secondary protein structure

Summary

Summary: The level of protein structure in which regular hydrogen-bond interactions within contiguous stretches of polypeptide chain give rise to alpha helices, beta strands (which align to form beta sheets) or other types of coils. This is the first folding level of protein conformation.

Top Publications

  1. ncbi AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR
    R A Laskowski
    Department of Biochemistry and Molecular Biology, University College London, UK
    J Biomol NMR 8:477-86. 1996
  2. ncbi Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes
    A Krogh
    Center for Biological Sequence Analysis, Technical University of Denmark, Building 208, 2800 Lyngby, Denmark
    J Mol Biol 305:567-80. 2001
  3. ncbi Protein secondary structure prediction based on position-specific scoring matrices
    D T Jones
    Department of Biological Sciences, University of Warwick, Coventry, CV4 7AL, United Kingdom
    J Mol Biol 292:195-202. 1999
  4. 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
  5. 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
  6. ncbi ESPript: analysis of multiple sequence alignments in PostScript
    P Gouet
    Laboratory of Molecular Biophysics, The Rex Richards Building, South Parks Road, Oxford OX1 3QU, UK
    Bioinformatics 15:305-8. 1999
  7. ncbi How to study proteins by circular dichroism
    Sharon M Kelly
    Division of Biochemistry and Molecular Biology, Institute of Biomedical and Life Sciences, Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, Scotland, UK
    Biochim Biophys Acta 1751:119-39. 2005
  8. ncbi The HMMTOP transmembrane topology prediction server
    G E Tusnády
    Institute of Enzymology, BRC, Hungarian Academy of Sciences, H 1518 Budapest, PO Box 7, Hungary
    Bioinformatics 17:849-50. 2001
  9. ncbi Mutation in the alpha-synuclein gene identified in families with Parkinson's disease
    M H Polymeropoulos
    Laboratory of Genetic Disease Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 1430, USA
    Science 276:2045-7. 1997
  10. pmc STRIDE: a web server for secondary structure assignment from known atomic coordinates of proteins
    Matthias Heinig
    Department of Genome Oriented Bioinformatics, Technical University of Munich, Wissenschaftszentrum Weihenstephan, 85354 Freising, Germany
    Nucleic Acids Res 32:W500-2. 2004

Research Grants

  1. Cloning of a type 2 diabetes modifier in obese mice
    Rudolph Leibel; Fiscal Year: 2006
  2. Probing the cellular Mechanisms of Transthyretin Cytotoxicity
    Natalia Reixach; Fiscal Year: 2010
  3. HEPATIC BIOSYNTHESIS OF CERULOPLASMIN
    Michael Schilsky; Fiscal Year: 1990
  4. VIRULENCE DETERMINANTS OF BARTONELLA BACILLIFORMIS
    MICHAEL MINNICK; Fiscal Year: 1993
  5. Cloning of a type 2 diabetes modifier in obese mice
    Rudolph Leibel; Fiscal Year: 2005
  6. Cloning of a type 2 diabetes modifier in obese mice
    Rudolph Leibel; Fiscal Year: 2003
  7. Cloning of a type 2 diabetes modifier in obese mice
    Rudolph Leibel; Fiscal Year: 2004
  8. PHOSPHATE TRANSPORT PATHS WITHIN HOMODIMERIC PTP
    Hartmut Wohlrab; Fiscal Year: 2001
  9. PHOSPHATE TRANSPORT PATHS WITHIN HOMODIMERIC PTP
    Hartmut Wohlrab; Fiscal Year: 2000
  10. PHOSPHATE TRANSPORT PATHS WITHIN HOMODIMERIC PTP
    Hartmut Wohlrab; Fiscal Year: 1999

Detail Information

Publications272 found, 100 shown here

  1. ncbi AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR
    R A Laskowski
    Department of Biochemistry and Molecular Biology, University College London, UK
    J Biomol NMR 8:477-86. 1996
    ..They are intended to be of use both to support ongoing NMR structure determination and in the validation of the final results...
  2. ncbi Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes
    A Krogh
    Center for Biological Sequence Analysis, Technical University of Denmark, Building 208, 2800 Lyngby, Denmark
    J Mol Biol 305:567-80. 2001
    ..We discuss the possible relevance of this finding for our understanding of membrane protein assembly mechanisms. A TMHMM prediction service is available at http://www.cbs.dtu.dk/services/TMHMM/...
  3. ncbi Protein secondary structure prediction based on position-specific scoring matrices
    D T Jones
    Department of Biological Sciences, University of Warwick, Coventry, CV4 7AL, United Kingdom
    J Mol Biol 292:195-202. 1999
    ..Given the success of the method in CASP3, it is reasonable to be confident that the evaluation presented here gives a fair indication of the performance of the method in general...
  4. 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...
  5. 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
    ....
  6. ncbi ESPript: analysis of multiple sequence alignments in PostScript
    P Gouet
    Laboratory of Molecular Biophysics, The Rex Richards Building, South Parks Road, Oxford OX1 3QU, UK
    Bioinformatics 15:305-8. 1999
    ..It can read secondary structure files (such as that created by the program DSSP) to produce a synthesis of both sequence and structural information...
  7. ncbi How to study proteins by circular dichroism
    Sharon M Kelly
    Division of Biochemistry and Molecular Biology, Institute of Biomedical and Life Sciences, Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, Scotland, UK
    Biochim Biophys Acta 1751:119-39. 2005
    ..In this article, we summarise the basis of the CD approach and its application to the study of proteins, and then present clear guidelines on how reliable data can be obtained and analysed...
  8. ncbi The HMMTOP transmembrane topology prediction server
    G E Tusnády
    Institute of Enzymology, BRC, Hungarian Academy of Sciences, H 1518 Budapest, PO Box 7, Hungary
    Bioinformatics 17:849-50. 2001
    ..This option improves the prediction accuracy as well as helps the interpretation of experimental results, i.e. in epitope insertion experiments...
  9. ncbi Mutation in the alpha-synuclein gene identified in families with Parkinson's disease
    M H Polymeropoulos
    Laboratory of Genetic Disease Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 1430, USA
    Science 276:2045-7. 1997
    ..This finding of a specific molecular alteration associated with PD will facilitate the detailed understanding of the pathophysiology of the disorder...
  10. pmc STRIDE: a web server for secondary structure assignment from known atomic coordinates of proteins
    Matthias Heinig
    Department of Genome Oriented Bioinformatics, Technical University of Munich, Wissenschaftszentrum Weihenstephan, 85354 Freising, Germany
    Nucleic Acids Res 32:W500-2. 2004
    ..A searchable database of STRIDE assignments for the latest PDB release is also provided. The STRIDE server is accessible from http://webclu.bio.wzw.tum.de/stride/...
  11. ncbi A reference database for circular dichroism spectroscopy covering fold and secondary structure space
    Jonathan G Lees
    Department of Crystallography, Birkbeck College, University of London, London WC1E 7HX, UK
    Bioinformatics 22:1955-62. 2006
    ..Hence, by combining new bioinformatics and biophysical methods, a database has been produced that should have wide applicability as a tool for structural molecular biology...
  12. 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..
  13. pmc Protein structure prediction servers at University College London
    Kevin Bryson
    Department of Computer Science, University College London Gower Street, London WC1E 6BT, UK
    Nucleic Acids Res 33:W36-8. 2005
    ..More recent servers include DISOPRED for the prediction of protein dynamic disorder and DomPred for domain boundary prediction. These servers are available from our software home page at http://bioinf.cs.ucl.ac.uk/software.html...
