protein conformation

Summary

Summary: The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).

Top Publications

  1. pmc The Protein Data Bank
    H M Berman
    Research Collaboratory for Structural Bioinformatics RCSB, Rutgers University, Piscataway, NJ 08854 8087, USA
    Nucleic Acids Res 28:235-42. 2000
  2. ncbi The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling
    Konstantin Arnold
    Biozentrum Basel, University of Basel Switzerland
    Bioinformatics 22:195-201. 2006
  3. ncbi Protein structure prediction on the Web: a case study using the Phyre server
    Lawrence A Kelley
    Structural Bioinformatics Group, Division of Molecular Biosciences, Department of Life Sciences, Imperial College London, South Kensington Campus, London, UK
    Nat Protoc 4:363-71. 2009
  4. ncbi Comparative protein modelling by satisfaction of spatial restraints
    A Sali
    Department of Crystallography, Birkbeck College, London, England
    J Mol Biol 234:779-815. 1993
  5. pmc I-TASSER server for protein 3D structure prediction
    Yang Zhang
    Center for Bioinformatics and Department of Molecular Bioscience, University of Kansas, 2030 Becker Dr, Lawrence, KS 66047, USA
    BMC Bioinformatics 9:40. 2008
  6. pmc MolProbity: all-atom contacts and structure validation for proteins and nucleic acids
    Ian W Davis
    Department of Biochemistry, Duke University, Durham, NC, USA
    Nucleic Acids Res 35:W375-83. 2007
  7. pmc The HHpred interactive server for protein homology detection and structure prediction
    Johannes Söding
    Department of Protein Evolution, Max Planck Institute for Developmental Biology Spemannstrasse 35, 72076 Tubingen, Germany
    Nucleic Acids Res 33:W244-8. 2005
  8. pmc The RCSB Protein Data Bank: redesigned web site and web services
    Peter W Rose
    San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093 0743, USA
    Nucleic Acids Res 39:D392-401. 2011
  9. ncbi Protein misfolding, functional amyloid, and human disease
    Fabrizio Chiti
    Dipartimento di Scienze Biochimiche, Universita degli Studi di Firenze, I 50134 Firenze, Italy
    Annu Rev Biochem 75:333-66. 2006
  10. ncbi Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy
    Richard A Friesner
    Department of Chemistry, Columbia University, New York, New York 10036, USA
    J Med Chem 47:1739-49. 2004

Detail Information

Publications276 found, 100 shown here

  1. pmc The Protein Data Bank
    H M Berman
    Research Collaboratory for Structural Bioinformatics RCSB, Rutgers University, Piscataway, NJ 08854 8087, USA
    Nucleic Acids Res 28:235-42. 2000
    ..This paper describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information, and near-term plans for the future development of the resource...
  2. ncbi The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling
    Konstantin Arnold
    Biozentrum Basel, University of Basel Switzerland
    Bioinformatics 22:195-201. 2006
    ....
  3. ncbi Protein structure prediction on the Web: a case study using the Phyre server
    Lawrence A Kelley
    Structural Bioinformatics Group, Division of Molecular Biosciences, Department of Life Sciences, Imperial College London, South Kensington Campus, London, UK
    Nat Protoc 4:363-71. 2009
    ..Phyre is widely used by the biological community, with >150 submissions per day, and provides a simple interface to results. Phyre takes 30 min to predict the structure of a 250-residue protein...
  4. ncbi Comparative protein modelling by satisfaction of spatial restraints
    A Sali
    Department of Crystallography, Birkbeck College, London, England
    J Mol Biol 234:779-815. 1993
    ..The method is automated and is illustrated by the modelling of trypsin from two other serine proteinases...
  5. pmc I-TASSER server for protein 3D structure prediction
    Yang Zhang
    Center for Bioinformatics and Department of Molecular Bioscience, University of Kansas, 2030 Becker Dr, Lawrence, KS 66047, USA
    BMC Bioinformatics 9:40. 2008
    ..Our laboratory has since then received numerous requests about the public availability of the I-TASSER algorithm and the usage of the I-TASSER predictions...
  6. pmc MolProbity: all-atom contacts and structure validation for proteins and nucleic acids
    Ian W Davis
    Department of Biochemistry, Duke University, Durham, NC, USA
    Nucleic Acids Res 35:W375-83. 2007
    ..This service is available free to all users at http://molprobity.biochem.duke.edu...
  7. pmc The HHpred interactive server for protein homology detection and structure prediction
    Johannes Söding
    Department of Protein Evolution, Max Planck Institute for Developmental Biology Spemannstrasse 35, 72076 Tubingen, Germany
    Nucleic Acids Res 33:W244-8. 2005
    ..A detailed help facility is available. As a demonstration, we analyze the sequence of SpoVT, a transcriptional regulator from Bacillus subtilis. HHpred can be accessed at http://protevo.eb.tuebingen.mpg.de/hhpred...
  8. pmc The RCSB Protein Data Bank: redesigned web site and web services
    Peter W Rose
    San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093 0743, USA
    Nucleic Acids Res 39:D392-401. 2011
    ..These improvements enable a range of new possibilities to analyze and understand structure data. The next generation of the RCSB PDB web site, as described here, provides a rich resource for research and education...
  9. ncbi Protein misfolding, functional amyloid, and human disease
    Fabrizio Chiti
    Dipartimento di Scienze Biochimiche, Universita degli Studi di Firenze, I 50134 Firenze, Italy
    Annu Rev Biochem 75:333-66. 2006
    ....
  10. ncbi Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy
    Richard A Friesner
    Department of Chemistry, Columbia University, New York, New York 10036, USA
    J Med Chem 47:1739-49. 2004
    ..Glide is also found to be more accurate than the recently described Surflex method...
  11. pmc ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids
    Haim Ashkenazy
    Department of Cell Research and Immunology, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
    Nucleic Acids Res 38:W529-33. 2010
    ..In addition, the new version of ConSurf calculates the evolutionary rates for nucleic acid sequences. The new version is freely available at: http://consurf.tau.ac.il/...
  12. ncbi A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
    Yong Duan
    Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
    J Comput Chem 24:1999-2012. 2003
    ..charge sets, as judged by overall agreement between dipole moments, allows a smooth transition to the new force field in the area of ligand-binding calculations. Test simulations on a large set of proteins are also discussed...
  13. pmc Structures of the CXCR4 chemokine GPCR with small-molecule and cyclic peptide antagonists
    Beili Wu
    Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    Science 330:1066-71. 2010
    ..These structures provide new clues about the interactions between CXCR4 and its natural ligand CXCL12, and with the HIV-1 glycoprotein gp120...
