arylphosphine ligands in Ni-based olefin polymerization catalysts, (ii) studied the synthesis of double-end-capped polyethylene using group 4 metal catalysts that contain tris-pyrazolylborate ligands, (iii) explored the ethylene insertion reactivity of group 4 metal tris-pyrazolyl-borate complexes, (iv) showed that (α-diimine)PdMe{sup +} species undergo multiple insertion of silyl vinyl ethers, (v) synthesized and explored the reactivity of base-free Ni benzyl complexes that contain ortho-phosphino-arene sulfonate ligands, (vi) established the mechanism of the reaction of vinyl chloride with (α-diimine)PdMe{sup +} catalysts, (vii) explored the role of cationic polymerization and insertion chemistry in the reactions of vinyl ethers with (α-diimine)PdMe{sup +} species, (viii) discovered a new class of self-assembled tetranuclear Pd catalysts that produce high molecular weight linear polyethylene and copolymerize ethylene and vinyl fluoride, and (ix) developed model systems that enabled investigation of cis-trans isomerization of {phosphine-sulfonate}Pd(II) complexes.

  2. Geometric isomerism in coordination cages based on tris-chelate vertices: a tool to control both assembly and host/guest chemistry.

    Science.gov (United States)

    Metherell, Alexander J; Ward, Michael D

    2016-10-18

    This 'Perspective' article summarises recent work from the authors' research group on the exploitation of the simple fac/mer geometric isomerism of octahedral metal tris-chelates as a tool to control the chemistry of coordination cages based on bis(pyrazolyl-pyridine) ligands, in two different respects. Firstly this geometric isomerism plays a major role in controlling the guest binding properties of cages because a fac tris-chelate arrangement of pyrazolyl-pyridine chelates around a metal ion vertex results in formation of a convergent set of inwardly-directed C-H protons in a region of high positive electrostatic potential close to a metal cation. This collection of δ+ protons therefore provides a charge-assisted hydrogen-bond donor site, which interacts with the electron-rich regions of guest molecules that are of the correct size and shape to occupy the cage cavity, and the strength of this hydrogen-bonding interaction plays a major role in guest recognition in non-aqueous solvents. Secondly the ability to prepare mononuclear complexes with either a fac or mer arrangement of ligands provides an entry into the controlled, stepwise assembly of heterometallic cages based on a combination of kinetically inert and kinetically labile metal ions at different sites. This has allowed introduction of useful physical properties such as redox activity or luminescence, commonly associated with inert metal ions which are not amenable to participation in thermodynamic self-assembly processes, to be incorporated in a predictable way into the superstructures of coordination cages at specific sites.

  3. Controlled-deactivation cannabinergic ligands.

    Science.gov (United States)

    Sharma, Rishi; Nikas, Spyros P; Paronis, Carol A; Wood, Jodianne T; Halikhedkar, Aneetha; Guo, Jason Jianxin; Thakur, Ganesh A; Kulkarni, Shashank; Benchama, Othman; Raghav, Jimit Girish; Gifford, Roger S; Järbe, Torbjörn U C; Bergman, Jack; Makriyannis, Alexandros

    2013-12-27

    We report an approach for obtaining novel cannabinoid analogues with controllable deactivation and improved druggability. Our design involves the incorporation of a metabolically labile ester group at the 2'-position on a series of (-)-Δ(8)-THC analogues. We have sought to introduce benzylic substituents α to the ester group which affect the half-lives of deactivation through enzymatic activity while enhancing the affinities and efficacies of individual ligands for the CB1 and CB2 receptors. The 1'-(S)-methyl, 1'-gem-dimethyl, and 1'-cyclobutyl analogues exhibit remarkably high affinities for both CB receptors. The novel ligands are susceptible to enzymatic hydrolysis by plasma esterases in a controllable manner, while their metabolites are inactive at the CB receptors. In further in vitro and in vivo experiments key analogues were shown to be potent CB1 receptor agonists and to exhibit CB1-mediated hypothermic and analgesic effects.

  4. Privileged chiral ligands and catalysts

    CERN Document Server

    Zhou, Qi-Lin

    2011-01-01

    This ultimate ""must have"" and long awaited reference for every chemist working in the field of asymmetric catalysis starts with the core structure of the catalysts, explaining why a certain ligand or catalyst is so successful. It describes in detail the history, the basic structural characteristics, and the applications of these ""privileged catalysts"". A novel concept that gives readers a much deeper insight into the topic.

  5. Vesicular Stomatitis Virus Infection Promotes Immune Evasion by Preventing NKG2D-Ligand Surface Expression

    DEFF Research Database (Denmark)

    Jensen, Helle; Andresen, Lars; Nielsen, Jens;

    2011-01-01

    Vesicular stomatitis virus (VSV) has recently gained attention for its oncolytic ability in cancer treatment. Initially, we hypothesized that VSV infection could increase immune recognition of cancer cells through induction of the immune stimulatory NKG2D-ligands. Here we show that VSV infection...... leads to a robust induction of MICA mRNA expression, however the subsequent surface expression is potently hindered. Thus, VSV lines up with human cytomegalovirus (HCMV) and adenovirus, which actively subvert the immune system by negatively affecting NKG2D-ligand surface expression. VSV infection caused...... an active suppression of NKG2D-ligand surface expression, affecting both endogenous and histone deacetylase (HDAC)-inhibitor induced MICA, MICB and ULBP-2 expression. The classical immune escape mechanism of VSV (i.e., the M protein blockade of nucleocytoplasmic mRNA transport) was not involved, as the VSV...

  6. Perspective: Geometrically frustrated assemblies

    Science.gov (United States)

    Grason, Gregory M.

    2016-09-01

    This perspective will overview an emerging paradigm for self-organized soft materials, geometrically frustrated assemblies, where interactions between self-assembling elements (e.g., particles, macromolecules, proteins) favor local packing motifs that are incompatible with uniform global order in the assembly. This classification applies to a broad range of material assemblies including self-twisting protein filament bundles, amyloid fibers, chiral smectics and membranes, particle-coated droplets, curved protein shells, and phase-separated lipid vesicles. In assemblies, geometric frustration leads to a host of anomalous structural and thermodynamic properties, including heterogeneous and internally stressed equilibrium structures, self-limiting assembly, and topological defects in the equilibrium assembly structures. The purpose of this perspective is to (1) highlight the unifying principles and consequences of geometric frustration in soft matter assemblies; (2) classify the known distinct modes of frustration and review corresponding experimental examples; and (3) describe outstanding questions not yet addressed about the unique properties and behaviors of this broad class of systems.

  7. Extending reference assembly models

    DEFF Research Database (Denmark)

    Church, Deanna M.; Schneider, Valerie A.; Steinberg, Karyn Meltz;

    2015-01-01

    The human genome reference assembly is crucial for aligning and analyzing sequence data, and for genome annotation, among other roles. However, the models and analysis assumptions that underlie the current assembly need revising to fully represent human sequence diversity. Improved analysis tools...

  8. Assembly of primary cilia

    DEFF Research Database (Denmark)

    Pedersen, Lotte B; Veland, Iben R; Schrøder, Jacob M

    2008-01-01

    in primary cilia assembly or function have been associated with a panoply of disorders and diseases, including polycystic kidney disease, left-right asymmetry defects, hydrocephalus, and Bardet Biedl Syndrome. Here we provide an up-to-date review focused on the molecular mechanisms involved in the assembly...

  9. Tumor targeting via integrin ligands

    Directory of Open Access Journals (Sweden)

    Udaya Kiran eMarelli

    2013-08-01

    Full Text Available Selective and targeted delivery of drugs to tumors is a major challenge for an effective cancer therapy and also to overcome the side effects associated with current treatments. Overexpression of various receptors on tumor cells is a characteristic structural and biochemical aspect of tumors and distinguishes them from physiologically normal cells. This abnormal feature is therefore suitable for selectively directing anticancer molecules to tumors by using ligands that can preferentially recognize such receptors. Several subtypes of integrin receptors that are crucial for cell adhesion, cell signaling, cell viability and motility have been shown to have an upregulated expression on cancer cells. Thus, ligands that recognize specific integrin subtypes represent excellent candidates to be conjugated to drugs or drug carrier systems and be targeted to tumors. In this regard, integrins recognizing the RGD cell adhesive sequence have been extensively targeted for tumor specific drug delivery. Here we review key recent examples on the presentation of RGD-based integrin ligands by means of distinct drug delivery systems, and discuss the prospects of such therapies to specifically target tumor cells.

  10. Equilibrium and kinetic aspects of protein-DNA recognition.

    Science.gov (United States)

    Livshitz, M A; Gursky, G V; Zasedatelev, A S; Volkenstein, M V

    1979-01-01

    The specificity of regulatory protein binding to DNA is due to a complementarity between the sequence of reaction centres on the protein and the base pair sequence in the specific DNA site allowing the formation of a number of specific noncovalent bonds between the interacting entities. In the present communication the thermodynamic and kinetic aspects of these interactions are considered. The extent of binding specificity is shown to increase with an increase of the bond stability constants and with an increase in the number of ligand reaction centres. Kinetic analysis is carried out assuming that association process is very fast and that dissociation of nonspecific complexes is a rate-limiting step in the recognition of a specific binding site on DNA. The calculations show that a ligand can recognize its specific binding site on DNA within a reasonably limited time interval if the number of its reaction centres and the corresponding stability constants are strongly limited.

  11. Superlattices assembled through shape-induced directional binding.

    Science.gov (United States)

    Lu, Fang; Yager, Kevin G; Zhang, Yugang; Xin, Huolin; Gang, Oleg

    2015-01-01

    Organization of spherical particles into lattices is typically driven by packing considerations. Although the addition of directional binding can significantly broaden structural diversity, nanoscale implementation remains challenging. Here we investigate the assembly of clusters and lattices in which anisotropic polyhedral blocks coordinate isotropic spherical nanoparticles via shape-induced directional interactions facilitated by DNA recognition. We show that these polyhedral blocks--cubes and octahedrons--when mixed with spheres, promote the assembly of clusters with architecture determined by polyhedron symmetry. Moreover, three-dimensional binary superlattices are formed when DNA shells accommodate the shape disparity between nanoparticle interfaces. The crystallographic symmetry of assembled lattices is determined by the spatial symmetry of the block's facets, while structural order depends on DNA-tuned interactions and particle size ratio. The presented lattice assembly strategy, exploiting shape for defining the global structure and DNA-mediation locally, opens novel possibilities for by-design fabrication of binary lattices.

  12. Assembly: a resource for assembled genomes at NCBI.

    Science.gov (United States)

    Kitts, Paul A; Church, Deanna M; Thibaud-Nissen, Françoise; Choi, Jinna; Hem, Vichet; Sapojnikov, Victor; Smith, Robert G; Tatusova, Tatiana; Xiang, Charlie; Zherikov, Andrey; DiCuccio, Michael; Murphy, Terence D; Pruitt, Kim D; Kimchi, Avi

    2016-01-04

    The NCBI Assembly database (www.ncbi.nlm.nih.gov/assembly/) provides stable accessioning and data tracking for genome assembly data. The model underlying the database can accommodate a range of assembly structures, including sets of unordered contig or scaffold sequences, bacterial genomes consisting of a single complete chromosome, or complex structures such as a human genome with modeled allelic variation. The database provides an assembly accession and version to unambiguously identify the set of sequences that make up a particular version of an assembly, and tracks changes to updated genome assemblies. The Assembly database reports metadata such as assembly names, simple statistical reports of the assembly (number of contigs and scaffolds, contiguity metrics such as contig N50, total sequence length and total gap length) as well as the assembly update history. The Assembly database also tracks the relationship between an assembly submitted to the International Nucleotide Sequence Database Consortium (INSDC) and the assembly represented in the NCBI RefSeq project. Users can find assemblies of interest by querying the Assembly Resource directly or by browsing available assemblies for a particular organism. Links in the Assembly Resource allow users to easily download sequence and annotations for current versions of genome assemblies from the NCBI genomes FTP site.

  13. Self-assembled nanostructures

    CERN Document Server

    Zhang, Jin Z; Liu, Jun; Chen, Shaowei; Liu, Gang-yu

    2003-01-01

    Nanostructures refer to materials that have relevant dimensions on the nanometer length scales and reside in the mesoscopic regime between isolated atoms and molecules in bulk matter. These materials have unique physical properties that are distinctly different from bulk materials. Self-Assembled Nanostructures provides systematic coverage of basic nanomaterials science including materials assembly and synthesis, characterization, and application. Suitable for both beginners and experts, it balances the chemistry aspects of nanomaterials with physical principles. It also highlights nanomaterial-based architectures including assembled or self-assembled systems. Filled with in-depth discussion of important applications of nano-architectures as well as potential applications ranging from physical to chemical and biological systems, Self-Assembled Nanostructures is the essential reference or text for scientists involved with nanostructures.

  14. Constrained space camera assembly

    Science.gov (United States)

    Heckendorn, Frank M.; Anderson, Erin K.; Robinson, Casandra W.; Haynes, Harriet B.

    1999-01-01

    A constrained space camera assembly which is intended to be lowered through a hole into a tank, a borehole or another cavity. The assembly includes a generally cylindrical chamber comprising a head and a body and a wiring-carrying conduit extending from the chamber. Means are included in the chamber for rotating the body about the head without breaking an airtight seal formed therebetween. The assembly may be pressurized and accompanied with a pressure sensing means for sensing if a breach has occurred in the assembly. In one embodiment, two cameras, separated from their respective lenses, are installed on a mounting apparatus disposed in the chamber. The mounting apparatus includes means allowing both longitudinal and lateral movement of the cameras. Moving the cameras longitudinally focuses the cameras, and moving the cameras laterally away from one another effectively converges the cameras so that close objects can be viewed. The assembly further includes means for moving lenses of different magnification forward of the cameras.

  15. Assembly and Characterization of Coordination Polymer Nanostructural Materials at Interfaces

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    1 Results Molecular self-assembly of one-/two-dimensional (1D/2D) nanostructures has recently received great interest because the specific structures of crystals determine their unique physical and chemical properties. Coordination polymers contain two central components, connectors and linkers. Transition metal ions are often used as versatile connectors, with coordination numbers ranging from 2 to 7 dependant on the oxidation states of the metal ions. Multidentate ligands are often used as linkers, wh...

  16. Creating molecular macrocycles for anion recognition

    Directory of Open Access Journals (Sweden)

    Amar H. Flood

    2016-03-01

    Full Text Available The creation and functionality of new classes of macrocycles that are shape persistent and can bind anions is described. The genesis of triazolophane macrocycles emerges out of activity surrounding 1,2,3-triazoles made using click chemistry; and the same triazoles are responsible for anion capture. Mistakes made and lessons learnt in anion recognition provide deeper understanding that, together with theory, now provides for computer-aided receptor design. The lessons are acted upon in the creation of two new macrocycles. First, cyanostars are larger and like to capture large anions. Second is tricarb, which also favors large anions but shows a propensity to self-assemble in an orderly and stable manner, laying a foundation for future designs of hierarchical nanostructures.

  17. Visual affect recognition

    CERN Document Server

    Stathopoulou, I-O

    2010-01-01

    It is generally known that human faces, as well as body motions and gestures, provide a wealth of information about a person, such as age, race, sex and emotional state. This monograph primarily studies the perception of facial expression of emotion, and secondarily of motion and gestures, with the purpose of developing a fully automated visual affect recognition system for use in modes of human/computer interaction. The book begins with a survey of the literature on emotion perception, followed by a description of empirical studies conducted with human participants and the construction of a '

  18. Advances in Speech Recognition

    CERN Document Server

    Neustein, Amy

    2010-01-01

    This volume is comprised of contributions from eminent leaders in the speech industry, and presents a comprehensive and in depth analysis of the progress of speech technology in the topical areas of mobile settings, healthcare and call centers. The material addresses the technical aspects of voice technology within the framework of societal needs, such as the use of speech recognition software to produce up-to-date electronic health records, not withstanding patients making changes to health plans and physicians. Included will be discussion of speech engineering, linguistics, human factors ana

  19. Contribution of Solvation Energy in Protein-Peptide Recognition Systems

    Institute of Scientific and Technical Information of China (English)

    LI,Fei; LI,Wei; SHEN,Jia-Cong

    2001-01-01

    The contribution of solvation energy to guding molecualr recognition for six rigid protein-peptide systems had been eval uated by the variation in the number of the identified native like configurations and in the driving force of specific interac tion resulting from the addition of the explicit solvation term in the force field function. The AMBER force field energy and the total energy including the force field energy and the WZS solvation energy were calculated for sampled configurations. The results obtained by the calculations of both force field and total energies were compared with each other. It suggests that specific recognition of the systems in which the ligands possess larger hydrophobic or aromatic residues while the protein re ceptors provide the active surfaces with hydrophobic property.