  14. ncbi Crystal structure of the extracellular segment of integrin alpha Vbeta3 in complex with an Arg-Gly-Asp ligand
    Jian Ping Xiong
    Renal Unit, Leukocyte Biology and Inflammation Program, Structural Biology Program, Massachusetts General Hospital, 149 13th Street, Charlestown, MA 02129, USA
    Science 296:151-5. 2002
    ..Ligand binding induces small changes in the orientation of alphaV relative to beta3...
  15. ncbi Blocker protection in the pore of a voltage-gated K+ channel and its structural implications
    D del Camino
    Department of Neurobiology, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nature 403:321-5. 2000
    ..This bend would occur at a Pro-X-Pro sequence that is highly conserved in Kv channels, near the site of activation gating...
  16. pmc Length-dependent prediction of protein intrinsic disorder
    Kang Peng
    Center for Information Science and Technology, Temple University, Philadelphia, PA 19122, USA
    BMC Bioinformatics 7:208. 2006
    ..However, these predictors are less successful on short disordered regions (< or =30 residues). A probable cause is a length-dependent amino acid compositions and sequence properties of disordered regions...
  17. pmc Statistical potential for assessment and prediction of protein structures
    Min Yi Shen
    Department of Biopharmaceutical Sciences, Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, California 94158, USA
    Protein Sci 15:2507-24. 2006
    ....
  18. ncbi The mechanism by which influenza A virus nucleoprotein forms oligomers and binds RNA
    Qiaozhen Ye
    Department of Biochemistry and Cell Biology, Rice University, 6100 Main Street, MS140, Houston, Texas 77005, USA
    Nature 444:1078-82. 2006
    ..Our results identify the tail loop binding pocket as a potential target for antiviral development...
  19. ncbi Recognition of transmembrane helices by the endoplasmic reticulum translocon
    Tara Hessa
    Department of Biochemistry and Biophysics, Stockholm University, SE 106 91 Stockholm, Sweden
    Nature 433:377-81. 2005
    ..Our results indicate that direct protein-lipid interactions are critical during translocon-mediated membrane insertion...
  20. ncbi MUSTANG: a multiple structural alignment algorithm
    Arun S Konagurthu
    Department of Computer Science and Software Engineering, The University of Melbourne, Parkville, Melbourne, Victoria, 3010 Australia
    Proteins 64:559-74. 2006
    ....
  21. pmc Multipass membrane protein structure prediction using Rosetta
    Vladimir Yarov-Yarovoy
    Department of Pharmacology, University of Washington, Seattle, Washington 98195, USA
    Proteins 62:1010-25. 2006
    ..In tests on 12 membrane proteins for which the structure is known, between 51 and 145 residues were predicted with root-mean-square deviation <4 A from the native structure...
  22. ncbi Design and evolution of new catalytic activity with an existing protein scaffold
    Hee Sung Park
    Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 373 1, Kusung dong, Yusung Gu, Daejon 305 701, Korea
    Science 311:535-8. 2006
    ..8 x 10(2) (mole/liter)(-1) second(-1), thus increasing resistance to Escherichia coli growth on cefotaxime by a factor of about 100...
  23. 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
    ....
  24. ncbi The structure of the potassium channel: molecular basis of K+ conduction and selectivity
    D A Doyle
    Laboratory of Molecular Neurobiology and Biophysics and the Howard Hughes Medical Institute, Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
    Science 280:69-77. 1998
    ..The architecture of the pore establishes the physical principles underlying selective K+ conduction...
  25. doi Fifty years of coiled-coils and alpha-helical bundles: a close relationship between sequence and structure
    David A D Parry
    Institute of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North, New Zealand
    J Struct Biol 163:258-69. 2008
    ..An important development has been the recognition that the delightful simplicity that exists between sequence and structure, and between structure and function, allows coiled coils with specialized features to be designed de novo...
  26. pmc DICHROWEB, an online server for protein secondary structure analyses from circular dichroism spectroscopic data
    Lee Whitmore
    Department of Crystallography, Birkbeck College, University of London, London WC1E 7HX, UK
    Nucleic Acids Res 32:W668-73. 2004
    ..The web pages associated with the server provide information on CD spectroscopic methods and terms, literature references and aids for interpreting the analysis results...
  27. ncbi The S4-S5 linker directly couples voltage sensor movement to the activation gate in the human ether-a'-go-go-related gene (hERG) K+ channel
    Tania Ferrer
    Department of Pediatrics, University of Utah, Salt Lake City, Utah 94113, USA
    J Biol Chem 281:12858-64. 2006
    ..Moreover, rather than functioning simply as a mechanical lever, these findings imply that specific interactions between the S4-S5 linker and the activation gate stabilize the closed channel conformation...
  28. doi Biophysical dissection of membrane proteins
    Stephen H White
    Department of Physiology and Biophysics, and Center for Biomembrane Systems, University of California, Irvine, California 92697, USA
    Nature 459:344-6. 2009
    ....
  29. ncbi BAR domains as sensors of membrane curvature: the amphiphysin BAR structure
    Brian J Peter
    Medical Research Council MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
    Science 303:495-9. 2004
    ..From this, we predict that BAR domains are in many protein families, including sorting nexins, centaurins, and oligophrenins. The universal and minimal BAR domain is a dimerization, membrane-binding, and curvature-sensing module...
  30. pmc GeneSilico protein structure prediction meta-server
    Michal A Kurowski
    Bioinformatics Laboratory, International Institute of Molecular and Cell Biology, Warsaw, Poland
    Nucleic Acids Res 31:3305-7. 2003
    ..The GeneSilico protein structure prediction meta-server is freely available for academic users at http://genesilico.pl/meta...
  31. ncbi Water permeation across biological membranes: mechanism and dynamics of aquaporin-1 and GlpF
    B L de Groot
    Theoretical Molecular Biophysics Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Gottingen, Germany
    Science 294:2353-7. 2001
    ..In AQP1, a fine-tuned water dipole rotation during passage is essential for water selectivity. In GlpF, a glycerol-mediated "induced fit" gating motion is proposed to generate selectivity for glycerol over water...
  32. ncbi Human brain neuroglobin structure reveals a distinct mode of controlling oxygen affinity
    Alessandra Pesce
    Department of Physics INFM and Centre for Excellence in Biomedical Research, University of Genova, Via Dodecaneso 33, I 16146 Genova, Italy
    Structure 11:1087-95. 2003
    ....
  33. ncbi A combined transmembrane topology and signal peptide prediction method
    LUKAS KALL
    Center for Genomics and Bioinformatics, Karolinska Institutet, SE 17 177 Stockholm, Sweden
    J Mol Biol 338:1027-36. 2004
    ..The method is available at as well as at..
  34. pmc SCRATCH: a protein structure and structural feature prediction server
    J Cheng
    Institute for Genomics and Bioinformatics, University of California Irvine, CA, USA
    Nucleic Acids Res 33:W72-6. 2005
    ..The user simply provides an amino acid sequence and selects the desired predictions, then submits to the server. Results are emailed to the user. The server is available at http://www.igb.uci.edu/servers/psss.html...