  14. pmc ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins
    Markus Wiederstein
    Center of Applied Molecular Engineering, Division of Bioinformatics, University of Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg, Austria
    Nucleic Acids Res 35:W407-10. 2007
    ..ProSA-web is accessible at https://prosa.services.came.sbg.ac.at...
  15. pmc High-resolution crystal structure of an engineered human beta2-adrenergic G protein-coupled receptor
    Vadim Cherezov
    Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037, USA
    Science 318:1258-65. 2007
    ....
  16. ncbi Crystal structure of the nucleosome core particle at 2.8 A resolution
    K Luger
    Institut fur Molekularbiologie und Biophysik, Zurich, Switzerland
    Nature 389:251-60. 1997
    ..The lack of uniformity between multiple histone/DNA-binding sites causes the DNA to deviate from ideal superhelix geometry...
  17. ncbi IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content
    Zsuzsanna Dosztanyi
    Institute of Enzymology, BRC, Hungarian Academy of Sciences, PO Box 7, H 1518 Budapest, Hungary
    Bioinformatics 21:3433-4. 2005
    ..Optional to the prediction are built-in parameter sets optimized for predicting short or long disordered regions and structured domains...
  18. ncbi Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions
    E Krissinel
    European Bioinformatics Institute, Genome Campus, Hinxton, Cambridge CB10 1SD, England
    Acta Crystallogr D Biol Crystallogr 60:2256-68. 2004
    ..A new score, balancing the r.m.s.d. and alignment length Nalign, is proposed. It is found that different servers agree reasonably well on the new score, while showing considerable differences in r.m.s.d. and Nalign...
  19. pmc The crystal structure of a voltage-gated sodium channel
    Jian Payandeh
    Department of Pharmacology, University of Washington, Seattle, Washington 98195, USA
    Nature 475:353-8. 2011
    ..This structure provides the template for understanding electrical signalling in excitable cells and the actions of drugs used for pain, epilepsy and cardiac arrhythmia at the atomic level...
  20. ncbi Molecular chaperones in the cytosol: from nascent chain to folded protein
    F Ulrich Hartl
    Department of Cellular Biochemistry, Max Planck Institut fur Biochemie, Am Klopferspitz 18a, D 82152 Martinsried, Germany
    Science 295:1852-8. 2002
    ..Understanding how the thousands of different proteins synthesized in a cell use this chaperone machinery has profound implications for biotechnology and medicine...
  21. ncbi Structure validation by Calpha geometry: phi,psi and Cbeta deviation
    Simon C Lovell
    Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
    Proteins 50:437-50. 2003
    ..To run our geometrical evaluations on a user-uploaded file, see MOLPROBITY (http://kinemage.biochem.duke.edu) or RAMPAGE (http://www-cryst.bioc.cam.ac.uk/rampage)...
  22. ncbi Structure of an HIV gp120 envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody
    P D Kwong
    Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
    Nature 393:648-59. 1998
    ..Our results provide a framework for understanding the complex biology of HIV entry into cells and should guide efforts to intervene...
  23. ncbi Protein folding and misfolding
    Christopher M Dobson
    University of Cambridge, Department of Chemistry, Lensfield Road, Cambridge CB2 1EW, UK
    Nature 426:884-90. 2003
    ..Aggregation of misfolded proteins that escape the cellular quality-control mechanisms is a common feature of a wide range of highly debilitating and increasingly prevalent diseases...
  24. ncbi Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations
    Alexander D MacKerell
    Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, Maryland 21201, USA
    J Comput Chem 25:1400-15. 2004
    ..This extension of the potential energy function is anticipated to facilitate improved treatment of biological macromolecules via MM approaches in general...
  25. ncbi Common structure of soluble amyloid oligomers implies common mechanism of pathogenesis
    Rakez Kayed
    Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697 3900, USA
    Science 300:486-9. 2003
    ..These results indicate that different types of soluble amyloid oligomers have a common structure and suggest they share a common mechanism of toxicity...
  26. pmc ExPASy: The proteomics server for in-depth protein knowledge and analysis
    Elisabeth Gasteiger
    Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel Servet, 1211 Geneva 4, Switzerland
    Nucleic Acids Res 31:3784-8. 2003
    ..ExPASy started to operate in 1993, as the first WWW server in the field of life sciences. In addition to the main site in Switzerland, seven mirror sites in different continents currently serve the user community...
  27. pmc Structure of a nanobody-stabilized active state of the β(2) adrenoceptor
    Søren G F Rasmussen
    Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, California 94305, USA
    Nature 469:175-80. 2011
    ..This structure provides insights into the process of agonist binding and activation...
  28. pmc Antibody recognition of a highly conserved influenza virus epitope
    Damian C Ekiert
    Department of Molecular Biology, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    Science 324:246-51. 2009
    ..The CR6261 epitope identified here should accelerate the design and implementation of improved vaccines that can elicit CR6261-like antibodies, as well as antibody-based therapies for the treatment of influenza...
  29. ncbi Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations
    Raphael Guerois
    EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    J Mol Biol 320:369-87. 2002
    ..FOLDEF is available via a web-interface at http://fold-x.embl-heidelberg.de..
  30. ncbi Very fast empirical prediction and rationalization of protein pKa values
    Hui Li
    Department of Chemistry, Center for Biocatalysis and Bioprocessing, The University of Iowa, Iowa City, Iowa 52242, USA
    Proteins 61:704-21. 2005
    ..89 from experimental values. Removal of the 29 pKa values that are upper or lower limits results in an RMSD = 0.79 for the remaining 285 pKa values...
  31. pmc ESPript/ENDscript: Extracting and rendering sequence and 3D information from atomic structures of proteins
    Patrice Gouet
    Laboratoire de BioCristallographie, IBCP CNRS UMR 5086 UCBL, 7 passage du Vercors, 69367 Lyon Cedex 07, France
    Nucleic Acids Res 31:3320-3. 2003
    ..ESPript and ENDscript are available at http://genopole.toulouse.inra.fr/ESPript...
  32. pmc Structure of the human dopamine D3 receptor in complex with a D2/D3 selective antagonist
    Ellen Y T Chien
    Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    Science 330:1091-5. 2010
    ..This difference provides direction to the design of D3R-selective agents for treating drug abuse and other neuropsychiatric indications...
