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 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
  2. 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
  3. 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
  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. 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
  7. 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
  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 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
  10. pmc Can correct protein models be identified?
    Björn Wallner
    Stockholm Bioinformatics Center, SCFAB, Stockholm University, SE 106 91 Stockholm, Sweden
    Protein Sci 12:1073-86. 2003

Research Grants

  1. Probing the cellular Mechanisms of Transthyretin Cytotoxicity
    Natalia Reixach; Fiscal Year: 2013
  2. HEPATIC BIOSYNTHESIS OF CERULOPLASMIN
    Michael Schilsky; Fiscal Year: 1993
  3. PHOSPHATE TRANSPORT PATHS WITHIN HOMODIMERIC PTP
    Hartmut Wohlrab; Fiscal Year: 2001
  4. STRUCTURAL ORGANIZATION AND PROTEOMICS OF TB
    Thomas Terwilliger; Fiscal Year: 2005
  5. MOLECULAR MECHANISMS OF PACEMAKER CHANNEL FUNCTION
    Michael Sanguinetti; Fiscal Year: 2008
  6. Structure and function of antimicrobial peptides
    Ayyalusamy Ramamoorthy; Fiscal Year: 2008
  7. HYBRID HYDROGELS SELF-ASSEMBLED FROM GRAFT COPOLYMERS
    Jindrich Kopecek; Fiscal Year: 2008
  8. Structure-Function Relationships in Lung Surfactants
    Joanna Long; Fiscal Year: 2008
  9. DNA Multiplex Hybridization Kinetics and SNP Assays
    ALBERT BENIGHT; Fiscal Year: 2007
  10. Structure/Function Studies on Flavoproteins
    Irina Sevrioukova; Fiscal Year: 2007

Detail Information

Publications305 found, 100 shown here

  1. 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...
  2. 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...
  3. 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/...
  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. 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...
  7. 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...
  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 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...
  10. pmc Can correct protein models be identified?
    Björn Wallner
    Stockholm Bioinformatics Center, SCFAB, Stockholm University, SE 106 91 Stockholm, Sweden
    Protein Sci 12:1073-86. 2003
    ..Pmodeller was successful in CASP5 and results from the latest LiveBench, LiveBench-6, indicating that Pmodeller has a higher specificity than Pcons alone...
  11. 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...
  12. 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
    ....
  13. 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...
  14. 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..
  15. 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...
  16. ncbi Toward high-resolution de novo structure prediction for small proteins
    Philip Bradley
    University of Washington, Department of Biochemistry, and Howard Hughes Medical Institute, Box 357350, Seattle, WA 98195, USA
    Science 309:1868-71. 2005
    ..5 angstroms) can be achieved for small protein domains (<85 residues). The primary bottleneck to consistent high-resolution prediction appears to be conformational sampling...
  17. ncbi X-ray structure of a protein-conducting channel
    Bert van den Berg
    Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA
    Nature 427:36-44. 2004
    ....
  18. 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...
  19. 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...
  20. ncbi Sar1p N-terminal helix initiates membrane curvature and completes the fission of a COPII vesicle
    Marcus C S Lee
    Department of Molecular and Cell Biology and Howard Hughes Medical Institute, University of California, Berkeley, California 94702, USA
    Cell 122:605-17. 2005
    ..Thus, the initiation of vesicle budding by Sar1p couples the generation of membrane curvature with coat-protein assembly and cargo capture...
  21. 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/...
  22. ncbi Preformed structural elements feature in partner recognition by intrinsically unstructured proteins
    Monika Fuxreiter
    Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Budapest, Hungary
    J Mol Biol 338:1015-26. 2004
    ..This finding implies that IUPs draw a functional advantage from preformed structural elements, as they enable their facile, kinetically and energetically less demanding, interaction with their physiological partner...
  23. 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...
  24. ncbi Structure and function of bacterial outer membrane proteins: barrels in a nutshell
    R Koebnik
    Biozentrum Basel, Abteilung Mikrobiologie, Klingelbergstr 50, CH 4056 Basel, Switzerland
    Mol Microbiol 37:239-53. 2000
    ..Our review is aimed at discussing their common principles and peculiarities as well as open questions associated with them...
