amino acid motifs

Summary

Summary: Commonly observed structural components of proteins formed by simple combinations of adjacent secondary structures. A commonly observed structure may be composed of a CONSERVED SEQUENCE which can be represented by a CONSENSUS SEQUENCE.

Top Publications

  1. ncbi Tsg101 and the vacuolar protein sorting pathway are essential for HIV-1 budding
    J E Garrus
    Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
    Cell 107:55-65. 2001
  2. ncbi T-Coffee: A novel method for fast and accurate multiple sequence alignment
    C Notredame
    National Institute for Medical Research, The Ridgeway, London, NW7 1AA, UK
    J Mol Biol 302:205-17. 2000
  3. pmc ELM--the database of eukaryotic linear motifs
    Holger Dinkel
    Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
    Nucleic Acids Res 40:D242-51. 2012
  4. pmc A quantitative atlas of mitotic phosphorylation
    Noah Dephoure
    Department of Cell Biology, Harvard University Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 105:10762-7. 2008
  5. ncbi Genome-wide mapping of in vivo protein-DNA interactions
    David S Johnson
    Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305 5120, USA
    Science 316:1497-502. 2007
  6. 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
  7. ncbi Atomic structure of a voltage-dependent K+ channel in a lipid membrane-like environment
    Stephen B Long
    Howard Hughes Medical Institute, Laboratory of Molecular Neurobiology and Biophysics, Rockefeller University, 1230 York Avenue, New York, New York 10065, USA
    Nature 450:376-82. 2007
  8. ncbi Locating proteins in the cell using TargetP, SignalP and related tools
    Olof Emanuelsson
    Stockholm Bioinformatics Center, AlbaNova, Stockholm University, SE 10691 Stockholm, Sweden
    Nat Protoc 2:953-71. 2007
  9. ncbi Attributes of short linear motifs
    Norman E Davey
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    Mol Biosyst 8:268-81. 2012
  10. pmc ELM: the status of the 2010 eukaryotic linear motif resource
    Cathryn M Gould
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 38:D167-80. 2010

Research Grants

  1. Potentiation of Glycine Receptors by Ethanol
    LUIS GERARDO AGUAYO; Fiscal Year: 2010
  2. DNA Helicases: Mechanisms and Functions
    Kevin D Raney; Fiscal Year: 2013
  3. MOLECULAR ASPECTS OF ORAL PLAQUE FORMATION
    Richard J Lamont; Fiscal Year: 2013
  4. The BARD1 tumor suppressor and breast cancer
    Richard J Baer; Fiscal Year: 2013
  5. Designing Spider Silk Proteins as Novel Biomaterials
    Randolph Lewis; Fiscal Year: 2009
  6. SIGNALING MECHANISMS OF SOMATOSTATIN RECEPTORS
    DIANE BARBER; Fiscal Year: 2002
  7. Structure-Function of UDP-Glucuronosyltransferases
    Anna Radominska Pandya; Fiscal Year: 2009
  8. DYNAMICS OF C-FOS PROTEIN INTERACTIONS
    EDWARD ZIFF; Fiscal Year: 2000
  9. MOLECULAR MECHANISMS OF ALPHA 2,8-POLYSIALYTRANSFERASES
    FREDERIC TROY; Fiscal Year: 2001
  10. MINORITY PREDOCTORAL FELLOWSHIP PROGRAM
    ADRIENNE COTTRELL; Fiscal Year: 2007

Detail Information

Publications270 found, 100 shown here

  1. ncbi Tsg101 and the vacuolar protein sorting pathway are essential for HIV-1 budding
    J E Garrus
    Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
    Cell 107:55-65. 2001
    ..These observations suggest that retroviruses bud by appropriating cellular machinery normally used in the Vps pathway to form multivesicular bodies...
  2. ncbi T-Coffee: A novel method for fast and accurate multiple sequence alignment
    C Notredame
    National Institute for Medical Research, The Ridgeway, London, NW7 1AA, UK
    J Mol Biol 302:205-17. 2000
    ..The improvement, especially clear with the more difficult test cases, is always visible, regardless of the phylogenetic spread of the sequences in the tests...
  3. pmc ELM--the database of eukaryotic linear motifs
    Holger Dinkel
    Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
    Nucleic Acids Res 40:D242-51. 2012
    ..The motif discovery portion of the ELM resource has added conservation, and structural attributes have been incorporated to aid users to discriminate biologically relevant motifs from stochastically occurring non-functional instances...
  4. pmc A quantitative atlas of mitotic phosphorylation
    Noah Dephoure
    Department of Cell Biology, Harvard University Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 105:10762-7. 2008
    ..Analysis of non-proline site-containing phosphopeptides identified two unique motifs that suggest there are at least two undiscovered mitotic kinases...
  5. ncbi Genome-wide mapping of in vivo protein-DNA interactions
    David S Johnson
    Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305 5120, USA
    Science 316:1497-502. 2007
    ..96] and statistical confidence (P <10(-4)), properties that were important for inferring new candidate interactions. These include key transcription factors in the gene network that regulates pancreatic islet cell development...
  6. 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...
  7. ncbi Atomic structure of a voltage-dependent K+ channel in a lipid membrane-like environment
    Stephen B Long
    Howard Hughes Medical Institute, Laboratory of Molecular Neurobiology and Biophysics, Rockefeller University, 1230 York Avenue, New York, New York 10065, USA
    Nature 450:376-82. 2007
    ..The detailed structure, which can be compared directly to a large body of functional data, explains charge stabilization within the membrane and suggests a mechanism for voltage-sensor movements and pore gating...
  8. ncbi Locating proteins in the cell using TargetP, SignalP and related tools
    Olof Emanuelsson
    Stockholm Bioinformatics Center, AlbaNova, Stockholm University, SE 10691 Stockholm, Sweden
    Nat Protoc 2:953-71. 2007
    ..In addition, we describe and provide web references to other useful subcellular localization predictors. Finally, we discuss predictive performance measures in general and the performance of TargetP and SignalP in particular...
  9. ncbi Attributes of short linear motifs
    Norman E Davey
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    Mol Biosyst 8:268-81. 2012
    ..Finally, the most interesting conclusions are examined in regard to their functional consequences...
  10. pmc ELM: the status of the 2010 eukaryotic linear motif resource
    Cathryn M Gould
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 38:D167-80. 2010
    ..Using the links, researchers can explore the motifs, proteins, complex structures and associated literature to evaluate whether candidate motifs might be worth experimental investigation...
  11. 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...