  35. ncbi Design of a novel globular protein fold with atomic-level accuracy
    Brian Kuhlman
    Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
    Science 302:1364-8. 2003
    ..2 angstroms) to the design model. The ability to design a new protein fold makes possible the exploration of the large regions of the protein universe not yet observed in nature...
  36. ncbi Atomic structures of the human immunophilin FKBP-12 complexes with FK506 and rapamycin
    G D Van Duyne
    Department of Chemistry, Cornell University Ithaca, NY 14853 1301
    J Mol Biol 229:105-24. 1993
    ..The different complexes are active in suppressing different steps of T cell activation, an activity seemingly unconnected with the PPIase activity...
  37. ncbi Structure of the MDM2 oncoprotein bound to the p53 tumor suppressor transactivation domain
    P H Kussie
    Cellular Biochemistry and Biophysics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
    Science 274:948-53. 1996
    ..The structure also suggests that the amphipathic alpha helix may be a common structural motif in the binding of a diverse family of transactivation factors to the TATA-binding protein-associated factors...
  38. ncbi Comparison of multiple Amber force fields and development of improved protein backbone parameters
    Viktor Hornak
    Center for Structural Biology, Stony Brook University, Stony Brook, New York 11794, USA
    Proteins 65:712-25. 2006
    ..It also accomplishes improved agreement with published experimental data for conformational preferences of short alanine peptides and better accord with experimental NMR relaxation data of test protein systems...
  39. pmc Structure of the cross-beta spine of amyloid-like fibrils
    Rebecca Nelson
    Howard Hughes Medical Institute, UCLA DOE Institute for Genomics and Proteomics, Box 951570, UCLA, Los Angeles, California 90095 1570, USA
    Nature 435:773-8. 2005
    ..The structure illuminates the stability of amyloid fibrils, their self-seeding characteristic and their tendency to form polymorphic structures...
  40. ncbi A study of the coevolutionary patterns operating within the env gene of the HIV-1 group M subtypes
    Simon A A Travers
    Molecular Evolution and Bioinformatics Laboratory, Department of Biology, National University of Ireland, Maynooth, Ireland
    Mol Biol Evol 24:2787-801. 2007
    ....
  41. ncbi Protein aggregation and neurodegenerative disease
    Christopher A Ross
    Division of Neurobiology, Department of Psychiatry, Johns Hopkins University School of Medicine, Ross Research Building, Room 618, 720 Rutland Avenue, Baltimore, Maryland 21205, USA
    Nat Med 10:S10-7. 2004
    ..There is now increased understanding of the pathways involved in protein aggregation, and some recent clues have emerged as to the molecular mechanisms of cellular toxicity. These are leading to approaches toward rational therapeutics...
  42. pmc NMR solution structure of the human prion protein
    R Zahn
    Institut fur Molekularbiologie und Biophysik, Eidgenossische Technische Hochschule Honggerberg, CH 8093 Zurich, Switzerland
    Proc Natl Acad Sci U S A 97:145-50. 2000
    ....
  43. ncbi Structure and mechanism of the lactose permease of Escherichia coli
    Jeff Abramson
    Department of Biological Sciences, Imperial College London, London SW7 2AZ, UK
    Science 301:610-5. 2003
    ..We propose a possible mechanism for lactose/proton symport (co-transport) consistent with both the structure and a large body of experimental data...
  44. ncbi Prediction of amyloid fibril-forming proteins
    Y Kallberg
    Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Medical Nobel Institute, Karolinska Institutet, S-171 77 Stockholm, Sweden
    J Biol Chem 276:12945-50. 2001
    ..Likewise, when Abeta residues 14-23 are removed or changed to a nondiscordant sequence, fibrils are no longer formed. We propose that alpha-helix/beta-strand-discordant stretches are associated with amyloid fibril formation...
  45. pmc Increasing protein stability by improving beta-turns
    Hailong Fu
    Department of Biochemistry and Biophysics, Texas A and M University, College Station, Texas, USA
    Proteins 77:491-8. 2009
    ..Improving beta-turns by substituting Pro residues is a generally useful way of increasing protein stability...
  46. pmc Crystal structure of a translation termination complex formed with release factor RF2
    Andrei Korostelev
    Center for Molecular Biology of RNA and Departments of Molecular, Cell and Developmental Biology and Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
    Proc Natl Acad Sci U S A 105:19684-9. 2008
    ..We show that when the H-bonding capability of the main-chain N-H of the conserved glutamine is eliminated by substitution with proline, peptidyl-tRNA esterase activity is abolished, consistent with its proposed role in catalysis...
  47. pmc Prediction of membrane-protein topology from first principles
    Andreas Bernsel
    Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE 106 91 Stockholm, Sweden
    Proc Natl Acad Sci U S A 105:7177-81. 2008
    ..This result suggests that prediction of membrane-protein topology and structure directly from first principles is an attainable goal, given the recently improved understanding of peptide recognition by the translocon...
  48. pmc The Jpred 3 secondary structure prediction server
    Christian Cole
    School of Life Sciences Research, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
    Nucleic Acids Res 36:W197-201. 2008
    ..A new software pipeline will enable Jnet/Jpred to continue to be updated in sync with major updates to SCOP and UniProt and so ensures that Jpred 3 will maintain high-accuracy predictions...
  49. pmc Natural and synthetic prion structure from X-ray fiber diffraction
    Holger Wille
    Institute for Neurodegenerative Diseases, Departments of Neurology and Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94143, USA
    Proc Natl Acad Sci U S A 106:16990-5. 2009
    ....
  50. ncbi Voltage-dependent gating of hyperpolarization-activated, cyclic nucleotide-gated pacemaker channels: molecular coupling between the S4-S5 and C-linkers
    Niels Decher
    Department of Physiology and Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah 84112 5000, USA
    J Biol Chem 279:13859-65. 2004
    ....
  51. pmc Identifying the amylome, proteins capable of forming amyloid-like fibrils
    Lukasz Goldschmidt
    Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095 1570, USA
    Proc Natl Acad Sci U S A 107:3487-92. 2010
    ..The implication is that chaperoning effects have evolved to constrain self-complementary segments from interaction with each other...
  52. ncbi Fibrillar aggregates of the tumor suppressor p53 core domain
    Daniella Ishimaru
    Departamento de Bioquímica Médica and Centro Nacional de Ressonância Magnética Nuclear, Universidade Federal do Rio de Janeiro, 21941 590 Rio de Janeiro, RJ, Brazil
    Biochemistry 42:9022-7. 2003
    ..Fibrillar aggregates of p53C contribute to the loss of function of p53 and seed the accumulation of conformationally altered protein in some cancerous cells...
  53. ncbi Prediction of protein B-factor profiles
    Zheng Yuan
    Institute for Molecular Bioscience and ARC Centre in Bioinformatics, The University of Queensland, St Lucia, Australia
    Proteins 58:905-12. 2005
    ..flexible). For almost all predicted B-factor thresholds, prediction accuracies (percent of correctly predicted residues) are greater than 70%. These results exceed the best results of other sequence-based prediction methods...
  54. pmc A structural model for Alzheimer's beta -amyloid fibrils based on experimental constraints from solid state NMR
    Aneta T Petkova
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 0520, USA
    Proc Natl Acad Sci U S A 99:16742-7. 2002
    ..The only charged sidechains in the core are those of D23 and K28, which form salt bridges. Fibrils with minimum mass-per-length and diameter consist of two cross-beta units with their hydrophobic faces juxtaposed...