  25. ncbi Analyzing protein circular dichroism spectra for accurate secondary structures
    W C Johnson
    Department of Biochemistry and Biophysics, Oregon State University, Corvallis 97331 7305, USA
    Proteins 35:307-12. 1999
    ..3% for alpha-helix, 2.6% for 3(10)-helix, 4.2% for beta-strand, 4.2% for beta-turn, 2.7% for poly(L-proline) II type 3(1)-helix, and 5.1% for other structures when compared with the X-ray structure...
  26. 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..
  27. 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...
  28. 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...
  29. 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
    ....
  30. 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...
  31. ncbi Prediction of "aggregation-prone" and "aggregation-susceptible" regions in proteins associated with neurodegenerative diseases
    Amol P Pawar
    Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
    J Mol Biol 350:379-92. 2005
    ....
  32. 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
    ....
  33. pmc Structural basis for the autoinhibition of focal adhesion kinase
    Daniel Lietha
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
    Cell 129:1177-87. 2007
    ..Our biochemical and structural analysis shows how the architecture of autoinhibited FAK orchestrates an activation sequence of FERM domain displacement, linker autophosphorylation, Src recruitment, and full catalytic activation...
  34. 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...
  35. 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...
  36. 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...
  37. 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...
  38. 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...
  39. 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
    ....
  40. ncbi Three-dimensional structure of the armadillo repeat region of beta-catenin
    A H Huber
    Department of Structural Biology, Stanford University School of Medicine, California 94305, USA
    Cell 90:871-82. 1997
    ..Although unrelated in sequence, the beta-catenin binding regions of cadherins, Tcfs, and APC are acidic and are proposed to interact with this groove...
  41. 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...
  42. 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...
  43. 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...
  44. ncbi 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...
  45. 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...
  46. 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...
  47. ncbi 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
    ....
  48. ncbi Structure and dynamics of micelle-bound human alpha-synuclein
    Tobias S Ulmer
    Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Biol Chem 280:9595-603. 2005
    ....
  49. ncbi Porter: a new, accurate server for protein secondary structure prediction
    Gianluca Pollastri
    Computer Science Department, University College Dublin, Belfield, Dublin 4, Ireland
    Bioinformatics 21:1719-20. 2005
    ..Porter's accuracy, tested by rigorous 5-fold cross-validation on a large set of proteins, exceeds 79%, significantly above a copy of the state-of-the-art SSpro server, better than any system published to date...
  50. 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...
  51. pmc CE-MC: a multiple protein structure alignment server
    Chittibabu Guda
    San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
    Nucleic Acids Res 32:W100-3. 2004
    ..For large-scale jobs and local installation of the CE-MC program, users can download the source code and precompiled binaries from the web server...
  52. 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...
  53. 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
    ....
  54. ncbi Structural basis for recognition of the tra mRNA precursor by the Sex-lethal protein
    N Handa
    Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Japan
    Nature 398:579-85. 1999
    ..This structure offers the first insight, to our knowledge, into how a protein binds specifically to a cognate RNA without any intramolecular base-pairing...
  55. 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...
  56. ncbi TPR proteins: the versatile helix
    Luca D D'Andrea
    Institute of Biostructure and Bioimaging, CNR, Via Mezzocannone 6, 80134, Naples, Italy
    Trends Biochem Sci 28:655-62. 2003
    ..Genomic analyses of the distribution of TPR domains are presented along with implications for protein engineering...
  57. 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...
  58. 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...
  59. 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...
  60. ncbi Conformational behavior and aggregation of alpha-synuclein in organic solvents: modeling the effects of membranes
    Larissa A Munishkina
    Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
    Biochemistry 42:2720-30. 2003
    ..At least to some extent, these conformational effects mimic those observed in the presence of phospholipid vesicles, and can explain some of the observed effects of membranes on alpha-synuclein fibrillation...
  61. ncbi Crystal structure of CD14 and its implications for lipopolysaccharide signaling
    Jung In Kim
    Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 305 701, Korea
    J Biol Chem 280:11347-51. 2005
    ..Ligand diversity of CD14 could be explained by the generous size of the pocket, the considerable flexibility of the rim of the pocket, and the multiplicity of grooves available for ligand binding...