  20. Chinese Local Government Delegation Attends 2005 National General Assembly Of Australian Local Government

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    <正>Invited by the Australian Local Government Association (ALGA), a 11-member delegation of the Chinese local government, sent by the CPAFFC, attended the 2005 National General Assembly of Australian Local Government from November 6 to 9 in Canberra. The National General Assembly The ALGA convenes a national general assembly annually to discuss issues concerning the local government. The theme of this General Assembly was Good to Great: Pursuing Progress Through Partnership, that is, asking the federal government to give the local government more financial support, equitable treatment and formal recognition. Local government representatives and well-known experts and scholars of Australia, and

  1. Recent progress in fingerprint recognition

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Fingerprint recognition has been increasingly used to realize personal identification in civilian's daily life, such as ID card, fingerprints hard disk and so on. Great improvement has been achieved in the on-line fingerprint sensing technology and automatic fingerprint recognition algorithms. Various fingerprint recognition techniques, including fingerprint acquisition, classification, enhancement and matching, are highly improved. This paper overviews recent advances in fingerprint recognition and summarizes the algorithm proposed for every step with special focuses on the enhancement of low-quality fingerprints and the matching of the distorted fingerprint images. Both issues are believed to be significant and challenging tasks. In addition, we also discuss the common evaluation for the fingerprint recognition algorithm of the Fingerprint Verification Competition 2004 (FVC2004) and the Fingerprint Vendor Technology Evaluation 2003 (FpVTE2003), based on which we could measure the performance of the recognition algorithm objectively and uniformly.

  2. Human activity recognition and prediction

    CERN Document Server

    2016-01-01

    This book provides a unique view of human activity recognition, especially fine-grained human activity structure learning, human-interaction recognition, RGB-D data based action recognition, temporal decomposition, and causality learning in unconstrained human activity videos. The techniques discussed give readers tools that provide a significant improvement over existing methodologies of video content understanding by taking advantage of activity recognition. It links multiple popular research fields in computer vision, machine learning, human-centered computing, human-computer interaction, image classification, and pattern recognition. In addition, the book includes several key chapters covering multiple emerging topics in the field. Contributed by top experts and practitioners, the chapters present key topics from different angles and blend both methodology and application, composing a solid overview of the human activity recognition techniques. .

  3. [Comparative studies of face recognition].

    Science.gov (United States)

    Kawai, Nobuyuki

    2012-07-01

    Every human being is proficient in face recognition. However, the reason for and the manner in which humans have attained such an ability remain unknown. These questions can be best answered-through comparative studies of face recognition in non-human animals. Studies in both primates and non-primates show that not only primates, but also non-primates possess the ability to extract information from their conspecifics and from human experimenters. Neural specialization for face recognition is shared with mammals in distant taxa, suggesting that face recognition evolved earlier than the emergence of mammals. A recent study indicated that a social insect, the golden paper wasp, can distinguish their conspecific faces, whereas a closely related species, which has a less complex social lifestyle with just one queen ruling a nest of underlings, did not show strong face recognition for their conspecifics. Social complexity and the need to differentiate between one another likely led humans to evolve their face recognition abilities.

  4. Genetic specificity of face recognition.

    Science.gov (United States)

    Shakeshaft, Nicholas G; Plomin, Robert

    2015-10-13

    Specific cognitive abilities in diverse domains are typically found to be highly heritable and substantially correlated with general cognitive ability (g), both phenotypically and genetically. Recent twin studies have found the ability to memorize and recognize faces to be an exception, being similarly heritable but phenotypically substantially uncorrelated both with g and with general object recognition. However, the genetic relationships between face recognition and other abilities (the extent to which they share a common genetic etiology) cannot be determined from phenotypic associations. In this, to our knowledge, first study of the genetic associations between face recognition and other domains, 2,000 18- and 19-year-old United Kingdom twins completed tests assessing their face recognition, object recognition, and general cognitive abilities. Results confirmed the substantial heritability of face recognition (61%), and multivariate genetic analyses found that most of this genetic influence is unique and not shared with other cognitive abilities.

  5. Star PolyMOCs with Diverse Structures, Dynamics, and Functions by Three-Component Assembly

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Yufeng [Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue Cambridge MA USA; Department of Chemistry, the University of Hong Kong, Pokfulam Road Hong Kong SAR China; Gu, Yuwei [Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue Cambridge MA USA; Keeler, Eric G. [Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue Cambridge MA USA; Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, 77 Massachusetts Avenue Cambridge MA USA; Park, Jiwon V. [Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue Cambridge MA USA; Griffin, Robert G. [Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue Cambridge MA USA; Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, 77 Massachusetts Avenue Cambridge MA USA; Johnson, Jeremiah A. [Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue Cambridge MA USA

    2016-12-05

    We report star polymer metal–organic cage (polyMOC) materials whose structures, mechanical properties, functionalities, and dynamics can all be precisely tailored through a simple three-component assembly strategy. The star polyMOC network is composed of tetra-arm star polymers functionalized with ligands on the chain ends, small molecule ligands, and palladium ions; polyMOCs are formed via metal–ligand coordination and thermal annealing. The ratio of small molecule ligands to polymer-bound ligands determines the connectivity of the MOC junctions and the network structure. The use of large M12L24 MOCs enables great flexibility in tuning this ratio, which provides access to a rich spectrum of material properties including tunable moduli and relaxation dynamics.

  6. Star PolyMOCs with Diverse Structures, Dynamics, and Functions by Three-Component Assembly.

    Science.gov (United States)

    Wang, Yufeng; Gu, Yuwei; Keeler, Eric G; Park, Jiwon V; Griffin, Robert G; Johnson, Jeremiah A

    2017-01-02

    We report star polymer metal-organic cage (polyMOC) materials whose structures, mechanical properties, functionalities, and dynamics can all be precisely tailored through a simple three-component assembly strategy. The star polyMOC network is composed of tetra-arm star polymers functionalized with ligands on the chain ends, small molecule ligands, and palladium ions; polyMOCs are formed via metal-ligand coordination and thermal annealing. The ratio of small molecule ligands to polymer-bound ligands determines the connectivity of the MOC junctions and the network structure. The use of large M12 L24 MOCs enables great flexibility in tuning this ratio, which provides access to a rich spectrum of material properties including tunable moduli and relaxation dynamics.

  7. Phenanthroline-2,9-bistriazoles as selective G-quadruplex ligands.

    Science.gov (United States)

    Nielsen, Mads Corvinius; Larsen, Anders Foller; Abdikadir, Faisal Hussein; Ulven, Trond

    2014-01-24

    G-quadruplex (G4) ligands are currently receiving considerable attention as potential anticancer therapeutics. A series of phenanthroline-2,9-bistriazoles carrying tethered positive end groups has been synthesized and evaluated as G4 stabilizers. The compounds were efficiently assembled by copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) in CH2Cl2 and water in the presence of a complexing agent. Characterization of the target compounds on telomeric and c-KIT G4 sequences led to the identification of guanidinium-substituted compounds as potent G4 DNA ligands with high selectivity over duplex DNA. The diisopropylguanidium ligands exhibited high selectivity for the proto-oncogenic sequence c-KIT over the human telomeric sequence in the surface plasmon resonance (SPR) assay, whereas the compounds appeared potent on both G4 structures in the FRET melting temperature assay. The phenanthroline-2,9-bistriazole ligands were thus identified as potent G4 ligands with high selectivity over duplex DNA, and preliminary results indicate that the scaffold may form basis for the development of subtype-specific G4 ligands.

  8. Why do receptor-ligand bonds in cell adhesion cluster into discrete focal-adhesion sites?

    Science.gov (United States)

    Gao, Zhiwen; Gao, Yanfei

    2016-10-01

    Cell adhesion often exhibits the clustering of the receptor-ligand bonds into discrete focal-adhesion sites near the contact edge, thus resembling a rosette shape or a contracting membrane anchored by a small number of peripheral forces. The ligands on the extracellular matrix are immobile, and the receptors in the cell plasma membrane consist of two types: high-affinity integrins (that bond to the substrate ligands and are immobile) and low-affinity integrins (that are mobile and not bonded to the ligands). Thus the adhesion energy density is proportional to the high-affinity integrin density. This paper provides a mechanistic explanation for the clustering/assembling of the receptor-ligand bonds from two main points: (1) the cellular contractile force leads to the density evolution of these two types of integrins, and results into a large high-affinity integrin density near the contact edge and (2) the front of a propagating crack into a decreasing toughness field will be unstable and wavy. From this fracture mechanics perspective, the chemomechanical equilibrium is reached when a small number of patches with large receptor-ligand bond density are anticipated to form at the cell periphery, as opposed to a uniform distribution of bonds on the entire interface. Cohesive fracture simulations show that the de-adhesion force can be significantly enhanced by this nonuniform bond density field, but the de-adhesion force anisotropy due to the substrate elastic anisotropy is significantly reduced.

  9. Speech recognition in university classrooms

    OpenAIRE

    Wald, Mike; Bain, Keith; Basson, Sara H

    2002-01-01

    The LIBERATED LEARNING PROJECT (LLP) is an applied research project studying two core questions: 1) Can speech recognition (SR) technology successfully digitize lectures to display spoken words as text in university classrooms? 2) Can speech recognition technology be used successfully as an alternative to traditional classroom notetaking for persons with disabilities? This paper addresses these intriguing questions and explores the underlying complex relationship between speech recognition te...

  10. Pilgrims Face Recognition Dataset -- HUFRD

    OpenAIRE

    Aly, Salah A.

    2012-01-01

    In this work, we define a new pilgrims face recognition dataset, called HUFRD dataset. The new developed dataset presents various pilgrims' images taken from outside the Holy Masjid El-Harram in Makkah during the 2011-2012 Hajj and Umrah seasons. Such dataset will be used to test our developed facial recognition and detection algorithms, as well as assess in the missing and found recognition system \\cite{crowdsensing}.

  11. Structure of the Membrane-tethering GRASP Domain Reveals a Unique PDZ Ligand Interaction That Mediates Golgi Biogenesis

    Energy Technology Data Exchange (ETDEWEB)

    S Truschel; D Sengupta; A Foote; A Heroux; M Macbeth; A Linstedt

    2011-12-31

    Biogenesis of the ribbon-like membrane network of the mammalian Golgi requires membrane tethering by the conserved GRASP domain in GRASP65 and GRASP55, yet the tethering mechanism is not fully understood. Here, we report the crystal structure of the GRASP55 GRASP domain, which revealed an unusual arrangement of two tandem PDZ folds that more closely resemble prokaryotic PDZ domains. Biochemical and functional data indicated that the interaction between the ligand-binding pocket of PDZ1 and an internal ligand on PDZ2 mediates the GRASP self-interaction, and structural analyses suggest that this occurs via a unique mode of internal PDZ ligand recognition. Our data uncover the structural basis for ligand specificity and provide insight into the mechanism of GRASP-dependent membrane tethering of analogous Golgi cisternae.

  12. Structure of the Membrane-tethering GRASP Domain Reveals a Unique PDZ Ligand Interaction That Mediates Golgi Biogenesis

    Energy Technology Data Exchange (ETDEWEB)

    Truschel, S.T.; Heroux, A.; Sengupta, D.; Foote, A.; Macbeth, M. R.; Linstedt, A. D.

    2011-06-10

    Biogenesis of the ribbon-like membrane network of the mammalian Golgi requires membrane tethering by the conserved GRASP domain in GRASP65 and GRASP55, yet the tethering mechanism is not fully understood. Here, we report the crystal structure of the GRASP55 GRASP domain, which revealed an unusual arrangement of two tandem PDZ folds that more closely resemble prokaryotic PDZ domains. Biochemical and functional data indicated that the interaction between the ligand-binding pocket of PDZ1 and an internal ligand on PDZ2 mediates the GRASP self-interaction, and structural analyses suggest that this occurs via a unique mode of internal PDZ ligand recognition. Our data uncover the structural basis for ligand specificity and provide insight into the mechanism of GRASP-dependent membrane tethering of analogous Golgi cisternae.

  13. Using chiral molecules as an approach to address low-druggability recognition sites.

    Science.gov (United States)

    Lucas, Xavier; Günther, Stefan

    2014-11-05

    The content of chiral carbon atoms or structural complexity, which is known to correlate well with relevant physicochemical properties of small molecules, represents a promising descriptor that could fill the gap in existing drug discovery between ligand library filtering rules and the corresponding properties of the target's recognition site. Herein, we present an in silico study on the yet unclear underlying correlations between molecular complexity and other more sophisticated physicochemical and biological properties. By analyzing thousands of protein-ligand complexes from DrugBank, we show that increasing molecular complexity of drugs is an approach to addressing particularly low-druggability and polar recognition sites. We also show that biologically relevant protein classes characteristically bind molecules with a certain degree of structural complexity. Three distinct behaviors toward drug recognition are described. The reported results set the basis for a better understanding of protein-drug recognition, and open the possibility of including target information in the filtering of large ligand libraries for screening.

  14. Speech Recognition on Mobile Devices

    DEFF Research Database (Denmark)

    Tan, Zheng-Hua; Lindberg, Børge

    2010-01-01

    The enthusiasm of deploying automatic speech recognition (ASR) on mobile devices is driven both by remarkable advances in ASR technology and by the demand for efficient user interfaces on such devices as mobile phones and personal digital assistants (PDAs). This chapter presents an overview of ASR...... in the mobile context covering motivations, challenges, fundamental techniques and applications. Three ASR architectures are introduced: embedded speech recognition, distributed speech recognition and network speech recognition. Their pros and cons and implementation issues are discussed. Applications within...... command and control, text entry and search are presented with an emphasis on mobile text entry....

  15. Frequency-Based Fingerprint Recognition

    Science.gov (United States)

    Aguilar, Gualberto; Sánchez, Gabriel; Toscano, Karina; Pérez, Héctor

    abstract Fingerprint recognition is one of the most popular methods used for identification with greater success degree. Fingerprint has unique characteristics called minutiae, which are points where a curve track ends, intersects, or branches off. In this chapter a fingerprint recognition method is proposed in which a combination of Fast Fourier Transform (FFT) and Gabor filters is used for image enhancement. A novel recognition stage using local features for recognition is also proposed. Also a verification stage is introduced to be used when the system output has more than one person.

  16. Markov Models for Handwriting Recognition

    CERN Document Server

    Plotz, Thomas

    2011-01-01

    Since their first inception, automatic reading systems have evolved substantially, yet the recognition of handwriting remains an open research problem due to its substantial variation in appearance. With the introduction of Markovian models to the field, a promising modeling and recognition paradigm was established for automatic handwriting recognition. However, no standard procedures for building Markov model-based recognizers have yet been established. This text provides a comprehensive overview of the application of Markov models in the field of handwriting recognition, covering both hidden

  17. Study of Face Recognition Techniques

    Directory of Open Access Journals (Sweden)

    Sangeeta Kaushik

    2014-12-01

    Full Text Available A study of both face recognition and detection techniques is carried out using the algorithms like Principal Component Analysis (PCA, Kernel Principal Component Analysis (KPCA, Linear Discriminant Analysis (LDA and Line Edge Map (LEM. These algorithms show different rates of accuracy under different conditions. The automatic recognition of human faces presents a challenge to the pattern recognition community. Typically, human faces are different in shapes with minor similarity from person to person. Furthermore, lighting condition changes, facial expressions and pose variations further complicate the face recognition task as one of the difficult problems in pattern analysis.