  12. pmc Comparative genomics of the neglected human malaria parasite Plasmodium vivax
    Jane M Carlton
    The Institute for Genomic Research J Craig Venter Institute, 9704 Medical Research Drive, Rockville, Maryland 20850, USA
    Nature 455:757-63. 2008
    ..Completion of the P. vivax genome provides the scientific community with a valuable resource that can be used to advance investigation into this neglected species...
  13. pmc Integrin ligands at a glance
    Jonathan D Humphries
    Wellcome Trust Centre for Cell Matrix Research, Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
    J Cell Sci 119:3901-3. 2006
  14. pmc Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis
    Claire Lurin
    Unite de Recherche en Genomique Vegetale, Institut National de la Recherche Agronomique Centre National de la Recherche Scientifique Université d Evry Val d Essone, CP 5708, 91057 Evry Cedex, France
    Plant Cell 16:2089-103. 2004
    ..These results confirm, but massively extend, the very sparse observations previously obtained from detailed characterization of individual mutants in other organisms...
  15. pmc SLiMSearch 2.0: biological context for short linear motifs in proteins
    Norman E Davey
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
    Nucleic Acids Res 39:W56-60. 2011
    ..Users can search motifs against the human proteome or a subset thereof defined by Uniprot accession numbers or GO term. The SLiMSearch server is available at: http://bioware.ucd.ie/slimsearch2.html...
  16. ncbi An EB1-binding motif acts as a microtubule tip localization signal
    Srinivas Honnappa
    Biomolecular Research, Structural Biology, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
    Cell 138:366-76. 2009
    ..Our findings establish a general "microtubule tip localization signal" (MtLS) and delineate a unifying mechanism for this subcellular protein targeting process...
  17. pmc STAMP: a web tool for exploring DNA-binding motif similarities
    Shaun Mahony
    Department of Computational Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
    Nucleic Acids Res 35:W253-8. 2007
    ..STAMP also directly accepts the output files from 12 supported motif-finders, enabling quick interpretation of motif-discovery analyses. STAMP is available at http://www.benoslab.pitt.edu/stamp...
  18. ncbi A translocation signal for delivery of oomycete effector proteins into host plant cells
    Stephen C Whisson
    Plant Pathology Programme, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK
    Nature 450:115-8. 2007
    ..infestans genome. Identification of this class of proteins provides unparalleled opportunities to determine how oomycetes manipulate hosts to establish infection...
  19. 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...
  20. ncbi Crystal structure of rhodopsin: A G protein-coupled receptor
    K Palczewski
    Department of Ophthalmology, University of Washington, Seattle, WA 98195, USA
    Science 289:739-45. 2000
    ..Identification of a set of residues that mediate interactions between the transmembrane helices and the cytoplasmic surface, where G-protein activation occurs, also suggests a possible structural change upon photoactivation...
  21. 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...
  22. 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...
  23. ncbi Structure of a beta-TrCP1-Skp1-beta-catenin complex: destruction motif binding and lysine specificity of the SCF(beta-TrCP1) ubiquitin ligase
    Geng Wu
    Cellular Biochemistry and Biophysics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
    Mol Cell 11:1445-56. 2003
    ....
  24. ncbi Role of Rpn11 metalloprotease in deubiquitination and degradation by the 26S proteasome
    Rati Verma
    Department of Biology and Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA
    Science 298:611-5. 2002
    ..Our findings reveal an unexpected coupling between substrate deubiquitination and degradation and suggest a unifying rationale for the presence of the lid in eukaryotic proteasomes...
  25. ncbi Feature-based prediction of non-classical and leaderless protein secretion
    Jannick Dyrløv Bendtsen
    Center for Biological Sequence Analysis BioCentrum DTU, Building 208, Technical University of Denmark, DK 2800 Lyngby, Denmark
    Protein Eng Des Sel 17:349-56. 2004
    ..By scanning the entire human proteome we identified new proteins potentially undergoing non-classical secretion. Predictions can be made at http://www.cbs.dtu.dk/services/SecretomeP...
  26. 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...
  27. 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...
  28. 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...
  29. pmc Structure of a beta1-adrenergic G-protein-coupled receptor
    Tony Warne
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
    Nature 454:486-91. 2008
    ....
  30. pmc Identification of a SUMO-binding motif that recognizes SUMO-modified proteins
    Jing Song
    Division of Immunology, Beckman Research Institute of the City of Hope, 1450 East Duarte Road, Duarte, CA 91010, USA
    Proc Natl Acad Sci U S A 101:14373-8. 2004
    ..The SUMO-binding motif exists in nearly all proteins known to be involved in SUMO-dependent processes, suggesting its general role in sumoylation-dependent cellular functions...
  31. ncbi Structural and biochemical studies of ALIX/AIP1 and its role in retrovirus budding
    Robert D Fisher
    Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
    Cell 128:841-52. 2007
    ..ALIX therefore serves as a flexible, extended scaffold that connects retroviral Gag proteins to ESCRT-III and other cellular-budding machinery...
  32. ncbi Casein kinase 1 gamma couples Wnt receptor activation to cytoplasmic signal transduction
    Gary Davidson
    Division of Molecular Embryology, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, D 69120 Heidelberg, Germany
    Nature 438:867-72. 2005
    ..Our results reveal an evolutionarily conserved mechanism that couples Wnt receptor activation to the cytoplasmic signal transduction apparatus...
  33. ncbi An iterative statistical approach to the identification of protein phosphorylation motifs from large-scale data sets
    Daniel Schwartz
    Department of Cell Biology, 240 Longwood Ave, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nat Biotechnol 23:1391-8. 2005
    ....
  34. ncbi SYFPEITHI: database for MHC ligands and peptide motifs
    H Rammensee
    Universitat Tubingen, Interfakultäres Institut für Zellbiologie, Abteilung Immunologie, Auf der Morgenstelle 15, D 72076 Tubingen, Germany
    Immunogenetics 50:213-9. 1999
    ..Hyperlinks to the EMBL and PubMed databases are included. In addition, ligand predictions are available for a number of MHC allelic products. The database content is restricted to published data only...
  35. ncbi Specification of SUMO1- and SUMO2-interacting motifs
    Christina Maria Hecker
    Institute for Biochemistry II, Goethe University Medical School, Theodor Stern Kai 7, 60590 Frankfurt, Germany
    J Biol Chem 281:16117-27. 2006
    ....
  36. pmc SUMO-targeted ubiquitin ligases in genome stability
    John Prudden
    Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
    EMBO J 26:4089-101. 2007
    ..The DNA repair factor Rad60 and its human homolog NIP45, which contain SLDs, are candidate STUbL targets. Consistently, Rad60 and Slx8-Rfp mutants have similar DNA repair defects...