  62. 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...
  63. ncbi Type II restriction endonucleases: structure and mechanism
    A Pingoud
    Institut fur Biochemie, Justus Liebig Universitat, Heinrich Buff Ring 58, 35392, Giessen, Germany
    Cell Mol Life Sci 62:685-707. 2005
    ..A major emphasis of this review will be on target site location and the mechanism of catalysis, two problems currently being addressed in the literature...
  64. pmc Molecular basis for amyloid fibril formation and stability
    O Sumner Makin
    Structural Medicine, Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Hills Road, Cambridge CB2 2XY, United Kingdom
    Proc Natl Acad Sci U S A 102:315-20. 2005
    ..These interactions are likely to be important in the formation and stability of other amyloid fibrils...
  65. pmc Thr729 in human topoisomerase I modulates anti-cancer drug resistance by altering protein domain communications as suggested by molecular dynamics simulations
    Giovanni Chillemi
    CASPUR Inter University Consortium for the Application of Super Computing for Universities and Research, Via dei Tizii 6, Rome 00185, Italy
    Nucleic Acids Res 36:5645-51. 2008
    ....
  66. pmc Molecular recognition of corticotropin-releasing factor by its G-protein-coupled receptor CRFR1
    Augen A Pioszak
    Laboratory of Structural Sciences, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA
    J Biol Chem 283:32900-12. 2008
    ..These structural studies provide a molecular framework for understanding peptide binding and specificity by the CRF receptors as well as a template for designing potent and selective CRFR1 antagonists for therapeutic applications...
  67. ncbi Pathway complexity of prion protein assembly into amyloid
    Ilia V Baskakov
    Institute for Neurodegenerative Diseases, University of California, San Francisco, California 94143, USA
    J Biol Chem 277:21140-8. 2002
    ....
  68. 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...
  69. ncbi Statistical analysis of atomic contacts at RNA-protein interfaces
    M Treger
    , , , 4 Rue Kirshleger, F-67000 Strasbourg, France
    J Mol Recognit 14:199-214. 2001
    ....
  70. ncbi Structural and functional constraints in the evolution of protein families
    Catherine L Worth
    Biochemistry Department, University of Cambridge, UK
    Nat Rev Mol Cell Biol 10:709-20. 2009
    ..These constraints arise from the need to conserve a specific architecture and to retain interactions that mediate functions in protein families and superfamilies...
  71. ncbi Coiled coils: a highly versatile protein folding motif
    P Burkhard
    M E Müller Institute for Structural Biology, Biozentrum, University of Basel, Klingelbergstrasse 70, 4056, Basel, Switzerland
    Trends Cell Biol 11:82-8. 2001
    ..Here we discuss this highly versatile protein folding and oligomerization motif with regard to its structural architecture and how this is related to its biological functions...
  72. ncbi HELANAL: a program to characterize helix geometry in proteins
    M Bansal
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore
    J Biomol Struct Dyn 17:811-9. 2000
    ..In addition to these, the program can also be used to characterise the helix start and end as well as other types of secondary structures...
  73. 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...
  74. 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...
  75. 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
    ....
  76. 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...
  77. 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...
  78. 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...
  79. 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...
  80. ncbi Peptide-based inhibitors of amyloid assembly
    Kimberly L Sciarretta
    The University of Chicago, Department of Pathology, Chicago, IL, USA
    Methods Enzymol 413:273-312. 2006
    ..Finally, we consider potential applications of inhibitor peptides to therapeutic strategies...
  81. ncbi The murine voltage-dependent anion channel gene family. Conserved structure and function
    M J Sampson
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
    J Biol Chem 272:18966-73. 1997
    ..VDAC3, however, is only able to partially complement the mutant phenotype, suggesting an alternative physiologic function for the VDAC3 protein...
  82. ncbi Crystal structure of intact elongation factor EF-Tu from Escherichia coli in GDP conformation at 2.05 A resolution
    H Song
    School of Biochemistry and Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
    J Mol Biol 285:1245-56. 1999
    ..Comparisons of the Mg2+ binding site with other guanine nucleotide binding proteins in GDP-bound forms show that the Mg2+ co-ordination patterns are well preserved among these structures...