  33. ncbi Protein structure modeling with MODELLER
    Narayanan Eswar
    Department of Biopharmaceutical Sciences and California Institute for Quantitative Biomedical Research, University of California at San Francisco, San Francisco, CA, USA
    Methods Mol Biol 426:145-59. 2008
    ..Automation of similar protocols (correction of protcols) has resulted in models of useful accuracy for domains in more than half of all known protein sequences...
  34. pmc The 2.6 angstrom crystal structure of a human A2A adenosine receptor bound to an antagonist
    Veli Pekka Jaakola
    Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037 USA
    Science 322:1211-7. 2008
    ....
  35. pmc PDBe: Protein Data Bank in Europe
    S Velankar
    Protein Data Bank in Europe, EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 40:D445-52. 2012
    ....
  36. pmc The FoldX web server: an online force field
    Joost Schymkowitz
    Switch Laboratory, Flanders Interuniversity Institute for Biotechnology VIB, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussel, Belgium
    Nucleic Acids Res 33:W382-8. 2005
    ..This core functionality will be further extended as more FoldX applications are developed...
  37. ncbi A general model of prion strains and their pathogenicity
    John Collinge
    MRC Prion Unit, Department of Neurodegenerative Disease, UCL Institute of Neurology, London WC1N 3BG, UK
    Science 318:930-6. 2007
    ..Recent advances suggest that prions themselves are not directly neurotoxic, but rather their propagation involves production of toxic species, which may be uncoupled from infectivity...
  38. ncbi The use of differential scanning fluorimetry to detect ligand interactions that promote protein stability
    Frank H Niesen
    Structural Genomics Consortium, Botnar Research Centre, Oxford University, Oxford, UK
    Nat Protoc 2:2212-21. 2007
    ..Results can be obtained in a single day...
  39. pmc Structure of P-glycoprotein reveals a molecular basis for poly-specific drug binding
    Stephen G Aller
    Department of Molecular Biology, Scripps Research Institute, 10550 North Torrey Pines Road, CB105, La Jolla, CA 92037, USA
    Science 323:1718-22. 2009
    ..The inward-facing conformation represents an initial stage of the transport cycle that is competent for drug binding...
  40. ncbi Atomic structure of a voltage-dependent K+ channel in a lipid membrane-like environment
    Stephen B Long
    Howard Hughes Medical Institute, Laboratory of Molecular Neurobiology and Biophysics, Rockefeller University, 1230 York Avenue, New York, New York 10065, USA
    Nature 450:376-82. 2007
    ..The detailed structure, which can be compared directly to a large body of functional data, explains charge stabilization within the membrane and suggests a mechanism for voltage-sensor movements and pore gating...
  41. ncbi Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening
    Thomas A Halgren
    Schrodinger, L L C, 120 W 45th Street, New York, New York 10036, USA
    J Med Chem 47:1750-9. 2004
    ..Comparisons to results for the thymidine kinase and estrogen receptors published by Rognan and co-workers (J. Med. Chem. 2000, 43, 4759-4767) show that Glide 2.5 performs better than GOLD 1.1, FlexX 1.8, or DOCK 4.01...
  42. pmc X-ray structures of LeuT in substrate-free outward-open and apo inward-open states
    Harini Krishnamurthy
    Vollum Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, USA
    Nature 481:469-74. 2012
    ..The new structures establish a structural framework for the mechanism of neurotransmitter sodium symporters and their modulation by therapeutic and illicit substances...
  43. pmc A series of PDB related databases for everyday needs
    Robbie P Joosten
    Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
    Nucleic Acids Res 39:D411-9. 2011
    ..All these systems are updated weekly. The data sets can be used for the analysis of properties of protein structures in areas ranging from structural genomics, to cancer biology and protein design...
  44. pmc The role of dynamic conformational ensembles in biomolecular recognition
    David D Boehr
    Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA
    Nat Chem Biol 5:789-96. 2009
    ....
  45. ncbi An allosteric mechanism for activation of the kinase domain of epidermal growth factor receptor
    Xuewu Zhang
    Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, 94720, USA
    Cell 125:1137-49. 2006
    ..The CDK/cyclin-like complex formed by two kinase domains thus explains the activation of EGFR-family receptors by homo- or heterodimerization...
  46. pmc Modeling of loops in protein structures
    A Fiser
    Laboratory of Molecular Biophysics, Pels Family Center for Biochemistry and Structural Biology, The Rockefeller University, New York, New York 10021, USA
    Protein Sci 9:1753-73. 2000
    ..Finally, it is shown that the average accuracy of prediction is limited primarily by the accuracy of the energy function rather than by the extent of conformational sampling...
  47. ncbi Crystal structure of the human beta2 adrenergic G-protein-coupled receptor
    Søren G F Rasmussen
    Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, Palo Alto, California 94305, USA
    Nature 450:383-7. 2007
    ..These differences may be responsible for the relatively high basal activity and structural instability of the beta2AR, and contribute to the challenges in obtaining diffraction-quality crystals of non-rhodopsin GPCRs...
  48. pmc The structure and function of G-protein-coupled receptors
    Daniel M Rosenbaum
    Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Palo Alto, California 94305, USA
    Nature 459:356-63. 2009
    ..Recent high-resolution structural studies have provided insights into the molecular mechanisms of GPCR activation and constitutive activity...
  49. pmc Structure of the human histamine H1 receptor complex with doxepin
    Tatsuro Shimamura
    Human Receptor Crystallography Project, ERATO, Japan Science and Technology Agency, Kyoto 606 8501, Japan
    Nature 475:65-70. 2011
    ..Our study sheds light on the molecular basis of H(1)R antagonist specificity against H(1)R...
  50. pmc Structure of the human κ-opioid receptor in complex with JDTic
    Huixian Wu
    Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
    Nature 485:327-32. 2012
    ....
  51. ncbi Optimal description of a protein structure in terms of multiple groups undergoing TLS motion
    Jay Painter
    Biomolecular Structure Center, Department of Biochemistry, University of Washington, Seattle, WA 98195 7742, USA
    Acta Crystallogr D Biol Crystallogr 62:439-50. 2006
    ..The models generated by TLSMD analysis can significantly improve the standard crystallographic residuals R and R(free) and can reveal intrinsic dynamic properties of the protein...
  52. ncbi Targeting cancer with small molecule kinase inhibitors
    Jianming Zhang
    Dana Farber Cancer Institute, Department of Cancer Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nat Rev Cancer 9:28-39. 2009
    ..This Review provides a broad overview of some of the approaches currently used to discover and characterize new kinase inhibitors...
  53. pmc Structure of a beta1-adrenergic G-protein-coupled receptor
    Tony Warne
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
    Nature 454:486-91. 2008
    ....