  18. Radically enhanced molecular recognition

    KAUST Repository

    Trabolsi, Ali

    2009-12-17

    The tendency for viologen radical cations to dimerize has been harnessed to establish a recognition motif based on their ability to form extremely strong inclusion complexes with cyclobis(paraquat-p-phenylene) in its diradical dicationic redox state. This previously unreported complex involving three bipyridinium cation radicals increases the versatility of host-guest chemistry, extending its practice beyond the traditional reliance on neutral and charged guests and hosts. In particular, transporting the concept of radical dimerization into the field of mechanically interlocked molecules introduces a higher level of control within molecular switches and machines. Herein, we report that bistable and tristable [2]rotaxanes can be switched by altering electrochemical potentials. In a tristable [2]rotaxane composed of a cyclobis(paraquat-p-phenylene) ring and a dumbbell with tetrathiafulvalene, dioxynaphthalene and bipyridinium recognition sites, the position of the ring can be switched. On oxidation, it moves from the tetrathiafulvalene to the dioxynaphthalene, and on reduction, to the bipyridinium radical cation, provided the ring is also reduced simultaneously to the diradical dication. © 2010 Macmillan Publishers Limited. All rights reserved.

  19. Modular assembled space telescope

    Science.gov (United States)

    Feinberg, Lee D.; Budinoff, Jason; MacEwen, Howard; Matthews, Gary; Postman, Marc

    2013-09-01

    We present a new approach to building a modular segmented space telescope that greatly leverages the heritage of the Hubble Space Telescope and the James Webb Space Telescope. The modular design in which mirror segments are assembled into identical panels allows for economies of scale and for efficient space assembly that make a 20-m aperture approach cost effective. This assembly approach can leverage NASA's future capabilities and has the power to excite the public's imagination. We discuss the science drivers, basic architecture, technology, and leveraged NASA infrastructure, concluding with a proposed plan for going forward.

  20. DC source assemblies

    Science.gov (United States)

    Campbell, Jeremy B; Newson, Steve

    2013-02-26

    Embodiments of DC source assemblies of power inverter systems of the type suitable for deployment in a vehicle having an electrically grounded chassis are provided. An embodiment of a DC source assembly comprises a housing, a DC source disposed within the housing, a first terminal, and a second terminal. The DC source also comprises a first capacitor having a first electrode electrically coupled to the housing, and a second electrode electrically coupled to the first terminal. The DC source assembly further comprises a second capacitor having a first electrode electrically coupled to the housing, and a second electrode electrically coupled to the second terminal.

  1. 从配位体到配位络合物结构:扫描隧道显微学的分子工程%From ligands to coordinated complex architectures:a molecular engineering with scanning tunneling microscopy

    Institute of Scientific and Technical Information of China (English)

    万立骏

    2006-01-01

    @@ With the development of modem coordination chemistry,various metal-ligand complexes with elaborate structures have been synthesized.[1]The structural complexities as well as the coordination processes of these metal-ligand complexes can be partially comparable to those in biology system formed by self-assembling with the weak intermolecular or intramolecular interactions.

  2. Synthesis and self-assembly of spin-labile and redox-active manganese(III) complexes.

    Science.gov (United States)

    Gandolfi, Claudio; Cotting, Tatiana; Martinho, Paulo N; Sereda, Olha; Neels, Antonia; Morgan, Grace G; Albrecht, Martin

    2011-03-07

    New amphiphilic and spin-labile Mn(III) complexes based on dianionic N(4)O(2)-hexadentate sal(2)trien or sal(2)bapen ligands, which contain OC(6)H(13), OC(12)H(25), or OC(18)H(37) alkoxy substituents at different positions of the salicylidene unit were prepared (H(2)sal(2)trien = N,N'''-bis(salicylidene)-1,4,7,10-tetraazadecane, H(2)sal(2)bapen = N,N'''-bis(salicylidene)-1,5,8,12-tetraazadodecane). According to electrochemical measurements, these complexes undergo two (quasi)reversible redox processes. Temperature-dependent magnetic measurements revealed a high-spin configuration for all sal(2)trien complexes (S = 2) and gradual spin crossover for sal(2)bapen complexes from high to low spin (S = 1). The chain length strongly influences the spin crossover, as C(18)-functionalization stabilizes the low spin state at much higher temperatures than shorter alkyl chains. Moreover, long alkyl chains allow for spontaneous self-assembly of the molecules, which was investigated in single crystals and in Langmuir-films at the air-water interface. Long alkyl chains (C(12) or C(18)) as well as a mutual syn-orientation of these molecular recognition sites were required for the Langmuir monolayers to be stable.

  3. Ligand placement based on prior structures: the guided ligand-replacement method

    Energy Technology Data Exchange (ETDEWEB)

    Klei, Herbert E. [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Bristol-Myers Squibb, Princeton, NJ 08543-4000 (United States); Moriarty, Nigel W., E-mail: nwmoriarty@lbl.gov; Echols, Nathaniel [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Terwilliger, Thomas C. [Los Alamos National Laboratory, Los Alamos, NM 87545-0001 (United States); Baldwin, Eric T. [Bristol-Myers Squibb, Princeton, NJ 08543-4000 (United States); Natural Discovery LLC, Princeton, NJ 08542-0096 (United States); Pokross, Matt; Posy, Shana [Bristol-Myers Squibb, Princeton, NJ 08543-4000 (United States); Adams, Paul D. [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); University of California at Berkeley, Berkeley, CA 94720-1762 (United States)

    2014-01-01

    A new module, Guided Ligand Replacement (GLR), has been developed in Phenix to increase the ease and success rate of ligand placement when prior protein-ligand complexes are available. The process of iterative structure-based drug design involves the X-ray crystal structure determination of upwards of 100 ligands with the same general scaffold (i.e. chemotype) complexed with very similar, if not identical, protein targets. In conjunction with insights from computational models and assays, this collection of crystal structures is analyzed to improve potency, to achieve better selectivity and to reduce liabilities such as absorption, distribution, metabolism, excretion and toxicology. Current methods for modeling ligands into electron-density maps typically do not utilize information on how similar ligands bound in related structures. Even if the electron density is of sufficient quality and resolution to allow de novo placement, the process can take considerable time as the size, complexity and torsional degrees of freedom of the ligands increase. A new module, Guided Ligand Replacement (GLR), was developed in Phenix to increase the ease and success rate of ligand placement when prior protein–ligand complexes are available. At the heart of GLR is an algorithm based on graph theory that associates atoms in the target ligand with analogous atoms in the reference ligand. Based on this correspondence, a set of coordinates is generated for the target ligand. GLR is especially useful in two situations: (i) modeling a series of large, flexible, complicated or macrocyclic ligands in successive structures and (ii) modeling ligands as part of a refinement pipeline that can automatically select a reference structure. Even in those cases for which no reference structure is available, if there are multiple copies of the bound ligand per asymmetric unit GLR offers an efficient way to complete the model after the first ligand has been placed. In all of these applications, GLR

  4. Attribute measure recognition approach and its applications to emitter recognition

    Institute of Scientific and Technical Information of China (English)

    GUAN Xin; HE You; YI Xiao

    2005-01-01

    This paper studies the emitter recognition problem. A new recognition method based on attribute measure for emitter recognition is put forward. The steps of the method are presented. The approach to determining the weight coefficient is also discussed. Moreover, considering the temporal redundancy of emitter information detected by multi-sensor system, this new recognition method is generalized to multi-sensor system. A method based on the combination of attribute measure and D-S evidence theory is proposed. The implementation of D-S reasoning is always restricted by basic probability assignment function. Constructing basic probability assignment function based on attribute measure is presented in multi-sensor recognition system. Examples of recognizing the emitter purpose and system are selected to demonstrate the method proposed. Experimental results show that the performance of this new method is accurate and effective.

  5. The Legal Recognition of Sign Languages

    Science.gov (United States)

    De Meulder, Maartje

    2015-01-01

    This article provides an analytical overview of the different types of explicit legal recognition of sign languages. Five categories are distinguished: constitutional recognition, recognition by means of general language legislation, recognition by means of a sign language law or act, recognition by means of a sign language law or act including…

  6. Designing Assemblies Of Plates

    Science.gov (United States)

    Williams, F. W.; Kennedy, D.; Butler, R.; Aston, G.; Anderson, M. S.

    1992-01-01

    VICONOPT calculates vibrations and instabilities of assemblies of prismatic plates. Designed for efficient, accurate analysis of buckling and vibration, and for optimum design of panels of composite materials. Written in FORTRAN 77.

  7. Ligand conjugation to bimodal poly(ethylene glycol) brush layers on microbubbles.

    Science.gov (United States)

    Chen, Cherry C; Borden, Mark A

    2010-08-17

    Using microbubbles as model systems, we examined molecular diffusion and binding to colloidal surfaces in bimodal poly(ethylene glycol) (PEG) brush layers. A microbubble is a gaseous colloidal particle with a diameter of less than 10 mum, of which the surface comprises amphiphilic phospholipids self-assembled to form a lipid monolayer shell. Due to the compressible gas core, microbubbles provide a sensitive acoustic response and are currently used as ultrasound contrast agents. Similar to the design of long circulating liposomes, PEG chains are typically incorporated into the shell of microbubbles to form a steric barrier against coalescence and adsorption of macromolecules to the microbubble surface. We introduced a buried-ligand architecture (BLA) design where the microbubble surface was coated with a bimodal PEG brush. After microbubbles were generated, fluorescent ligands with different molecular weights were conjugated to the tethered functional groups on the shorter PEG chains, while the longer PEG chains served as a shield to protect these ligands from exposure to the surrounding environment. BLA microbubbles reduced the binding of macromolecules (>10 kDa) to the tethers due to the steric hindrance of the PEG overbrush while allowing the uninhibited attachment of small molecules (microbubbles compared to exposed-ligand architecture (ELA) microbubbles. The binding of SA-FITC to BLA microbubbles suggested a possible phase separation between the lipid species on the surface leading to populations of revealed and concealed ligands. Ligand conjugation kinetics was independent of microbubble size, regardless of ligand size or microbubble architecture. We observed, for the first time, streptavidin-induced surface structure formation for ELA microbubbles and proposed that this phenomenon may be correlated to flow cytometry scattering measurements. We therefore demonstrated the feasibility of postlabeling for small-molecule ligands to BLA microbubbles to generate

  8. Neat and complete: Thiolate-ligand exchange on a silver molecular nanoparticle

    KAUST Repository

    AbdulHalim, Lina G.

    2014-11-12

    Atomically precise thiolate-protected noble metal molecular nanoparticles are a promising class of model nanomaterials for catalysis, optoelectronics, and the bottom-up assembly of true molecular crystals. However, these applications have not fully materialized due to a lack of ligand exchange strategies that add functionality, but preserve the properties of these remarkable particles. Here we present a method for the rapid (<30 s) and complete thiolate-for-thiolate exchange of the highly sought after silver molecular nanoparticle [Ag44(SR)30]-4. Only by using this method were we able to preserve the precise nature of the particles and simultaneously replace the native ligands with ligands containing a variety of functional groups. Crucially, as a result of our method we were able to process the particles into smooth thin films, paving the way for their integration into solution-processed devices.

  9. Rotational Control of a Dirhodium-Centered Supramolecular Four-Gear System by Ligand Exchange.

    Science.gov (United States)

    Sanada, Kazuma; Ube, Hitoshi; Shionoya, Mitsuhiko

    2016-03-09

    Self-assembled molecular machines have great potential to enable noncovalent regulation of a coupled motion of the building blocks. Herein we report the synthesis and the rotational control of a lantern-type dirhodium complex with circularly arranged four 2,3,6,7,14,15-hexamethyltriptycene carboxylates as gears and two axial ligands as the rate control elements. The rotating rates in solution were markedly affected by the coordination ability and the bulkiness of axial ligands. Notably, the rate changes were closely correlated with the changes in the electronic states of the dirhodium center. Such ligand exchange-based control of rotational motions with color changes would advance stimulus-responsive metallo-molecular multirotors.

  10. Dithiocarbamate Assembly on Gold

    OpenAIRE

    Yan ZHAO; Perez-Segarra, Waleska; Shi, Qicun; Wei, Alexander

    2005-01-01

    Metal surfaces are functionalized by stable dithiocarbamate ligands when exposed to carbon disulfide and secondary amines. The adsorbed dithiocarbamates are robust under a wide pH range and can resist displacement by other chemisorptive surfactants, providing an attractive method for conjugating sensitive molecules onto metal surfaces.

  11. Composite organization of the cobalamin binding and cubilin recognition sites of intrinsic factor

    DEFF Research Database (Denmark)

    Fedosov, Sergey N; Fedosova, Natalya U; Berglund, Lars

    2005-01-01

    ; however, efficient retention of the ligand required the presence of both fragments. Detailed schemes of the interaction of Cbl with IF(50) and with IF(30) and IF(20) are presented, where the sequential attachment of Cbl to the IF(20) and IF(30) domains plays the key role in recognition and retention...... of the ligand. Each isolated fragment of IF was tested for the binding to the specific receptor cubilin in the presence or absence of Cbl. Neither apo nor holo forms of IF(20) and IF(30) were recognized by the receptor. When two fragments were mixed and incubated with Cbl, they associated into a stable complex...

  12. Polymer Directed Protein Assemblies

    Directory of Open Access Journals (Sweden)

    Patrick van Rijn

    2013-05-01

    Full Text Available Protein aggregation and protein self-assembly is an important occurrence in natural systems, and is in some form or other dictated by biopolymers. Very obvious influences of biopolymers on protein assemblies are, e.g., virus particles. Viruses are a multi-protein assembly of which the morphology is dictated by poly-nucleotides namely RNA or DNA. This “biopolymer” directs the proteins and imposes limitations on the structure like the length or diameter of the particle. Not only do these bionanoparticles use polymer-directed self-assembly, also processes like amyloid formation are in a way a result of directed protein assembly by partial unfolded/misfolded biopolymers namely, polypeptides. The combination of proteins and synthetic polymers, inspired by the natural processes, are therefore regarded as a highly promising area of research. Directed protein assembly is versatile with respect to the possible interactions which brings together the protein and polymer, e.g., electrostatic, v.d. Waals forces or covalent conjugation, and possible combinations are numerous due to the large amounts of different polymers and proteins available. The protein-polymer interacting behavior and overall morphology is envisioned to aid in clarifying protein-protein interactions and are thought to entail some interesting new functions and properties which will ultimately lead to novel bio-hybrid materials.

  13. Iris Recognition Using Wavelet

    Directory of Open Access Journals (Sweden)

    Khaliq Masood

    2013-08-01

    Full Text Available Biometric systems are getting more attention in the present era. Iris recognition is one of the most secure and authentic among the other biometrics and this field demands more authentic, reliable and fast algorithms to implement these biometric systems in real time. In this paper, an efficient localization technique is presented to identify pupil and iris boundaries using histogram of the iris image. Two small portions of iris have been used for polar transformation to reduce computational time and to increase the efficiency of the system. Wavelet transform is used for feature vector generation. Rotation of iris is compensated without shifts in the iris code. System is tested on Multimedia University Iris Database and results show that proposed system has encouraging performance.

  14. Chemical recognition software

    Energy Technology Data Exchange (ETDEWEB)

    Wagner, J.S.; Trahan, M.W.; Nelson, W.E.; Hargis, P.H. Jr.; Tisone, G.C.

    1994-06-01

    We have developed a capability to make real time concentration measurements of individual chemicals in a complex mixture using a multispectral laser remote sensing system. Our chemical recognition and analysis software consists of three parts: (1) a rigorous multivariate analysis package for quantitative concentration and uncertainty estimates, (2) a genetic optimizer which customizes and tailors the multivariate algorithm for a particular application, and (3) an intelligent neural net chemical filter which pre-selects from the chemical database to find the appropriate candidate chemicals for quantitative analyses by the multivariate algorithms, as well as providing a quick-look concentration estimate and consistency check. Detailed simulations using both laboratory fluorescence data and computer synthesized spectra indicate that our software can make accurate concentration estimates from complex multicomponent mixtures, even when the mixture is noisy and contaminated with unknowns.