  83. ncbi Solution structure of the N-terminal RNP domain of U1A protein: the role of C-terminal residues in structure stability and RNA binding
    J M Avis
    MRC Laboratory of Molecular Biology, Cambridge, UK
    J Mol Biol 257:398-411. 1996
    ..The movement of helix C mainly involves changes in the main-chain torsion angles of Thr89, Asp90 and Ser91, the helix thereby acting as a "lid" over the RNA binding surface...
  84. pmc The structure of the RNA-dependent RNA polymerase from bovine viral diarrhea virus establishes the role of GTP in de novo initiation
    Kyung H Choi
    Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907, USA
    Proc Natl Acad Sci U S A 101:4425-30. 2004
    ..The putative binding sites of previously reported BVDV inhibitors are also discussed...
  85. pmc Structural basis for translational inhibition by the tumour suppressor Pdcd4
    Portia G Loh
    Institute of Molecular and Cell Biology, Proteos, Singapore
    EMBO J 28:274-85. 2009
    ..Our structural and mutational analyses reveal that Pdcd4 inhibits translation initiation by trapping eIF4A in an inactive conformation, and blocking its incorporation into the eIF4F complex...
  86. ncbi Stretching single talin rod molecules activates vinculin binding
    Armando Del Rio
    Department of Biological Sciences, Columbia University, New York, NY 10027, USA
    Science 323:638-41. 2009
    ..Such protein stretching may be a more general mechanism for force transduction...
  87. 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...
  88. 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...
  89. 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...
  90. 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...
  91. 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
    ....
  92. 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...
  93. 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
    ....
  94. 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
    ....
  95. 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
    ....
  96. 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...
  97. 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...
  98. 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...
  99. 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...
  100. 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...
  101. 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
    ....

Research Grants69

  1. Probing the cellular Mechanisms of Transthyretin Cytotoxicity
    Natalia Reixach; Fiscal Year: 2013
    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 ..
  2. HEPATIC BIOSYNTHESIS OF CERULOPLASMIN
    Michael Schilsky; Fiscal Year: 1993
    ..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...
  3. 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 ..
  4. 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. ..
  5. MOLECULAR MECHANISMS OF PACEMAKER CHANNEL FUNCTION
    Michael Sanguinetti; Fiscal Year: 2008
    ..These studies promise to further our understanding of the biological oscillator that controls heart rhythm. ..
  6. Structure and function of antimicrobial peptides
    Ayyalusamy Ramamoorthy; Fiscal Year: 2008
    ..These peptides have therapeutic potential as antibiotics and have particular importance for cystic fibrosis patients. ..
  7. HYBRID HYDROGELS SELF-ASSEMBLED FROM GRAFT COPOLYMERS
    Jindrich Kopecek; Fiscal Year: 2008
    ..In addition, the possibility to join non-compatible materials, such as hydrophobic muscle mimics from liquid crystalline polymers and hydrogels, may open a new field of research. ..
  8. Structure-Function Relationships in Lung Surfactants
    Joanna Long; Fiscal Year: 2008
    ..We will be using novel, sensitive solid state NMR experiments which allow us to determine at atomic resolution these parameters at low concentrations in complex lipid environments. ..
  9. DNA Multiplex Hybridization Kinetics and SNP Assays
    ALBERT BENIGHT; Fiscal Year: 2007
    ..unreadable] [unreadable] [unreadable]..
  10. Structure/Function Studies on Flavoproteins
    Irina Sevrioukova; Fiscal Year: 2007
    ..unreadable] [unreadable]..
  11. MECHANISMS OF CURRENT MODULATION IN CARDIAC MYOCYTES
    DAVID GADSBY; Fiscal Year: 2007
    ..CFTR channels[unreadable] thus offer an opportunity, unprecedented in biology, to examine individual[unreadable] ATP hydrolysis cycles in a single protein molecule, in its natural[unreadable] environment, in real time.[unreadable]..
  12. INHIBITION OF PTH SECRETION: CaR AND THE CYTOSKELETON
    Edward M Brown; Fiscal Year: 2007
    ..Phosphorylation of caveolin-1 under high Ca 2+ conditions may anchor the CaR-PTH unit to the plasma membrane, limiting PTH secretion. ..