  37. ncbi Prediction of peroxisomal targeting signal 1 containing proteins from amino acid sequence
    Georg Neuberger
    Research Institute of Molecular Pathology, Dr Bohrgasse 7, A 1030 Vienna, Austria
    J Mol Biol 328:581-92. 2003
    ..The predicted presence of a PTS1 signal implies peroxisomal localisation in the absence of N-terminal targeting sequences such as the mitochondrial import signal...
  38. ncbi Tumor suppressor LATS1 is a negative regulator of oncogene YAP
    Yawei Hao
    Department of Pathology and Molecular Medicine, Queen s University, Kingston, Ontario K7L 3N6, Canada
    J Biol Chem 283:5496-509. 2008
    ..These research findings will have profound impacts on our understanding of the molecular mechanism of the LATS tumor suppressor and the emerging Hippo-LATS/Warts pathway...
  39. ncbi Role of SUMO-interacting motif in Daxx SUMO modification, subnuclear localization, and repression of sumoylated transcription factors
    Ding Yen Lin
    Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan, Republic of China
    Mol Cell 24:341-54. 2006
    ..Our results provide mechanistic insights into Daxx in SUMO-dependent transcriptional control and subnuclear compartmentalization...
  40. ncbi Prediction, conservation analysis, and structural characterization of mammalian mucin-type O-glycosylation sites
    Karin Julenius
    Center for Biological Sequence Analysis, BioCentrum, Building 208, Technical University of Denmark, DK 2800 Lyngby, Denmark
    Glycobiology 15:153-64. 2005
    ..NetOGlyc 3.1 is made available at www.cbs.dtu.dk/services/netoglyc...
  41. pmc Repression domains of class II ERF transcriptional repressors share an essential motif for active repression
    M Ohta
    Gene Discovery Research Center, National Institute of Advanced Industrial Science and Technology AIST, Central 6, Tsukuba 305 8566, Japan
    Plant Cell 13:1959-68. 2001
    ..These zinc finger proteins functioned as repressors, and their repression domains were identified as regions that contained an EAR motif...
  42. pmc Keap1 recruits Neh2 through binding to ETGE and DLG motifs: characterization of the two-site molecular recognition model
    Kit I Tong
    Graduate School of Life and Environmental Sciences, University of Tsukuba, 1 1 1 Tennoudai, Tsukuba 305 8572, Japan
    Mol Cell Biol 26:2887-900. 2006
    ..Based on these observations, we propose that Keap1 recruits Nrf2 by the ETGE motif and that the DLG motif of the Neh2 domain locks its lysine-rich central alpha-helix in a correct position to benefit ubiquitin signaling...
  43. pmc The extended PP1 toolkit: designed to create specificity
    Mathieu Bollen
    Laboratory of Biosignaling and Therapeutics, Department of Molecular Cell Biology, University of Leuven, B 3000 Leuven, Belgium
    Trends Biochem Sci 35:450-8. 2010
    ..These novel insights offer perspectives for the therapeutic targeting of PP1 by interfering with the binding of PIPs or substrates...
  44. ncbi Small ubiquitin-like modifier (SUMO) recognition of a SUMO binding motif: a reversal of the bound orientation
    Jing Song
    Division of Immunology and Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, California 91010, USA
    J Biol Chem 280:40122-9. 2005
    ..This study provides a clear mechanism of the SBM sequence variations and its recognition of the SUMO moiety in sumoylated proteins...
  45. pmc Structure of the Keap1:Nrf2 interface provides mechanistic insight into Nrf2 signaling
    Shih Ching Lo
    Department of Biochemistry, University of Missouri Columbia, Columbia, MO 65211, USA
    EMBO J 25:3605-17. 2006
    ..Our results provide a detailed picture of how a BTB-Kelch substrate adaptor protein binds to its cognate substrate and will enable the rational design of novel chemopreventive agents...
  46. ncbi Molecular architecture and functional model of the endocytic AP2 complex
    Brett M Collins
    Cambridge Institute for Medical Research, University of Cambridge, Department of Clinical Biochemistry, Wellcome Trust MRC Building, Hills Road, United Kingdom
    Cell 109:523-35. 2002
    ..A model for AP2 recruitment and activation is proposed...
  47. ncbi Linear motif atlas for phosphorylation-dependent signaling
    Martin Lee Miller
    Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark
    Sci Signal 1:ra2. 2008
    ..The atlas is available as a community resource (http://netphorest.info)...
  48. pmc A dual-kinase mechanism for Wnt co-receptor phosphorylation and activation
    Xin Zeng
    Neurobiology Program, Children s Hospital Boston, Department of Neurology, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nature 438:873-7. 2005
    ....
  49. ncbi WW domain-containing protein YAP associates with ErbB-4 and acts as a co-transcriptional activator for the carboxyl-terminal fragment of ErbB-4 that translocates to the nucleus
    Akihiko Komuro
    Department of Medicine, Mount Sinai School of Medicine, New York, New York 10029, USA
    J Biol Chem 278:33334-41. 2003
    ..Our data indicate that YAP is a potential signaling partner of the full-length ErbB4 receptor at the membrane and of the COOH-terminal fragment of ErbB-4 that translocates to the nucleus to regulate transcription...
  50. pmc RNF8 transduces the DNA-damage signal via histone ubiquitylation and checkpoint protein assembly
    Michael S Y Huen
    Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
    Cell 131:901-14. 2007
    ..Together, our study implicates RNF8 as a novel DNA-damage-responsive protein that integrates protein phosphorylation and ubiquitylation signaling and plays a critical role in the cellular response to genotoxic stress...
  51. pmc Comparative analysis of mRNA targets for human PUF-family proteins suggests extensive interaction with the miRNA regulatory system
    Alessia Galgano
    Institute of Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland
    PLoS ONE 3:e3164. 2008
    ..Our work suggests extensive connections between the RBP and miRNA post-transcriptional regulatory systems and provides a framework for deciphering the molecular mechanism by which PUF proteins regulate their target mRNAs...
  52. ncbi The structure of the beta-catenin/E-cadherin complex and the molecular basis of diverse ligand recognition by beta-catenin
    A H Huber
    Departments of Structural Biology and Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
    Cell 105:391-402. 2001
    ..APC contains sequences homologous to the phosphorylated region of cadherin, and is likely to bind similarly...
  53. ncbi Cloning of the Arabidopsis clock gene TOC1, an autoregulatory response regulator homolog
    C Strayer
    Department of Cell Biology, Scripps Research Institute, La Jolla, CA 92037, USA
    Science 289:768-71. 2000
    ..TOC1 is itself circadianly regulated and participates in a feedback loop to control its own expression...
