tertiary protein structure

Summary

Summary: The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.

Top Publications

  1. ncbi Integrins: bidirectional, allosteric signaling machines
    Richard O Hynes
    Howard Hughes Medical Institute, Center for Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Cell 110:673-87. 2002
  2. ncbi Translating the histone code
    T Jenuwein
    Research Institute of Molecular Pathology IMP at the Vienna Biocenter, Dr Bohrgasse 7, A 1030 Vienna, Austria
    Science 293:1074-80. 2001
  3. ncbi The protein kinase complement of the human genome
    G Manning
    SUGEN Inc, 230 East Grand Avenue, South San Francisco, CA 94080, USA
    Science 298:1912-34. 2002
  4. ncbi Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure
    J Gough
    Laboratory of Molecular Biology, MRC, Hills Road, Cambridge, CB2 2QH, UK
    J Mol Biol 313:903-19. 2001
  5. ncbi PRODRG: a tool for high-throughput crystallography of protein-ligand complexes
    Alexander W Schuttelkopf
    Division of Biological Chemistry and Molecular Microbiology, Wellcome Trust Biocentre, School of Life Sciences, University of Dundee, Dow Street, DD1 5EH, Scotland
    Acta Crystallogr D Biol Crystallogr 60:1355-63. 2004
  6. ncbi Systematic functional analysis of the Caenorhabditis elegans genome using RNAi
    Ravi S Kamath
    Wellcome Trust Cancer Research UK Institute and Department of Genetics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
    Nature 421:231-7. 2003
  7. pmc ESPript/ENDscript: Extracting and rendering sequence and 3D information from atomic structures of proteins
    Patrice Gouet
    Laboratoire de BioCristallographie, IBCP CNRS UMR 5086 UCBL, 7 passage du Vercors, 69367 Lyon Cedex 07, France
    Nucleic Acids Res 31:3320-3. 2003
  8. ncbi The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)
    G A Tuskan
    Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
    Science 313:1596-604. 2006
  9. ncbi Signals for sorting of transmembrane proteins to endosomes and lysosomes
    Juan S Bonifacino
    Cell Biology and Metabolism Branch, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
    Annu Rev Biochem 72:395-447. 2003
  10. ncbi The RNA helicase RIG-I has an essential function in double-stranded RNA-induced innate antiviral responses
    Mitsutoshi Yoneyama
    Department of Tumor Cell Biology, Tokyo Metropolitan Institute of Medical Science, Tokyo Metropolitan Organization for Medical Research, 3 18 22 Honkomagome, Bunkyo ku, Tokyo 113 8613, Japan
    Nat Immunol 5:730-7. 2004

Detail Information

Publications291 found, 100 shown here

  1. ncbi Integrins: bidirectional, allosteric signaling machines
    Richard O Hynes
    Howard Hughes Medical Institute, Center for Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Cell 110:673-87. 2002
    ..Long-range conformational changes couple these functions via allosteric equilibria...
  2. ncbi Translating the histone code
    T Jenuwein
    Research Institute of Molecular Pathology IMP at the Vienna Biocenter, Dr Bohrgasse 7, A 1030 Vienna, Austria
    Science 293:1074-80. 2001
    ....
  3. ncbi The protein kinase complement of the human genome
    G Manning
    SUGEN Inc, 230 East Grand Avenue, South San Francisco, CA 94080, USA
    Science 298:1912-34. 2002
    ..We also identified 106 protein kinase pseudogenes. Chromosomal mapping revealed several small clusters of kinase genes and revealed that 244 kinases map to disease loci or cancer amplicons...
  4. ncbi Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure
    J Gough
    Laboratory of Molecular Biology, MRC, Hills Road, Cambridge, CB2 2QH, UK
    J Mol Biol 313:903-19. 2001
    ..The annotations derived from these matches are available from a public web server at: http://stash.mrc-lmb.cam.ac.uk/SUPERFAMILY. This server also enables users to match their own sequences against the SUPERFAMILY model library...
  5. ncbi PRODRG: a tool for high-throughput crystallography of protein-ligand complexes
    Alexander W Schuttelkopf
    Division of Biological Chemistry and Molecular Microbiology, Wellcome Trust Biocentre, School of Life Sciences, University of Dundee, Dow Street, DD1 5EH, Scotland
    Acta Crystallogr D Biol Crystallogr 60:1355-63. 2004
    ..However, tests with distorted starting coordinates show that PRODRG topologies perform better, both in terms of ligand geometry and of crystallographic R factors...
  6. ncbi Systematic functional analysis of the Caenorhabditis elegans genome using RNAi
    Ravi S Kamath
    Wellcome Trust Cancer Research UK Institute and Department of Genetics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
    Nature 421:231-7. 2003
    ..Our resulting data set and reusable RNAi library of 16,757 bacterial clones will facilitate systematic analyses of the connections among gene sequence, chromosomal location and gene function in C. elegans...
  7. pmc ESPript/ENDscript: Extracting and rendering sequence and 3D information from atomic structures of proteins
    Patrice Gouet
    Laboratoire de BioCristallographie, IBCP CNRS UMR 5086 UCBL, 7 passage du Vercors, 69367 Lyon Cedex 07, France
    Nucleic Acids Res 31:3320-3. 2003
    ..ESPript and ENDscript are available at http://genopole.toulouse.inra.fr/ESPript...
  8. ncbi The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)
    G A Tuskan
    Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
    Science 313:1596-604. 2006
    ..Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport...
  9. ncbi Signals for sorting of transmembrane proteins to endosomes and lysosomes
    Juan S Bonifacino
    Cell Biology and Metabolism Branch, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
    Annu Rev Biochem 72:395-447. 2003
    ..This complex array of signals and recognition proteins ensures the dynamic but accurate distribution of transmembrane proteins to different compartments of the endosomal-lysosomal system...
  10. ncbi The RNA helicase RIG-I has an essential function in double-stranded RNA-induced innate antiviral responses
    Mitsutoshi Yoneyama
    Department of Tumor Cell Biology, Tokyo Metropolitan Institute of Medical Science, Tokyo Metropolitan Organization for Medical Research, 3 18 22 Honkomagome, Bunkyo ku, Tokyo 113 8613, Japan
    Nat Immunol 5:730-7. 2004
    ..Subsequent gene activation by these factors induced antiviral functions, including type I interferon production. Thus, RIG-I is key in the detection and subsequent eradication of the replicating viral genomes...