  55. pmc Random-coil behavior and the dimensions of chemically unfolded proteins
    Jonathan E Kohn
    Interdepartmental Program in Biomolecular Science and Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA
    Proc Natl Acad Sci U S A 101:12491-6. 2004
    ..588 predicted for an excluded volume random coil. Therefore, it appears that the mean dimensions of the large majority of chemically denatured proteins are effectively indistinguishable from the mean dimensions of a random-coil ensemble...
  56. pmc Structural basis for high-affinity peptide inhibition of p53 interactions with MDM2 and MDMX
    Marzena Pazgier
    Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
    Proc Natl Acad Sci U S A 106:4665-70. 2009
    ....
  57. pmc Flexibility, conformational diversity and two dimerization modes in complexes of ribosomal protein L12
    M C Wahl
    Max Planck Institut fur Biochemie, Abteilung Strukturforschung, Am Klopferspitz 18a, D 82152 Martinsried, Germany
    EMBO J 19:174-86. 2000
    ..The structures have been submitted to the Protein Databank (http://www.rcsb.org/pdb) under accession numbers 1DD3 and 1DD4...
  58. ncbi The needle component of the type III secreton of Shigella regulates the activity of the secretion apparatus
    Roma Kenjale
    Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
    J Biol Chem 280:42929-37. 2005
    ..Most types of mutants were defective in interactions with host cells. Together, these data indicate that the needle directly controls the activity of the TTSS and suggest that it may be used to "sense" host cells...
  59. pmc Novel protein folds and their nonsequential structural analogs
    Aysam Guerler
    Department of Chemistry and Biochemistry, Freie Universitat Berlin, 14195 Berlin, Germany
    Protein Sci 17:1374-82. 2008
    ..A web server is available at http://agknapp.chemie.fu-berlin.de/gplus for pairwise alignment, visualization, and database comparison...
  60. ncbi Functional interactions at the interface between voltage-sensing and pore domains in the Shaker K(v) channel
    Gilberto J Soler-Llavina
    Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892, USA
    Neuron 52:623-34. 2006
    ....
  61. ncbi Developments in the CCP4 molecular-graphics project
    Liz Potterton
    Department of Chemistry, University of York, England
    Acta Crystallogr D Biol Crystallogr 60:2288-94. 2004
    ..As well as providing a carefully designed user interface to advanced algorithms of model building and analysis, CCP4 mg is intended to present a graphical toolkit to developers of novel algorithms in these fields...
  62. ncbi FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties
    J Shi
    Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Old Addenbrookes Site, Cambridge, CB2 1GA, UK
    J Mol Biol 310:243-57. 2001
    ..We demonstrate that the combination of these three key features implemented in FUGUE improves both homology recognition performance and alignment accuracy...
  63. ncbi JOY: protein sequence-structure representation and analysis
    K Mizuguchi
    Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
    Bioinformatics 14:617-23. 1998
    ..It was developed to display 3D structural information in a sequence alignment and to help understand the conservation of amino acids in their specific local environments...
  64. pmc Prediction of the plant beta-barrel proteome: a case study of the chloroplast outer envelope
    Enrico Schleiff
    Botanisches Institut der Ludwig Maximilian Universität München, 80368 München, Germany
    Protein Sci 12:748-59. 2003
    ..In addition to the known components, four new proteins of the outer envelope membranes were identified in this study...
  65. ncbi Unexpected modes of PDZ domain scaffolding revealed by structure of nNOS-syntrophin complex
    B J Hillier
    Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA
    Science 284:812-5. 1999
    ..This structure explains how PDZ domains can participate in diverse interaction modes to assemble protein networks...
  66. ncbi Structure of a HoxB1-Pbx1 heterodimer bound to DNA: role of the hexapeptide and a fourth homeodomain helix in complex formation
    D E Piper
    Department of Biophysics and Biophysical Chemistry and Howard Hughes Medical Institute, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
    Cell 96:587-97. 1999
    ..The structure suggests a model for modulation of Hox DNA binding activity by Pbx1 and related proteins...
  67. pmc A conformation-specific monoclonal antibody reacting with fusion-active gp41 from the human immunodeficiency virus type 1 envelope glycoprotein
    S Jiang
    Lindsley F Kimball Research Institute, New York Blood Center, New York, New York 10021, USA
    J Virol 72:10213-7. 1998
    ....
  68. ncbi The use of circular dichroism in the investigation of protein structure and function
    S M Kelly
    Division of Biochemistry and Molecular Biology, Institute of Biomedical and Life Sciences, University of Glasgow, Scotland, G12 8QQ, UK
    Curr Protein Pept Sci 1:349-84. 2000
    ..It is therefore evident that CD is a versatile technique in structural biology, with an increasingly wide range of applications...
  69. ncbi Techniques to study amyloid fibril formation in vitro
    Melanie R Nilsson
    Department of Chemistry, McDaniel College, Eaton Hall, 2 College Hill, Westminster, MD 21157, USA
    Methods 34:151-60. 2004
    ....
  70. doi HIV-1 broadly neutralizing antibody extracts its epitope from a kinked gp41 ectodomain region on the viral membrane
    Zhen Yu J Sun
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
    Immunity 28:52-63. 2008
    ....
  71. ncbi A hidden Markov model for predicting transmembrane helices in protein sequences
    E L Sonnhammer
    National Center for Biotechnology Information, NLM NIH, Bethesda, Maryland 20894, USA
    Proc Int Conf Intell Syst Mol Biol 6:175-82. 1998
    ..The same accuracy was achieved on a larger dataset of 160 proteins. These results compare favourably with existing methods...
  72. ncbi In vitro generation of infectious scrapie prions
    Joaquin Castilla
    Department of Neurology, University of Texas Medical Branch, Galveston, Texas 77555, USA
    Cell 121:195-206. 2005
    ..These findings demonstrate that prions can be generated in vitro and provide strong evidence in support of the protein-only hypothesis of prion transmission...
  73. doi Passing the baton in class B GPCRs: peptide hormone activation via helix induction?
    Christoph Parthier
    Institut für Biochemie und Biotechnologie, Martin Luther Universitat Halle Wittenberg, Kurt Mothes Strasse 3, D 06120 Halle Saale, Germany
    Trends Biochem Sci 34:303-10. 2009
    ..The structures reveal similar modes of ligand binding, with concomitant alpha-helical structuring of the ligand. The latter suggests an attractive mechanical model for class B GPCR activation...
  74. ncbi CD81 (TAPA-1): a molecule involved in signal transduction and cell adhesion in the immune system
    S Levy
    Department of Medicine, Stanford University Medical Center, California 94305, USA
    Annu Rev Immunol 16:89-109. 1998
    ..Like CD81, several tetraspanins are involved in cell adhesion, motility, and metastasis, as well as cell activation and signal transduction...
  75. pmc WoLF PSORT: protein localization predictor
    Paul Horton
    Computational Biology Research Center, AIST, Tokyo, Japan
    Nucleic Acids Res 35:W585-7. 2007
    ..Taken together, this information allows a user to understand the evidence (or lack thereof) behind the predictions made for particular proteins. WoLF PSORT is available at wolfpsort.org...