  54. ncbi HIV-1 and Ebola virus encode small peptide motifs that recruit Tsg101 to sites of particle assembly to facilitate egress
    J Martin-Serrano
    Aaron Diamond AIDS Research Center and The Rockefeller University, New York, New York, USA
    Nat Med 7:1313-9. 2001
    ..Because the Tsg101 is recruited by small, conserved viral sequence motifs, agents that mimic these structures are potential inhibitors of the replication of these lethal human pathogens...
  55. pmc Rules for nuclear localization sequence recognition by karyopherin beta 2
    Brittany J Lee
    Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park, Dallas, TX 75390, USA
    Cell 126:543-58. 2006
    ..These studies define and validate a new NLS that could not be predicted by primary sequence analysis alone...
  56. pmc Akt-RSK-S6 kinase signaling networks activated by oncogenic receptor tyrosine kinases
    Albrecht Moritz
    Cell Signaling Technology Inc, Danvers, MA 01923, USA
    Sci Signal 3:ra64. 2010
    ..Our approach provides a new view of RTK and Akt-RSK-S6 kinase signaling, revealing previously unidentified Akt-RSK-S6 kinase substrates that merit further consideration as targets for combination therapy with RTKIs...
  57. ncbi Histone demethylation by a family of JmjC domain-containing proteins
    Yu Ichi Tsukada
    Howard Hughes Medical Institute, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599 7295, USA
    Nature 439:811-6. 2006
    ..Thus, we identify the JmjC domain as a novel demethylase signature motif and uncover a protein demethylation mechanism that is conserved from yeast to human...
  58. pmc Conserved function of RNF4 family proteins in eukaryotes: targeting a ubiquitin ligase to SUMOylated proteins
    Huaiyu Sun
    Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
    EMBO J 26:4102-12. 2007
    ..Hence, we describe a family of SIM-containing RING-finger proteins that potentially regulates eukaryotic genome stability through linking SUMO-interaction with ubiquitin conjugation...
  59. ncbi C-type lectin DC-SIGN modulates Toll-like receptor signaling via Raf-1 kinase-dependent acetylation of transcription factor NF-kappaB
    Sonja I Gringhuis
    Department of Molecular Cell Biology and Immunology, VU University Medical Center, 1007 MB Amsterdam, The Netherlands
    Immunity 26:605-16. 2007
    ..Thus, this pathway is involved in regulation of adaptive immunity by DCs to bacterial, fungal, and viral pathogens...
  60. ncbi The leucine-rich repeat as a protein recognition motif
    B Kobe
    Department of Biochemistry and Molecular Biology Institute for Molecular Bioscience, University of Queensland, Brisbane, 4072, Queensland, Australia
    Curr Opin Struct Biol 11:725-32. 2001
    ....
  61. pmc Prediction of lipid posttranslational modifications and localization signals from protein sequences: big-Pi, NMT and PTS1
    Frank Eisenhaber
    Research Institute of Molecular Pathology, Dr Bohr Gasse 7, A 1030 Vienna, Republic of Austria
    Nucleic Acids Res 31:3631-4. 2003
    ..Guidelines for application of the three WWW-based predictors (http://mendel.imp.univie.ac.at/) and for the interpretation of their output are described...
  62. pmc HMM Logos for visualization of protein families
    Benjamin Schuster-Böckler
    Department of Mathematics and Computer Science, Freie Universitat Berlin, Germany
    BMC Bioinformatics 5:7. 2004
    ..Profile Hidden Markov Models (pHMMs) are a widely used tool for protein family research. Up to now, however, there exists no method to visualize all of their central aspects graphically in an intuitively understandable way...
  63. ncbi Close encounters of the third kind: disordered domains and the interactions of proteins
    Peter Tompa
    Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Budapest, Hungary
    Bioessays 31:328-35. 2009
    ..With these points, we argue that these long disordered regions should be recognized as a distinct class of biologically functional protein domains...
  64. ncbi Crystal structure of opsin in its G-protein-interacting conformation
    Patrick Scheerer
    Institut für Medizinische Physik und Biophysik CC2, Charite Universitatsmedizin Berlin, Chariteplatz 1, D 10117 Berlin, Germany
    Nature 455:497-502. 2008
    ..On the basis of the Ops*-GalphaCT structure and known conformational changes in Galpha, we discuss signal transfer from the receptor to the G protein nucleotide-binding site...
  65. ncbi Defining the specificity space of the human SRC homology 2 domain
    Haiming Huang
    Department of Biochemistry, Siebens Drake Medical Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario N6A 5C1, Canada
    Mol Cell Proteomics 7:768-84. 2008
    ..The definition of the specificity space of the human SH2 domain provides both the necessary molecular basis and a platform for future exploration of the functions for SH2-containing proteins in cells...
  66. ncbi PML protein isoforms and the RBCC/TRIM motif
    K Jensen
    Centre for Structural Biology, Imperial College of Science, Technology and Medicine, Flowers Building, Armstrong Road, London SW7 2AZ, UK
    Oncogene 20:7223-33. 2001
    ..In APL oligomerization mediated by the RBCC/TRIM motif is essential for the transformation potential of the PML-RARalpha fusion protein...
  67. ncbi Auto-regulation of the circadian slave oscillator component AtGRP7 and regulation of its targets is impaired by a single RNA recognition motif point mutation
    Jan C Schöning
    Department of Molecular Cell Physiology, University of Bielefeld, D 33615 Bielefeld, Germany
    Plant J 52:1119-30. 2007
    ....
  68. pmc Identification of a novel, widespread, and functionally important PCNA-binding motif
    Karin M Gilljam
    Department of Cancer Research and Molecular Medicine, Faculty of Medicine, Norwegian University of Science and Technology, N 7489 Trondheim, Norway
    J Cell Biol 186:645-54. 2009
    ..Thus, APIM is likely to mediate PCNA binding in many proteins involved in DNA repair and cell cycle control during genotoxic stress...
  69. ncbi Structure-function analysis of the NB-ARC domain of plant disease resistance proteins
    Gerben van Ooijen
    Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, PO Box 94062, 1090 GB Amsterdam, The Netherlands
    J Exp Bot 59:1383-97. 2008
    ..The presented 3D model provides a framework for the formulation of hypotheses on how mutations in the NB-ARC exert their effects...
  70. ncbi Cyclin specificity in the phosphorylation of cyclin-dependent kinase substrates
    Mart Loog
    Department of Physiology, University of California, San Francisco, California 94143 2200, USA
    Nature 434:104-8. 2005
    ..Thus, Clb5 and Clb2 use distinct mechanisms to enhance the phosphorylation of S-phase and M-phase substrates...