  54. ncbi Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy
    Peter B Rosenthal
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
    J Mol Biol 333:721-45. 2003
    ..7A resolution, according to a new objective criterion for resolution assessment proposed here...
  55. pmc Improved prediction of protein side-chain conformations with SCWRL4
    Georgii G Krivov
    Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, Pennsylvania 19111, USA
    Proteins 77:778-95. 2009
    ..The new program maintains its simple command-line interface, designed for homology modeling, and is now available as a dynamic-linked library for incorporation into other software programs...
  56. pmc Structural definition of a conserved neutralization epitope on HIV-1 gp120
    Tongqing Zhou
    Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
    Nature 445:732-7. 2007
    ..A site of vulnerability, related to a functional requirement for efficient association with CD4, can therefore be targeted by antibody to neutralize HIV-1...
  57. ncbi Crystal structure of a bacterial homologue of glucose transporters GLUT1-4
    Linfeng Sun
    State Key Laboratory of Bio membrane and Membrane Biotechnology, Center for Structural Biology, Tsinghua University, Beijing 100084, China
    Nature 490:361-6. 2012
    ..The structural and biochemical information reported here constitutes an important framework for mechanistic understanding of glucose transporters and sugar porters in general...
  58. pmc How significant is a protein structure similarity with TM-score = 0.5?
    Jinrui Xu
    Department of Medical School, Center for Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA
    Bioinformatics 26:889-95. 2010
    ..This article aims to answer two questions: (i) what is the statistical significance of TM-score? (ii) What is the probability of two proteins having the same fold given a specific TM-score?..
  59. ncbi Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations
    Jeffrey J Gray
    Howard Hughes Medical Institute and Department of Biochemistry, University of Washington, J 567 Health Sciences, Box 357350, Seattle, WA 98195, USA
    J Mol Biol 331:281-99. 2003
    ....
  60. pmc BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities
    Tiqing Liu
    Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, 9600 Gudelsky Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 35:D198-201. 2007
    ..The data in BindingDB are linked both to structural data in the PDB via PDB IDs and chemical and sequence searches, and to the literature in PubMed via PubMed IDs...
  61. pmc Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing
    D I Svergun
    European Molecular Biology Laboratory, Hamburg, Germany and Institute of Crystallography, Russian Academy of Sciences, Moscow, Russia
    Biophys J 76:2879-86. 1999
    ..Application of the method is illustrated by the restoration of a ribosome-like model structure and more realistically by the determination of the shape of several proteins from experimental x-ray scattering data...
  62. pmc Protein structure prediction and analysis using the Robetta server
    David E Kim
    Structural Genomics of Pathogenic Protozoa, Department of Biochemistry, University of Washington, Seattle WA 98195, USA
    Nucleic Acids Res 32:W526-31. 2004
    ..The Rosetta protein design and protein-protein docking methodologies will soon be available through the server as well...
  63. pmc Induced fit, conformational selection and independent dynamic segments: an extended view of binding events
    Peter Csermely
    Department of Medical Chemistry, Semmelweis University, PO Box 260, H 1444 Budapest 8, Hungary
    Trends Biochem Sci 35:539-46. 2010
    ..Additionally, we highlight the dynamic complexity of binding scenarios as they relate to events such as aggregation and signalling, and the crowded cellular environment...
  64. pmc Structural basis of preexisting immunity to the 2009 H1N1 pandemic influenza virus
    Rui Xu
    Department of Molecular Biology, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    Science 328:357-60. 2010
    ..Thus, antigenic similarity between the 2009 and 1918-like viruses provides an explanation for the age-related immunity to the current influenza pandemic...
  65. ncbi Structure of staphylococcal alpha-hemolysin, a heptameric transmembrane pore
    L Song
    Department of Biochemistry, University of Chicago, 920 East 58 Street, Chicago, IL 60637, USA
    Science 274:1859-66. 1996
    ....
  66. pmc PDBsum new things
    Roman A Laskowski
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 37:D355-9. 2009
    ..Furthermore, it now accepts users' own PDB format files and generates a private set of analyses for each uploaded structure...
  67. pmc Crystal structure of a lipid G protein-coupled receptor
    Michael A Hanson
    Receptos, 10835 Road to the Cure, San Diego, CA 92121, USA
    Science 335:851-5. 2012
    ....
  68. ncbi Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
    W Kabsch
    Biopolymers 22:2577-637. 1983
  69. ncbi ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information
    Fabian Glaser
    The George S Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
    Bioinformatics 19:163-4. 2003
    ..We present a new web server, ConSurf, which automates these algorithmic tools. ConSurf may be used for high-throughput characterization of functional regions in proteins...
  70. pmc Structure of a V3-containing HIV-1 gp120 core
    Chih Chin Huang
    Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA
    Science 310:1025-8. 2005
    ..The extended nature and antibody accessibility of V3 explain its immunodominance. Together, the results provide a structural rationale for the role of V3 in HIV entry and neutralization...
  71. ncbi Automated NMR structure calculation with CYANA
    Peter Güntert
    RIKEN Genomic Sciences Center, Yokohama, Japan
    Methods Mol Biol 278:353-78. 2004
    ....
  72. ncbi Structural characterization of flexible proteins using small-angle X-ray scattering
    Pau Bernado
    European Molecular Biology Laboratory, Hamburg Outstation, 22603 Hamburg, Germany
    J Am Chem Soc 129:5656-64. 2007
    ..In the latter case, EOM is able to distinguish between rigid and flexible proteins and to directly assess the interdomain contacts...
  73. ncbi Refinement of severely incomplete structures with maximum likelihood in BUSTER-TNT
    E Blanc
    Global Phasing Ltd, Sheraton House, Castle Park, Cambridge CB3 0AX, England
    Acta Crystallogr D Biol Crystallogr 60:2210-21. 2004
    ....
  74. ncbi Recognition of errors in three-dimensional structures of proteins
    M J Sippl
    Center for Applied Molecular Engineering, University of Salzburg, Austria
    Proteins 17:355-62. 1993
    ..The techniques are even applicable in cases where only the C alpha trace of a protein conformation is available. The capabilities of the technique are demonstrated using correct and incorrect protein folds.
  75. ncbi Atomic-level characterization of the structural dynamics of proteins
    David E Shaw
    D E Shaw Research, 120 West 45th Street, New York, NY 10036, USA
    Science 330:341-6. 2010
    ....