  76. pmc A novel GJA8 mutation (p.I31T) causing autosomal dominant congenital cataract in a Chinese family
    Kaijie Wang
    Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology and Visual Sciences Key Lab, Beijing, China
    Mol Vis 15:2813-20. 2009
    ..To identify the genetic defect associated with autosomal dominant congenital nuclear cataract in a Chinese family...
  77. pmc REPETITA: detection and discrimination of the periodicity of protein solenoid repeats by discrete Fourier transform
    Luca Marsella
    CECAM, Lyon, France
    Bioinformatics 25:i289-95. 2009
    ....
  78. pmc Characterization of molecular recognition features, MoRFs, and their binding partners
    Vladimir Vacic
    Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
    J Proteome Res 6:2351-66. 2007
    ..Implications of these findings for the development of MoRF-partner interaction predictors are discussed. In addition, structural changes upon MoRF-to-partner complex formation were examined for several illustrative examples...
  79. pmc Experimental evidence for a frustrated energy landscape in a three-helix-bundle protein family
    Beth G Wensley
    Department of Chemistry, University of Cambridge, MRC Centre for Protein Engineering, Lensfield Rd, Cambridge CB2 1EW UK
    Nature 463:685-8. 2010
    ....
  80. ncbi A mutation in the nerve growth factor beta gene (NGFB) causes loss of pain perception
    Elisabet Einarsdottir
    Department of Medical Biosciences, Unit of Clinical and Medical Genetics, Umea University, SE 90187 Umea, Sweden
    Hum Mol Genet 13:799-805. 2004
    ..This mutation could therefore potentially provide an important tool to study different roles of NGF, and of pain control...
  81. ncbi Mutations that reduce aggregation of the Alzheimer's Abeta42 peptide: an unbiased search for the sequence determinants of Abeta amyloidogenesis
    Christine Wurth
    Department of Chemistry, Princeton University, NJ 08544, USA
    J Mol Biol 319:1279-90. 2002
    ..Some of the variants, however, contain amino acid substitutions not implicated in pre-existing models of Abeta amyloidogenesis...
  82. ncbi New phosphorylation sites identified in hyperphosphorylated tau (paired helical filament-tau) from Alzheimer's disease brain using nanoelectrospray mass spectrometry
    D P Hanger
    Department of Neuroscience, Institute of Psychiatry, London, England, UK
    J Neurochem 71:2465-76. 1998
    ..We identified 22 phosphorylation sites in PHF-tau, including five sites not previously identified. The combination of our new data with previous reports shows that PHF-tau can be phosphorylated on at least 25 different sites...
  83. pmc Solving structures of protein complexes by molecular replacement with Phaser
    Airlie J McCoy
    University of Cambridge, Department of Haematology, Cambridge Institute for Medical Research, Wellcome Trust MRC Building, Hills Road, Cambridge CB2 2XY, England
    Acta Crystallogr D Biol Crystallogr 63:32-41. 2007
    ..Two case studies are presented to illustrate how Phaser can be used to best advantage in the standard ;automated MR' mode and two case studies are used to show how to modify the automated search strategy for problematic cases...
  84. pmc The fold of alpha-synuclein fibrils
    Marçal Vilar
    The Salk Institute for Biological Studies, North Torrey Pines Road, La Jolla, CA 92037, USA
    Proc Natl Acad Sci U S A 105:8637-42. 2008
    ..5 nm. Based on the combination of these data and published structural studies, a fold of alpha-syn in the fibrils is proposed and discussed...
  85. ncbi X-ray structure of recombinant ricin A-chain at 1.8 A resolution
    S A Weston
    Protein Structure Laboratory, Zeneca Pharmaceuticals, Macclesfield, Cheshire, United Kingdom
    J Mol Biol 244:410-22. 1994
    ..The structures suggest that Glu177 is better positioned for the activation of the catalytic water molecule than Arg180...
  86. ncbi Mechanisms of specificity in protein phosphorylation
    Jeffrey A Ubersax
    Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305 5174, USA
    Nat Rev Mol Cell Biol 8:530-41. 2007
    ..The responsibility for the recognition of substrates by protein kinases appears to be distributed among a large number of independent, imperfect specificity mechanisms...
  87. ncbi Specific interactions for ab initio folding of protein terminal regions with secondary structures
    Yuedong Yang
    Indiana University School of Informatics, Indianapolis, Indiana 46202, USA
    Proteins 72:793-803. 2008
    ..The result has significant implications on the theoretical and experimental searches for specific interactions involved in protein folding and molecular recognition between proteins and other biologically active molecules...
  88. pmc The peripheral membrane subunits of the SAM complex function codependently in mitochondrial outer membrane biogenesis
    Nickie C Chan
    Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia
    Mol Biol Cell 19:126-36. 2008
    ..Very different environments surround bacteria and mitochondria, and we discuss the role of Sam35 and Sam37 in terms of the problems peculiar to mitochondrial protein substrates...
  89. ncbi Structure of the cytochrome b6f complex of oxygenic photosynthesis: tuning the cavity
    Genji Kurisu
    Department of Biological Sciences, 915 West State Street, Purdue University, West Lafayette, IN 47907 2054, USA
    Science 302:1009-14. 2003
    ..The motion of the Rieske iron-sulfur protein extrinsic domain, essential for electron transfer, must also be different in the b6f complex...
  90. pmc A conserved trimerization motif controls the topology of short coiled coils
    Richard A Kammerer
    Wellcome Trust Centre for Cell Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 PT, United Kingdom
    Proc Natl Acad Sci U S A 102:13891-6. 2005
    ..In addition to being of particular interest for the biotechnological production of candidate therapeutic proteins, these findings may be of interest for viral drug development strategies...
  91. pmc Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web server
    LUKAS KALL
    Center for Genomics and Bioinformatics, Karolinska Institutet, S 17177 Stockholm, Sweden
    Nucleic Acids Res 35:W429-32. 2007
    ..We here present a web interface (http://phobius.cgb.ki.se and http://phobius.binf.ku.dk) to access Phobius...
  92. pmc Detecting coevolution without phylogenetic trees? Tree-ignorant metrics of coevolution perform as well as tree-aware metrics
    J Gregory Caporaso
    Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO, USA
    BMC Evol Biol 8:327. 2008
    ..We further considered the influence of sequence recoding using reduced-state amino acid alphabets, a common tactic employed in coevolutionary analyses to improve both statistical and computational performance...
  93. pmc DiANNA: a web server for disulfide connectivity prediction
    F Ferre
    Department of Biology, Boston College, Chestnut Hill, MA 02467, USA
    Nucleic Acids Res 33:W230-2. 2005
    ..Our novel neural network-based approach achieves results that are comparable and in some cases better than the current state-of-the-art methods...
  94. pmc The structure of an open form of an E. coli mechanosensitive channel at 3.45 A resolution
    Wenjian Wang
    Centre for Biomolecular Sciences, The North Haugh, University of St Andrews, KY16 9ST, Scotland, UK
    Science 321:1179-83. 2008
    ..Support for this mechanism is provided by single-channel analysis of mutants with altered gating characteristics...
  95. ncbi Docking of HIV-1 Vpr to the nuclear envelope is mediated by the interaction with the nucleoporin hCG1
    Erwann Le Rouzic
    Institut Cochin, Department of Infectious Diseases, CNRS UMR8104, INSERM U567, Universite Paris 5, Paris, France
    J Biol Chem 277:45091-8. 2002
    ..This association of Vpr with a component of the nuclear pore complex may contribute to the disruption of the nuclear envelope and to the nuclear import of the viral DNA...