  11. ncbi Scoring function for automated assessment of protein structure template quality
    Yang Zhang
    Center of Excellence in Bioinformatics, University at Buffalo, Buffalo, New York 14203, USA
    Proteins 57:702-10. 2004
    ..These data suggest that the TM-score is a useful complement to the fully automated assessment of protein structure predictions. The executable program of TM-score is freely downloadable at http://bioinformatics.buffalo.edu/TM-score...
  12. ncbi Cellular motility driven by assembly and disassembly of actin filaments
    Thomas D Pollard
    Department of Cellular, Molecular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
    Cell 112:453-65. 2003
    ..Profilin catalyzes the exchange of ADP for ATP, refilling the pool of ATP-actin monomers bound to profilin, ready for elongation...
  13. ncbi An allosteric mechanism for activation of the kinase domain of epidermal growth factor receptor
    Xuewu Zhang
    Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, 94720, USA
    Cell 125:1137-49. 2006
    ..The CDK/cyclin-like complex formed by two kinase domains thus explains the activation of EGFR-family receptors by homo- or heterodimerization...
  14. ncbi GEF means go: turning on RHO GTPases with guanine nucleotide-exchange factors
    Kent L Rossman
    Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
    Nat Rev Mol Cell Biol 6:167-80. 2005
    ..The failure to do so can have significant consequences and is reflected in the aberrant function of Dbl-family GEFs in some human diseases...
  15. ncbi Intrinsically unstructured proteins and their functions
    H Jane Dyson
    Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
    Nat Rev Mol Cell Biol 6:197-208. 2005
    ..Many disordered segments fold on binding to their biological targets (coupled folding and binding), whereas others constitute flexible linkers that have a role in the assembly of macromolecular arrays...
  16. ncbi The genome sequence of Schizosaccharomyces pombe
    V Wood
    The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nature 415:871-80. 2002
    ....
  17. ncbi Cardif is an adaptor protein in the RIG-I antiviral pathway and is targeted by hepatitis C virus
    Etienne Meylan
    Department of Biochemistry, University of Lausanne, BIL Biomedical Research Center, Chemin des Boveresses 155, CH 1066 Epalinges, Switzerland
    Nature 437:1167-72. 2005
    ..Cardif thus functions as an adaptor, linking the cytoplasmic dsRNA receptor RIG-I to the initiation of antiviral programmes...
  18. pmc MEME: discovering and analyzing DNA and protein sequence motifs
    Timothy L Bailey
    Institute of Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
    Nucleic Acids Res 34:W369-73. 2006
    ..This article describes the freely accessible web server and its architecture, and discusses ways to use MEME effectively to find new sequence patterns in biological sequences and analyze their significance...
  19. ncbi Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites
    Alasdair T R Laurie
    School of Biochemistry and Microbiology, University of Leeds, UK
    Bioinformatics 21:1908-16. 2005
    ..Energetically favourable probe sites are clustered according to their spatial proximity and clusters are then ranked according to the sum of interaction energies for sites within each cluster...
  20. ncbi EGFR mutations in lung cancer: correlation with clinical response to gefitinib therapy
    J Guillermo Paez
    Departments of Medical Oncology and Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02115, USA
    Science 304:1497-500. 2004
    ..These results suggest that EGFR mutations may predict sensitivity to gefitinib...
  21. ncbi Structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF ubiquitin ligase complex
    Ning Zheng
    Cellular Biochemistry and Biophysics Program, Memorial Sloan Kettering Cancer Center, New York 10021, USA
    Nature 416:703-9. 2002
    ..The structure suggests that Cul1 may contribute to catalysis through the positioning of the substrate and the ubiquitin-conjugating enzyme, and this model is supported by Cul1 mutations designed to eliminate the rigidity of the scaffold...
  22. ncbi Membrane recognition by phospholipid-binding domains
    Mark A Lemmon
    Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, 809C Stellar Chance Laboratories, 422 Curie Boulevard, Philadelphia, Pennsylvania 19104 6059, USA
    Nat Rev Mol Cell Biol 9:99-111. 2008
    ..A full appreciation of these processes is crucial for understanding how protein localization and membrane topography and trafficking are regulated in cells...
  23. ncbi Role for a bidentate ribonuclease in the initiation step of RNA interference
    E Bernstein
    Cold Spring Harbor Laboratory, New York 11724, USA
    Nature 409:363-6. 2001
    ..The enzyme has a distinctive structure, which includes a helicase domain and dual RNase III motifs. Dicer also contains a region of homology to the RDE1/QDE2/ARGONAUTE family that has been genetically linked to RNAi...
  24. ncbi Modeller: generation and refinement of homology-based protein structure models
    Andras Fiser
    Department of Biochemistry and Seaver Foundation Center for Bioinformatics, Albert Einstein College of Medicine, Bronz, New York 10461, USA
    Methods Enzymol 374:461-91. 2003
  25. ncbi AIP1/ALIX is a binding partner for HIV-1 p6 and EIAV p9 functioning in virus budding
    Bettina Strack
    Department of Cancer Immunology and AIDS, Dana Farber Cancer Institute and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
    Cell 114:689-99. 2003
    ..These observations identify AIP1 as a component of the viral budding machinery, which serves to link a distinct region in the L domain of HIV-1 p6 and EIAV p9 to ESCRT-III...
  26. pmc SETDB1: a novel KAP-1-associated histone H3, lysine 9-specific methyltransferase that contributes to HP1-mediated silencing of euchromatic genes by KRAB zinc-finger proteins
    David C Schultz
    The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
    Genes Dev 16:919-32. 2002
    ..Thus, KAP-1 is a molecular scaffold that is targeted by KRAB-ZFPs to specific loci and coordinates both histone methylation and the deposition of HP1 proteins to silence gene expression...
  27. pmc Data growth and its impact on the SCOP database: new developments
    Antonina Andreeva
    MRC Centre for Protein Engineering, Hills Road, Cambridge CB2 0QH, UK
    Nucleic Acids Res 36:D419-25. 2008
    ..SCOP can be accessed at http://scop.mrc-lmb.cam.ac.uk/scop...
  28. ncbi Shelterin: the protein complex that shapes and safeguards human telomeres
    Titia de Lange
    The Rockefeller University, New York, New York 10021, USA
    Genes Dev 19:2100-10. 2005
    ..Six shelterin subunits: TRF1, TRF2, TIN2, Rap1, TPP1, and POT1...
  29. pmc Carbohydrate-binding modules: fine-tuning polysaccharide recognition
    Alisdair B Boraston
    Biochemistry and Microbiology, University of Victoria, PO Box 3055 STN CSC, Victoria, BC, Canada V8W 3P6
    Biochem J 382:769-81. 2004
    ..The present review summarizes the impact structural biology has had on our understanding of the mechanisms by which CBMs bind to their target ligands...