  15. Chemical recognition software

    Energy Technology Data Exchange (ETDEWEB)

    Wagner, J.S.; Trahan, M.W.; Nelson, W.E.; Hargis, P.J. Jr.; Tisone, G.C.

    1994-12-01

    We have developed a capability to make real time concentration measurements of individual chemicals in a complex mixture using a multispectral laser remote sensing system. Our chemical recognition and analysis software consists of three parts: (1) a rigorous multivariate analysis package for quantitative concentration and uncertainty estimates, (2) a genetic optimizer which customizes and tailors the multivariate algorithm for a particular application, and (3) an intelligent neural net chemical filter which pre-selects from the chemical database to find the appropriate candidate chemicals for quantitative analyses by the multivariate algorithms, as well as providing a quick-look concentration estimate and consistency check. Detailed simulations using both laboratory fluorescence data and computer synthesized spectra indicate that our software can make accurate concentration estimates from complex multicomponent mixtures. even when the mixture is noisy and contaminated with unknowns.

  16. SAR: Stroke Authorship Recognition

    KAUST Repository

    Shaheen, Sara

    2015-10-15

    Are simple strokes unique to the artist or designer who renders them? If so, can this idea be used to identify authorship or to classify artistic drawings? Also, could training methods be devised to develop particular styles? To answer these questions, we propose the Stroke Authorship Recognition (SAR) approach, a novel method that distinguishes the authorship of 2D digitized drawings. SAR converts a drawing into a histogram of stroke attributes that is discriminative of authorship. We provide extensive classification experiments on a large variety of data sets, which validate SAR\\'s ability to distinguish unique authorship of artists and designers. We also demonstrate the usefulness of SAR in several applications including the detection of fraudulent sketches, the training and monitoring of artists in learning a particular new style and the first quantitative way to measure the quality of automatic sketch synthesis tools. © 2015 The Eurographics Association and John Wiley & Sons Ltd.

  17. Endocytosis via galactose receptors in vivo. Ligand size directs uptake by hepatocytes and/or liver macrophages

    Energy Technology Data Exchange (ETDEWEB)

    Schlepper-Schaefer, J.; Huelsmann, D.; Djovkar, A.; Meyer, H.E.; Herbertz, L.; Kolb, H.; Kolb-Bachofen, V.

    1986-01-01

    The intrahepatic binding and uptake of variously sized ligands with terminal galactosyl residues is rat liver was followed. The ligands were administered to prefixed livers in binding studies and in vivo and in situ (serum-free perfused livers) in uptake studies. Gold sols with different particle diameters were prepared: 5 nm (Au/sub 5/), 17 nm (Au/sub 17/), 50 nm (Au/sub 50/) and coated with galactose exposing glycoproteins (asialofetuin (ASF) or lactosylated BSA (LacBSA)). Electron microscopy of mildly prefixed livers perfused with LacBSA-Au/sub 5/ in serum-free medium showed ligand binding to liver macrophages, hepatocytes and endothelial cells. Ligands bound to prefixed cell surfaces reflect the initial distribution of receptor activity: pre-aggregated clusters of ligands are found on liver macrophages, single particles statistically distributed on hepatocytes and pre-aggregated clusters of particles restricted to coated pits on endothelial cells. Ligand binding is prevented in the presence of 80 mM N-acetylgalactosamine (GalNAc), while N-acetylglucosamine (GlcNAc) is without effect. Electron microscopy of livers after ligand injection into the tail vein shows that in vivo uptake of electron-dense galactose particles by liver cells is size-dependent. In vivo uptake by liver macrophages is mediated by galactose-specific recognition as shown by inhibition with GalNAc.

  18. Insights into ligand binding to PreQ1 Riboswitch Aptamer from molecular dynamics simulations.

    Directory of Open Access Journals (Sweden)

    Zhou Gong

    Full Text Available Riboswitches play roles in transcriptional or translational regulation through specific ligand binding of their aptamer domains. Although a number of ligand-bound aptamer complex structures have been solved, it is important to know ligand-free conformations of the aptamers in order to understand the mechanism of specific binding by ligands. In this paper, preQ1 riboswitch aptamer domain from Bacillus subtilis is studied by overall 1.5 μs all-atom molecular dynamics simulations We found that the ligand-free aptamer has a stable state with a folded P1-L3 and open binding pocket. The latter forms a cytosine-rich pool in which the nucleotide C19 oscillates between close and open positions, making it a potential conformation for preQ1 entrance. The dynamic picture further suggests that the specific recognition of preQ1 by the aptamer domain is not only facilitated by the key nucleotide C19 but also aided and enhanced by other cytosines around the binding pocket. These results should help to understand the details of preQ1 binding.

  19. Bovine Norovirus: Carbohydrate Ligand, Environmental Contamination, and Potential Cross-Species Transmission via Oysters ▿ †

    Science.gov (United States)

    Zakhour, Maha; Maalouf, Haifa; Di Bartolo, Ilaria; Haugarreau, Larissa; Le Guyader, Françoise S.; Ruvoën-Clouet, Nathalie; Le Saux, Jean-Claude; Ruggeri, Franco Maria; Pommepuy, Monique; Le Pendu, Jacques

    2010-01-01

    Noroviruses (NoV) are major agents of acute gastroenteritis in humans and the primary pathogens of shellfish-related outbreaks. Previous studies showed that some human strains bind to oyster tissues through carbohydrate ligands that are similar to their human receptors. Thus, based on presentation of shared norovirus carbohydrate ligands, oysters could selectively concentrate animal strains with increased ability to overcome species barriers. In comparison with human GI and GII strains, bovine GIII NoV strains, although frequently detected in bovine feces and waters of two estuaries of Brittany, were seldom detected in oysters grown in these estuaries. Characterization of the carbohydrate ligand from a new GIII strain indicated recognition of the alpha-galactosidase (α-Gal) epitope not expressed by humans, similar to the GIII.2 Newbury2 strain. This ligand was not detectable on oyster tissues, suggesting that oysters may not be able to accumulate substantial amounts of GIII strains due to the lack of shared carbohydrate ligand and that they should be unable to contribute to select GIII strains with an increased ability to recognize humans. PMID:20709837

  20. pK(a) based protonation states and microspecies for protein-ligand docking.

    Science.gov (United States)

    ten Brink, Tim; Exner, Thomas E

    2010-11-01

    In this paper we present our reworked approach to generate ligand protonation states with our structure preparation tool SPORES (Structure PrOtonation and REcognition System). SPORES can be used for the preprocessing of proteins and protein-ligand complexes as e.g. taken from the Protein Data Bank as well as for the setup of 3D ligand databases. It automatically assigns atom and bond types, generates different protonation, tautomeric states as well as different stereoisomers. In the revised version, pKa calculations with the ChemAxon software MARVIN are used either to determine the likeliness of a combinatorial generated protonation state or to determine the titrable atoms used in the combinatorial approach. Additionally, the MARVIN software is used to predict microspecies distributions of ligand molecules. Docking studies were performed with our recently introduced program PLANTS (Protein-Ligand ANT System) on all protomers resulting from the three different selection methods for the well established CCDC/ASTEX clean data set demonstrating the usefulness of especially the latter approach.

  1. Forensic Face Recognition: A Survey

    NARCIS (Netherlands)

    Ali, Tauseef; Veldhuis, Raymond; Spreeuwers, Luuk

    2010-01-01

    Beside a few papers which focus on the forensic aspects of automatic face recognition, there is not much published about it in contrast to the literature on developing new techniques and methodologies for biometric face recognition. In this report, we review forensic facial identification which is t

  2. Side-View Face Recognition

    NARCIS (Netherlands)

    Santemiz, Pinar; Spreeuwers, Luuk J.; Veldhuis, Raymond N.J.; Biggelaar , van den Olivier

    2011-01-01

    As a widely used biometrics, face recognition has many advantages such as being non-intrusive, natural and passive. On the other hand, in real-life scenarios with uncontrolled environment, pose variation up to side-view positions makes face recognition a challenging work. In this paper we discuss th

  3. Quantum-Limited Image Recognition

    Science.gov (United States)

    1989-12-01

    J. S. Bomba ,’Alpha-numeric character recognition using local operations,’ Fall Joint Comput. Conf., 218-224 (1959). 53. D. Barnea and H. Silverman...for Chapter 6 1. J. S. Bomba ,’Alpha-numeric character recognition using local operations,’ Fall Joint Comput. Conf., 218-224 (1959). 2. D. Bamea and H

  4. FILTWAM and Voice Emotion Recognition

    NARCIS (Netherlands)

    Bahreini, Kiavash; Nadolski, Rob; Westera, Wim

    2014-01-01

    This paper introduces the voice emotion recognition part of our framework for improving learning through webcams and microphones (FILTWAM). This framework enables multimodal emotion recognition of learners during game-based learning. The main goal of this study is to validate the use of microphone d

  5. Coordinate Transformations in Object Recognition

    Science.gov (United States)

    Graf, Markus

    2006-01-01

    A basic problem of visual perception is how human beings recognize objects after spatial transformations. Three central classes of findings have to be accounted for: (a) Recognition performance varies systematically with orientation, size, and position; (b) recognition latencies are sequentially additive, suggesting analogue transformation…

  6. Bile salt recognition by human liver fatty acid binding protein.

    Science.gov (United States)

    Favretto, Filippo; Santambrogio, Carlo; D'Onofrio, Mariapina; Molinari, Henriette; Grandori, Rita; Assfalg, Michael

    2015-04-01

    Fatty acid binding proteins (FABPs) act as intracellular carriers of lipid molecules, and play a role in global metabolism regulation. Liver FABP (L-FABP) is prominent among FABPs for its wide ligand repertoire, which includes long-chain fatty acids as well as bile acids (BAs). In this work, we performed a detailed molecular- and atomic-level analysis of the interactions established by human L-FABP with nine BAs to understand the binding specificity for this important class of cholesterol-derived metabolites. Protein-ligand complex formation was monitored using heteronuclear NMR, steady-state fluorescence spectroscopy, and mass spectrometry. BAs were found to interact with L-FABP with dissociation constants in the narrow range of 0.6-7 μm; however, the diverse substitution patterns of the sterol nucleus and the presence of side-chain conjugation resulted in complexes endowed with various degrees of conformational heterogeneity. Trihydroxylated BAs formed monomeric complexes in which single ligand molecules occupied similar internal binding sites, based on chemical-shift perturbation data. Analysis of NMR line shapes upon progressive addition of taurocholate indicated that the binding mechanism departed from a simple binary association equilibrium, and instead involved intermediates along the binding path. The co-linear chemical shift behavior observed for L-FABP complexes with cholate derivatives added insight into conformational dynamics in the presence of ligands. The observed spectroscopic features of L-FABP/BA complexes, discussed in relation to ligand chemistry, suggest possible molecular determinants of recognition, with implications regarding intracellular BA transport. Our findings suggest that human L-FABP is a poorly selective, universal BA binder.

  7. CB receptor ligands from plants.

    Science.gov (United States)

    Woelkart, Karin; Salo-Ahen, Outi M H; Bauer, Rudolf

    2008-01-01

    Advances in understanding the physiology and pharmacology of the endogenous cannabinoid system have potentiated the interest of cannabinoid receptors as potential therapeutic targets. Cannabinoids have been shown to modulate a variety of immune cell functions and have therapeutic implications on central nervous system (CNS) inflammation, chronic inflammatory conditions such as arthritis, and may be therapeutically useful in treating autoimmune conditions such as multiple sclerosis. Many of these drug effects occur through cannabinoid receptor signalling mechanisms and the modulation of cytokines and other gene products. Further, endocannabinoids have been found to have many physiological and patho-physiological functions, including mood alteration and analgesia, control of energy balance, gut motility, motor and co-ordination activities, as well as alleviation of neurological, psychiatric and eating disorders. Plants offer a wide range of chemical diversity and have been a growing domain in the search for effective cannabinoid ligands. Cannabis sativa L. with the known plant cannabinoid, Delta(9-)tetrahydrocannabinol (THC) and Echinacea species with the cannabinoid (CB) receptor-binding lipophilic alkamides are the best known herbal cannabimimetics. This review focuses on the state of the art in CB ligands from plants, as well their possible therapeutic and immunomodulatory effects.

  8. Ligand photo-isomerization triggers conformational changes in iGluR2 ligand binding domain.

    Directory of Open Access Journals (Sweden)

    Tino Wolter

    Full Text Available Neurological glutamate receptors bind a variety of artificial ligands, both agonistic and antagonistic, in addition to glutamate. Studying their small molecule binding properties increases our understanding of the central nervous system and a variety of associated pathologies. The large, oligomeric multidomain membrane protein contains a large and flexible ligand binding domains which undergoes large conformational changes upon binding different ligands. A recent application of glutamate receptors is their activation or inhibition via photo-switchable ligands, making them key systems in the emerging field of optochemical genetics. In this work, we present a theoretical study on the binding mode and complex stability of a novel photo-switchable ligand, ATA-3, which reversibly binds to glutamate receptors ligand binding domains (LBDs. We propose two possible binding modes for this ligand based on flexible ligand docking calculations and show one of them to be analogues to the binding mode of a similar ligand, 2-BnTetAMPA. In long MD simulations, it was observed that transitions between both binding poses involve breaking and reforming the T686-E402 protein hydrogen bond. Simulating the ligand photo-isomerization process shows that the two possible configurations of the ligand azo-group have markedly different complex stabilities and equilibrium binding modes. A strong but slow protein response is observed after ligand configuration changes. This provides a microscopic foundation for the observed difference in ligand activity upon light-switching.

  9. Regulation of DnaA Assembly and Activity: Taking Directions From the Genome

    OpenAIRE

    2011-01-01

    To ensure proper timing of chromosome duplication during the cell cycle, bacteria must carefully regulate the activity of initiator protein, DnaA, and its interactions with the unique replication origin, oriC. Although several protein regulators of DnaA are known, recent evidence suggests that DnaA recognition sites, in multiple genomic locations, also play an important role in controlling assembly of pre-replication complexes. In oriC, closely spaced high and low affinity recognition sites d...

  10. Measurement of protein-ligand complex formation.

    Science.gov (United States)

    Lowe, Peter N; Vaughan, Cara K; Daviter, Tina

    2013-01-01

    Experimental approaches to detect, measure, and quantify protein-ligand binding, along with their theoretical bases, are described. A range of methods for detection of protein-ligand interactions is summarized. Specific protocols are provided for a nonequilibrium procedure pull-down assay, for an equilibrium direct binding method and its modification into a competition-based measurement and for steady-state measurements based on the effects of ligands on enzyme catalysis.

  11. Killer immunoglobulin-like receptor (KIR) and KIR-ligand genotype do not correlate with clinical outcome of renal cell carcinoma patients receiving high-dose IL2.

    Science.gov (United States)

    Wang, Wei; Erbe, Amy K; Gallenberger, Mikayla; Kim, KyungMann; Carmichael, Lakeesha; Hess, Dustin; Mendonca, Eneida A; Song, Yiqiang; Hank, Jacquelyn A; Cheng, Su-Chun; Signoretti, Sabina; Atkins, Michael; Carlson, Alexander; Weiss, Jonathan M; Mier, James; Panka, David; McDermott, David F; Sondel, Paul M

    2016-12-01

    NK cells play a role in many cancer immunotherapies. NK cell activity is tightly regulated by killer immunoglobulin-like receptor (KIR) and KIR-ligand interactions. Inhibitory KIR-ligands have been identified as HLA molecules, while activating KIR-ligands are largely unknown. Individuals that have not inherited the corresponding KIR-ligand for at least one inhibitory KIR gene are termed the "KIR-ligand missing" genotype, and they are thought to have a subset of NK cells that express inhibitory KIRs for which the corresponding KIR-ligand is missing on autologous tissue, and thus will not be inhibited through KIR-ligand recognition. In some settings where an anticancer immunotherapeutic effect is likely mediated by NK cells, individuals with a KIR-ligand missing genotype have shown improved clinical outcome compared to individuals with an "all KIR-ligands present" genotype. In addition, patients receiving hematopoietic stem cell transplants for leukemia may do better if their donor has more activating KIR genes (i.e., KIR haplotype-B). In a recent multi-institution clinical trial of patients with metastatic renal cell carcinoma receiving high-dose IL2 (HD-IL2), 25 % of patients showed a complete or partial tumor response to this therapy. We genotyped KIR and KIR-ligand genes for these patients (n = 107) and tested whether KIR/KIR-ligand genotypes correlated with patient clinical outcomes. In these analyses, we did not find any significant association of KIR/KIR-ligand genotype (either KIR-ligand missing or the presence of KIR haplotype-B) with patient outcome in response to the HD-IL2 therapy.