  71. ncbi Multi-domain conformational selection underlies pre-mRNA splicing regulation by U2AF
    Cameron D Mackereth
    Institute of Structural Biology, Helmholtz Zentrum Munchen, Ingolstadter Landstrasse 1, 85764 Neuherberg, Germany
    Nature 475:408-11. 2011
    ..Similar mechanisms of cooperative multi-domain conformational selection may operate more generally in the recognition of degenerate nucleotide or amino acid motifs by multi-domain proteins.
  72. pmc On the detection and refinement of transcription factor binding sites using ChIP-Seq data
    Ming Hu
    Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
    Nucleic Acids Res 38:2154-67. 2010
    ..These findings may offer new biological insights into the mechanisms of transcription factor regulation...
  73. pmc Discovering sequence motifs with arbitrary insertions and deletions
    Martin C Frith
    Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology AIST, Tokyo, Japan
    PLoS Comput Biol 4:e1000071. 2008
    ..It may be equally useful for arbitrarily gapped motifs in DNA and RNA, although fewer examples of such motifs are known at present. GLAM2 is public domain software, available for download at http://bioinformatics.org.au/glam2...
  74. ncbi Mechanistic insight into pentatricopeptide repeat proteins as sequence-specific RNA-binding proteins for organellar RNAs in plants
    Takahiro Nakamura
    Department of Research Superstar Program, Institute of Advanced Study, Kyushu University, Fukuoka 812 8581, Japan
    Plant Cell Physiol 53:1171-9. 2012
    ..Here, we summarize recent studies addressing the mechanistic aspect of PPR proteins...
  75. ncbi The Q motif: a newly identified motif in DEAD box helicases may regulate ATP binding and hydrolysis
    N Kyle Tanner
    Departement de Biochimie Medicale, Centre Medical Universitaire, 1, rue Michel Servet, 1211 Geneva 4, Switzerland
    Mol Cell 11:127-38. 2003
    ..These results are consistent with computer studies of the solved crystal structures...
  76. ncbi Adaptors for clathrin coats: structure and function
    David J Owen
    Cambridge Institute for Medical Research, Department of Clinical Biochemistry, University of Cambridge, Cambridge CB2 2XY, UK
    Annu Rev Cell Dev Biol 20:153-91. 2004
    ..This review focuses on the structure of clathrin adaptors and how these structures provide functional information on the mechanism of CCV formation...
  77. ncbi Prediction of short linear protein binding regions
    Catherine Mooney
    Complex and Adaptive Systems Laboratory, University College Dublin, Dublin, Ireland
    J Mol Biol 415:193-204. 2012
    ..We conclude that, despite the diversity of motif sequences and structures, SLiMPred is a valuable tool for prioritizing potential interaction motifs in proteins...
  78. ncbi Computational identification and analysis of protein short linear motifs
    Norman E Davey
    UCD Complex and Adaptive Systems Laboratory, University College Dublin, Dublin, Ireland
    Front Biosci (Landmark Ed) 15:801-25. 2010
    ..g. of physical protein interactions) as input for computational discovery...
  79. ncbi Determination of protease cleavage site motifs using mixture-based oriented peptide libraries
    B E Turk
    Department of Medicine, Beth Israel Deaconess Medical Center, Department of Cell Biology, Harvard Medical School, 330 Brookline Avenue, Boston, MA 02215, USA
    Nat Biotechnol 19:661-7. 2001
    ..Our results indicate that a small set of libraries can be used to quickly profile an expanding protease family, providing information applicable to the design of inhibitors and to the identification of protein substrates...
  80. pmc Secretion modification region-derived peptide disrupts HIV-1 Nef's interaction with mortalin and blocks virus and Nef exosome release
    Martin N Shelton
    Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, Georgia, USA
    J Virol 86:406-19. 2012
    ..Taken together, this work constitutes a significant step in understanding the underlying mechanism of exNef secretion, identifies a novel host-pathogen interaction, and introduces an HIV-derived peptide with antiviral properties...
  81. ncbi Parallels between cytokinesis and retroviral budding: a role for the ESCRT machinery
    Jez G Carlton
    Department of Infectious Diseases, King s College London School of Medicine, London, UK
    Science 316:1908-12. 2007
    ..Thus, HIV-1 budding and cytokinesis use a similar subset of cellular components to carry out topologically similar membrane fission events...
  82. ncbi Identification of sequence motifs that target neuronal nicotinic receptors to dendrites and axons
    Jian Xu
    Molecular Neurobiology Laboratory, The Salk Institute, La Jolla, California 92037, USA
    J Neurosci 26:9780-93. 2006
    ..These results provide valuable information in understanding diverse roles of neuronal nAChRs in mediating and modulating synaptic transmission, synaptic plasticity, and nicotine addiction...
  83. pmc Extensive phosphorylation with overlapping specificity by Mycobacterium tuberculosis serine/threonine protein kinases
    Sladjana Prisic
    Division of Infectious Diseases, Children s Hospital Boston, Harvard Medical School, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 107:7521-6. 2010
    ..tuberculosis and create a resource for understanding how specific phosphorylation events modulate protein activity. The results further provide the potential to predict likely cognate STPKs for newly identified phosphoproteins...
  84. ncbi Cracking the RNA polymerase II CTD code
    Sylvain Egloff
    Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
    Trends Genet 24:280-8. 2008
    ..How and when is the code written and read? How does it contribute to transcription and coordinate RNA processing?..
  85. pmc GlobPlot: Exploring protein sequences for globularity and disorder
    Rune Linding
    European Molecular Biology Laboratory, Biocomputing Unit, D 69117 Heidelberg, Germany
    Nucleic Acids Res 31:3701-8. 2003
    ..GlobPlot has a pipeline interface--GlobPipe--for the advanced user to do whole proteome analysis. GlobPlot can also be used as a generic infrastructure package for graphical displaying of any possible propensity...
  86. ncbi Systematic sequence analysis and identification of tissue-specific or stress-responsive genes of NAC transcription factor family in rice
    Yujie Fang
    National Center of Plant Gene Research, Huazhong Agricultural University, 430070, Wuhan, China
    Mol Genet Genomics 280:547-63. 2008
    ..Considering the fact that a very limited number of genes of the NAC family have been characterized, our data provide a very useful reference for functional analysis of this family in rice...