  30. ncbi Activating mutations of NOTCH1 in human T cell acute lymphoblastic leukemia
    Andrew P Weng
    Department of Pathology, Brigham and Women s Hospital, Harvard Medical School, Boston, MA 02115, USA
    Science 306:269-71. 2004
    ..These findings greatly expand the role of activated NOTCH1 in the molecular pathogenesis of human T-ALL and provide a strong rationale for targeted therapies that interfere with NOTCH signaling...
  31. ncbi FOXP3 controls regulatory T cell function through cooperation with NFAT
    Yongqing Wu
    Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO 80309, USA
    Cell 126:375-87. 2006
    ..Thus by switching transcriptional partners, NFAT converts the acute T cell activation program into the suppressor program of Tregs...
  32. 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...
  33. ncbi Structure of the guide-strand-containing argonaute silencing complex
    Yanli Wang
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
    Nature 456:209-13. 2008
    ....
  34. pmc InterProScan: protein domains identifier
    E Quevillon
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 33:W116-20. 2005
    ..O'Reilly Publishers, Sebastopol, CA, http://www.w3.org/TR/soap/] are also available to the users. Various output formats are supported and include text tables, XML documents, as well as various graphs to help interpret the results...
  35. ncbi Structure of the dengue virus envelope protein after membrane fusion
    Yorgo Modis
    Howard Hughes Medical Institute, Children s Hospital and Harvard Medical School, 320 Longwood Avenue, Boston, Massachusetts 02115, USA
    Nature 427:313-9. 2004
    ..Specific features of the folded-back structure suggest strategies for inhibiting flavivirus entry...
  36. ncbi Mutations of the BRAF gene in human cancer
    Helen Davies
    Cancer Genome Project, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK
    Nature 417:949-54. 2002
    ..As BRAF is a serine/threonine kinase that is commonly activated by somatic point mutation in human cancer, it may provide new therapeutic opportunities in malignant melanoma...
  37. ncbi Function and regulation of cullin-RING ubiquitin ligases
    Matthew D Petroski
    Division of Biology and Howard Hughes Medical Institute, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, USA
    Nat Rev Mol Cell Biol 6:9-20. 2005
    ..In this review, we focus on the composition, regulation and function of cullin-RING ligases, and describe how these enzymes can be characterized by a set of general principles...
  38. ncbi Crystal structure of the TLR1-TLR2 heterodimer induced by binding of a tri-acylated lipopeptide
    Mi Sun Jin
    Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejon, Korea 305 701
    Cell 130:1071-82. 2007
    ..We propose that formation of the TLR1-TLR2 heterodimer brings the intracellular TIR domains close to each other to promote dimerization and initiate signaling...
  39. ncbi DNA damage-induced phosphorylation of p53 alleviates inhibition by MDM2
    S Y Shieh
    Department of Biological Sciences, Columbia University, New York, New York 10027, USA
    Cell 91:325-34. 1997
    ..Our studies provide a plausible mechanism by which the induction of p53 can be modulated by DNA-PK (or other protein kinases with similar specificity) in response to DNA damage...
  40. pmc Molecular dynamics and protein function
    M Karplus
    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
    Proc Natl Acad Sci U S A 102:6679-85. 2005
    ..We also describe results for the F(1) ATPase molecular motor and the Src family of signaling proteins as examples of applications of simulations to specific biological systems...
  41. ncbi IPS-1, an adaptor triggering RIG-I- and Mda5-mediated type I interferon induction
    Taro Kawai
    Exploratory Research for Advanced Technology, Japan Science and Technology Agency
    Nat Immunol 6:981-8. 2005
    ..Knockdown' of IPS-1 by small interfering RNA blocked interferon induction by virus infection. Thus, IPS-1 is an adaptor involved in RIG-I- and Mda5-mediated antiviral immune responses...
  42. ncbi GPCR engineering yields high-resolution structural insights into beta2-adrenergic receptor function
    Daniel M Rosenbaum
    Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
    Science 318:1266-73. 2007
    ..Amino acids known to regulate receptor function are linked through packing interactions and a network of hydrogen bonds, suggesting a conformational pathway from the ligand-binding pocket to regions that interact with G proteins...
  43. pmc SMART 6: recent updates and new developments
    Ivica Letunic
    EMBL, Meyerhofstrasse 1, 69012 Heidelberg, Germany
    Nucleic Acids Res 37:D229-32. 2009
    ..In addition to the standard web access to the database, users can now query SMART using distributed annotation system (DAS) or through a simple object access protocol (SOAP) based web service...
  44. ncbi Methylated lysine 79 of histone H3 targets 53BP1 to DNA double-strand breaks
    Yentram Huyen
    Wistar Institute, Philadelphia, Pennsylvania 19104 4268, USA
    Nature 432:406-11. 2004
    ..Because methylation of histone H3 Lys 79 was unaltered in response to DNA damage, we propose that 53BP1 senses DSBs indirectly through changes in higher-order chromatin structure that expose the 53BP1 binding site...
  45. ncbi Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa
    Toru Sengoku
    Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7 3 1 Hongo, Tokyo 113 0033, Japan
    Cell 125:287-300. 2006
    ..This mechanism, which differs from those for canonical translocating helicases, may enable the targeted modulation of intricate RNA structures...
  46. pmc Structural basis of integrin regulation and signaling
    Bing Hao Luo
    The CBR Institute for Biomedical Research, Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA
    Annu Rev Immunol 25:619-47. 2007
    ..In this review, we focus on integrin structure as it relates to affinity modulation, ligand binding, outside-in signaling, and cell surface distribution dynamics...
  47. pmc The Pfam protein families database
    Alex Bateman
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nucleic Acids Res 32:D138-41. 2004
    ..Pfam is available on the web in the UK (http://www.sanger.ac.uk/Software/Pfam/), the USA (http://pfam.wustl.edu/), France (http://pfam.jouy.inra.fr/) and Sweden (http://Pfam.cgb.ki.se/)...
  48. ncbi The importance of being proline: the interaction of proline-rich motifs in signaling proteins with their cognate domains
    B K Kay
    Department of Pharmacology, University of Wisconsin Madison, Madison, Wisconsin 53706 1532, USA
    FASEB J 14:231-41. 2000
    ..Kay, B. K., Williamson, M. P., Sudol, M. The importance of being proline: the interaction of proline-rich motifs in signaling proteins with their cognate domains...
  49. ncbi The transcriptional coactivators p300 and CBP are histone acetyltransferases
    V V Ogryzko
    Laboratory of Molecular Growth Regulation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892 2753, USA
    Cell 87:953-9. 1996
    ..p300/CBP acetylates all four core histones in nucleosomes. These observations suggest that p300/CBP acetylates nucleosomes in concert with PCAF...