  12. Interactive Systems for Designing Machine Elements and Assemblies

    Directory of Open Access Journals (Sweden)

    Kacalak Wojciech

    2015-09-01

    Full Text Available The article describes the development of fundamentals of machine elements and assemblies design processes automation using artificial intelligence, and descriptions of structural elements’ features in a natural language. In the proposed interactive automated design systems, computational artificial intelligence methods allow communication by speech and natural language, resulting in analyses of design engineer’s messages, analyses of constructions, encoding and assessments of constructions, CAD system controlling and visualizations. The system is equipped with several adaptive intelligent layers for human biometric identification, recognition of speech and handwriting, recognition of words, analyses and recognition of messages, enabling interpretation of messages, and assessments of human reactions. The article proposes a concept of intelligent processing for analysis of descriptions of machine elements’ structural features in a natural language. It also presents the developed methodology for similarity analysis between structural features of designed machine elements and corresponding antipatterns allowing normalization of parameters of the analysed structural solutions.

  13. Pattern Recognition by Combined Invariants

    Institute of Scientific and Technical Information of China (English)

    WANG Xiaohong; ZHAO Rongchun

    2001-01-01

    A feature-based recognition of objectsor patterns independent of their position, size, orien-tation and other variations has been the goal of muchrecent research. The existing approaches to invarianttwo-dimensional pattern recognition are useless whenpattern is blurred. In this paper, we present a novelpattern recognition system which can solve the prob-lem by using combined invariants as image features.The classification technique we choose for our systemis weighted normalized cross correlation. The mean ofthe intraclass standard deviations of the kth featureover the total number of prototypes for each class isused as a weighting factor during the classification pro-cess to improve recognition accuracy. The feasibilityof our pattern recognition system and the invarianceof the combined features with respect to translation,scaling, rotation and blurring are approved by numer-ical experiments on head images.

  14. Online handwritten mathematical expression recognition

    Science.gov (United States)

    Büyükbayrak, Hakan; Yanikoglu, Berrin; Erçil, Aytül

    2007-01-01

    We describe a system for recognizing online, handwritten mathematical expressions. The system is designed with a user-interface for writing scientific articles, supporting the recognition of basic mathematical expressions as well as integrals, summations, matrices etc. A feed-forward neural network recognizes symbols which are assumed to be single-stroke and a recursive algorithm parses the expression by combining neural network output and the structure of the expression. Preliminary results show that writer-dependent recognition rates are very high (99.8%) while writer-independent symbol recognition rates are lower (75%). The interface associated with the proposed system integrates the built-in recognition capabilities of the Microsoft's Tablet PC API for recognizing textual input and supports conversion of hand-drawn figures into PNG format. This enables the user to enter text, mathematics and draw figures in a single interface. After recognition, all output is combined into one LATEX code and compiled into a PDF file.

  15. Viewpoint Manifolds for Action Recognition

    Directory of Open Access Journals (Sweden)

    Souvenir Richard

    2009-01-01

    Full Text Available Abstract Action recognition from video is a problem that has many important applications to human motion analysis. In real-world settings, the viewpoint of the camera cannot always be fixed relative to the subject, so view-invariant action recognition methods are needed. Previous view-invariant methods use multiple cameras in both the training and testing phases of action recognition or require storing many examples of a single action from multiple viewpoints. In this paper, we present a framework for learning a compact representation of primitive actions (e.g., walk, punch, kick, sit that can be used for video obtained from a single camera for simultaneous action recognition and viewpoint estimation. Using our method, which models the low-dimensional structure of these actions relative to viewpoint, we show recognition rates on a publicly available dataset previously only achieved using multiple simultaneous views.

  16. Viewpoint Manifolds for Action Recognition

    Directory of Open Access Journals (Sweden)

    Richard Souvenir

    2009-01-01

    Full Text Available Action recognition from video is a problem that has many important applications to human motion analysis. In real-world settings, the viewpoint of the camera cannot always be fixed relative to the subject, so view-invariant action recognition methods are needed. Previous view-invariant methods use multiple cameras in both the training and testing phases of action recognition or require storing many examples of a single action from multiple viewpoints. In this paper, we present a framework for learning a compact representation of primitive actions (e.g., walk, punch, kick, sit that can be used for video obtained from a single camera for simultaneous action recognition and viewpoint estimation. Using our method, which models the low-dimensional structure of these actions relative to viewpoint, we show recognition rates on a publicly available dataset previously only achieved using multiple simultaneous views.

  17. Optimizing Face Recognition Using PCA

    Directory of Open Access Journals (Sweden)

    Manal Abdullah

    2012-03-01

    Full Text Available Principle Component Analysis PCA is a classical feature extraction and data representation technique widely used in pattern recognition. It is one of the most successful techniques in face recognition. But it has drawback of high computational especially for big size database. This paper conducts a study to optimize the time complexity of PCA (eigenfaces that does not affects the recognition performance. The authors minimize the participated eigenvectors which consequently decreases the computational time. A comparison is done to compare the differences between the recognition time in the original algorithm and in the enhanced algorithm. The performance of the original and the enhanced proposed algorithm is tested on face94 face database. Experimental results show that the recognition time is reduced by 35% by applying our proposed enhanced algorithm. DET Curves are used to illustrate the experimental results.

  18. Optimizing Face Recognition Using PCA

    Directory of Open Access Journals (Sweden)

    Manal Abdullah

    2012-04-01

    Full Text Available Principle Component Analysis PCA is a classical feature extraction and data representation technique widely used in pattern recognition. It is one of the most successful techniques in face recognition. But it has drawback of high computational especially for big size database. This paper conducts a study to optimize the time complexity of PCA (eigenfaces that does not affects the recognition performance. The authorsminimize the participated eigenvectors which consequently decreases the computational time. A comparison is done to compare the differences between the recognition time in the original algorithm and in the enhanced algorithm. The performance of the original and the enhanced proposed algorithm is tested on face94 face database. Experimental results show that the recognition time is reduced by 35% by applying our proposed enhanced algorithm. DET Curves are used to illustrate the experimental results.

  19. The broad pattern recognition spectrum of the Toll-like receptor in mollusk Zhikong scallop Chlamys farreri.

    Science.gov (United States)

    Wang, Mengqiang; Wang, Lingling; Guo, Ying; Sun, Rui; Yue, Feng; Yi, Qilin; Song, Linsheng

    2015-10-01

    Toll-like receptors (TLRs) are among the most studied pattern recognition receptors (PRRs) playing essential roles in innate immune defenses. In the present study, the basic features of CfTLR in mollusk Zhikong scallop Chlamys farreri, including sequence homology, tissue distribution, subcellular localization and ligands spectrum, were investigated to elucidate its pattern recognition. The elements of extracellular domains (ECD) in CfTLR displayed high homology to the corresponding parts of the ECDs in TLRs from Homo sapiens. CfTLR protein was detected in hemocytes, mantle, gills, hepatopancreas, kidney and gonad of the scallops, and it was localized in both the plasma membranes and the lysosomes in HEK293T cells. CfTLR could activate NFκB in response to multiple HsTLR ligands including Pam3CSK4, glucan (GLU), peptidoglycan (PGN), polyriboinosinic:polyribocytidylic acid (poly I:C), Imiquimod and three types of CpG. Additionally, the scallop serum could enhance the induction of NFκB in the CfTLR expressing cells elicited by most PAMPs, including GLU, PGN, Imiquimod and four types of CpG. It could be concluded that this primitive mollusk TLR shared a hybrid function in pattern recognition and could recognize broader ligands than mammalian TLRs, and its mosaic capability of pathogen associated molecular pattern (PAMP) recognition might be based on the basic features of its structure, ligand properties and the assistance of some components in scallop serum.

  20. Reversible Guest Exchange Mechanisms in Supramolecular Host-GuestAssemblies

    Energy Technology Data Exchange (ETDEWEB)

    Pluth, Michael D.; Raymond, Kenneth N.

    2006-09-01

    Synthetic chemists have provided a wide array of supramolecular assemblies able to encapsulate guest molecules. The scope of this tutorial review focuses on supramolecular host molecules capable of reversibly encapsulating polyatomic guests. Much work has been done to determine the mechanism of guest encapsulation and guest release. This review covers common methods of monitoring and characterizing guest exchange such as NMR, UV-VIS, mass spectroscopy, electrochemistry, and calorimetry and also presents representative examples of guest exchange mechanisms. The guest exchange mechanisms of hemicarcerands, cucurbiturils, hydrogen-bonded assemblies, and metal-ligand assemblies are discussed. Special attention is given to systems which exhibit constrictive binding, a motif common in supramolecular guest exchange systems.

  1. Human Assisted Assembly Processes

    Energy Technology Data Exchange (ETDEWEB)

    CALTON,TERRI L.; PETERS,RALPH R.

    2000-01-01

    Automatic assembly sequencing and visualization tools are valuable in determining the best assembly sequences, but without Human Factors and Figure Models (HFFMs) it is difficult to evaluate or visualize human interaction. In industry, accelerating technological advances and shorter market windows have forced companies to turn to an agile manufacturing paradigm. This trend has promoted computerized automation of product design and manufacturing processes, such as automated assembly planning. However, all automated assembly planning software tools assume that the individual components fly into their assembled configuration and generate what appear to be a perfectly valid operations, but in reality the operations cannot physically be carried out by a human. Similarly, human figure modeling algorithms may indicate that assembly operations are not feasible and consequently force design modifications; however, if they had the capability to quickly generate alternative assembly sequences, they might have identified a feasible solution. To solve this problem HFFMs must be integrated with automated assembly planning to allow engineers to verify that assembly operations are possible and to see ways to make the designs even better. Factories will very likely put humans and robots together in cooperative environments to meet the demands for customized products, for purposes including robotic and automated assembly. For robots to work harmoniously within an integrated environment with humans the robots must have cooperative operational skills. For example, in a human only environment, humans may tolerate collisions with one another if they did not cause much pain. This level of tolerance may or may not apply to robot-human environments. Humans expect that robots will be able to operate and navigate in their environments without collisions or interference. The ability to accomplish this is linked to the sensing capabilities available. Current work in the field of cooperative

  2. Recognition memory impairments caused by false recognition of novel objects.

    Science.gov (United States)

    Yeung, Lok-Kin; Ryan, Jennifer D; Cowell, Rosemary A; Barense, Morgan D

    2013-11-01

    A fundamental assumption underlying most current theories of amnesia is that memory impairments arise because previously studied information either is lost rapidly or is made inaccessible (i.e., the old information appears to be new). Recent studies in rodents have challenged this view, suggesting instead that under conditions of high interference, recognition memory impairments following medial temporal lobe damage arise because novel information appears as though it has been previously seen. Here, we developed a new object recognition memory paradigm that distinguished whether object recognition memory impairments were driven by previously viewed objects being treated as if they were novel or by novel objects falsely recognized as though they were previously seen. In this indirect, eyetracking-based passive viewing task, older adults at risk for mild cognitive impairment showed false recognition to high-interference novel items (with a significant degree of feature overlap with previously studied items) but normal novelty responses to low-interference novel items (with a lower degree of feature overlap). The indirect nature of the task minimized the effects of response bias and other memory-based decision processes, suggesting that these factors cannot solely account for false recognition. These findings support the counterintuitive notion that recognition memory impairments in this memory-impaired population are not characterized by forgetting but rather are driven by the failure to differentiate perceptually similar objects, leading to the false recognition of novel objects as having been seen before.

  3. Genome filtering using methylation-sensitive restriction enzymes with six-base pair recognition sites

    Science.gov (United States)

    The large fraction of repetitive DNA in many plant genomes has complicated all aspects of DNA sequencing and assembly, and thus techniques that enrich for genes and low-copy sequences have been employed to isolate gene space. Methyl sensitive restriction enzymes with six base pair recognition sites...

  4. A microprocessor-based single board computer for high energy physics event pattern recognition

    CERN Document Server

    Bernstein, H; Imossi, R; Kopp, J K; Kramer, M A; Love, W A; Ozaki, S; Platner, E D

    1981-01-01

    A single board MC 68000 based computer has been assembled and benchmarked against the CDC 7600 running portions of the pattern recognition code used at the MPS. This computer has a floating coprocessor to achieve throughputs equivalent to several percent that of the 7600. A major part of this work was the construction of a FORTR

  5. Selectivity in ligand binding to uranyl compounds: A synthetic, structural, thermodynamic and computational study

    Energy Technology Data Exchange (ETDEWEB)

    Arnold, John [Univ. of California, Berkeley, CA (United States)

    2015-01-21

    The uranyl cation (UO₂²⁺) is the most abundant form of uranium on the planet. It is estimated that 4.5 billion tons of uranium in this form exist in sea water. The ability to bind and extract the uranyl cation from aqueous solution while separating it from other elements would provide a limitless source of nuclear fuel. A large body of research concerns the selective recognition and extraction of uranyl. A stable molecule, the cation has a linear O=U=O geometry. The short U-O bonds (1.78 Å) arise from the combination of uranium 5f/6d and oxygen 2p orbitals. Due to the oxygen moieties being multiply bonded, these sites were not thought to be basic enough for Lewis acidic coordination to be a viable approach to sequestration. The goal of this research is thus to broaden the coordination chemistry of the uranyl ion by studying new ligand systems via synthetic, structural, thermodynamic and computational methods. It is anticipated that this fundamental science will find use beyond actinide separation technologies in areas such as nuclear waste remediation and nuclear materials. The focus of this study is to synthesize uranyl complexes incorporating amidinate and guanidinate ligands. Both synthetic and computational methods are used to investigate novel equatorial ligand coordination and how this affects the basicity of the oxo ligands. Such an understanding will later apply to designing ligands incorporating functionalities that can bind uranyl both equatorially and axially for highly selective sequestration. Efficient and durable chromatography supports for lanthanide separation will be generated by (1) identifying robust peptoid-based ligands capable of binding different lanthanides with variable affinities, and (2) developing practical synthetic methods for the attachment of these ligands to Dowex ion exchange resins.

  6. Controlled self-assembly of hydrophobic quantum dots through silanization.

    Science.gov (United States)

    Yang, Ping; Ando, Masanori; Murase, Norio

    2011-09-01

    We demonstrate the formation of one-, two-, and three-dimensional nanocomposites through the self-assembly of silanized CdSe/ZnS quantum dots (QDs) by using a controlled sol-gel process. The self-assembly behavior of the QDs was created when partially hydrolyzed silicon alkoxide monomers replaced hydrophobic ligands on the QDs. We examined systematically self-assembly conditions such as solvent components and QD sizes in order to elucidate the formation mechanism of various QD nanocomposites. The QD nanocomposites were assembled in water phase or on the interface of water and oil phase in emulsions. The partially hydrolyzed silicon alkoxides act as intermolecules to assemble the QDs. The QD nanocomposites with well-defined solid or hollow spherical, fiber-like, sheet-like, and pearl-like morphologies were prepared by adjusting the experimental conditions. The high photoluminescence efficiency of the prepared QD nanocomposites suggests partially hydrolyzed silicon alkoxides reduced the surface deterioration of QDs during self-assembly. These techniques are applicable to other hydrophobic QDs for fabricating complex QD nanocomposites.