  76. pmc Structure of an agonist-bound human A2A adenosine receptor
    Fei Xu
    Department of Molecular Biology, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    Science 332:322-7. 2011
    ..The results define the molecule UK-432097 as a "conformationally selective agonist" capable of receptor stabilization in a specific active-state configuration...
  77. pmc Structure and function of an irreversible agonist-β(2) adrenoceptor complex
    Daniel M Rosenbaum
    Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, California 94305, USA
    Nature 469:236-40. 2011
    ....
  78. pmc Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex
    Yanli Wang
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
    Nature 456:921-6. 2008
    ..Consistent with the geometry of the ternary complex, bulges residing in the seed segments of the target, but not the guide strand, were better accommodated and their complexes were catalytically active...
  79. ncbi How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers
    Sean D Taverna
    Laboratory of Chromatin Biology, The Rockefeller University, New York, New York 10021, USA
    Nat Struct Mol Biol 14:1025-40. 2007
    ..Changes in these interactions may have far-reaching implications for human biology and disease, notably cancer...
  80. ncbi Thermofluor-based high-throughput stability optimization of proteins for structural studies
    Ulrika B Ericsson
    Department of Biochemistry and Biophysics, Stockholm University, Stockholm SE 109 51, Sweden
    Anal Biochem 357:289-98. 2006
    ..This suggests that thermofluor constitutes an efficient generic high-throughput method for identification of protein properties predictive of crystallizability...
  81. pmc SNAP: predict effect of non-synonymous polymorphisms on function
    Yana Bromberg
    Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th St, New York, NY 10032, USA
    Nucleic Acids Res 35:3823-35. 2007
    ..This measure will allow users to focus on the most accurate predictions and/or the most severe effects. Available at http://www.rostlab.org/services/SNAP...
  82. ncbi Function and structure of inherently disordered proteins
    A Keith Dunker
    Center for Computational Biology and Bioinformatics, Institute for Intrinsically Disordered Protein Research, Indiana University Schools of Medicine and Informatics, Indianapolis, IN 46202, USA
    Curr Opin Struct Biol 18:756-64. 2008
    ....
  83. ncbi Protein structure homology modeling using SWISS-MODEL workspace
    Lorenza Bordoli
    Biozentrum, University of Basel, Klingelbergstrasse 50 70, CH 4056 Basel, Switzerland
    Nat Protoc 4:1-13. 2009
    ..However, this does not include the time required for visualization and interpretation of the model, which may vary depending on personal experience working with protein structures...
  84. ncbi Sirtuin 2 inhibitors rescue alpha-synuclein-mediated toxicity in models of Parkinson's disease
    Tiago Fleming Outeiro
    Alzheimer s Research Unit, MGH, Harvard Medical School, CNY 114, 16th Street, Charlestown, MA 02129, USA
    Science 317:516-9. 2007
    ..Furthermore, the inhibitors protected against dopaminergic cell death both in vitro and in a Drosophila model of Parkinson's disease. The results suggest a link between neurodegeneration and aging...
  85. ncbi The guanine nucleotide-binding switch in three dimensions
    I R Vetter
    , 44227 Dortmund, Germany
    Science 294:1299-304. 2001
    ..Here we will try to define some underlying principles...
  86. pmc Linking folding and binding
    Peter E Wright
    Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States
    Curr Opin Struct Biol 19:31-8. 2009
    ....
  87. pmc Molecular dynamics and protein function
    M Karplus
    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
    Proc Natl Acad Sci U S A 102:6679-85. 2005
    ..We also describe results for the F(1) ATPase molecular motor and the Src family of signaling proteins as examples of applications of simulations to specific biological systems...
  88. pmc DNA binding site sequence directs glucocorticoid receptor structure and activity
    Sebastiaan H Meijsing
    Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
    Science 324:407-10. 2009
    ..We therefore propose that DNA is a sequence-specific allosteric ligand of GR that tailors the activity of the receptor toward specific target genes...
  89. ncbi Crystal structure of opsin in its G-protein-interacting conformation
    Patrick Scheerer
    Institut für Medizinische Physik und Biophysik CC2, Charite Universitatsmedizin Berlin, Chariteplatz 1, D 10117 Berlin, Germany
    Nature 455:497-502. 2008
    ..On the basis of the Ops*-GalphaCT structure and known conformational changes in Galpha, we discuss signal transfer from the receptor to the G protein nucleotide-binding site...
  90. ncbi Biological and chemical approaches to diseases of proteostasis deficiency
    Evan T Powers
    Departments of Chemistry and Molecular and Experimental Medicine and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
    Annu Rev Biochem 78:959-91. 2009
    ..We propose that such therapeutic strategies, including combination therapies, represent a new approach for treating a range of diverse human maladies...
  91. pmc Global dynamics of proteins: bridging between structure and function
    Ivet Bahar
    Department of Computational Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
    Annu Rev Biophys 39:23-42. 2010
    ..These observed correlations suggest that computational methods may be advantageously employed for assessing functional changes in structure and allosteric mechanisms intrinsically favored by the native fold...
  92. pmc The origin of allosteric functional modulation: multiple pre-existing pathways
    Antonio del Sol
    Bioinformatics Research Unit, Research and Development Division, Fujirebio Inc, Hachioji shi, Tokyo, Japan
    Structure 17:1042-50. 2009
    ....
  93. pmc Benchmarking sets for molecular docking
    Niu Huang
    Department of Pharmaceutical Chemistry, University of California San Francisco, QB3 Building, 1700 4th Street, Box 2550, San Francisco, California 94143 2550, USA
    J Med Chem 49:6789-801. 2006
    ..DUD is freely available online as a benchmarking set for docking at http://blaster.docking.org/dud/...
  94. pmc Conformational selection and induced fit mechanism underlie specificity in noncovalent interactions with ubiquitin
    Tomasz Wlodarski
    Laboratory of Bioinformatics and Bioengineering, Interdisciplinary Centre for Mathematical and Computational Modeling, University of Warsaw, Zwirki i Wigury 93 02 089, Warsaw, Poland
    Proc Natl Acad Sci U S A 106:19346-51. 2009
    ..Our final model of ubiquitin binding blends conformational selection with the subsequent induced fit and provides a quantitative measure of their respective contributions...
  95. ncbi Structure and mechanism of helicases and nucleic acid translocases
    Martin R Singleton
    Macromolecular Structure and Function Laboratory, The London Research Institute, London WC2A 3PX, United Kingdom
    Annu Rev Biochem 76:23-50. 2007
    ..As a result, each superfamily is subdivided, where appropriate, on the basis of mechanistic understanding, which we hope will provide a framework for classification of new superfamily members as they are discovered and characterized...