  13. CA2+-RECEPTOR: IMMUNE MODULATION IN VIVO AND IN VITRO
    Edward M Brown; Fiscal Year: 2007
    ..3) To develop an animal model of activating and/or inactivating antibodies by immunization with the CaR's extracellular domain. [unreadable] [unreadable]..
  14. Purchase of a 500 MHz Solid State NMR Spectrometer
    Ayyalusamy Ramamoorthy; Fiscal Year: 2007
    ..unreadable] [unreadable] All the major users of the instrument are supported by NIH R01 grants. [unreadable] [unreadable] [unreadable]..
  15. ApoA1 Determining HDL Subclasses and Atherosclerosis
    GODFREY GETZ; Fiscal Year: 2006
    ..The final specific aim will examine how the mutants or the engineered HDLs generated in vivo interact with enzymes and receptors that are involved in HDL remodeling and cholesterol efflux. ..
  16. Biochemical Studies of Worm Insulins
    Michael Weiss; Fiscal Year: 2006
    ..abstract_text> ..
  17. ABCA1 agonist peptides for therapeutic use
    JOHN BIELICKI; Fiscal Year: 2008
    ..The research is likely to have a high impact on public health, since the therapeutics will be amenable to the widespread treatment of atherosclerosis. [unreadable] [unreadable] [unreadable] [unreadable]..
  18. Lipid mediators of inflammation and insulin resistance in adipocytes and adipose
    Andisheh Abedini; Fiscal Year: 2007
    ..unreadable] [unreadable] [unreadable] [unreadable]..
  19. Structural studies on the Initiator protein, IBP39.
    Maria Schumacher; Fiscal Year: 2008
    ..vaginalis suggests it is a possible target for the treatment of trichomoniasis, which afflicts over 170 million individuals each _,ear, ..
  20. Structural mechanism of DNA segregation by the pSK41 par system
    Maria Schumacher; Fiscal Year: 2010
    ..Thus, understanding the structural basis for DNA segregation by this par system will provide several points of potential therapeutic intervention against pSK41 harboring multidrug resistant S. aureus strains. ..
  21. Structure Function Studies of DNA Mismatch Repair
    Dorothy A Erie; Fiscal Year: 2010
    ....
  22. Chemical Models of Protein beta-Sheet Interactions
    James Nowick; Fiscal Year: 2009
    ..These insights and new compounds may eventually pave the way to new drugs to treat diseases and improve human health. ..
  23. STRUCTURE AND FUNCTION OF THE GLUCOSE TRANSPORTER
    Mike M Mueckler; Fiscal Year: 2010
    ..This aim will be conducted in collaboration with Dr. Da-Neng Wang at NYU. ..
  24. LIPID MODULATION OF RHODOPSIN SIGNALING IN MEMBRANES
    Michael F Brown; Fiscal Year: 2010
    ..This work is pertinent to the role of polyunsaturated lipids in the function and dysfunction of central nervous system of humans with attendant insights that may be of eventual therapeutic benefit. ..
  25. A POLYMERIC DRUG DELIVERY SYSTEM FOR CANCER THERAPY
    JINDRICH H KOPECEK; Fiscal Year: 2010
    ..The concept of double-targeted macromolecular therapeutics provides a new paradigm for the design of efficient anticancer drugs for the treatment of ovarian cancer. ..
  26. Peptide-amphiphile biomimetics for targeted therapies
    GREGG FIELDS; Fiscal Year: 2008
    ..The selectivity of peptideamphiphile colloidal delivery vehicles will be analyzed using metastatic melanoma cells and other cell types (fibroblasts, endothelial cells) found in the melanoma microenvironment. ..
  27. Lymphotoxin/LIGHT in Lipoprotein Metabolism and Atherosclerosis
    GODFREY GETZ; Fiscal Year: 2009
    ..These studies will further our understanding of how the immune system influences these processes and may point to potential sites for therapeutic intervention. ..
  28. Amyloid beta Peptide and Apolipoprotein E
    Thomas Wisniewski; Fiscal Year: 2009
    ..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. ..