  7. Silver, Gold, Palladium Nanoparticles: Ligand Design, Synthesis and Polymer Composites

    Science.gov (United States)

    Iqbal, Muhammad

    Metal nanoparticles, especially gold nanoparticles (AuNPs), have been extensively studied due to their interesting optical properties and potential applications in emerging technologies like drug delivery, cancer therapy, catalysis, chemical and bio-sensing and microelectronics devices. Alkyl thiol ligands in the form of self assembled monolayers are often used to stabilize and functionalize the gold nanoparticles while other types of ligands have been rarely employed and the properties of AuNPs protected by different types of ligands have not been studied comprehensively and comparatively. This dissertation reports the first comparative studies on the thermal and chemical stability of AuNPs protected by alkyl thiolates, alkyl selenolates, dialkyl dithiophosphinates, and dialkyl dithiophosphates (Chapters 2 and 3). AuNPs protected by dialkyl dithiophosphinates and dialkyl dithiophosphates are unprecedented. All AuNPs were prepared from amine protected precursor AuNPs by ligand exchange to ensure similar size, size distribution, and chemical composition. They were extensively characterized by solution 1H-NMR and UV-VIS spectroscopy, transmission electron microscopy (TEM), thermal analysis, X-ray photoelectron spectroscopy (XPS), and X-ray diffraction (XRD) analysis. For the first time, thermal stability was investigated by differential scanning calorimetry (DSC) that provided more accurate decomposition temperatures and enthalpies, whereas chemical stability was tested as the availability of the gold surface towards etching with cyanide in different solvents. Surprisingly, alkyl selenolate protected AuNPs are thermally less stable than alkyl thiolate protected AuNPs despite their proposed stronger binding to the gold surface and a much more crystalline monolayer, which suggests that different decomposition mechanisms apply to alkyl thiolate and alkyl selenolate protected AuNPs. Dialkyl dithiophosphinates and dialkyl dithiophosphates protected AuNPs are thermally

  8. Kernel learning algorithms for face recognition

    CERN Document Server

    Li, Jun-Bao; Pan, Jeng-Shyang

    2013-01-01

    Kernel Learning Algorithms for Face Recognition covers the framework of kernel based face recognition. This book discusses the advanced kernel learning algorithms and its application on face recognition. This book also focuses on the theoretical deviation, the system framework and experiments involving kernel based face recognition. Included within are algorithms of kernel based face recognition, and also the feasibility of the kernel based face recognition method. This book provides researchers in pattern recognition and machine learning area with advanced face recognition methods and its new

  9. Photovoltaic self-assembly.

    Energy Technology Data Exchange (ETDEWEB)

    Lavin, Judith; Kemp, Richard Alan; Stewart, Constantine A.

    2010-10-01

    This late-start LDRD was focused on the application of chemical principles of self-assembly on the ordering and placement of photovoltaic cells in a module. The drive for this chemical-based self-assembly stems from the escalating prices in the 'pick-and-place' technology currently used in the MEMS industries as the size of chips decreases. The chemical self-assembly principles are well-known on a molecular scale in other material science systems but to date had not been applied to the assembly of cells in a photovoltaic array or module. We explored several types of chemical-based self-assembly techniques, including gold-thiol interactions, liquid polymer binding, and hydrophobic-hydrophilic interactions designed to array both Si and GaAs PV chips onto a substrate. Additional research was focused on the modification of PV cells in an effort to gain control over the facial directionality of the cells in a solvent-based environment. Despite being a small footprint research project worked on for only a short time, the technical results and scientific accomplishments were significant and could prove to be enabling technology in the disruptive advancement of the microelectronic photovoltaics industry.

  10. Spectral recognition of graphs

    Directory of Open Access Journals (Sweden)

    Cvetković Dragoš

    2012-01-01

    Full Text Available At some time, in the childhood of spectral graph theory, it was conjectured that non-isomorphic graphs have different spectra, i.e. that graphs are characterized by their spectra. Very quickly this conjecture was refuted and numerous examples and families of non-isomorphic graphs with the same spectrum (cospectral graphs were found. Still some graphs are characterized by their spectra and several mathematical papers are devoted to this topic. In applications to computer sciences, spectral graph theory is considered as very strong. The benefit of using graph spectra in treating graphs is that eigenvalues and eigenvectors of several graph matrices can be quickly computed. Spectral graph parameters contain a lot of information on the graph structure (both global and local including some information on graph parameters that, in general, are computed by exponential algorithms. Moreover, in some applications in data mining, graph spectra are used to encode graphs themselves. The Euclidean distance between the eigenvalue sequences of two graphs on the same number of vertices is called the spectral distance of graphs. Some other spectral distances (also based on various graph matrices have been considered as well. Two graphs are considered as similar if their spectral distance is small. If two graphs are at zero distance, they are cospectral. In this sense, cospectral graphs are similar. Other spectrally based measures of similarity between networks (not necessarily having the same number of vertices have been used in Internet topology analysis, and in other areas. The notion of spectral distance enables the design of various meta-heuristic (e.g., tabu search, variable neighbourhood search algorithms for constructing graphs with a given spectrum (spectral graph reconstruction. Several spectrally based pattern recognition problems appear in many areas (e.g., image segmentation in computer vision, alignment of protein-protein interaction networks in bio

  11. Enantioselective self-assembly of antiferromagnetic hexacopper(II) wheels with chiral amino acid oxamates.

    Science.gov (United States)

    Grancha, Thais; Ferrando-Soria, Jesús; Cano, Joan; Lloret, Francesc; Julve, Miguel; De Munno, Giovanni; Armentano, Donatella; Pardo, Emilio

    2013-07-01

    The Cu(2+)-mediated self-assembly of oxamato-based ligands derived from either the (S)- or (R)-enantiomers of the amino acid valine leads to the formation of two antiferromagnetically coupled homochiral anionic hexacopper(II) wheels in the presence of templating tetramethylammonium countercations.

  12. Nucleobase assemblies supported by uranyl cation coordination and other non-covalent interactions

    Indian Academy of Sciences (India)

    Jitendra Kumar; Sandeep Verma

    2011-11-01

    We describe synthesis and solid state structural description of uranyl complexes of carboxylate functionalized adenine and uracil derivatives. The metal coordination through carboxylate pendant leads to the formation of dimeric assemblies, whereas the directional nature of hydrogen bonding interaction supported by nucleobases and aqua ligands, result in the generation of complex 3-D architectures containing embedded nucleobase ribbons.

  13. Apoptotic cell and phagocyte interplay: recognition and consequences in different cell systems

    Directory of Open Access Journals (Sweden)

    Moreira Maria Elisabete C.

    2004-01-01

    Full Text Available Cell death by apoptosis is characterized by specific biochemical changes, including the exposure of multiple ligands, expected to tag the dying cell for prompt recognition by phagocytes. In non-pathological conditions, an efficient clearance is assured by the redundant interaction between apoptotic cell ligands and multiple receptor molecules present on the engulfing cell surface. This review concentrates on the molecular interactions operating in mammalian and non-mammalian systems for apoptotic cell recognition, as well as on the consequences of their signaling. Furthermore, some cellular models where the exposure of the phosphatidylserine (PS phospholipid, a classical hallmark of the apoptotic phenotype, is not followed by cell death will be discussed.

  14. Self-Assembled Pyridine-Dipyrrolate Cages.

    Science.gov (United States)

    Zhang, Huacheng; Lee, Juhoon; Lammer, Aaron D; Chi, Xiaodong; Brewster, James T; Lynch, Vincent M; Li, Hao; Zhang, Zhan; Sessler, Jonathan L

    2016-04-06

    An inherently nonlinear pyridine dipyrrolate ligand, namely 2,6-bis(3,4-diethyl-5-carboxy-1H-pyrrol-2yl)pyridine (compound 1), is able to distinguish between different zinc(II) cation sources, namely Zn(acac)2 and Zn(OAc)2, respectively. This differentiation is manifest both in terms of the observed fluorescent behavior in mixed organic media and the reaction chemistry. Treatment of 1 with Zn(acac)2 gives rise to a cage dimer, cage-1, wherein two molecules of compound 1 act as double bridging units to connect two individual cage subunits. As inferred from X-ray crystallographic studies, this cage system consists of discrete zinc dimers with hydroxide bridges that, with the assistance of bound DMF solvent molecules, serve to fix the geometry and orientation of the pyridine dipyrrolate building blocks. When a different zinc source, Zn(OAc)2, is used to carry out an ostensibly similar complexation reaction with compound 1, an acetate-bridged 1D abacus-like cage polymer is obtained as inferred from X-ray diffraction analysis. This extended solid state structure, cage-2, contains individual zinc dimer cage submits and appears stabilized by solvent molecules (DMF) and the counteranion (acetate). Rod-like assemblies are also observed by DLS and SEM. This construct, in contrast to cage-1, proved fluorescent in mixed organic media. The structure of the ligand itself (i.e., in the absence of Zn(II)) was confirmed by X-ray crystallographic analysis and was found to assemble into a supramolecular polymer. Conversion to a dimer form was seen upon the addition of TBAOAc. On the basis of the metric parameters, the structures seen in the solid state are stabilized via hydrogen bonding interactions involving solvent molecules.

  15. Logo Recognition Theory and Practice

    CERN Document Server

    Chen, Jingying

    2011-01-01

    Used by companies, organizations, and even individuals to promote recognition of their brand, logos can also act as a valuable means of identifying the source of a document. E-business applications can retrieve and catalog products according to their logos. Governmental agencies can easily inspect goods using smart mobile devices that use logo recognition techniques. However, because logos are two-dimensional shapes of varying complexity, the recognition process can be challenging. Although promising results have been found for clean logos, they have not been as robust for noisy logos. Logo Re

  16. In vitro kinetochore assembly

    Science.gov (United States)

    Miell, Matthew D D; Straight, Aaron F

    2016-01-01

    The kinetochore is the primary site of interaction between chromosomes and microtubules of the mitotic spindle during chromosome segregation. The kinetochore is a complex of more than 100 proteins that transiently assemble during mitosis at a single defined region on each chromosome, known as the centromere. Kinetochore assembly and activity must be tightly regulated to ensure proper microtubule interaction and faithful chromosome segregation because perturbation of kinetochores often results in aneuploidy and cell lethality. As such, cell free and reconstituted systems to analyze kinetochore formation and function are invaluable in probing the biochemical activities of kinetochores. In vitro approaches to studying kinetochores have enabled the manipulation of kinetochore protein structure, function, interactions and regulation that are not possible in cells. Here we outline a cell-free approach for the assembly of centromeres and recruitment of functional kinetochores that enables their manipulation and analysis. PMID:27193846

  17. Assembling Sustainable Territories

    DEFF Research Database (Denmark)

    Vandergeest, Peter; Ponte, Stefano; Bush, Simon

    2015-01-01

    The authors show how certification assembles ‘sustainable’ territories through a complex layering of regulatory authority in which both government and nongovernment entities claim rule-making authority, sometimes working together, sometimes in parallel, sometimes competitively. It is argued...... that territorialisation is accomplished not just through (re)defining bounded space, but more broadly through the assembling of four elements: space, subjects, objects, and expertise. Four case studies of sustainability certification in seafood are analyzed to show that ‘green gabbing’ is not necessarily the central...... dynamic in assembling sustainable territories, and that certification always involves state agencies in determining how the key elements that comprise it are defined. Whereas some state agencies have been suspicious of sustainability certification, others have embraced it or even used it to extend...

  18. Power module assembly

    Science.gov (United States)

    Campbell, Jeremy B [Torrance, CA; Newson, Steve [Redondo Beach, CA

    2011-11-15

    A power module assembly of the type suitable for deployment in a vehicular power inverter, wherein the power inverter has a grounded chassis, is provided. The power module assembly comprises a conductive base layer electrically coupled to the chassis, an insulating layer disposed on the conductive base layer, a first conductive node disposed on the insulating layer, a second conductive node disposed on the insulating layer, wherein the first and second conductive nodes are electrically isolated from each other. The power module assembly also comprises a first capacitor having a first electrode electrically connected to the conductive base layer, and a second electrode electrically connected to the first conductive node, and further comprises a second capacitor having a first electrode electrically connected to the conductive base layer, and a second electrode electrically connected to the second conductive node.

  19. Blade attachment assembly

    Science.gov (United States)

    Garcia-Crespo, Andres Jose; Delvaux, John McConnell; Miller, Diane Patricia

    2016-05-03

    An assembly and method for affixing a turbomachine rotor blade to a rotor wheel are disclosed. In an embodiment, an adaptor member is provided disposed between the blade and the rotor wheel, the adaptor member including an adaptor attachment slot that is complementary to the blade attachment member, and an adaptor attachment member that is complementary to the rotor wheel attachment slot. A coverplate is provided, having a coverplate attachment member that is complementary to the rotor wheel attachment slot, and a hook for engaging the adaptor member. When assembled, the coverplate member matingly engages with the adaptor member, and retains the blade in the adaptor member, and the assembly in the rotor wheel.

  20. Integrated magnetic transformer assembly

    DEFF Research Database (Denmark)

    2014-01-01

    The present invention relates to an integrated magnetics transformer assembly comprising a first magnetically permeable core forming a first substantially closed magnetic flux path and a second magnetically permeable core forming a second substantially closed magnetic flux path. A first input...... inductor winding is wound around a first predetermined segment of the first magnetically permeable core and a second input inductor winding is wound around a first predetermined segment of the second magnetically permeable core. The integrated magnetics transformer assembly further comprises a first output......-winding of the first output inductor winding and the first half-winding of the second output inductor winding are configured to produce aligned, i.e. in the same direction, magnetic fluxes through the first substantially closed magnetic flux path. The integrated magnetics transformer assembly is well- suited for use...

  1. Rhodium olefin complexes of diiminate type ligands

    NARCIS (Netherlands)

    Willems, Sander Theodorus Hermanus

    2003-01-01

    The mono-anionic beta-diiminate ligand (ArNC(CH3)CHC(CH3)NAr) on several previous occasions proved useful in stabilising low coordination numbers for both early and late transition metals. In this thesis the reactivity of the rhodium olefin complexes of one of these beta-diiminate ligands (Ar = 2,6-

  2. Ligand sphere conversions in terminal carbide complexes

    DEFF Research Database (Denmark)

    Morsing, Thorbjørn Juul; Reinholdt, Anders; Sauer, Stephan P. A.

    2016-01-01

    Metathesis is introduced as a preparative route to terminal carbide complexes. The chloride ligands of the terminal carbide complex [RuC(Cl)2(PCy3)2] (RuC) can be exchanged, paving the way for a systematic variation of the ligand sphere. A series of substituted complexes, including the first exam...

  3. Flexible Ligand Docking Using Evolutionary Algorithms

    DEFF Research Database (Denmark)

    Thomsen, Rene

    2003-01-01

    The docking of ligands to proteins can be formulated as a computational problem where the task is to find the most favorable energetic conformation among the large space of possible protein–ligand complexes. Stochastic search methods such as evolutionary algorithms (EAs) can be used to sample large...

  4. Geometrical assembly of ultrastable protein templates for nanomaterials

    Science.gov (United States)

    Glover, Dominic J.; Giger, Lars; Kim, Steve S.; Naik, Rajesh R.; Clark, Douglas S.

    2016-06-01

    The fabrication of nanoscale devices requires architectural templates on which to position functional molecules in complex arrangements. Protein scaffolds are particularly promising templates for nanomaterials due to inherent molecular recognition and self-assembly capabilities combined with genetically encoded functionalities. However, difficulties in engineering protein quaternary structure into stable and well-ordered shapes have hampered progress. Here we report the development of an ultrastable biomolecular construction kit for the assembly of filamentous proteins into geometrically defined templates of controllable size and symmetry. The strategy combines redesign of protein-protein interaction specificity with the creation of tunable connector proteins that govern the assembly and projection angles of the filaments. The functionality of these nanoarchitectures is illustrated by incorporation of nanoparticles at specific locations and orientations to create hybrid materials such as conductive nanowires. These new structural components facilitate the manufacturing of nanomaterials with diverse shapes and functional properties over a wide range of processing conditions.