  50. pmc Structural classification of zinc fingers: survey and summary
    S Sri Krishna
    Department of Biochemistry, University of Texas, Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390 9050, USA
    Nucleic Acids Res 31:532-50. 2003
    ..The classification helps in understanding the relationship between the structure, function and evolutionary history of these domains. The results are available as an online database of zinc finger structures...
  51. ncbi A structural perspective of the flavivirus life cycle
    Suchetana Mukhopadhyay
    Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, Indiana 47907 2054, USA
    Nat Rev Microbiol 3:13-22. 2005
    ..This review focuses mainly on structural studies of dengue virus...
  52. ncbi R2D2, a bridge between the initiation and effector steps of the Drosophila RNAi pathway
    Qinghua Liu
    Howard Hughes Medical Institute and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
    Science 301:1921-5. 2003
    ..These results indicate that R2D2 bridges the initiation and effector steps of the Drosophila RNAi pathway by facilitating siRNA passage from Dicer to RISC...
  53. pmc Protein structure prediction and analysis using the Robetta server
    David E Kim
    Structural Genomics of Pathogenic Protozoa, Department of Biochemistry, University of Washington, Seattle WA 98195, USA
    Nucleic Acids Res 32:W526-31. 2004
    ..The Rosetta protein design and protein-protein docking methodologies will soon be available through the server as well...
  54. ncbi Fuzzy complexes: polymorphism and structural disorder in protein-protein interactions
    Peter Tompa
    Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Budapest, Hungary
    Trends Biochem Sci 33:2-8. 2008
    ..Given the crucial role of protein disorder in protein-protein interactions and in regulatory processes, we envision that fuzziness will become integral to understanding the interactome...
  55. ncbi FAK integrates growth-factor and integrin signals to promote cell migration
    D J Sieg
    Department of Immunology, The Scripps Research Institute, La Jolla, CA 92037, USA
    Nat Cell Biol 2:249-56. 2000
    ..Our results establish that FAK is an important receptor-proximal link between growth-factor-receptor and integrin signalling pathways...
  56. ncbi Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 A resolution
    Dmitry G Vassylyev
    Cellular Signaling Laboratory, RIKEN Harima Institute at SPring 8, 1 1 1 Kouto, Mikazuki cho, Sayo, Hyogo 679 5148, Japan
    Nature 417:712-9. 2002
    ..The holoenzyme structure provides insight into the structural organization of transcription intermediate complexes and into the mechanism of transcription initiation...
  57. pmc Diversity and complexity in DNA recognition by transcription factors
    Gwenael Badis
    Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada
    Science 324:1720-3. 2009
    ..This complexity in DNA recognition may be important in gene regulation and in the evolution of transcriptional regulatory networks...
  58. ncbi Double chromodomains cooperate to recognize the methylated histone H3 tail
    John F Flanagan
    Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia 22908, USA
    Nature 438:1181-5. 2005
    ..Furthermore, unique inserts within chromodomain 1 of CHD1 block the expected site of H3 tail binding seen in HP1 and Polycomb, instead directing H3 binding to a groove at the inter-chromodomain junction...
  59. ncbi The DEAD-box protein family of RNA helicases
    Olivier Cordin
    Département de Microbiologie et Médecine Moléculaire, Centre Medical Universitaire, 1 rue Michel Servet, 1211, Geneve 4, Switzerland
    Gene 367:17-37. 2006
    ..This review will focus on the description of the molecular characteristics of members of the DEAD-box protein family and on the enzymatic activities they possess...
  60. pmc Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs
    John C Obenauer
    Center for Cancer Research, E18 580, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
    Nucleic Acids Res 31:3635-41. 2003
    ..In addition, a new series of Sequence Match programs for non-quantitative user-defined motifs has been implemented. Scansite is available via the World Wide Web at http://scansite.mit.edu...
  61. ncbi The SRA protein Np95 mediates epigenetic inheritance by recruiting Dnmt1 to methylated DNA
    Jafar Sharif
    Tohoku University Biomedical Engineering Research Organization TUBERO, 2 1 Seiryo machi, Aoba ku, Sendai 980 8575, Japan
    Nature 450:908-12. 2007
    ..The link between hemi-methylated DNA, Np95 and Dnmt1 thus establishes key steps of the mechanism for epigenetic inheritance of DNA methylation...
  62. pmc Edc3p and a glutamine/asparagine-rich domain of Lsm4p function in processing body assembly in Saccharomyces cerevisiae
    Carolyn J Decker
    Department of Molecular and Cellular Biology and Howard Hughes Medical Institute, University of Arizona, Tucson, AZ 85721
    J Cell Biol 179:437-49. 2007
    ..These results suggest a stepwise model for P-body assembly with the initial formation of a core mRNA-protein complex that then aggregates through multiple specific mechanisms...
  63. ncbi DNA-binding specificity of the ERF/AP2 domain of Arabidopsis DREBs, transcription factors involved in dehydration- and cold-inducible gene expression
    Yoh Sakuma
    Biological Resources Division, Japan International Research Center for Agricultural Sciences JIRCAS, 1 1 Ohwashi, Tsukuba, Ibaraki, 305 8686, Japan
    Biochem Biophys Res Commun 290:998-1009. 2002
    ..The DREB subfamily included three novel DREB1A- and six DREB2A-related proteins. We analyzed expression of novel genes for these proteins and discuss their roles in stress-responsive gene expression...
  64. pmc The CATH classification revisited--architectures reviewed and new ways to characterize structural divergence in superfamilies
    Alison L Cuff
    Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
    Nucleic Acids Res 37:D310-4. 2009
    ..Information on the degree of structural diversity in each superfamily and structural overlaps between superfamilies can now be downloaded from the CATH website...
  65. ncbi JmjC-domain-containing proteins and histone demethylation
    Robert J Klose
    Howard Hughes Medical Institute, Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599 7295, USA
    Nat Rev Genet 7:715-27. 2006
    ..Here we analyse the evolutionary relationship between Jumonji C (JmjC)-domain-containing proteins and discuss their cellular functions in relation to their potential enzymatic activities...
  66. ncbi Fibronectin at a glance
    Roumen Pankov
    Craniofacial Developmental Biology and Regeneration Branch, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA
    J Cell Sci 115:3861-3. 2002
  67. ncbi Purified Argonaute2 and an siRNA form recombinant human RISC
    Fabiola V Rivas
    Cold Spring Harbor Laboratory, Watson School of Biological Sciences, New York 11724, USA
    Nat Struct Mol Biol 12:340-9. 2005
    ..These studies demonstrate that Argonaute proteins catalyze mRNA cleavage within RISC and provide a source of recombinant enzyme for detailed biochemical studies of the RNAi effector complex...