  87. ncbi FANMOD: a tool for fast network motif detection
    Sebastian Wernicke
    Institut fur Informatik, Friedrich Schiller Universität Jena Ernst Abbe Platz 2, 07743 Jena, Germany
    Bioinformatics 22:1152-3. 2006
    ..Additional benefits of FANMOD are the ability to analyze colored networks, a graphical user interface and the ability to export results to a variety of machine- and human-readable file formats including comma-separated values and HTML...
  88. pmc A PPxY motif within the VP40 protein of Ebola virus interacts physically and functionally with a ubiquitin ligase: implications for filovirus budding
    R N Harty
    Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, 3800 Spruce Street, Philadelphia, PA 19104 6049, USA
    Proc Natl Acad Sci U S A 97:13871-6. 2000
    ..Last, these studies imply that VP40 likely plays an important role in filovirus budding, and that budding of retroviruses, rhabdoviruses, and filoviruses may proceed via analogous mechanisms...
  89. 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...
  90. ncbi Somatic diversification of variable lymphocyte receptors in the agnathan sea lamprey
    Zeev Pancer
    Division of Developmental and Clinical Immunology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
    Nature 430:174-80. 2004
    ..Different evolutionary strategies were thus used to generate highly diverse lymphocyte receptors through rearrangement of LRR modules in agnathans (jawless fish) and of immunoglobulin gene segments in gnathostomes (jawed vertebrates)...
  91. pmc Minimotif Miner 3.0: database expansion and significantly improved reduction of false-positive predictions from consensus sequences
    Tian Mi
    Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269 2155, USA
    Nucleic Acids Res 40:D252-60. 2012
    ..This online database can be used to predict new functions in proteins and causes of disease...
  92. ncbi Motif switches: decision-making in cell regulation
    Kim Van Roey
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
    Curr Opin Struct Biol 22:378-85. 2012
    ....
  93. pmc c-Src and c-Abl kinases control hierarchic phosphorylation and function of the CagA effector protein in Western and East Asian Helicobacter pylori strains
    Doreen Mueller
    University of Magdeburg, Department of Medical Microbiology, Magdeburg, Germany
    J Clin Invest 122:1553-66. 2012
    ..These results provide insight for clinical H. pylori typing and clarify the role of phosphorylated bacterial effector proteins in pathogenesis...
  94. pmc SUMO pathway dependent recruitment of cellular repressors to herpes simplex virus type 1 genomes
    Delphine Cuchet-Lourenço
    MRC University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
    PLoS Pathog 7:e1002123. 2011
    ..We conclude that recruitment of ND10 components to sites associated with HSV-1 genomes reflects a cellular defence against invading pathogen DNA that is regulated through the SUMO modification pathway...
  95. pmc SLiMFinder: a web server to find novel, significantly over-represented, short protein motifs
    Norman E Davey
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
    Nucleic Acids Res 38:W534-9. 2010
    ..Returned motifs can also be compared with known SLiMs from the literature using CompariMotif. All results are available for download. The SLiMFinder server is available at: http://bioware.ucd.ie/slimfinder.html...
  96. pmc Partitioning of minimotifs based on function with improved prediction accuracy
    Sanguthevar Rajasekaran
    Department of Computer Science and Engineering, University of Connecticut, Storrs, Connecticut, United States of America
    PLoS ONE 5:e12276. 2010
    ..As a step toward resolving this problem we have built, implemented, and tested a new data-driven algorithm that reduces false-positive predictions...
  97. pmc Crystal structure of Toll-like receptor adaptor MAL/TIRAP reveals the molecular basis for signal transduction and disease protection
    Eugene Valkov
    School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia
    Proc Natl Acad Sci U S A 108:14879-84. 2011
    ..Jointly, our results provide a molecular and structural basis for the role of MAL in TLR signaling and disease protection...
  98. pmc Specific protein domains mediate cooperative assembly of HuR oligomers on AU-rich mRNA-destabilizing sequences
    Elizabeth J Fialcowitz-White
    Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
    J Biol Chem 282:20948-59. 2007
    ..Together, the results define distinct roles for the HuR hinge and RRM3 domains in formation of cooperative HuR.ARE complexes in solution...
  99. ncbi Noxa, a BH3-only member of the Bcl-2 family and candidate mediator of p53-induced apoptosis
    E Oda
    Department of Immunology, Graduate School of Medicine and Faculty of Medicine, University of Tokyo, Hongo 7 3 1, Bunkyo ku, Tokyo 113 0033, Japan
    Science 288:1053-8. 2000
    ..We also demonstrate that blocking the endogenous Noxa induction results in the suppression of apoptosis. Noxa may thus represent a mediator of p53-dependent apoptosis...
  100. pmc Mining protein loops using a structural alphabet and statistical exceptionality
    Leslie Regad
    MTI, INSERM UMR S 973, Universite Paris Diderot Paris 7, Paris, F 75205 Cedex 13, France
    BMC Bioinformatics 11:75. 2010
    ..Due to data sparsity, long loops have rarely been systematically studied...
  101. 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...

Research Grants62

  1. Potentiation of Glycine Receptors by Ethanol
    LUIS GERARDO AGUAYO; Fiscal Year: 2010
    ..Specifically, using a series of GlyR mutants, the presence of basic amino acid motifs that are responsible for G beta gamma binding and receptor modulation were discovered...
  2. DNA Helicases: Mechanisms and Functions
    Kevin D Raney; Fiscal Year: 2013
    ..Specific amino acid motifs are known to make contact with DNA, but the dynamic role of these motifs has only been inferred...
  3. MOLECULAR ASPECTS OF ORAL PLAQUE FORMATION
    Richard J Lamont; Fiscal Year: 2013
    ..gingivalis that engage the Ssp surface proteins of S. gordonii. Within SspB several amino acid motifs within a region spanning residues 1167-1193 (designated BAR), dictate binding activity and specificity...
  4. The BARD1 tumor suppressor and breast cancer
    Richard J Baer; Fiscal Year: 2013
    ..tumor-associated BARD1 mutations specifically eliminate the coding potential for one or both of the two BRCT amino acid motifs that lie at the C-terminus of the BARD1 polypeptide...
  5. Designing Spider Silk Proteins as Novel Biomaterials
    Randolph Lewis; Fiscal Year: 2009
    ..A number of spider silk genes have been cloned and sequenced revealing specific amino acid motifs that have been conserved for over 125 million years...
  6. SIGNALING MECHANISMS OF SOMATOSTATIN RECEPTORS
    DIANE BARBER; Fiscal Year: 2002
    ..will be investigated by determining whether inhibition of NHE1 is mediated by receptor subtype-specific amino acid motifs, G alpha 12, and the novel NHE1-regulatory protein CHP, and by determining whether NHE1 and CHP mediate ..