  96. ncbi Structural basis of multiple drug-binding capacity of the AcrB multidrug efflux pump
    Edward W Yu
    Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720 3202, USA
    Science 300:976-80. 2003
    ..Each ligand uses a slightly different subset of AcrB residues for binding. The bound ligand molecules often interact with each other, stabilizing the binding...
  97. ncbi Solution NMR studies of the A beta(1-40) and A beta(1-42) peptides establish that the Met35 oxidation state affects the mechanism of amyloid formation
    Liming Hou
    Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106 7078, USA
    J Am Chem Soc 126:1992-2005. 2004
    ....
  98. pmc Solution structure of dengue virus capsid protein reveals another fold
    Lixin Ma
    Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA
    Proc Natl Acad Sci U S A 101:3414-9. 2004
    ..We propose a model for the interaction of dengue C protein with RNA and the viral membrane that is based on the asymmetric charge distribution of the protein and is consistent with previously reported results...
  99. ncbi A novel lytic peptide composed of DL-amino acids selectively kills cancer cells in culture and in mice
    Niv Papo
    Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, 76100 Israel
    J Biol Chem 278:21018-23. 2003
    ....
  100. ncbi Self-propagating, molecular-level polymorphism in Alzheimer's beta-amyloid fibrils
    Aneta T Petkova
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health NIH, Bethesda, MD 20892 0520, USA
    Science 307:262-5. 2005
    ..These results have implications for the mechanism of amyloid formation, the phenomenon of strains in prion diseases, the role of amyloid fibrils in amyloid diseases, and the development of amyloid-based nano-materials...
  101. ncbi The membrane-proximal tryptophan-rich region of the HIV glycoprotein, gp41, forms a well-defined helix in dodecylphosphocholine micelles
    D J Schibli
    Department of Biological Sciences, University of Calgary, Alberta, Canada
    Biochemistry 40:9570-8. 2001
    ..This work shows that the Trp-rich membrane-proximal region of HIV and related viruses can bind to the surfaces of zwitterioninc membranes in a "Velcro-like" manner...

Research Grants165 found, 100 shown here

  1. Cloning of a type 2 diabetes modifier in obese mice
    Rudolph Leibel; Fiscal Year: 2006
    ..4.) computational assessment of effects of coding and non-coding variants on secondary protein structure/function and transcription. 5...
  2. Probing the cellular Mechanisms of Transthyretin Cytotoxicity
    Natalia Reixach; Fiscal Year: 2010
    DESCRIPTION (provided by applicant): The transthyretin (TTR) amyloidoses are fatal disorders of secondary protein structure characterized by extracellular deposition of aggregates, including amyloid fibrils, derived from the secreted ..
  3. HEPATIC BIOSYNTHESIS OF CERULOPLASMIN
    Michael Schilsky; Fiscal Year: 1990
    ..This will be accomplished for the primary and secondary protein structure by peptide mapping, and amino acid modification of native proteins followed by peptide mapping...
  4. VIRULENCE DETERMINANTS OF BARTONELLA BACILLIFORMIS
    MICHAEL MINNICK; Fiscal Year: 1993
    ..DNA sequence analysis of each determinant gene will provide a means of predicting primary and secondary protein structure and will allow us to compare the gene or protein to database homologues from other bacteria...
  5. Cloning of a type 2 diabetes modifier in obese mice
    Rudolph Leibel; Fiscal Year: 2005
    ..4.) computational assessment of effects of coding and non-coding variants on secondary protein structure/function and transcription. 5...
  6. Cloning of a type 2 diabetes modifier in obese mice
    Rudolph Leibel; Fiscal Year: 2003
    ..4.) computational assessment of effects of coding and non-coding variants on secondary protein structure/function and transcription. 5...
  7. Cloning of a type 2 diabetes modifier in obese mice
    Rudolph Leibel; Fiscal Year: 2004
    ..4.) computational assessment of effects of coding and non-coding variants on secondary protein structure/function and transcription. 5...
  8. PHOSPHATE TRANSPORT PATHS WITHIN HOMODIMERIC PTP
    Hartmut Wohlrab; Fiscal Year: 2001
    ..The aim now is to identify transmembrane secondary protein structure elements that line the Pi transport path through PTP and to demonstrate that they undergo Pi-induced ..
  9. PHOSPHATE TRANSPORT PATHS WITHIN HOMODIMERIC PTP
    Hartmut Wohlrab; Fiscal Year: 2000
    ..The aim now is to identify transmembrane secondary protein structure elements that line the Pi transport path through PTP and to demonstrate that they undergo Pi-induced ..
  10. PHOSPHATE TRANSPORT PATHS WITHIN HOMODIMERIC PTP
    Hartmut Wohlrab; Fiscal Year: 1999
    ..The aim now is to identify transmembrane secondary protein structure elements that line the Pi transport path through PTP and to demonstrate that they undergo Pi-induced ..
  11. STRUCTURAL ORGANIZATION AND PROTEOMICS OF TB
    Thomas Terwilliger; Fiscal Year: 2005
    ..The structural and functional information obtained in this project is to be placed in the public domain by timely deposition in publicly available databases. ..
  12. Integrated Center for Structure and Function Innovation
    Thomas Terwilliger; Fiscal Year: 2008
    ..Technologies and results will be made available to other Centers and the broader structural biology community through workshops, publications, personnel exchanges, and the web. ..
  13. LIGAND BASED STUDIES OF NUCLEAR RECEPTORS
    Thomas Scanlan; Fiscal Year: 2003
    ..Moreover, these selective ligands could be useful as therapeutics for the treatment of human disease associated with thyroid hormone regulation. ..
  14. Structural Studies of Metabolic Membrane Proteins
    Joanne Yeh; Fiscal Year: 2002
    ..Our specific aims are to obtain atomic resolution structures of both membrane proteins, both of which are likely to be novel targets for antibiotic design and therapy. ..
  15. Protein interactions underlying actin-based motility
    David Sept; Fiscal Year: 2002
    ..This work will give perspective, not only into dendritic nucleation, but the motility of bacteria such as Listeria, and the function of the cell as a whole. ..
  16. Cold Neutrons For Biology And Technology
    Stephen White; Fiscal Year: 2002
    ..We foresee a future when computer simulations will allow three-dimensional detail to be inferred routinely from 1- and 2-dimensional neutron and X-ray data. ..
  17. Selective Induction of Estrogen Conjugative Metabolism
    Bao Ting Zhu; Fiscal Year: 2003
    ..These studies will also provide examinations of the important roles of bioactive estrogen metabolites (e.g., 4-OH-E2 and 16alpha-OH-E2) in estrogen-induced cancers. ..
  18. CHEMICAL MODELS OF PROTEIN BETA SHEET INTERACTIONS
    James Nowick; Fiscal Year: 2002
    ..5) Artificial beta-sheets designed to block beta-amyloid aggregation will be synthesized, and their abilities to block its aggregation and deposition will be studied using in vitro assays. ..
  19. ANNEXIN PHOSPHORYLATION: CAUSES AND CONSEQUENCES
    CARL CREUTZ; Fiscal Year: 2002
    ....
  20. CELL BIOLOGY OF THE NEURONAL SODIUM CHANNEL
    William Catterall; Fiscal Year: 2005
    ..Our results will add substantially to understanding of the cell biology of the Na channel and the functional significance of Na channel signaling complexes. ..