  68. ncbi Refined structure of the nicotinic acetylcholine receptor at 4A resolution
    Nigel Unwin
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
    J Mol Biol 346:967-89. 2005
    ..Access to the pore on the intracellular side is further influenced by narrow lateral windows, which would be expected to screen out electrostatically ions of the wrong charge and size...
  69. ncbi Prions affect the appearance of other prions: the story of [PIN(+)]
    I L Derkatch
    Laboratory for Molecular Biology, Department of Biological Sciences, University of Illinois at Chicago, 900 South Ashland Avenue, Chicago, IL 60607, USA
    Cell 106:171-82. 2001
    ..Importantly, the de novo appearance of Rnq1::GFP prion aggregates also requires the presence of other prions, suggesting the existence of a general mechanism by which the appearance of prions is enhanced by heterologous prion aggregates...
  70. pmc Structures of lung cancer-derived EGFR mutants and inhibitor complexes: mechanism of activation and insights into differential inhibitor sensitivity
    Cai Hong Yun
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, MA 02115, USA
    Cancer Cell 11:217-27. 2007
    ..Strikingly, direct binding measurements show that gefitinib binds 20-fold more tightly to the L858R mutant than to the wild-type enzyme...
  71. ncbi Crystal structure of a mammalian voltage-dependent Shaker family K+ channel
    Stephen B Long
    Howard Hughes Medical Institute, Laboratory of Molecular Neurobiology and Biophysics, Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
    Science 309:897-903. 2005
    ..Electrostatic properties of the side portals and positions of the T1 domain and beta subunit are consistent with electrophysiological studies of inactivation gating and with the possibility of K+ channel regulation by the beta subunit...
  72. ncbi Themes and variations on ubiquitylation
    A M Weissman
    Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892 1152, USA
    Nat Rev Mol Cell Biol 2:169-78. 2001
    ..A few years ago, we could only have dreamt of the complex arsenal of enzymes dedicated to ubiquitylation. Why has nature come up with so many ways of doing what seems to be such a simple job?..
  73. pmc DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA
    Steen K T Ooi
    Department of Genetics and Development, College of Physicians and Surgeons of Columbia University, New York, New York 10032, USA
    Nature 448:714-7. 2007
    ..These data indicate that DNMT3L recognizes histone H3 tails that are unmethylated at lysine 4 and induces de novo DNA methylation by recruitment or activation of DNMT3A2...
  74. ncbi Smad7 binds to Smurf2 to form an E3 ubiquitin ligase that targets the TGF beta receptor for degradation
    P Kavsak
    Program in Molecular Biology and Cancer, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto M5G 1X5, Canada
    Mol Cell 6:1365-75. 2000
    ..These studies thus define Smad7 as an adaptor in an E3 ubiquitin-ligase complex that targets the TGF beta receptor for degradation...
  75. ncbi Crystal structure of the TLR4-MD-2 complex with bound endotoxin antagonist Eritoran
    Ho Min Kim
    Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejon, Korea 305 701
    Cell 130:906-17. 2007
    ..The interaction with Eritoran is mediated by a hydrophobic internal pocket in MD-2. Based on structural analysis and mutagenesis experiments on MD-2 and TLR4, we propose a model of TLR4-MD-2 dimerization induced by LPS...
  76. ncbi Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes
    J L Riechmann
    Mendel Biotechnology, 21375 Cabot Boulevard, Hayward, CA 94545, USA
    Science 290:2105-10. 2000
    ..The genome-wide comparison reveals the evolutionary generation of diversity in the regulation of transcription...
  77. ncbi Evolution of protein kinase signaling from yeast to man
    Gerard Manning
    Sugen Inc 230 East Grand Ave, South San Francisco, CA 94080, USA
    Trends Biochem Sci 27:514-20. 2002
    ....
  78. ncbi Structure of a bacterial multidrug ABC transporter
    Roger J P Dawson
    Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
    Nature 443:180-5. 2006
    ....
  79. ncbi The guanine nucleotide-binding switch in three dimensions
    I R Vetter
    , 44227 Dortmund, Germany
    Science 294:1299-304. 2001
    ..Here we will try to define some underlying principles...
  80. ncbi Ubiquitin-binding domains in Y-family polymerases regulate translesion synthesis
    Marzena Bienko
    Institute for Biochemistry II, Goethe University Medical School, Theodor Stern Kai 7, 60590 Frankfurt, Germany
    Science 310:1821-4. 2005
    ..Our results indicate that Ub-binding domains of Y-family polymerases play crucial regulatory roles in TLS...
  81. pmc PDBsum new things
    Roman A Laskowski
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 37:D355-9. 2009
    ..Furthermore, it now accepts users' own PDB format files and generates a private set of analyses for each uploaded structure...
  82. ncbi Clinical resistance to STI-571 cancer therapy caused by BCR-ABL gene mutation or amplification
    M E Gorre
    Department of Medicine, Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
    Science 293:876-80. 2001
    ..These studies provide evidence that genetically complex cancers retain dependence on an initial oncogenic event and suggest a strategy for identifying inhibitors of STI-571 resistance...
  83. ncbi Macromolecular TLS refinement in REFMAC at moderate resolutions
    Martyn D Winn
    Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, United Kingdom
    Methods Enzymol 374:300-21. 2003
  84. 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...
  85. ncbi The molecular architecture of axonemes revealed by cryoelectron tomography
    Daniela Nicastro
    Laboratory for 3D Electron Microscopy of Cells, Department of Molecular, Cellular, and Developmental Biology, CB 347, University of Colorado, Boulder, CO 80309 0347, USA
    Science 313:944-8. 2006
    ..Periodic densities were also observed inside doublet microtubules; these may contribute to doublet stability...
  86. ncbi Insights into DNA recombination from the structure of a RAD51-BRCA2 complex
    Luca Pellegrini
    University of Cambridge, Department of Biochemistry, Tennis Court Road, Cambridge CB2 1GA, UK
    Nature 420:287-93. 2002
    ..Cancer-associated mutations that affect the BRC repeat disrupt its predicted interaction with RAD51, yielding structural insight into mechanisms for cancer susceptibility...
  87. ncbi Role of histone H3 lysine 9 methylation in epigenetic control of heterochromatin assembly
    J Nakayama
    Cold Spring Harbor Laboratory, Post Office Box 100, Cold Spring Harbor, NY 11724, USA
    Science 292:110-3. 2001
    ..These data define a conserved pathway wherein sequential histone modifications establish a "histone code" essential for the epigenetic inheritance of heterochromatin assembly...