  29. Insulin Formulations of Enhanced Stability
    Michael Weiss; Fiscal Year: 2009
    ..Accordingly, our strategy may generalize to enhance the utility of diverse protein pharmaceuticals in the post-genomic era. ..
  30. LIGAND PHARMACOLOGY OF ESTROGEN RECEPTORS
    Thomas Scanlan; Fiscal Year: 2008
    ..unreadable] [unreadable]..
  31. TRAINING IN MOLECULAR NEUROBIOLOGY
    William Catterall; Fiscal Year: 2008
    ..The training program will integrate the substantial expertise of this group of faculty in a coordinated pre-doctoral and post-doctoral training effort. ..
  32. Protein interactions underlying actin-based motility
    David Sept; Fiscal Year: 2006
    ..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. ..
  33. REGULATION OF CONTRACTION IN MUSCLE AND NONMUSCLE CELLS
    Sarah Hitchcock DeGregori; Fiscal Year: 2006
    ..unreadable] [unreadable]..
  34. DEGRADABLE HYDROGELS FOR ORAL DELIVERY OF CALCITONIN
    Jindrich Kopecek; Fiscal Year: 2003
    ..Based on in vivo animal data criteria will be studied. Based on in vivo animal data criteria will be established for the design of an oral hCT and CKI delivery system for the treatment of postmenopausal osteoporosis. ..
  35. FOLDING OF THE INTRACELLULAR LIPID-BINDING PROTEINS
    Ira Ropson; Fiscal Year: 2003
    ..Single-site mutant proteins will be generated and studied for their effects on the transition state in protein folding. ..
  36. OPTICAL PROPERTIES OF BIOLOGICAL MACROMOLECULES
    ROBERT WOODY; Fiscal Year: 2003
    ..Models of multi-heme proteins obtained by protein design (maquettes) will be studied experimentally and theoretically. ..
  37. Proteomics Reagents in Diabetes & Metabolism
    Michael Weiss; Fiscal Year: 2003
    ..The proposed pilot studies will dissect an insulin signaling pathway in a genetic model of senescence and aging (Aim 1) and a novel mechanism of metabolic homeostasis and insulin resistance in human obesity. ..
  38. PRESERVATION OF HDL FUNCTION DURING EARLY ATHEROGENESIS
    JOHN BIELICKI; Fiscal Year: 2002
    ..Moreover, the research will uncover novel mechanisms for preserving HDL/LCAT function that can be utilized therapeutically to fight the onset of cardiovascular disease. ..
  39. CALCIUM DEPENDENT MEMBRANE BINDING PROTEINS
    CARL CREUTZ; Fiscal Year: 2002
    ....
  40. COLLAGEN STRUCTURAL MODULATION OF TUMOR BEHAVIORS
    GREGG FIELDS; Fiscal Year: 2002
    ..The manner in which the protein three-dimensional structure impacts protein-protein interactions, such as receptor binding to ligand, and subsequent signaling activities will also be better understood. ..
  41. VASCULAR SMOOTH MUSCLE GROWTH AND FIBRONECTIN MATRIX
    GODFREY GETZ; Fiscal Year: 2002
    ..By understanding the role of the ECM in pathological processes such as restenosis and atherosclerosis we may begin to design more effective treatments for these conditions. ..
  42. OPTICAL PROPERTIES OF BIOLOGICAL MACROMOLECULES
    ROBERT WOODY; Fiscal Year: 2002
    ..Models of multi-heme proteins obtained by protein design (maquettes) will be studied experimentally and theoretically. ..
  43. Ultra-shielded 600 MHz NMR spectrometer with a cryprobe
    Michael Weiss; Fiscal Year: 2002
    ..It will not only make an impact on research projects of Cleveland structural biology community but also create an active core of NMR structural biology experts trained in the most current and sophisticated techniques. ..
  44. APOPROTEIN E AND NEURITE OUTGROWTH
    GODFREY GETZ; Fiscal Year: 2001
    ..These results should provide important information about the physiological role of apoE in neuronal growth and differentiation. ..
  45. TISSUE ENGINEERING USING PEPTIDE AMPHIPHILE BIOMIMETICS
    GREGG FIELDS; Fiscal Year: 2001
    ..For building materials with molecular and cellular recognition capacity, these PAs may provide an important approach for producing characteristic structures at surfaces and interfaces. ..