  21. FOLDING OF THE INTRACELLULAR LIPID-BINDING PROTEINS
    Ira Ropson; Fiscal Year: 2002
    ..Single-site mutant proteins will be generated and studied for their effects on the transition state in protein folding. ..
  22. STRUCTURE AND STABILITY OF SINGLE-LAYER BETA-SHEETS
    Shohei Koide; Fiscal Year: 2001
    ..Outcomes of this study will also provide important information for structural genomics and de novo protein design. ..
  23. MOLECULAR PROPERTIES OF VOLTAGE SENSITIVE CA++ CHANNELS
    William Catterall; Fiscal Year: 2000
    ..abstract_text> ..
  24. PROTEIN FOLDING AND MISFOLDING
    Michael Weiss; Fiscal Year: 1999
    ..This differential property is the basis on which Dr. Weiss proposes to identify factors responsible for on-pathway and off-pathway oxidative folding. ..
  25. TISSUE ENGINEERING USING PEPTIDE AMPHIPHILE BIOMIMETICS
    GREGG FIELDS; Fiscal Year: 1999
    ..For building materials with molecular and cellular recognition capacity, these PAs may provide an important approach for producing characteristic structures at surfaces and interfaces. ..
  26. Molecular Mechanisms of Regulation of Contraction
    Sarah Hitchcock DeGregori; Fiscal Year: 2003
    ..The results will help understand how the cytoskeleton is remodeled during complex functions such as leucocyte chemotaxis and growth factor-stimulated cellular outgrowth, processes important in both normal and pathological states. ..
  27. REGULATION OF THE GLUCOSE TRANSPORTER
    Michael Mueckler; Fiscal Year: 2003
    ..This isoform will be thoroughly characterized with respect to its substrate specificity, tissue distribution, regulation, and possible role in insulin regulated metabolite uptake. ..
  28. Therapeutic Approaches for Prion Disease
    Thomas Wisniewski; Fiscal Year: 2005
    ..In vivo imaging will also be done with 2 photon microscopy and non-toxic, Congo red analogs. Our novel imaging techniques will be used to monitor our therapeutic experiments. ..
  29. CELL BIOLOGY OF THE NEURONAL SODIUM CHANNEL
    William A Catterall; Fiscal Year: 2010
    ..This project will use a mouse genetic model of this disease to determine how this gene defect causes epilepsy and to test new drug combinations for control of this intractable epilepsy syndrome. ..
  30. Factors influencing regulation of the dynamics of the actin filament pointed end
    Alla S Kostyukova; Fiscal Year: 2010
    ..The information obtained in this study will help us to understand the formation of the capping complex at the pointed end and its function in regulating dynamics of the actin filament in cells and tissues. ..
  31. Dietary Polyphenols Are Consequential Epigenetic Modulators of Gene Expression
    BAOTING ZHU; Fiscal Year: 2009
    ..It is expected that the outcomes of the proposed studies will have direct clinical utility in the near future and far-reaching human health implications. ..
  32. Receptors Mediating Lymphotoxin Effects on Athersclerosis
    GODFREY GETZ; Fiscal Year: 2009
    ..This will be done in the LDLR-/- mouse background and will involve the expression of the ligands LIGHT and lymphotoxin beta at physiological levels and LIGHT overexpression in T cells. ..
  33. Biomolecular Analysis of Proteins in Visual Disease
    ESTHER BISWAS FISS; Fiscal Year: 2007
    ..unreadable] [unreadable] [unreadable]..
  34. Membrane Protein Folding and Assembly
    Stephen White; Fiscal Year: 2007
    ..The information obtained will help us understand how to predict the topology and structure of unusual membrane proteins, such as the CIC chloride channel. [unreadable] [unreadable] [unreadable]..
  35. Amyloid beta Peptide and Apolipoprotein E
    Thomas Wisniewski; Fiscal Year: 2006
    ..These studies will test our central hypothesis that blocking the Aa/apoE interaction can serve as a novel, non-toxic therapeutic target for Alzheimer's disease. ..
  36. INTRACELLULAR SIGNALING BY BACTERIAL CHEMORECEPTORS
    John Parkinson; Fiscal Year: 2006
    ..These studies will provide important new perspectives on the issue of receptor clustering, a hallmark of biological signaling systems at every complexity level. [unreadable] [unreadable] [unreadable]..
  37. CALCIUM RECEPTOR SIGNAL RECOGNITION AND TRANSDUCTION
    Edward M Brown; Fiscal Year: 2006
    ..abstract_text> ..
  38. Cold Neutrons For Biology And Technology
    Stephen White; Fiscal Year: 2005
    ..We foresee a future when computer simulations will allow three-dimensional detail to be inferred routinely from 1- and 2-dimensional neutron and X-ray data. ..
  39. Insulin Signaling in a Cell-Free System
    Michael Mueckler; Fiscal Year: 2005
    ..abstract_text> ..
  40. Structural and biochemical characterization of the OprD membrane protein family
    Bert van den Berg; Fiscal Year: 2009
    ..Besides being important from a fundamental point of view, such knowledge could also be used by pharmaceutical companies to design better drugs against disease-causing bacteria. ..
  41. Concerted membrane diffraction and simulation studies
    Stephen White; Fiscal Year: 2005
    ....
  42. LIGAND PHARMACOLOGY OF ESTROGEN RECEPTORS
    Thomas Scanlan; Fiscal Year: 2005
    ..This research aims to define the molecular mechanisms and Uganda-activation parameters of rapid, non-genomic estrogen signaling which could lead to much needed safe therapeutics for treating the symptoms of menopause. ..
  43. HIV Protease Inhibitors & Glucose Transport
    Michael Mueckler; Fiscal Year: 2005
    ..2) To test the hypothesis that PI-mediated inhibition of glucose transport directly contributes to lipodystrophy by suppressing adipogenesis and/or by enhancing adipocyte apoptosis. ..
  44. How Insulin Binds to the Insulin Receptor
    MICHAEL AARON WEISS; Fiscal Year: 2010
    ..To demonstrate proof-of- principle, respective application of this enabling technology to the liver and pancreatic p cells of LIRKO and PIRKO mice is planned in collaboration with C. R. Kahn (Joslin Diabetes Center, Boston). ..
  45. NA/K PUMP CURRENT IN ISOLATED HEART CELLS
    DAVID GADSBY; Fiscal Year: 1992
    ..We will also begin structure/function studies of exogenous Na/K pumps expressed in Xenopus oocytes from injected mRNA...
  46. VOLTAGE-SENSITIVE SODIUM CHANNELS IN BRAIN
    William Catterall; Fiscal Year: 1991
    ..These studies will provide essential information to understanding the molecular basis of electrical excitability...
  47. ADVANCED SEQUENCE BASED PREDICTION OF PROTEIN FUNCTION
    ANDREW NEUWALD; Fiscal Year: 1999
    ..A comprehensive database of protein domains will be made available to the biomedical community through the National Center for Biotechnology Information. ..
  48. VOLTAGE-SENSITIVE SODIUM CHANNELS IN BRAIN
    William Catterall; Fiscal Year: 1992
    ....
  49. FLUID BILAYER INTERACTIONS WITH PEPTIDES
    Stephen White; Fiscal Year: 1999
    ..5) Clarify the role of tryptophan in membrane protein assembly and stability through studies of the interactions of indole compounds with lipid bilayers. ..