  5. Self assembling proteins

    Science.gov (United States)

    Yeates, Todd O.; Padilla, Jennifer; Colovos, Chris

    2004-06-29

    Novel fusion proteins capable of self-assembling into regular structures, as well as nucleic acids encoding the same, are provided. The subject fusion proteins comprise at least two oligomerization domains rigidly linked together, e.g. through an alpha helical linking group. Also provided are regular structures comprising a plurality of self-assembled fusion proteins of the subject invention, and methods for producing the same. The subject fusion proteins find use in the preparation of a variety of nanostructures, where such structures include: cages, shells, double-layer rings, two-dimensional layers, three-dimensional crystals, filaments, and tubes.

  6. Low inductance connector assembly

    Science.gov (United States)

    Holbrook, Meghan Ann; Carlson, Douglas S

    2013-07-09

    A busbar connector assembly for coupling first and second terminals on a two-terminal device to first and second contacts on a power module is provided. The first terminal resides proximate the first contact and the second terminal resides proximate the second contact. The assembly comprises a first bridge having a first end configured to be electrically coupled to the first terminal, and a second end configured to be electrically coupled to the second contact, and a second bridge substantially overlapping the first bridge and having a first end electrically coupled to the first contact, and a second end electrically coupled to the second terminal.

  7. 柔性配体癸二酸构筑的镍多孔配位聚合物的合成和晶体结构%Self-assembly of Nickel(Ⅱ) Coordination Polymer Based on a Flexible Sebacic Acid Ligand

    Institute of Scientific and Technical Information of China (English)

    赵国良; 沈金杯; 咸会朵

    2011-01-01

    由硫酸镍和癸二酸(C10H18O4)合成了配合物:[Ni(C10H16O4)(H2O)4]·1.5H2O,并通过元素分析、红外光谱、热重分析对其进行表征,用单晶X-射线衍射方法测定了配合物的晶体结构.配合物属于正交晶系,空间群Cmca,晶胞参数:a=0.753820(10) nm,b=1.076 97(2)nm,c=4.130 42(8) nm,晶胞体积:V=3.353 25(10) nm3,晶胞内结构基元数Z=4,分子量Mr=358.02,电子数F(000)=1 528,密度Dc=1.418 9·cm-3,吸收系数μ(Mo Kα)=1.195mm-1.%A nickel(Ⅱ) complex [Ni(C10H16O4)(H2O)4]·1.5H2O (C10H18O4=sebacic acid), was synthesized and characterized by elemental analysis, Infrared radiation (IR) and thermogravimetry-derivative thermogravimetry (TG-DTG). Its crystal structure was determined by single crystal X-ray diffraction method. The complex, C10H27O93Ni, crystallizes in the orthorhombic system, space group Cmca,with cell parameters: a=0.753 820(10) nm, 6=1.07697(2) nm, c= 4.13042(8) nm, cell volume: F=3.353 25(10) nm3, number of molecules inside the cell: Z=A, relative molecular mass: Mr=358.02, numbers of electrons: F(000)=l 528, density calculated: DC=1.418 g·cm-3, absorptive parameter: μ(Mo Kα)=l.l95 mm-1. The coordination polymer was constructed by molecular self-assembly from hydrogen-bonding interactions. CCDC: 728231.

  8. Ligand binding mechanics of maltose binding protein.

    Science.gov (United States)

    Bertz, Morten; Rief, Matthias

    2009-11-13

    In the past decade, single-molecule force spectroscopy has provided new insights into the key interactions stabilizing folded proteins. A few recent studies probing the effects of ligand binding on mechanical protein stability have come to quite different conclusions. While some proteins seem to be stabilized considerably by a bound ligand, others appear to be unaffected. Since force acts as a vector in space, it is conceivable that mechanical stabilization by ligand binding is dependent on the direction of force application. In this study, we vary the direction of the force to investigate the effect of ligand binding on the stability of maltose binding protein (MBP). MBP consists of two lobes connected by a hinge region that move from an open to a closed conformation when the ligand maltose binds. Previous mechanical experiments, where load was applied to the N and C termini, have demonstrated that MBP is built up of four building blocks (unfoldons) that sequentially detach from the folded structure. In this study, we design the pulling direction so that force application moves the two MBP lobes apart along the hinge axis. Mechanical unfolding in this geometry proceeds via an intermediate state whose boundaries coincide with previously reported MBP unfoldons. We find that in contrast to N-C-terminal pulling experiments, the mechanical stability of MBP is increased by ligand binding when load is applied to the two lobes and force breaks the protein-ligand interactions directly. Contour length measurements indicate that MBP is forced into an open conformation before unfolding even if ligand is bound. Using mutagenesis experiments, we demonstrate that the mechanical stabilization effect is due to only a few key interactions of the protein with its ligand. This work illustrates how varying the direction of the applied force allows revealing important details about the ligand binding mechanics of a large protein.

  9. Metal Nanoparticle/Block Copolymer Composite Assembly and Disassembly.

    Science.gov (United States)

    Li, Zihui; Sai, Hiroaki; Warren, Scott C; Kamperman, Marleen; Arora, Hitesh; Gruner, Sol M; Wiesner, Ulrich

    2009-01-01

    Ligand-stabilized platinum nanoparticles (Pt NPs) were self-assembled with poly(isoprene-block-dimethylaminoethyl methacrylate) (PI-b-PDMAEMA) block copolymers to generate organic-inorganic hybrid materials. High loadings of NPs in hybrids were achieved through usage of N,N-di-(2-(allyloxy)ethyl)-N-3-mercaptopropyl-N-3-methylammonium chloride as the ligand, which provided high solubility of NPs in various solvents as well as high affinity to PDMAEMA. From NP synthesis, existence of sub-1 nm Pt NPs was confirmed by high-angle annular dark field scanning transmission electron microscopy (HAADF-STEM) images. Estimations of the Pt NP ligand head group density based on HAADF-STEM images and thermogravimetric analysis (TGA) data yielded results comparable to what has been found for alkanethiol self-assembled monolayers (SAMs) on flat Pt {111} surfaces. Changing the volume fraction of Pt NPs in block copolymer-NP composites yielded hybrids with spherical micellar, wormlike micellar, lamellar and inverse hexagonal morphologies. Disassembly of hybrids with spherical, wormlike micellar, and lamellar morphologies generated isolated metal-NP based nano-spheres, cylinders and sheets, respectively. Results suggest the existence of powerful design criteria for the formation of metal-based nanostructures from designer blocked macromolecules.

  10. An Interactive Assembly Process Planner

    Institute of Scientific and Technical Information of China (English)

    廖华飞; 张林鍹; 肖田元; 曾理; 古月

    2004-01-01

    This paper describes the implementation and performance of the virtual assembly support system (VASS), a new system that can provide designers and assembly process engineers with a simulation and visualization environment where they can evaluate the assemblability/disassemblability of products, and thereby use a computer to intuitively create assembly plans and interactively generate assembly process charts. Subassembly planning and assembly priority reasoning techniques were utilized to find heuristic information to improve the efficiency of assembly process planning. Tool planning was implemented to consider tool requirements in the product design stage. New methods were developed to reduce the computation amount involved in interference checking. As an important feature of the VASS, human interaction was integrated into the whole process of assembly process planning, extending the power of computer reasoning by including human expertise, resulting in better assembly plans and better designs.

  11. Fire resistant PV shingle assembly

    Science.gov (United States)

    Lenox, Carl J.

    2012-10-02

    A fire resistant PV shingle assembly includes a PV assembly, including PV body, a fire shield and a connection member connecting the fire shield below the PV body, and a support and inter-engagement assembly. The support and inter-engagement assembly is mounted to the PV assembly and comprises a vertical support element, supporting the PV assembly above a support surface, an upper interlock element, positioned towards the upper PV edge, and a lower interlock element, positioned towards the lower PV edge. The upper interlock element of one PV shingle assembly is inter-engageable with the lower interlock element of an adjacent PV shingle assembly. In some embodiments the PV shingle assembly may comprise a ventilation path below the PV body. The PV body may be slidably mounted to the connection member to facilitate removal of the PV body.

  12. Effective indexing for face recognition

    Science.gov (United States)

    Sochenkov, I.; Sochenkova, A.; Vokhmintsev, A.; Makovetskii, A.; Melnikov, A.

    2016-09-01

    Face recognition is one of the most important tasks in computer vision and pattern recognition. Face recognition is useful for security systems to provide safety. In some situations it is necessary to identify the person among many others. In this case this work presents new approach in data indexing, which provides fast retrieval in big image collections. Data indexing in this research consists of five steps. First, we detect the area containing face, second we align face, and then we detect areas containing eyes and eyebrows, nose, mouth. After that we find key points of each area using different descriptors and finally index these descriptors with help of quantization procedure. The experimental analysis of this method is performed. This paper shows that performing method has results at the level of state-of-the-art face recognition methods, but it is also gives results fast that is important for the systems that provide safety.

  13. Iris Recognition using Orthogonal Transforms

    Directory of Open Access Journals (Sweden)

    M.Mani Roja

    2012-12-01

    Full Text Available Iris Recognition is a biometric recognition technique in which features of the iris are used to uniquely identify individuals. Iris recognition has over the years emerged as one of the most accuratebiometric techniques as opposed to other biometric techniques like face, signature and fingerprint. First, the iris image is pre processed using canny edge detector using a Gaussian filter. The iris edge and the pupil edge are extracted using image morphological operation, image opening. After normalization of red, green and blue components of the colour iris using Euclidean distance method, they are combined to form the localized colour iris. For feature vectors extraction, orthogonal transforms like discrete cosine transform, discrete sine transform and discrete Fourier transform have been considered. The proposed iris recognition system is very time efficient and it takes less than 1 second to grant authentication.

  14. Similarity measures for face recognition

    CERN Document Server

    Vezzetti, Enrico

    2015-01-01

    Face recognition has several applications, including security, such as (authentication and identification of device users and criminal suspects), and in medicine (corrective surgery and diagnosis). Facial recognition programs rely on algorithms that can compare and compute the similarity between two sets of images. This eBook explains some of the similarity measures used in facial recognition systems in a single volume. Readers will learn about various measures including Minkowski distances, Mahalanobis distances, Hansdorff distances, cosine-based distances, among other methods. The book also summarizes errors that may occur in face recognition methods. Computer scientists "facing face" and looking to select and test different methods of computing similarities will benefit from this book. The book is also useful tool for students undertaking computer vision courses.

  15. Gesture recognition on smart cameras

    Science.gov (United States)

    Dziri, Aziz; Chevobbe, Stephane; Darouich, Mehdi

    2013-02-01

    Gesture recognition is a feature in human-machine interaction that allows more natural interaction without the use of complex devices. For this reason, several methods of gesture recognition have been developed in recent years. However, most real time methods are designed to operate on a Personal Computer with high computing resources and memory. In this paper, we analyze relevant methods found in the literature in order to investigate the ability of smart camera to execute gesture recognition algorithms. We elaborate two hand gesture recognition pipelines. The first method is based on invariant moments extraction and the second on finger tips detection. The hand detection method used for both pipeline is based on skin color segmentation. The results obtained show that the un-optimized versions of invariant moments method and finger tips detection method can reach 10 fps on embedded processor and use about 200 kB of memory.

  16. Pattern recognition and string matching

    CERN Document Server

    Cheng, Xiuzhen

    2002-01-01

    The research and development of pattern recognition have proven to be of importance in science, technology, and human activity. Many useful concepts and tools from different disciplines have been employed in pattern recognition. Among them is string matching, which receives much theoretical and practical attention. String matching is also an important topic in combinatorial optimization. This book is devoted to recent advances in pattern recognition and string matching. It consists of twenty eight chapters written by different authors, addressing a broad range of topics such as those from classifica­ tion, matching, mining, feature selection, and applications. Each chapter is self-contained, and presents either novel methodological approaches or applications of existing theories and techniques. The aim, intent, and motivation for publishing this book is to pro­ vide a reference tool for the increasing number of readers who depend upon pattern recognition or string matching in some way. This includes student...

  17. Defect Recognition in Thermosonic Imaging

    Institute of Scientific and Technical Information of China (English)

    CHEN Dapeng; WU Naiming; ZHANG Zheng

    2012-01-01

    This work is aimed at developing an effective method for defect recognition in thermosonic imaging.The heat mechanism of thermosonic imaging is introduced,and the problem for defect recognition is discussed.For this purpose,defect existing in the inner wall of a metal pipeline specimen and defects embedded in a carbon fiber reinforced plastic (CFRP) laminate are tested.The experimental data are processed by pulse phase thermography (PPT) method to show the phase images at different frequencies,and the characteristic of phase angle vs frequency curve of thermal anomalies and sound area is analyzed.A binary image,which is based on the characteristic value of defects,is obtained by a new recognition algorithm to show the defects.Results demonstrate good defect recognition performance for thermosonic imaging,and the reliability of this technique can be improved by the method.

  18. A Method for Designing Assembly Tolerance Networks of Mechanical Assemblies

    Directory of Open Access Journals (Sweden)

    Yi Zhang

    2012-01-01

    Full Text Available When designing mechanical assemblies, assembly tolerance design is an important issue which must be seriously considered by designers. Assembly tolerances reflect functional requirements of assembling, which can be used to control assembling qualities and production costs. This paper proposes a new method for designing assembly tolerance networks of mechanical assemblies. The method establishes the assembly structure tree model of an assembly based on its product structure tree model. On this basis, assembly information model and assembly relation model are set up based on polychromatic sets (PS theory. According to the two models, the systems of location relation equations and interference relation equations are established. Then, using methods of topologically related surfaces (TTRS theory and variational geometric constraints (VGC theory, three VGC reasoning matrices are constructed. According to corresponding relations between VGCs and assembly tolerance types, the reasoning matrices of tolerance types are also established by using contour matrices of PS. Finally, an exemplary product is used to construct its assembly tolerance networks and meanwhile to verify the feasibility and effectiveness of the proposed method.

  19. Pattern Recognition Theory of Mind

    OpenAIRE

    2009-01-01

    I propose that pattern recognition, memorization and processing are key concepts that can be a principle set for the theoretical modeling of the mind function. Most of the questions about the mind functioning can be answered by a descriptive modeling and definitions from these principles. An understandable consciousness definition can be drawn based on the assumption that a pattern recognition system can recognize its own patterns of activity. The principles, descriptive modeling and definiti...

  20. [Neurological disease and facial recognition].

    Science.gov (United States)

    Kawamura, Mitsuru; Sugimoto, Azusa; Kobayakawa, Mutsutaka; Tsuruya, Natsuko

    2012-07-01

    To discuss the neurological basis of facial recognition, we present our case reports of impaired recognition and a review of previous literature. First, we present a case of infarction and discuss prosopagnosia, which has had a large impact on face recognition research. From a study of patient symptoms, we assume that prosopagnosia may be caused by unilateral right occipitotemporal lesion and right cerebral dominance of facial recognition. Further, circumscribed lesion and degenerative disease may also cause progressive prosopagnosia. Apperceptive prosopagnosia is observed in patients with posterior cortical atrophy (PCA), pathologically considered as Alzheimer's disease, and associative prosopagnosia in frontotemporal lobar degeneration (FTLD). Second, we discuss face recognition as part of communication. Patients with Parkinson disease show social cognitive impairments, such as difficulty in facial expression recognition and deficits in theory of mind as detected by the reading the mind in the eyes test. Pathological and functional imaging studies indicate that social cognitive impairment in Parkinson disease is possibly related to damages in the amygdalae and surrounding limbic system. The social cognitive deficits can be observed in the early stages of Parkinson disease, and even in the prodromal stage, for example, patients with rapid eye movement (REM) sleep behavior disorder (RBD) show impairment in facial expression recognition. Further, patients with myotonic dystrophy type 1 (DM 1), which is a multisystem disease that mainly affects the muscles, show social cognitive impairment similar to that of Parkinson disease. Our previous study showed that facial expression recognition impairment of DM 1 patients is associated with lesion in the amygdalae and insulae. Our study results indicate that behaviors and personality traits in DM 1 patients, which are revealed by social cognitive impairment, are attributable to dysfunction of the limbic system.