  46. BIOPHYSICAL AND SCANNING FORCE MICROSCOPY STUDIES
    DOROTHY ERIE; Fiscal Year: 2001
    ..3) How do polymorphisms affect the above properties? ..
  47. TRANSCRIPTION RELATED STRUCTURAL MODULES
    Michael Weiss; Fiscal Year: 2001
    ..The systems under study are of broad biological interest with application to cancer biology and AIDS. ..
  48. ANNEXIN PHOSPHORYLATION: CAUSES AND CONSEQUENCES
    CARL CREUTZ; Fiscal Year: 2004
    ....
  49. CA2+ RECEPTOR, PTHRP & MALIGNANCY-INDUCED OSTEOLYSIS
    Edward M Brown; Fiscal Year: 2004
    ..abstract_text> ..
  50. Concerted membrane diffraction and simulation studies
    Stephen White; Fiscal Year: 2006
    ..unreadable] [unreadable]..
  51. Selective Induction of Estrogen Conjugative Metabolism
    Bao Ting Zhu; Fiscal Year: 2006
    ..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. ..
  52. VIRUS CHROMOSOME STRUCTURE: ROLE IN DEVELOPMENT
    Michael Feiss; Fiscal Year: 2005
    ..We will also look at the ability of terminase to move DNA, and to pursue a structural analysis of functional domains of terminase. ..
  53. ApoA-I Helical Domains and Cardiovascular Aging
    JOHN BIELICKI; Fiscal Year: 2005
    ..These studies are relevant for devising novel strategies to combat cardiovascular aging. ..
  54. Advanced Sequence-Based Prediction of Protein Function
    ANDREW NEUWALD; Fiscal Year: 2005
    ..abstract_text> ..
  55. MARINER TRANSPOSONS OF MAMMALS
    Hugh Robertson; Fiscal Year: 2001
    ..It will also reveal how occasionally particular copies of transposons can become integral parts of their host genetic complements. ..
  56. FLUID BILAYER INTERACTIONS WITH PEPTIDES
    Stephen White; Fiscal Year: 2004
    ..5) Expand and improve physicochemical rules for predicting the binding and folding of peptides at membrane interfaces, and establish a structural context for them. ..
  57. PROTEIN FOLDING AND MISFOLDING
    Michael Weiss; Fiscal Year: 2003
    ..This differential property is the basis on which Dr. Weiss proposes to identify factors responsible for on-pathway and off-pathway oxidative folding. ..
  58. Kinetic Studies of Transcription Elongation
    DOROTHY ERIE; Fiscal Year: 2005
    ..Accordingly, we will use this information to begin to understand, at the amino acid level, the role of NTP binding and conformational transitions in the regulation of elongation. ..
  59. 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. ..
  60. Biomolecular Analysis of Proteins in Visual Disease
    ESTHER BISWAS FISS; Fiscal Year: 2007
    ..unreadable] [unreadable] [unreadable]..
  61. CALCIUM RECEPTOR SIGNAL RECOGNITION AND TRANSDUCTION
    Edward M Brown; Fiscal Year: 2006
    ..abstract_text> ..
  62. 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. ..
  63. 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. ..
  64. 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. ..
  65. X-ray diffraction analysis of human adenovirus
    Vijay Reddy; Fiscal Year: 2006
    ..et al. Science 309: 1090-1092, 2005). [unreadable] [unreadable] [unreadable]..
  66. 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. ..
  67. Determinants of Folding Mechanism in Small Proteins
    Ray Luo; Fiscal Year: 2008
    ..unreadable] [unreadable]..
  68. Transcriptional Regulation of a Surfactant Enzyme
    RAMA MALLAMPALLI; Fiscal Year: 2005
    ..Ultimately, the results from these studies could lead to therapeutic strategies directed at modulating expression of this key surfactant enzyme at the molecular level. ..
  69. Hydrophobics transport across the outer membrane
    Bert van den Berg; Fiscal Year: 2009
    ..These structures will also allow us to determine whether mechanistic differences exist between LCFA and xenobiotics transport. ..