  7. Structure-Function of UDP-Glucuronosyltransferases
    Anna Radominska Pandya; Fiscal Year: 2009
    ..3. To sequence photolabeled polypeptides by mass spectrometry. 4. To modify amino acid motifs of putative binding sites by site-directed mutagenesis and catalytically characterize the generated mutants...
  8. DYNAMICS OF C-FOS PROTEIN INTERACTIONS
    EDWARD ZIFF; Fiscal Year: 2000
    ..The zipper interaction juxtaposes basic amino acid motifs of both proteins which form a sequence specific DNA binding domain...
  9. MOLECULAR MECHANISMS OF ALPHA 2,8-POLYSIALYTRANSFERASES
    FREDERIC TROY; Fiscal Year: 2001
    ..to be tested is that PST, STX and NeuS achieve the same catalytic functions by rearranging conserved amino acid motifs spatially in their active sites to bind CMP-Sia and initiate polySia chain synthesis while bound to the ..
  10. MINORITY PREDOCTORAL FELLOWSHIP PROGRAM
    ADRIENNE COTTRELL; Fiscal Year: 2007
    ..novel family of DNA recombinases, the Piv/MooV recombinase family, which does not share any of the conserved amino acid motifs found in the other DNA recombinase families...
  11. Identification of targeting motifs in K+ channels
    Jacqueline Rivera; Fiscal Year: 2005
    ..We hypothesize that the peptide sequences of K+ channels contain amino acid motifs that target them to distinct neuronal compartments...
  12. HOXA13 AMINO-TERMINAL FUNCTIONAL DOMAINS
    JEFFREY INNIS; Fiscal Year: 2004
    ..In Aim III we will use homologous recombination in ES cells to modify evolutionarily-conserved HOXA13 amino acid motifs known from work in Aim I to be critical for specific transcriptional activities in vitro...
  13. Botulinum Neurotoxin Substrate Specificity
    Neil Green; Fiscal Year: 2006
    ..abstract_text> ..
  14. BIOGENESIS OF RHOPTRIES IN TOXOPLASMA GONDII
    Keith Joiner; Fiscal Year: 2003
    ..transmembrane proteins to diverse intracellular locations based on the recognition of tyrosine-containing amino acid motifs in their cytoplasmic tails...
  15. DOPAMINERGIC SIGNALING IN NEUROLOGICAL DISORDERS
    Anita Sidhu; Fiscal Year: 2005
    ..Using progressively shorter synthetic peptides directed against specific amino acid motifs of intracellular loops of the D1 and D5 receptor, we will map the domains through which D1 couples to G(s)..
  16. 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. ..
  17. FUNCTION AND DYSFUNCTION IN HUMAN ANTITHROMBINS
    PETER GETTINS; Fiscal Year: 2007
    ..For antithrombins that have been activated by mutation,[unreadable] x-ray crystallography, through collaboration with Dr. Robin Carrell,[unreadable] will be used.[unreadable]..
  18. CELLULAR AND MOLECULAR STUDIES OF VESTIBULAR HAIR CELLS
    MANNING CORREIA; Fiscal Year: 2007
    ..The two specific aims of this project are linked in that one drives studies of the the effector pKir2.1 and the second directs studies the msucarinic receptors in the pathway proposed above. ..
  19. STRUCTURAL INVESTIGATION OF FOCAL ADHESION MOLECULES
    Jie Zheng; Fiscal Year: 2007
    ..abstract_text> ..
  20. 900MHz NMR for Structural Biology in Chicago
    PETER GETTINS; Fiscal Year: 2007
    ..As part of the facility, a resource will be established for development of procedures for intein-based segmental isotopic labeling of proteins, as well as for production of segmentally labeled DNA and RNA species. ..
  21. ASSEMBLY AND TRAFFICKING OF MHC CLASS II MOLECULES
    Hidde Ploegh; Fiscal Year: 2008
    ..H2 H4 mouse (autoimmune thyroiditis). We have backcrossed the CatB, CatL and CatS -/- mutations onto the NOD background and will explore the consequences of these cathepsin deficiencies for onset and severity of disease. ..
  22. VIRAL EVASION STRATEGIES: ANALYSIS OF HERPES VIRUSES HSV, VZV AND HHV-6-7
    Hidde Ploegh; Fiscal Year: 2007
    ..This analysis should reveal if and to what extent the MHC alleles in the human population help shape the "repertoire" of immunoevasins. ..
  23. A New Approach to Rapid Protein-Protein Docking
    Chandrajit Bajaj; Fiscal Year: 2008
    ..abstract_text> ..
  24. HMPV Fusion protein-host cell interactions
    REBECCA DUTCH; Fiscal Year: 2008
    ..This research will address significant questions concerning the cellular factors which interact with the HMPV fusion protein to facilitate attachment of the virus and entry into cells. [unreadable] [unreadable] [unreadable]..
  25. Hierarchical Methods for Large BioMolecular Complexes
    Chandrajit L Bajaj; Fiscal Year: 2010
    ..AIM 4: To implement, test, package and freely distribute our structural feature determination and fast search/fitting techniques. ..
  26. Hepatoma derived growth factor and vascular smooth muscle cell proliferation
    Allen D Everett; Fiscal Year: 2010
    ..We propose here to determine the mechanism regulating the activity of this protein to provide the basis for the future design of new drugs to treat cardiovascular disease. ..
  27. E6 Interaction with Cellular PDZ Proteins
    SCOTT BRIAN VANDE POL; Fiscal Year: 2010
    ..The purpose of this application is to characterize the PDZ complexes we have identified, and to explore the biological significance of E6-PDZ protein interactions. ..
  28. NEUROPEPTIDES IN THE CNS WITH NEW MASS SPECTROMETRIC SAMPLING PROTOCOLS
    Jonathan V Sweedler; Fiscal Year: 2010
    ..By developing powerful new proteomics-based technologies to answer questions about the most complex and elusive set of neuromodulators, the neuropeptides, basic insight into the effects of drugs of abuse on the CNS will be gained. ..
  29. Software Maintenance for Biomolecular Complexes
    Chandrajit L Bajaj; Fiscal Year: 2010
    ..3. Continued documentation and web based dissemination of all the components (libraries and tools) of our MVP. (http://ccvweb.csres.utexas.edu/software/). ..
  30. Molecular determinants of lung barrier function
    Michael Koval; Fiscal Year: 2009
    ....
  31. Phosphorylation of Estrogen Receptor and Coregulators
    BRIAN ROWAN; Fiscal Year: 2009
    ..abstract_text> ..