  1. On Tangut Historical Documents Recognition*

    Science.gov (United States)

    Liu, Changqing

    As the Tangut studies have made progress, a considerable number of Tangut historical documents' copies have been published. It is of great importance to carry out digitalization and domestication of these copies. The paper firstly makes an initial processing of images by global threshold, then dissect the photocopies by scanning. Finally adopts the recognition approach of principal component analysis. The experiment shows that a better recognition can be achieved by calculation without extra time.

  2. Voice congruency facilitates word recognition.

    Directory of Open Access Journals (Sweden)

    Sandra Campeanu

    Full Text Available Behavioral studies of spoken word memory have shown that context congruency facilitates both word and source recognition, though the level at which context exerts its influence remains equivocal. We measured event-related potentials (ERPs while participants performed both types of recognition task with words spoken in four voices. Two voice parameters (i.e., gender and accent varied between speakers, with the possibility that none, one or two of these parameters was congruent between study and test. Results indicated that reinstating the study voice at test facilitated both word and source recognition, compared to similar or no context congruency at test. Behavioral effects were paralleled by two ERP modulations. First, in the word recognition test, the left parietal old/new effect showed a positive deflection reflective of context congruency between study and test words. Namely, the same speaker condition provided the most positive deflection of all correctly identified old words. In the source recognition test, a right frontal positivity was found for the same speaker condition compared to the different speaker conditions, regardless of response success. Taken together, the results of this study suggest that the benefit of context congruency is reflected behaviorally and in ERP modulations traditionally associated with recognition memory.

  3. Pattern Recognition Using Neural Networks

    Directory of Open Access Journals (Sweden)

    Santaji Ghorpade

    2010-12-01

    Full Text Available Face Recognition has been identified as one of the attracting research areas and it has drawn the attention of many researchers due to its varying applications such as security systems, medical systems,entertainment, etc. Face recognition is the preferred mode of identification by humans: it is natural,robust and non-intrusive. A wide variety of systems requires reliable personal recognition schemes to either confirm or determine the identity of an individual requesting their services. The purpose of such schemes is to ensure that the rendered services are accessed only by a legitimate user and no one else.Examples of such applications include secure access to buildings, computer systems, laptops, cellular phones, and ATMs. In the absence of robust personal recognition schemes, these systems are vulnerable to the wiles of an impostor.In this paper we have developed and illustrated a recognition system for human faces using a novel Kohonen self-organizing map (SOM or Self-Organizing Feature Map (SOFM based retrieval system.SOM has good feature extracting property due to its topological ordering. The Facial Analytics results for the 400 images of AT&T database reflects that the face recognition rate using one of the neural network algorithm SOM is 85.5% for 40 persons.

  4. Holistic processing predicts face recognition.

    Science.gov (United States)

    Richler, Jennifer J; Cheung, Olivia S; Gauthier, Isabel

    2011-04-01

    The concept of holistic processing is a cornerstone of face-recognition research. In the study reported here, we demonstrated that holistic processing predicts face-recognition abilities on the Cambridge Face Memory Test and on a perceptual face-identification task. Our findings validate a large body of work that relies on the assumption that holistic processing is related to face recognition. These findings also reconcile the study of face recognition with the perceptual-expertise work it inspired; such work links holistic processing of objects with people's ability to individuate them. Our results differ from those of a recent study showing no link between holistic processing and face recognition. This discrepancy can be attributed to the use in prior research of a popular but flawed measure of holistic processing. Our findings salvage the central role of holistic processing in face recognition and cast doubt on a subset of the face-perception literature that relies on a problematic measure of holistic processing.

  5. Metaphase Spindle Assembly

    Directory of Open Access Journals (Sweden)

    Tarun M. Kapoor

    2017-02-01

    Full Text Available A microtubule-based bipolar spindle is required for error-free chromosome segregation during cell division. In this review I discuss the molecular mechanisms required for the assembly of this dynamic micrometer-scale structure in animal cells.

  6. Dump valve assembly

    Science.gov (United States)

    Owen, T.J.

    1984-01-01

    A dump valve assembly comprising a body having a bore defined by a tapered wall and a truncated spherical valve member adapted to seat along a spherical surface portion thereof against said tapered wall. Means are provided for pivoting said valve member between a closed position engagable with said tapered wall and an open position disengaged therefrom.

  7. Ordinary General Assembly

    CERN Multimedia

    Staff Association

    2010-01-01

    Tuesday 20 April at 10.00 Council Chamber, Bldg 503 In conformity with the Statutes of the Staff Association, an ordinary General Assembly is organized once a year (article IV.2.1). Agenda   Adoption of the Agenda Approval of the Draft Minutes of the Ordinary General Assembly of 12 May 2009 Presentation and approval of the Activity Report 2009 Presentation and approval of the Financial Report 2009 Presentation and approval of the Auditors Report 2009 Programme for 2010 Presentation et and approval of the draft budget and subscription rate 2010 Election of the Election Committee Election of the Board of Auditors Miscellaneous We remind members of article IV.3.4 in the Statutes of the Association which reads: “After having dealt with all the items on the agenda, the members may, with the consent of the Assembly, have other matters discussed, but decisions may be taken only on the items listed on the agenda. Nevertheless, the Assembly may require t...

  8. Ordinary General Assembly

    CERN Multimedia

    Staff Association

    2011-01-01

    Tuesday 12 April at 14.00 Council Chamber, Bldg 503 In conformity with the Statutes of the Staff Association, an ordinary General Assembly is organized once a year (article IV.2.1). Agenda   Adoption of the Agenda Approval of the Draft Minutes of the Ordinary General Assembly of 20 April 2010 Presentation and approval of the Activity Report 2010 Presentation and approval of the Financial Report 2010 Presentation and approval of the Auditors Report 2010 Programme for 2011 Presentation et and approval of the draft budget and subscription rate 2012 Election of the Election Committee Election of the Board of Auditors Miscellaneous We remind members of article IV.3.4 in the Statutes of the Association which reads: “After having dealt with all the items on the agenda, the members may, with the consent of the Assembly, have other matters discussed, but decisions may be taken only on the items listed on the agenda. Nevertheless, the Assembly ma...

  9. Ordinary General Assembly

    CERN Multimedia

    Staff Association

    2011-01-01

    Tuesday 12 April at 14.00 Council Chamber, Bldg 503 In conformity with the Statutes of the Staff Association, an ordinary General Assembly is organized once a year (article IV.2.1). Agenda   Adoption of the Agenda Approval of the Draft Minutes of the Ordinary General Assembly of 20 April 2010 Presentation and approval of the Activity Report 2010 Presentation and approval of the Financial Report 2010 Presentation and approval of the Auditors Report 2010 Programme for 2011 Presentation and approval of the draft budget and subscription rate 2012 Election of the Election Committee Election of the Board of Auditors Miscellaneous We remind members of article IV.3.4 in the Statutes of the Association which reads: “After having dealt with all the items on the agenda, the members may, with the consent of the Assembly, have other matters discussed, but decisions may be taken only on the items listed on the agenda. Nevertheless, the Assembly may r...

  10. Supramolecular Assemblies in Photosynthesis

    Science.gov (United States)

    Wrachtrup, J.; Tietz, C.; Jelezko, F.; Gerken, U.; Schuler, S.; Götze, B.; Volkmer, A.

    2002-10-01

    The photosynthetic apparatus contains a wealth of supramolecular assemblies that are optimized for charge and energy transfer. Various techniques have been applied to investigate these functions that rely on the electronic interaction among pigment molecules. In this contribution we will present single-molecule studies of pigment protein complexes. They reveal new information about electronic interactions between chlorophyll molecules in light harvesting complexes.

  11. Turbomachine blade assembly

    Energy Technology Data Exchange (ETDEWEB)

    Garcia Crespo, Andres Jose

    2016-11-01

    Embodiments of the present disclosure include a system comprising a turbomachine blade assembly having a blade portion, a shank portion, and a mounting portion, wherein the blade portion, the shank portion, and the mounting portion comprise a first plurality of plies extending from a tip of the airfoil to a base of the dovetail.

  12. America's Assembly Line

    DEFF Research Database (Denmark)

    Nye, David Edwin

    A social history of the assembly line, invented in 1913. Both praised as a boon to consumers and as a curse for workers, it has been satirized, imitated, and celebrated for 100 years. It has inspired fiction, comedy, cafeteria layouts, and suburban housing. It transformed industrial labor...

  13. Industrial Assembly Cases

    DEFF Research Database (Denmark)

    Ellekilde, Lars-Peter; Buch, Jacob Pørksen; Iversen, Thorbjørn Mosekjær;

    This technical report presents 13 different industrial assembly tasks, which are composed of 70 different operations. The report is written to provide an overview and do as such not contain product specific information such as object weights, dimensions etc. The operations are classified into a set...

  14. Assembling Sustainable Territories

    DEFF Research Database (Denmark)

    Vandergeest, Peter; Ponte, Stefano; Bush, Simon

    2015-01-01

    that territorialisation is accomplished not just through (re)defining bounded space, but more broadly through the assembling of four elements: space, subjects, objects, and expertise. Four case studies of sustainability certification in seafood are analyzed to show that ‘green gabbing’ is not necessarily the central...

  15. Role of peripheral phenanthroline groups in the self-assembly of self-assembled molecular triangles

    Indian Academy of Sciences (India)

    Mili C Naranthatta; V Ramkumar; Dillip Kumar Chand

    2015-02-01

    Self-assembled molecular triangles [Pd3(phen)3(imidazolate)3](NO3)3, 1a and [Pd3(phen)3 (imidazolate)3](PF6)3, 1b are prepared by the combination of imidazole with Pd(phen)(NO3)2 and Pd(phen) (PF6)2, respectively. Imidazole was deprotonated during the complexation reactions and the imidazolate so formed acted as a bis-monodentate bridging ligand to form the bowl-shaped trinuclear architectures of 1a/b. Relative orientation of the imidazolate moieties can be best described as syn,anti,anti as observed in the crystal structure of 1b. However, in solution state, slow conformational changes are assumed on the basis of 1HNMR spectral data. The molecular triangles are crafted with three peripheral phen units capable of − stacking interactions. Well-fashioned intermolecular − interactions are observed in the solid-state, wherein further self-assembly of already self-assembled triangle is observed.

  16. Correcting ligands, metabolites, and pathways

    Directory of Open Access Journals (Sweden)

    Vriend Gert

    2006-11-01

    Full Text Available Abstract Background A wide range of research areas in bioinformatics, molecular biology and medicinal chemistry require precise chemical structure information about molecules and reactions, e.g. drug design, ligand docking, metabolic network reconstruction, and systems biology. Most available databases, however, treat chemical structures more as illustrations than as a datafield in its own right. Lack of chemical accuracy impedes progress in the areas mentioned above. We present a database of metabolites called BioMeta that augments the existing pathway databases by explicitly assessing the validity, correctness, and completeness of chemical structure and reaction information. Description The main bulk of the data in BioMeta were obtained from the KEGG Ligand database. We developed a tool for chemical structure validation which assesses the chemical validity and stereochemical completeness of a molecule description. The validation tool was used to examine the compounds in BioMeta, showing that a relatively small number of compounds had an incorrect constitution (connectivity only, not considering stereochemistry and that a considerable number (about one third had incomplete or even incorrect stereochemistry. We made a large effort to correct the errors and to complete the structural descriptions. A total of 1468 structures were corrected and/or completed. We also established the reaction balance of the reactions in BioMeta and corrected 55% of the unbalanced (stoichiometrically incorrect reactions in an automatic procedure. The BioMeta database was implemented in PostgreSQL and provided with a web-based interface. Conclusion We demonstrate that the validation of metabolite structures and reactions is a feasible and worthwhile undertaking, and that the validation results can be used to trigger corrections and improvements to BioMeta, our metabolite database. BioMeta provides some tools for rational drug design, reaction searches, and

  17. Self-assembly of tetravalent Goldberg polyhedra from 144 small components

    Science.gov (United States)

    Fujita, Daishi; Ueda, Yoshihiro; Sato, Sota; Mizuno, Nobuhiro; Kumasaka, Takashi; Fujita, Makoto

    2016-12-01

    Rational control of the self-assembly of large structures is one of the key challenges in chemistry, and is believed to become increasingly difficult and ultimately impossible as the number of components involved increases. So far, it has not been possible to design a self-assembled discrete molecule made up of more than 100 components. Such molecules—for example, spherical virus capsids—are prevalent in nature, which suggests that the difficulty in designing these very large self-assembled molecules is due to a lack of understanding of the underlying design principles. For example, the targeted assembly of a series of large spherical structures containing up to 30 palladium ions coordinated by up to 60 bent organic ligands was achieved by considering their topologies. Here we report the self-assembly of a spherical structure that also contains 30 palladium ions and 60 bent ligands, but belongs to a shape family that has not previously been observed experimentally. The new structure consists of a combination of 8 triangles and 24 squares, and has the symmetry of a tetravalent Goldberg polyhedron. Platonic and Archimedean solids have previously been prepared through self-assembly, as have trivalent Goldberg polyhedra, which occur naturally in the form of virus capsids and fullerenes. But tetravalent Goldberg polyhedra have not previously been reported at the molecular level, although their topologies have been predicted using graph theory. We use graph theory to predict the self-assembly of even larger tetravalent Goldberg polyhedra, which should be more stable, enabling another member of this polyhedron family to be assembled from 144 components: 48 palladium ions and 96 bent ligands.

  18. Comparing Face Detection and Recognition Techniques

    OpenAIRE

    Korra, Jyothi

    2016-01-01

    This paper implements and compares different techniques for face detection and recognition. One is find where the face is located in the images that is face detection and second is face recognition that is identifying the person. We study three techniques in this paper: Face detection using self organizing map (SOM), Face recognition by projection and nearest neighbor and Face recognition using SVM.

  19. Interaction Entropy: A New Paradigm for Highly Efficient and Reliable Computation of Protein-Ligand Binding Free Energy.

    Science.gov (United States)

    Duan, Lili; Liu, Xiao; Zhang, John Z H

    2016-05-04

    Efficient and reliable calculation of protein-ligand binding free energy is a grand challenge in computational biology and is of critical importance in drug design and many other molecular recognition problems. The main challenge lies in the calculation of entropic contribution to protein-ligand binding or interaction systems. In this report, we present a new interaction entropy method which is theoretically rigorous, computationally efficient, and numerically reliable for calculating entropic contribution to free energy in protein-ligand binding and other interaction processes. Drastically different from the widely employed but extremely expensive normal mode method for calculating entropy change in protein-ligand binding, the new method calculates the entropic component (interaction entropy or -TΔS) of the binding free energy directly from molecular dynamics simulation without any extra computational cost. Extensive study of over a dozen randomly selected protein-ligand binding systems demonstrated that this interaction entropy method is both computationally efficient and numerically reliable and is vastly superior to the standard normal mode approach. This interaction entropy paradigm introduces a novel and intuitive conceptual understanding of the entropic effect in protein-ligand binding and other general interaction systems as well as a practical method for highly efficient calculation of this effect.

  20. Multicomponent mixtures for cryoprotection and ligand solubilization

    Directory of Open Access Journals (Sweden)

    Lidia Ciccone

    2015-09-01

    Full Text Available Mixed cryoprotectants have been developed for the solubilization of ligands for crystallization of protein–ligand complexes and for crystal soaking. Low affinity lead compounds with poor solubility are problematic for structural studies. Complete ligand solubilization is required for co-crystallization and crystal soaking experiments to obtain interpretable electron density maps for the ligand. Mixed cryo-preserving compounds are needed prior to X-ray data collection to reduce radiation damage at synchrotron sources. Here we present dual-use mixes that act as cryoprotectants and also promote the aqueous solubility of hydrophobic ligands. Unlike glycerol that increases protein solubility and can cause crystal melting the mixed solutions of cryo-preserving compounds that include precipitants and solubilizers, allow for worry-free crystal preservation while simultaneously solubilizing relatively hydrophobic ligands, typical of ligands obtained in high-throughput screening. The effectiveness of these mixture has been confirmed on a human transthyretin crystals both during crystallization and in flash freezing of crystals.