  88. pmc Transcriptional control by the TGF-beta/Smad signaling system
    J Massague
    Cell Biology Program and Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
    EMBO J 19:1745-54. 2000
  89. ncbi SKP1 connects cell cycle regulators to the ubiquitin proteolysis machinery through a novel motif, the F-box
    C Bai
    Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas 77030, USA
    Cell 86:263-74. 1996
    ..Different skp1 mutants arrest cells in either G1 or G2, suggesting a connection between regulation of proteolysis in different stages of the cycle...
  90. pmc Crystal structure of the extracellular segment of integrin alpha Vbeta3
    J P Xiong
    Renal Unit, Leukocyte Biology and Inflammation Program, Structural Biology Program, Massachusetts General Hospital and Harvard Medical School, 149 13th Street, Charlestown, MA 02129, USA
    Science 294:339-45. 2001
    ..MIDAS lies adjacent to a calcium-binding site with a potential regulatory function...
  91. ncbi Dynamic interaction of BiP and ER stress transducers in the unfolded-protein response
    A Bertolotti
    Skirball Institute of Biomolecular Medicine, Departments of Medicine and Cell Biology and the Kaplan Cancer Center, New York University School of Medicine, New York, New York 10016, USA
    Nat Cell Biol 2:326-32. 2000
    ..These findings are consistent with a model in which BiP represses signalling through PERK and IRE1 and protein misfolding relieves this repression by effecting the release of BiP from the PERK and IRE1 lumenal domains...
  92. 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...
  93. ncbi Dynamin and the actin cytoskeleton cooperatively regulate plasma membrane invagination by BAR and F-BAR proteins
    Toshiki Itoh
    Department of Cell Biology and Howard Hughes Medical Institute, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06510, USA
    Dev Cell 9:791-804. 2005
    ..These results suggest a close interplay between the mechanisms that control actin dynamics and those that mediate plasma membrane invagination and fission...
  94. ncbi Shared and unique functions of the DExD/H-box helicases RIG-I, MDA5, and LGP2 in antiviral innate immunity
    Mitsutoshi Yoneyama
    Antiviral Innate Immunity Project, Tokyo Metropolitan Institute of Medical Science, Tokyo Metropolitan Organization for Medical Research, Honkomagome, Tokyo, Japan
    J Immunol 175:2851-8. 2005
    ..These results highlight ingenious mechanisms for initiating antiviral innate immune responses and the action of virus-encoded inhibitors...
  95. ncbi The structural basis for cap binding by influenza virus polymerase subunit PB2
    Delphine Guilligay
    Grenoble Outstation, European Molecular Biology Laboratory, 6 rue Jules Horowitz, BP181, 38042 Grenoble Cedex 9, France
    Nat Struct Mol Biol 15:500-6. 2008
    ..These findings clarify the nature of the cap binding site in PB2 and will allow efficient structure-based design of new anti-influenza compounds inhibiting viral transcription...
  96. ncbi Proteome-wide analysis of chaperonin-dependent protein folding in Escherichia coli
    Michael J Kerner
    Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Cell 122:209-20. 2005
    ..We suggest that the chaperonin system may have facilitated the evolution of this fold into a versatile platform for the implementation of numerous enzymatic functions...
  97. pmc CD-Search: protein domain annotations on the fly
    Aron Marchler-Bauer
    Computational Biology Branch, NCBI, National Library of Medicine, NIH, Building 38A, Room 5S508, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 32:W327-31. 2004
    ..CD-Search can be accessed at http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi...
  98. ncbi Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain
    A J Bannister
    Wellcome CRC Institute and Department of Pathology, University of Cambridge, UK
    Nature 410:120-4. 2001
    ..This model may also explain the stable inheritance of the heterochromatic state...
  99. ncbi Identification of FAAP24, a Fanconi anemia core complex protein that interacts with FANCM
    Alberto Ciccia
    Cancer Research UK, London Research Institute, Clare Hall Laboratories, South Mimms, Herts, UK
    Mol Cell 25:331-43. 2007
    ..Our data indicate that the FANCM/FAAP24 complex may play a key role in recruitment of the FA core complex to damaged DNA...
  100. pmc Coupling of the nucleus and cytoplasm: role of the LINC complex
    Melissa Crisp
    Department of Anatomy and Cell Biology, University of Florida, Gainesville, FL 32610
    J Cell Biol 172:41-53. 2006
    ..2005), support a model in which Sun proteins tether nesprins in the ONM via interactions spanning the PNS. In this way, Sun proteins and nesprins form a complex that links the nucleoskeleton and cytoskeleton (the LINC complex)...
  101. ncbi A transcriptionally [correction of transcriptively] active complex of APP with Fe65 and histone acetyltransferase Tip60
    X Cao
    The Center for Basic Neuroscience, Department of Molecular Genetics, and Howard Hughes Medical Institute, The University of Texas Southwestern Medical Center, Dallas, TX 75390 9111 USA
    Science 293:115-20. 2001
    ..This complex potently stimulates transcription via heterologous Gal4- or LexA-DNA binding domains, suggesting that release of the cytoplasmic tail of APP by gamma-cleavage may function in gene expression...

Research Grants64

  1. ApoE4 Structure Correctors as a Therapeutic Approach for Alzheimers Disease
    Robert W Mahley; Fiscal Year: 2013
    ..This amino acid difference gives rise to profound differences in the tertiary protein structure and function...
  2. Oral administration of TeaMemTM inhibits Alzheimer's disease pathogenesis
    Jun Tan; Fiscal Year: 2009
    ..These studies will lay the foundation for AD clinical trials with pure TeaMemTM or/and piperine (an alkaloid derived from black pepper) in the near future. ..
  3. Assembly and Function of the Septal Ring in E. coli
    PIET A DE BOER; Fiscal Year: 2013
    ..A number of SR proteins are, or are actively pursued as, drug targets. This project may lead to the identification of additional promising targets for, and rational designs of, new anti-bacterial drugs. ..
  4. Synthetic Nanofiber Vaccines for Cocaine Addiction
    Jia Zhou; Fiscal Year: 2013
    ..Also, more broadly, completion of the proposed work will integrate the fields of synthetic chemistry, nanotechnology, immunology, and addiction to significantly impact human health. ..
  5. Aptamers to distinguish functional modification of target proteins by affinity pr
    STEVEN SULJAK; Fiscal Year: 2009
    ..Such aptamers could be used for signaling the presence of proteins associated with particular disease states, or potentially as pharmaceutical agents that can block or modify the action of these proteins. ..