  96. pmc Structure of the Ebola virus glycoprotein bound to an antibody from a human survivor
    Jeffrey E Lee
    Department of Immunology and Microbial Science, The Scripps Research Institute, 10550 North Torrey Pines Road, Mail Drop IMM 2, La Jolla, California 92037, USA
    Nature 454:177-82. 2008
    ..This structure provides a template for unravelling the mechanism of EBOV GP-mediated fusion and for future immunotherapeutic development...
  97. ncbi EGFR mutations in lung cancer: correlation with clinical response to gefitinib therapy
    J Guillermo Paez
    Departments of Medical Oncology and Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02115, USA
    Science 304:1497-500. 2004
    ..These results suggest that EGFR mutations may predict sensitivity to gefitinib...
  98. pmc Crystal structure of the extracellular segment of integrin alpha Vbeta3
    J P Xiong
    Renal Unit, Leukocyte Biology and Inflammation Program, Structural Biology Program, Massachusetts General Hospital and Harvard Medical School, 149 13th Street, Charlestown, MA 02129, USA
    Science 294:339-45. 2001
    ..MIDAS lies adjacent to a calcium-binding site with a potential regulatory function...
  99. ncbi Crystal structure of the ligand-free G-protein-coupled receptor opsin
    Jung Hee Park
    Institut für Medizinische Physik und Biophysik CC2, Charite Universitatsmedizin Berlin, Chariteplatz 1, D 10117 Berlin, Germany
    Nature 454:183-7. 2008
    ..The opsin structure sheds new light on ligand binding to GPCRs and on GPCR activation...
  100. ncbi Force fields for protein simulations
    Jay W Ponder
    Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, Missouri 63110, USA
    Adv Protein Chem 66:27-85. 2003
  101. pmc Structural basis of toll-like receptor 3 signaling with double-stranded RNA
    Lin Liu
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    Science 320:379-81. 2008
    ..This juxtaposition could mediate downstream signaling by dimerizing the cytoplasmic Toll interleukin-1 receptor (TIR) domains. The overall shape of the TLR3-ECD does not change upon binding to dsRNA...

Research Grants63

  1. NIH Director's Pioneer Award
    Junying Yuan; Fiscal Year: 2009
    ..No Abstract provided ..
  2. The Role of MYST Histone Acetyltransferase in Genome Stability
    M Mitchell Smith; Fiscal Year: 2013
    ..will specifically challenge the molecular switch model using genetic suppressors and biochemical assays of protein conformation in recombinant picNuA4...
  3. Role of TPH2 and 5HT Neuronal Loss in Non-motor Symptoms of Parkinson's
    Donald M Kuhn; Fiscal Year: 2012
    ..Modification of cysteines by oxidation can change protein conformation in a rapid and reversible way as part of a controlled signaling process...
  4. Vibrio cholerae-host interaction at the Intestinal Interface
    Jun Zhu; Fiscal Year: 2013
    ..and genetic methods to test our hypotheses that VIF-1 may directly interact with TcpP proteins to affect protein conformation and function...
  5. LIPID MODULATION OF RHODOPSIN SIGNALING IN MEMBRANES
    Michael F Brown; Fiscal Year: 2010
    ..transfer (FRET), and plasmon waveguide resonance (PWR) spectroscopy will elucidate the retinal environment, protein conformation, and oligomerization or association of rhodopsin in the dark, Meta I, and Meta II states...
  6. Unfolded Protein Response in Lens Epithelial Cells
    Toshimichi Shinohara; Fiscal Year: 2012
    ..One form of stress, so called endoplasmic reticulum (ER) stress, is caused by misfolded protein conformation. The ER stress produces reactive oxygen species (ROS) to oxidize free glutathione and proteins and induces ..
  7. Cytoskeletal Pliability within Cells under Stress: RBCs and Marrow-derived SCs
    Dennis E Discher; Fiscal Year: 2012
    ..We will use similar methods in Aim 2 to gain insight into protein conformation and assembly in the two main types of human marrow-derived Stem Cells, particularly focusing on how elastic ..
  8. Ribonucleotide Reductase: Structure and Function
    JoAnne Stubbe; Fiscal Year: 2013
    ..coli RNR, and are sensitive to changes in protein conformation, hydrogen bonding networks, and redox potentials...
  9. High Density Peptide Arrays for Cancer-Related Post-Translational Modifications
    Christopher L Warren; Fiscal Year: 2013
    ..role in cancer etiology and progression by altering protein-protein interactions, enzymatic activity, and protein conformation. Peptide arrays have played a significant role in cancer-related discoveries, such as cancer biomarkers, ..
  10. Proteolytic and chaperone machines implicated in virulence and disease
    Robert T Sauer; Fiscal Year: 2013
    ..and molecular genetics to determine how protease versus chaperone activities are mediated by changes in protein conformation or assembly and are regulated by the binding of substrates and adaptor proteins...
  11. Ethanol and Bcl-2 Gene Interactions in the Developing CNS
    Marieta B Heaton; Fiscal Year: 2012
    ..In addition, purified P4 and P7 Bax will be subjected to CD analyses of protein conformation at the two ages, and ethanol effects on this conformation.
  12. Upgrade of Our Thermo LTQ to a LTQ Orbitrap XL ETD Mass Spectrometer
    C Robert Matthews; Fiscal Year: 2010
    ..include in-depth proteome identification, identification of large MHC class II peptides, determination of protein conformation and contact points within protein complexes and aggregates through chemical cross-linking, site-specific ..
  13. Molecular Mechanisms of Prion and Amyloid Propagation
    Christopher P Jaroniec; Fiscal Year: 2013
    ..More recently, the prion hypothesis has been extended further to include the phenomenon of protein conformation-based inheritance in yeast and other fungi...
  14. Sensing Protein Folding Capacity in the Cell During Aging
    ROCKLAND L WISEMAN; Fiscal Year: 2010
    ..These innovative probes will assess the consequences of protein damage, cell stress, aging and diseases of protein conformation that influence human longevity...
  15. Aging and the Tissue Response to Misfolded Proteins
    Joel N Buxbaum; Fiscal Year: 2012
    Disorders of protein conformation of wild type proteins increase in frequency with aging...
  16. Mass Spectrometry of Protein Assemblies
    Joseph A Loo; Fiscal Year: 2012
    ..Information related to protein size, protein folding, and protein conformation that can be used to complement information derived from more traditional high resolution structural methods ..