  50. CHEMICAL MODELS OF PROTEIN BETA SHEET INTERACTIONS
    James Nowick; Fiscal Year: 1999
    ..5) Artificial beta-sheets designed to block beta-amyloid aggregation will be synthesized, and their abilities to block its aggregation and deposition will be studied using in vitro assays. ..
  51. CONFORMATIONAL STABILITY OF GLOBULAR PROTEINS
    CARLOS PACE; Fiscal Year: 1991
    ..These unfolded states will be compared with the thermally unfolded states and the unfolded states that exist under physiological conditions. The influence of the disulfide bonds on the unfolded conformations will also be studied...
  52. CONFORMATIONAL STABILITY OF GLOBULAR PROTEINS
    CARLOS PACE; Fiscal Year: 1999
    ..its conformational stability and other physical and chemical properties? 6) What determines the pK values of the ionizable groups in folded and unfolded proteins and how do they effect the conformational stability? ..
  53. CELL BIOLOGY OF THE NEURONAL SODIUM CHANNEL
    William Catterall; Fiscal Year: 1991
    ..The results will define the functional roles of these proteins in the development and maintenance of normal electrical excitability in central neurons...
  54. STRUCTURE AND FUNCTION OF THE GLUCOSE TRANSPORTER
    Michael Mueckler; Fiscal Year: 1991
    ....
  55. MOLECULAR MECHANISM OF RENAL NA+ DEPENDENT COTRANSPORT
    Ana Pajor; Fiscal Year: 2004
    ..abstract_text> ..
  56. GENETICS OF CHEMOTACTIC BEHAVIOR IN ESCHERICHIA COLI
    John Parkinson; Fiscal Year: 1991
    ..The DNA sequence changes in selected mutants will be determined in order to delineate functional domains within the proteins. From these studies, structurefunction models will be devised that can be tested by sitespecific mutagenesis...
  57. MOLECULAR MECHANISM OF RENAL NA+ DEPENDENT COTRANSPORT
    Ana Pajor; Fiscal Year: 1999
    ..These studies should provide fundamental information on the functional properties of this family of sodium-dependent transporters, and on the physiological role of these transporters in the kidney. ..
  58. MOLECULAR MECHANISM OF RENAL NA+ DEPENDENT COTRANSPORT
    Ana Pajor; Fiscal Year: 2006
    ..abstract_text> ..
  59. Arg199: key player in electron transfer in NOS enzyme
    Valentin Gogonea; Fiscal Year: 2004
    ..Primary focus is placed on how Arg199 modulates the electron transfer in NOS a role only revealed during the dynamics of the system. ..
  60. PROTON & ELECTRON TRANSFER & ENERGY COUPLING IN SITE I
    Tomoko Ohnishi; Fiscal Year: 2009
    ..Using this new strategy, we found that both cluster N2 and flavin can generate superoxide. We will solidify this exciting finding and study its relevance to complex I function under physiological and pathological conditions. ..
  61. INTRACELLULAR SIGNALING BY BACTERIAL CHEMORECEPTORS
    John Parkinson; Fiscal Year: 2004
    ..These studies will provide important new perspectives on the issue of receptor clustering, a hallmark of biological signaling systems at every complexity level. ..
  62. INTRACELLULAR SIGNALING BY BACTERIAL CHEMORECEPTORS
    John Parkinson; Fiscal Year: 2008
    ....
  63. X-ray diffraction analysis of human adenovirus
    Vijay Reddy; Fiscal Year: 2008
    ..The proposed studies are aimed at determining the crystal structure of the entire human adenovirus virion at near atomic resolution employing x-ray diffraction methods. ..
  64. MOLECULAR MECHANISM OF RENAL NA+ DEPENDENT COTRANSPORT
    Ana Pajor; Fiscal Year: 2002
    ..abstract_text> ..
  65. MOLECULAR MECHANISM OF RENAL NA+ DEPENDENT COTRANSPORT
    Ana Pajor; Fiscal Year: 2007
    ..Understanding how NaDC1 and SdcS work will help us to develop treatments for NaDC1-mediated diseases. ..
  66. INTRACELLULAR SIGNALING BY BACTERIAL CHEMORECEPTORS
    John Parkinson; Fiscal Year: 2007
    ....
  67. MOLECULAR MECHANISM OF RENAL NA+ DEPENDENT COTRANSPORT
    Ana Pajor; Fiscal Year: 2005
    ..abstract_text> ..
  68. GENETICS OF CHEMOTACTIC BEHAVIOR IN ESCHERICHIA COLI
    John Parkinson; Fiscal Year: 1990
    ..The DNA sequence changes in selected mutants will be determined in order to delineate functional domains within the proteins. From these studies, structurefunction models will be devised that can be tested by sitespecific mutagenesis...
  69. X-ray diffraction analysis of human adenovirus
    Vijay Reddy; Fiscal Year: 2006
    ..et al. Science 309: 1090-1092, 2005). [unreadable] [unreadable] [unreadable]..
  70. X-ray diffraction analysis of human adenovirus
    Vijay S Reddy; Fiscal Year: 2010
    ..The proposed studies are aimed at determining the crystal structure of the entire human adenovirus virion at near atomic resolution employing x-ray diffraction methods. ..
  71. MOLECULAR MECHANISM OF RENAL NA+ DEPENDENT COTRANSPORT
    Ana Pajor; Fiscal Year: 2001
    ..These studies should provide fundamental information on the functional properties of this family of sodium-dependent transporters, and on the physiological role of these transporters in the kidney. ..
  72. PROTON & ELECTRON TRANSFER & ENERGY COUPLING IN SIT I
    Tomoko Ohnishi; Fiscal Year: 2001
    ..5) We have developed an exciting bacterial model system, which allows us to study mechanisms of mitochondria-linked diseases by making clinically significant point mutations. ..
  73. MOLECULAR MECHANISM OF RENAL NA+ DEPENDENT COTRANSPORT
    Ana Pajor; Fiscal Year: 2009
    ..Understanding how NaDC1 and SdcS work will help us to develop treatments for NaDC1-mediated diseases. ..
  74. PROTON & ELECTRON TRANSFER & ENERGY COUPLING IN SITE I
    Tomoko Ohnishi; Fiscal Year: 2000
    ..The P.I. will collaborate on this project with a multi-disciplinary research team, consisting of renowned experts of molecular biology, mitochondrial disease, biochemistry and biophysics. ..
  75. MOLECULAR MECHANISM OF RENAL NA+ DEPENDENT COTRANSPORT
    Ana M Pajor; Fiscal Year: 2010
    ..Understanding how NaDC1 and SdcS work will help us to develop treatments for NaDC1-mediated diseases. ..
  76. INTRACELLULAR SIGNALING BY BACTERIAL CHEMORECEPTORS
    John Parkinson; Fiscal Year: 2003
    ..These studies will provide important new perspectives on the issue of receptor clustering, a hallmark of biological signaling systems at every complexity level. ..
  77. PROTON & ELECTRON TRANSFER & ENERGY COUPLING IN SITE I
    TOMOKO NONE OHNISHI; Fiscal Year: 2010
    ..Using this new strategy, we found that both cluster N2 and flavin can generate superoxide. We will solidify this exciting finding and study its relevance to complex I function under physiological and pathological conditions. ..