  6. Translocation through TonB-dependent transporters
    Karen Jakes; Fiscal Year: 2013
    ..Better understanding the mechanisms that mobilize that uptake will allow design of means to inhibit that essential process. ..
  7. Octyl gallate (OG) and Promotion of non-amyloidogenic processing of APP
    Jun Tan; Fiscal Year: 2013
    ..At the end of these experiments, these studies will provide the molecular basis for the future development of OG as novel and pharmacologically safe agents for Alzheimer's disease prevention/treatment. ..
  8. CONTENT AND ASSEMBLAGE OF PLATELET GRANULE PROTEINS
    Daniel Walz; Fiscal Year: 1993
    ..These studies should provide a better understanding of the role of thrombospondin in platelet aggregation, fibrin formation and fibrinolysis and permit the development of synthetic peptides which prevent or attenuate these processes...
  9. Protein Structure Prediction Using First Principles
    CHRISTODOULOS ACHILLEUS FLOUDAS; Fiscal Year: 2011
    ..and torsional angle dynamics, and (f) a new proposed approach for the selection of the predicted tertiary protein structure, from the ensemble of low energy protein structures, using a distance dependent force field developed ..
  10. MMP1 & MMP9: Mechanism of Activation & Substrate Binding
    Gregory Goldberg; Fiscal Year: 2009
    ..Specific Aims 2 and 3 propose to start with the gelatinase model to define biochemical interactions of gelatinases with substrate and to examine how these can enable processive diffusion and enzyme activation. ..
  11. LOX Pro-peptide Inhibition of FGF Signaling in Oral Cancer
    AMITHA PALAMAKUMBURA; Fiscal Year: 2009
    ..These studies will be of great importance to develop new therapeutic agents for oral cancer. ..
  12. RXR-Heterodimeric Receptors in the GI Tract
    Ellen Li; Fiscal Year: 2006
    ..We propose to study intraheterodimerization interactions between RXR and the minimal peptide by nuclear magnetic resonance techniques. ..
  13. I-TASSER based atomic-level protein structure prediction
    Yang Zhang; Fiscal Year: 2013
    ..I-TASSER and QUARK methods, the project aims to significantly improving the state of the art of tertiary protein structure prediction, especially for the non- and distant-homology proteins, so that the computational structure ..
  14. VIRUS RECEPTOR INTERACTION IN ECHOVIRUS INFECTION
    Jeffrey Bergelson; Fiscal Year: 1999
    ..James Hogle, determine the virus structure by X-ray diffraction. Knowledge of the virus structure, and the isolation of viral cDNA, will facilitate future genetic experiments to identify the viral sites for receptor binding. ..
  15. Structure-based Directed Evolution of Fast-Maturing GFPs
    Rebekka Wachter; Fiscal Year: 2007
    ..may depend on the strength of a base positioned close to the chromophore-forming amino acids in the tertiary protein structure. Therefore, specific sets of residues in the immediate chromophore environment will be the primary ..
  16. Determination of ab initio conformational shifts
    HAROLD SCHERAGA; Fiscal Year: 2005
    ..the results provided by this proposed research would provide additional assistance for an accurate tertiary protein structure prediction and, consequently, make a significant contribution to the solution of the, as yet unsolved, ..
  17. 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. ..
  18. Software tools for analysis and visulaization of protein structure
    Ethan A Merritt; Fiscal Year: 2010
    ..The algorithms and computation tools developed as part of this work will be distributed freely, and we will provide web-based state of the art analysis of structures submitted by external researchers. ..
  19. EXPANDED PROTEIN STRUCTURE REFINEMENT AND VALIDATION
    Ethan Merritt; Fiscal Year: 2005
    ..This, in turn, will make it easier to identify key biological features such as the presence and conformation of bound ligands, and the nature of hinge and inter-domain motions. ..
  20. 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. ..
  21. ENHANCING COLLECTIN MEDIATED HOST DEFENSE
    Kevan Hartshorn; Fiscal Year: 2001
    ..These experiments should yield important insights into basic collection biology and demonstrate that enhancement of collectin-mediated pulmonary host defense can be achieved in vivo through rational alteration of wild type collectins. ..
  22. Mechanisms and Function in HAD Phosphotransferases
    Karen Allen; Fiscal Year: 2009
    ..abstract_text> ..
  23. 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, ..
  24. Proteomic biomarkers for lymphoma
    GERALD DENIS; Fiscal Year: 2008
    ..The heuristic should be adaptable and extendable to a wide spectrum of human hematologic malignancies, including myeloid leukemias. [unreadable] [unreadable] [unreadable]..
  25. [Ca2+]i and Secretory Dynamics in Parotid Acinar Cells
    David Yule; Fiscal Year: 2007
    ..abstract_text> ..
  26. Novel Context-Activated Protide Anti-Infectives
    Michael Yeaman; Fiscal Year: 2008
    ..These advances would represent major breakthroughs in the prevention and treatment of these common and increasingly difficult-to-treat infections. [unreadable] [unreadable] [unreadable]..
  27. Membrane Targeting by PI-binding Domains
    TATIANA KUTATELADZE; Fiscal Year: 2009
    ..The results generated by this research may provide new approaches to rational design of anti-tumor therapeutic agents and systems for delivering drugs into cancer cells. ..
  28. 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. ..
  29. The role of srcasm in keratinocyte biology
    John Seykora; Fiscal Year: 2009
    ..The in vivo effects of SFKs and Srcasm on epidermal development and function will be determined by characterizing double transgenic strains over-expressing SFKs and Srcasm. ..
  30. Structural basis of signaling by ING2 PHD
    Tatiana G Kutateladze; Fiscal Year: 2010
    ..These studies will aid in deeper understanding of how the critical ING2-p53 pathways can be therapeutically manipulated and may help to identify new diagnostic markers and targets to prevent and treat cancer. ..
  31. Regulation of NF-kB by the Akt kinase
    Lawrence P Kane; Fiscal Year: 2010
    ..Such knowledge may eventually lead to more specific and efficacious treatments for tumors with dysregulated Akt. ..
  32. The FIAT-ATF4 interaction and the control of bone mass
    Rene St Arnaud; Fiscal Year: 2010
    ..These experiments will elucidate the molecular mechanisms through which FIAT regulates bone mass accrual in vivo. ..
  33. CELL SURFACE STRUCTURE AND TRANSFORMATIONS
    Richard Hynes; Fiscal Year: 2005
    ..Evaluation of the functions of cell adhesion proteins and the consequences of their misexpression in metastatic cells will lead to new leads for therapeutic interventions against metastasis. ..