  17. The Comprehensive Center for Chemical Probe Discovery and Optimization at Scripps
    Hugh Rosen; Fiscal Year: 2013
    ..as well as whole-cell reporter gene, second messenger, membrane potential, ion flux, complementation, protein conformation, renaturation and toxicity assays...
  18. Arbitrary Pulse Shaping to Advance Electron Paramagnetic Resonance Tools for Biom
    SongI Han; Fiscal Year: 2011
    ..effects can be effectively mapped out by directly probing the enzyme activity, through the modulation of protein conformation and hydration dynamics...
  19. Role of the Groucho/Grg/TLE corepressor protein in delaying tissue specification
    Kimberly Blahnik; Fiscal Year: 2013
    ..Specific Aim 1 will directly test the hypothesis that a protein conformation change upon recruitment to the DNA is required for the repressive activity of Grg proteins...
  20. Proteostasis sensors to assess the cellular protein folding capacity
    RICHARD I contact MORIMOTO; Fiscal Year: 2010
    ..of the cell and to assess the consequences of protein damage, cell stress, aging, and diseases of protein conformation. These tools will be initially developed for use in C...
  21. Static and dynamic light scattering instrumentation for macromolecular characteri
    Brian R Crane; Fiscal Year: 2010
    ..to analyzing intact and exchanging protein complexes, protein-protein/ligand interactions and probing protein conformation. Accurate assessment of protein size and shape is a critical first step in molecular characterization...
  22. Impaired Protein Degradation Pathways in Cardiac Proteinopathy
    Patrick M McLendon; Fiscal Year: 2013
    ..targeting the conformation of a cytotoxic pre-amyloid oligomer (PAO), suggesting that DRM is a cardiac protein conformation disease which may be prevalent in many forms of human heart failure...
  23. VON WILLEBRAND FACTOR STRUCTURE AND FUNCTION UNDER FLUID FLOW
    Sriram Neelamegham; Fiscal Year: 2013
    ..Functional/structural studies are carried out to measure VWF binding, protein conformation change, platelet adhesion and activation using both flow cytometry and fluorescence/confocal microscopy...
  24. Mutant Laminin Chains and Nephrotic Syndrome
    YING MAGGIE CHEN; Fiscal Year: 2013
    ..chaperones, such as taurodeoxycholic acid (TUDCA), are low molecular weight compounds that can stabilize protein conformation and rescue trafficking-defective misfolded proteins...
  25. Structural determinants of amelogenin function in regulating enamel formation
    Henry C Margolis; Fiscal Year: 2013
    ..nanoparticles of ACP, to test the hypothesis that phosphorylation of the single serine-16 site affects protein conformation and structural changes that uniquely enhance the capacity of the full-length amelogenin to interact with ..
  26. Arbitrary Pulse Shaping to Advance Electron Paramagnetic Resonance Tools for Biom
    SongI Han; Fiscal Year: 2013
    ..effects can be effectively mapped out by directly probing the enzyme activity, through the modulation of protein conformation and hydration dynamics...
  27. Study Protein-Nanomaterial Interactions and Their Impacts on Protein Activities
    Wenwan Zhong; Fiscal Year: 2011
    ..Such interactions could alter the protein conformation and thus protein function...
  28. Allosteric Binding in Antibodies and Protein Antigens
    Robert C Blake; Fiscal Year: 2011
    ..goal of this aim is to quantify the relative contributions of both avidity effects and binding-dependent protein conformation changes to the apparent synergy of binding...
  29. Investigation of the yeast prion factor [PSI+]
    Susan W Liebman; Fiscal Year: 2012
    ..but also because they suggest an important new mechanism of genetic variation operating at the level of protein conformation rather than nucleic acids...
  30. Tools to Connect Protein Conformations, Dynamics, and Associations
    Daniel Schwartz; Fiscal Year: 2013
    ..methods that will enable mechanistic studies of the ways in which surface chemistry affects adsorbed protein conformation and intermolecular associations...
  31. Protein conformational change upon membrane association
    John R Engen; Fiscal Year: 2012
    DESCRIPTION (provided by applicant): Protein conformation can be influenced by lipid membranes. This fact seems to be an essential contributor to the function of the HIV accessory protein Nef...
  32. Conformations of c-type cytochrome self-assembling complexes
    KRISTY LYNN MARDIS; Fiscal Year: 2010
    ..Our long-term goal is to determine the role of protein conformation on ET. This requires the construction and investigation of model supramolecular assemblies capable of ET...
  33. Single molecule imaging of beta2 adrenergic receptor activation
    Jonathan A Javitch; Fiscal Year: 2013
    ..time, providing a means of making direct measurements of the rates and amplitudes of transient changes in protein conformation during function...
  34. Investigations of interactions in dynamic protein complexes by mass spectrometry
    Igor A Kaltashov; Fiscal Year: 2013
    ..spectrometry (ESI MS) detection that use an array of gas phase ion fragmentation techniques to characterize protein conformation and dynamics at an unprecedented level of detail...
  35. Acquisition of a Hybrid Quadrupole, Ion Mobility Separation, Orthogonal Accelerat
    Sheng Zhang; Fiscal Year: 2009
    ..its applications for analysis of intact protein complexes, protein-protein/ligand interactions and probing protein conformation. This highly sensitive and accurate mass instrument will provide capabilities in protein domain mapping and ..
  36. Targeting the MSH2-dependent Apoptotic Pathway
    Freddie R Salsbury; Fiscal Year: 2013
    ..i) computational modeling incorporating protein dynamics to screen for compounds that favor a particular protein conformation and with that best induce cell death, followed by refinement to predict more efficient compounds;(ii) ..
  37. Analysis of PH1-associated alanine:glyoxylate aminotranferase (AGT) using yeast
    Chandra L Tucker; Fiscal Year: 2011
    ..chaperones, which are small molecules that are able to restore protein function by stabilizing a native protein conformation. While such an approach for AGT has great promise, a major impediment is the lack of simple cost-effective ..
  38. Analysis of De Novo Protein Folding by Fluorescence Resonance Energy Transfer
    Silvia Cavagnero; Fiscal Year: 2013
    ..nascent proteins is largely unexplored by methodologies able to provide a direct assessment of protein conformation. The goal of this research is to investigate the short-range helical secondary structure and degree of ..
  39. Modeling Prion Dynamics
    Suzanne Sindi; Fiscal Year: 2011
    ..The combination of experimental tractability in the yeast system, which allows direct observations of protein conformation and activity in live cells, and the development of an accurate mathematical model provide a unique ..