  32. Characterizing novel adult neuronal survival factors
    James Morgan; Fiscal Year: 2009
    ....
  33. Structural examination of serpin-protein interactions
    PETER GETTINS; Fiscal Year: 2009
    ..Dudley Strickland. ..
  34. TECHNOLOGIES FOR CELLULAR NEUROMETABOLOMICS
    Jonathan Sweedler; Fiscal Year: 2006
    ..The technology will be tailored to and validated on the most heterogeneous samples known - the mammalian brain. ..
  35. Mechanism of Meclp in the Checkpoint Response
    GEORGE BRUSH; Fiscal Year: 2006
    ..It is expected that these studies will provide significant insight into the molecular mechanisms underlying maintenance of the non-cancerous state under genotoxic conditions. ..
  36. HLA-G AND EQUIVALENT AND FETO-MATERNAL INTERACTION
    Hidde Ploegh; Fiscal Year: 2003
    ....
  37. Probing the pore of CFTR using chemical modification
    Xuehong Liu; Fiscal Year: 2003
    ..mechanism to explain how HFS type diets cause insulin resistance. and hypertension, and how a LFCC diet, antioxidant therapy or exercise training aid in the control of insulin resistance and hypertension. ..
  38. ULTRASENSITIVE CALORIMETRY SYSTEM FOR BIOMOLECULES
    PETER GETTINS; Fiscal Year: 2001
    ..abstract_text> ..
  39. NANOLITER VOLUME NUCLEAR MAGNETIC RESONANCE
    Jonathan Sweedler; Fiscal Year: 2003
    ..abstract_text> ..
  40. PHOSPHATIDYLINOSITOL 3 KINASE IN B CELL ACTIVATION
    KENNETH COGGESHALL; Fiscal Year: 2003
    ..Such information may reveal novel therapeutic targets in a variety of pathologic conditions and contribute to the etiology of such diseases. ..
  41. CELL SURFACE ACTIVITIES IN LIPOPROTEIN CATABOLISM
    ROBERT ORLANDO; Fiscal Year: 2003
    ....
  42. CELL BIOLOGY OF HEAT SHOCK PROTEIN MEDIATED IMMUNIZATION
    Hidde Ploegh; Fiscal Year: 2002
    ....
  43. 3rd Intl Symp on Serpin Biology, Structure and Function
    PETER GETTINS; Fiscal Year: 2002
    ..v) To provide an opportunity for promising junior scientists and minorities to play a major role in the meeting. ..
  44. Proteomics: The Next Grand Biological Challenge
    Walter Chazin; Fiscal Year: 2002
    ..A concentrated effort will be made to attract ethnic minorities, women and persons with disabilities as participants, organizers, and speakers. ..
  45. Dynamic Interactions of IP3 Receptor Ligands
    BARBARA EHRLICH; Fiscal Year: 2004
    ....
  46. ABI 3730 Capillary Sequencers
    Jonathan Sweedler; Fiscal Year: 2004
    ..abstract_text> ..
  47. Multifunctional Nanoparticles for Intracellular Delivery
    Stefan Franzen; Fiscal Year: 2006
    ..5. Develop strategies for covalent attachment of proteins and oligonucleotides to nanoparticles. 6. Determine of the efficiency of regulated in vitro protein expression using a well-characterized model system. ..
  48. PAPILLOMAVIRUS TRANSFORMATION
    Scott Vande Pol; Fiscal Year: 2006
    ..We will define how paxillin association with virally transduced oncogenes results in cellular transformation. ..
  49. Signaling by IgG receptors leading to phagocytosis
    KENNETH COGGESHALL; Fiscal Year: 2006
    ..The results will provide a better understanding of molecular process involved in clearance of infectious agents in humans. ..
  50. BETA H-SPECTRIN--ROLES IN CELL POLARITY AND SIGNALING
    Graham Thomas; Fiscal Year: 2001
    ..They will also illuminate the relationship between ras signaling and the cytoskeleton, a relationship that is important for oncogenic and metastatic processes. ..
  51. EMPTY CLASS II MHC PROTEINS: TRAFFICKING AND FUNCTION
    Laura Santambrogio; Fiscal Year: 2005
    ..The proposed research is part of an interactive research project grant. The companion project will focus on the biochemical aspects of antigen processing and peptide loading as part of the characterization of this novel pathway. ..
  52. Nucleic Acid Gordon Research Conference
    ANNA PYLE; Fiscal Year: 2004
    ..Poster sessions and optional recreational activities will stimulate informal interactions among participants. ..
  53. Aerotactic Signaling by the Escherichia coli Aer Protein
    John Parkinson; Fiscal Year: 2004
    ..Moreover, the existence of Aer homologs in pathogenic bacteria suggests that aerotactic behavior might play a role in virulence. Thus, a molecular understanding of Aer signal transduction could lead to new anti-infection agents. ..
  54. ROLE OF GLIA IN PARKINSON'S DISEASE
    James Morgan; Fiscal Year: 2004
    ..Furthermore, as dopamine but not other catecholamines triggers this pathway it can account for the neuronal specificity of MPTP killing. ..
  55. CONTROL OF CONNEXIN TRANSPORT AND ASSEMBLY
    Michael Koval; Fiscal Year: 2004
    ....
  56. QUANTITATIVE STUDY OF PRESYNAPTIC FACILITATION
    Maria Bykhovskaia; Fiscal Year: 2010
    ..All the developed computational algorithms will be available to other scholars. ..
  57. Structural Studies of AIDS-Responsive Drugs
    Vivian Cody; Fiscal Year: 2010
    ..These results will help guide the design of species selective inhibitors. Mutagenesis studies will be carried out to test these possibilitiesin the structure-based correlations to help design novel pjDHFRinhibitors. ..
  58. NEUROPEPTIDES IN THE CNS WITH IMAGING MASS SPECTROMETRY
    Jonathan Sweedler; Fiscal Year: 2002
    ..By developing powerful new proteomics-based technologies to answer questions about the most complex and elusive set of neuromodulators, and neuropeptides, basic insight into the effects of drugs of abuse on the CNS will be gained. ..
  59. PROTECTIVE ANTIGENS FROM HISTOPLASMA CAPSULATUM
    GEORGE DEEPE; Fiscal Year: 2007
    ..abstract_text> ..
  60. Regulation of the Atrial Natriuretic Peptide Receptor
    LINCOLN POTTER; Fiscal Year: 2005
    ..dependent regulation of natriuretic peptide receptors and to use this knowledge as a stepping stone towards the development of effective therapeutic agents for the treatment of cardiovascular diseases. ..