  34. 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. ..
  35. gp120 covalent analogs as candidate HIV vaccines
    Sudhir Paul; Fiscal Year: 2008
    ..Novel vaccination strategies and HIV-1 neutralizing Abs will emerge from these studies if the physiological barriers to catalytic Ab synthesis can be bypassed. [unreadable] [unreadable]..
  36. Proteolytic Antibody HIVcides
    Sudhir Paul; Fiscal Year: 2007
    ..These studies may identify proteolytic antibodies suitable for further development as a topical HIVcide. [unreadable] [unreadable] [unreadable]..
  37. Cell Biology of Human Thiamine Transporters
    VEEDAMALI SUBRAMANIAN; Fiscal Year: 2005
    ....
  38. DETERMINANTS IN PLATELET MICROBICIDAL PROTEINS
    Michael Yeaman; Fiscal Year: 2004
    ..Thus, these studies will significantly advance our understanding of antimicrobial host defense, and may yield new modes for its amplification. ..
  39. X-Ray Optics and Area Detector
    Lin Chen; Fiscal Year: 2004
    ..Pardi) Structural biology and biochemistry of Telomeres (Cdc13) (Deborah Wuttke) Structural studies of the prokaryotic and eukaryotic chemotaxis pathways (Joseph Falke) Structure and mechanism at the chemical synapse (Michael Stowell) ..
  40. ANNEXIN PHOSPHORYLATION: CAUSES AND CONSEQUENCES
    CARL CREUTZ; Fiscal Year: 2004
    ....
  41. Develop Peptide Inhibitors of the NFAT/AP-1 Complex
    Lin Chen; Fiscal Year: 2003
    ..These inhibitors may be important tools for studying the basic molecular mechanisms of tolerance induction and may lead to clinical drugs for invoking antigen specific long-term immune tolerance. ..
  42. GLOMERULAR LAMININS: STRUCTURE AND FUNCTION
    Christine Abrass; Fiscal Year: 2003
    ....
  43. 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. ..
  44. STRUCTURE/FUNCTION OF GTC, A NOVEL GOLGI PROTEIN COMPLEX
    FREDERICK HUGHSON; Fiscal Year: 2002
    ..These studies will provide the first insights into the role of this novel protein complex in the process of intracellular protein traffic. ..
  45. HUMAN HEPATIC & INTESTINAL UDP GLUCURONOSYLTRANSFERASES
    Anna Radominska Pandya; Fiscal Year: 2002
    ..abstract_text> ..
  46. COPPER METALLOBIOCHEMISTRY IN SACCHAROMYCES CEREVISAE
    DANIEL KOSMAN; Fiscal Year: 2002
    ..Thus, elucidation of the function and modulation of Mac1p in yeast will be broadly relevant to eukaryotic copper and iron metabolism in general. ..
  47. Matrix and Morphogenesis Conference
    MARION GORDON; Fiscal Year: 2002
    ..This meeting provides a unique opportunity for senior and junior scientists to gather and discuss the latest and most advanced results in the field of extracellular matrix and morphogenesis. ..
  48. Structural studies of bacterial quorum sensing regulator
    Mair Churchill; Fiscal Year: 2005
    ..Study the structures and mechanisms to determine similarities to other AHL synthases. ..
  49. Inhibition of Scar by the HEM2/Abi2/Pir121 Complex
    SHAE PADRICK; Fiscal Year: 2005
    ..NMR line broadening experiments will then determine the binding site in terms of specific amino acids and the site will be confirmed by designed point mutants testing the HAP or Arp2/3 binding interfaces. ..
  50. METABOTROPIC GLUTAMATE RECEPTORS IN BASAL GANGLIA
    COLLEEN NISWENDER; Fiscal Year: 2009
    ..Furthermore, we will test the hypothesis that agonists or allosteric potentiators of this receptor can provide palliative relief in rodent models of PD by actions in the GP. ..
  51. Structure:function studies of the glucocorticoid receptor
    Raj Kumar; Fiscal Year: 2007
    ..unreadable] [unreadable]..
  52. X-ray diffraction analysis of human adenovirus
    Vijay Reddy; Fiscal Year: 2006
    ..et al. Science 309: 1090-1092, 2005). [unreadable] [unreadable] [unreadable]..
  53. STRUCTURE/FUNCTION OF SURFACTANT PROTEIN D
    Erika Crouch; Fiscal Year: 2006
    ..As in the past, secreted recombinant proteins with novel structural attributes will be characterized and utilized for collaborative studies of SP-D function. [unreadable] [unreadable]..
  54. Iron Trafficking to Ribonucleotide Reductases
    DANIEL KOSMAN; Fiscal Year: 2006
    ..This work should provide new insight into the assembly of a critical iron prosthetic group in vivo and evidence that this process can be a target for intervention in a viral infection. ..
  55. Molecular mechanisms of voltage-gated ion channels
    Hans Peter Larsson; Fiscal Year: 2006
    ..These measurements will be used to determine how S4 moves in the different channels and will further our understanding of the different mechanisms of opening of these two classes of channels. ..
  56. Gene Therapy of Muscle Wasting From Uremia
    Xiaonan Wang; Fiscal Year: 2005
    ..We believe that the experimental results will shed the insight on the mechanisms of muscle protein degradation, and provide a possible new approach to treat the pathological process of muscle wasting. ..
  57. THE ROLE OF RB IN THE RETINA & OTHER TISSUES
    JAMES HARBOUR; Fiscal Year: 2009
    ..Consequently, these aims are highly relevant to the vision statement of the NEI, and they address several major program goals and objectives of the Retinal Diseases Program. ..
  58. STRUCTURAL STUDIES OF CHROMOSOMAL PROTEIN/DNA COMPLEXES
    Mair Churchill; Fiscal Year: 2002
    ..Structural studies with HMG-D will be valuable for understanding DNA recognition at a level of detail that will be helpful in the design of improved anti-tumor drugs. ..
  59. Molecular Mechanisms of Mesangial Sclerosis
    Christine Abrass; Fiscal Year: 2009
    ..Understanding transcriptional control of LN isoform expression will add new insights into the role that LN plays in normal glomerulogenesis and that becomes disordered in glomerular disease. ..
  60. 2005 Bones & Teeth Gordon Conference
    Rene St Arnaud; Fiscal Year: 2005
    ..These funds, if granted, will aid immeasurably in allowing the Gordon Research Conference to fulfill its function to stimulate further creativity in bone, cartilage and tooth research. ..
  61. MOLECULAR ANGLE TRANSITIONS IN MUSCLE
    THOMAS BURGHARDT; Fiscal Year: 2001
    ....