  40. An LTQ-Orbitrap Elite with ETD for the Keck Proteomics Facility
    Yinsheng Wang; Fiscal Year: 2013
    ..proteome quantification, large-scale mapping of post-translational modifications, protein complex, and protein conformation studies...
  41. Celestrols for Treatment of Neurodegenerative Diseases
    Richard Silverman; Fiscal Year: 2007
    ..A feature common to diseases of protein conformation is the appearance of folded intermediates that self-associate to form protein aggregates and inclusions...
  42. Structural Basis for Long-Range Genetic Interactions in Retroviral CA Assembly
    Rebecca Craven; Fiscal Year: 2009
    ..expertise of two investigators to directly test the role of the 12 helix of the CTD in achieving a protein conformation that is competent for assembly of functional capsids...
  43. INTERNAL BONDING IN PROTEINS
    Harold A Scheraga; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): Our long-term objective is to ascertain how protein conformation plays a role in biological function and in various diseases...
  44. New Computational Methods for Data-driven Protein Structure Prediction
    Jinbo Xu; Fiscal Year: 2013
    ..using a machine learning method to combine both residue-level and atom-level features;Aim 2) to improve protein conformation sampling in a continuous space and thus template-free modeling by three independent but complementary ..
  45. DIRECT OBSERVATION OF INTERFACIAL PROCESS
    Vladimir Hlady; Fiscal Year: 2003
    ..variation of surface properties, - related dynamics of protein- surface interactions, and surface - induced protein conformation, and to identify the critical parameters in these processes...
  46. DIRECT OBSERVATION OF INTERFACIAL PROCESS
    Vladimir Hlady; Fiscal Year: 2001
    ..variation of surface properties, - related dynamics of protein- surface interactions, and surface - induced protein conformation, and to identify the critical parameters in these processes...
  47. Circular Dichroism Spectropolarimeter with fluorescence acquisition and temperatu
    Robert M Straubinger; Fiscal Year: 2010
    ..this proposal, Circular Dichroism (CD) spectropolarimetry provides a unique window into dynamic aspects of protein conformation and unfolding, conformational transitions accompanying peptide-membrane interaction and insertion, the ..
  48. QUANTITATIVE MASS SPECTROMETRY TO PROBE FIBRINOGEN CONFORMATIONS ON BIOMATERIALS
    DONALD ELBERT; Fiscal Year: 2009
    ..The combination of methods, chemical labeling of adsorbed proteins to detect changes in protein conformation and quantitative mass spectrometry, may lead to advances in the study of protein adsorption on biomaterials...
  49. Optimizing and defining the mechanism of alpha-synuclein disaggregation by Hsp104
    MORGAN DESANTIS; Fiscal Year: 2013
    ..In PD, ? -syn misfolds into an aberrant protein conformation, termed amyloid, which is highly stable, possesses a characteristic cross-?? structure, and is largely ..
  50. PHYSICAL STUDIES OF CONFORMATIONAL CHANGE IN CHROMATIN
    RODNEY HARRINGTON; Fiscal Year: 1990
    Physical methods sensitive to DNA and protein conformation and structure will be used to characterize the structure and conformation of chromatin from the naturally mitotically synchronous slime mold Physarum polycephalum...
  51. APPROACHES TO DESIGNED METALLOPROTEINS
    David Benson; Fiscal Year: 2000
    ..metal ions in the proposed systems mirror their roles in nature, for example as allosteric regulators of protein conformation and as templates for protein folding...
  52. CooA: A Hemoprotein CO Sensor
    Judith Burstyn; Fiscal Year: 2005
    ..outlined in this proposal is to correlate changes in the heme coordination state of CooA with changes in protein conformation in order to understand how the heme serves to regulate protein function...
  53. Study protein folding mechanism using a roadmap-based approach
    Shuanghong Huo; Fiscal Year: 2013
    ..Our approach will utilize a roadmap (or a graph) to capture most important features of protein conformation space and energy landscape as proposed in Aim 1, in turn, rich thermodynamic and kinetic information will ..
  54. Conformational linkage during catalysis by TrpRS
    Charles Carter; Fiscal Year: 2005
    ..Rather, protein conformation may itself play an unprecedented, and more active role...
  55. STRUCTURE/FUNCTION IN IMMOBILIZED PROTEIN FILMS
    STEVEN SAAVEDRA; Fiscal Year: 1999
    ..2) Native protein conformation and biofunction in the outermost protein layer may be perturbed by the immobilization process; the degree ..
  56. CNS DEGENERATION CAUSED BY NOVEL PATHOGENS
    STANLEY PRUSINER; Fiscal Year: 2002
    ..Much evidence argues that prion diseases are disorders of protein conformation. Investigation directed toward elucidating the molecular mechanism of conversion of the cellular prion ..
  57. PHOSPHOPROTEIN INTERACTIONS WITH IRON AND OTHER METALS
    GEORGE TABORSKY; Fiscal Year: 1990
    ..such coordination may be non-uniform within and among given proteins, the effects that metal binding and protein conformation may mutually exert on each other, and the minimal structure required for the maintenance of the static and ..
  58. ANALYSIS OF MOTOR PROTEIN FUNCTION
    Edward Pate; Fiscal Year: 2004
    ..structural data from both kinesin-family and myosin-family motor proteins to better define the changes in protein conformation that produce force and work...
  59. Side Chain Driven Refinement of Protein Structure
    JERRY W TSAI; Fiscal Year: 2010
    ..In particular, our analysis will more clearly define the contributions to protein conformation from multi-bodied, tertiary interactions versus those determined by the linear protein backbone...
  60. MEMBRANE PROTEIN STRUCTURE
    JAMES STAROS; Fiscal Year: 1990
    ..Laboratory, and the conference on "Experimental and Theoretical Aspects of the Interactions the Determine Protein Conformation" held in January 1989, at the National Institution of Health...
  61. A Protein Footprinting Toolbox
    PEHR HARBURY; Fiscal Year: 2007
    ..unreadable] [unreadable] Understanding protein conformation, interactions and ligand binding is essential to all biological inquiry...
  62. MOLECULAR CONFORMATION, COMPARISON AND INTERACTION
    Michael Connolly; Fiscal Year: 1991
    ..This proposal presents a protein conformation comparison method that accomplishes the first objective by taking into account the topology, not just the ..
  63. PROTEIN BEHAVIOR AT SILICONE--A SINGLE MOLECULE STUDY
    Viola Vogel; Fiscal Year: 2002
    ..Our hypothesis is that the difficulty in deriving t quantitative information how protein conformation relates to cell behavior, which has troubled the biomaterials community for a long time, originates at ..