proteins

Summary

Summary: Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.

Top Publications

  1. pmc ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins
    Markus Wiederstein
    Center of Applied Molecular Engineering, Division of Bioinformatics, University of Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg, Austria
    Nucleic Acids Res 35:W407-10. 2007
  2. ncbi Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments
    Gerard Talavera
    Department of Physiology, Institute of Molecular Biology of Barcelona, Barcelona, Spain
    Syst Biol 56:564-77. 2007
  3. pmc PID: the Pathway Interaction Database
    Carl F Schaefer
    National Cancer Institute, Center for Biomedical Informatics and Information Technology, Rockville MD, USA
    Nucleic Acids Res 37:D674-9. 2009
  4. pmc Reactome knowledgebase of human biological pathways and processes
    Lisa Matthews
    Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
    Nucleic Acids Res 37:D619-22. 2009
  5. pmc Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    S F Altschul
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 25:3389-402. 1997
  6. pmc The Pfam protein families database
    Marco Punta
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
    Nucleic Acids Res 40:D290-301. 2012
  7. pmc KEGG: kyoto encyclopedia of genes and genomes
    M Kanehisa
    Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
    Nucleic Acids Res 28:27-30. 2000
  8. ncbi Comparative protein modelling by satisfaction of spatial restraints
    A Sali
    Department of Crystallography, Birkbeck College, London, England
    J Mol Biol 234:779-815. 1993
  9. pmc InterPro: the integrative protein signature database
    Sarah Hunter
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nucleic Acids Res 37:D211-5. 2009
  10. pmc Jalview Version 2--a multiple sequence alignment editor and analysis workbench
    Andrew M Waterhouse
    School of Life Sciences Research, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
    Bioinformatics 25:1189-91. 2009

Detail Information

Publications334 found, 100 shown here

  1. pmc ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins
    Markus Wiederstein
    Center of Applied Molecular Engineering, Division of Bioinformatics, University of Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg, Austria
    Nucleic Acids Res 35:W407-10. 2007
    ..ProSA-web is accessible at https://prosa.services.came.sbg.ac.at...
  2. ncbi Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments
    Gerard Talavera
    Department of Physiology, Institute of Molecular Biology of Barcelona, Barcelona, Spain
    Syst Biol 56:564-77. 2007
    ..This indicates that divergent and problematic alignment regions may lead, when present, to apparently better supported although, in fact, more biased topologies...
  3. pmc PID: the Pathway Interaction Database
    Carl F Schaefer
    National Cancer Institute, Center for Biomedical Informatics and Information Technology, Rockville MD, USA
    Nucleic Acids Res 37:D674-9. 2009
    ..The database is updated with new pathway content every month and supplemented by specially commissioned articles on the practical uses of other relevant online tools...
  4. pmc Reactome knowledgebase of human biological pathways and processes
    Lisa Matthews
    Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
    Nucleic Acids Res 37:D619-22. 2009
    ..Its current release includes 2975 human proteins, 2907 reactions and 4455 literature citations...
  5. pmc Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    S F Altschul
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 25:3389-402. 1997
    ..PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily...
  6. pmc The Pfam protein families database
    Marco Punta
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
    Nucleic Acids Res 40:D290-301. 2012
    ..Second, we discuss some of the features of domains of unknown function (also known as DUFs), which constitute a rapidly growing class of families within Pfam...
  7. pmc KEGG: kyoto encyclopedia of genes and genomes
    M Kanehisa
    Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
    Nucleic Acids Res 28:27-30. 2000
    ..The KEGG databases are daily updated and made freely available (http://www. genome.ad.jp/kegg/)...
  8. ncbi Comparative protein modelling by satisfaction of spatial restraints
    A Sali
    Department of Crystallography, Birkbeck College, London, England
    J Mol Biol 234:779-815. 1993
    ..Several such pdfs are obtained from the correlations between structural features in 17 families of homologous proteins which have been aligned on the basis of their 3D structures...
  9. pmc InterPro: the integrative protein signature database
    Sarah Hunter
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nucleic Acids Res 37:D211-5. 2009
    ..data, such as structural data, in new XML files on our FTP site, as well as the inclusion of matchless UniProtKB proteins in the existing match XML files...
  10. pmc Jalview Version 2--a multiple sequence alignment editor and analysis workbench
    Andrew M Waterhouse
    School of Life Sciences Research, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
    Bioinformatics 25:1189-91. 2009
    ..53 compliant sequence or annotation server...
  11. ncbi Inference of macromolecular assemblies from crystalline state
    Evgeny Krissinel
    European Bioinformatics Institute, Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    J Mol Biol 372:774-97. 2007
    ..The method is implemented as a public WWW service...
  12. pmc BLAT--the BLAST-like alignment tool
    W James Kent
    Department of Biology and Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA 95064, USA
    Genome Res 12:656-64. 2002
    ..BLAT is compared with other alignment programs on various test sets and then used in several genome-wide applications. http://genome.ucsc.edu hosts a web-based BLAT server for the human genome...
  13. doi MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification
    Jürgen Cox
    Department for Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Nat Biotechnol 26:1367-72. 2008
    ..MaxQuant automatically quantifies several hundred thousand peptides per SILAC-proteome experiment and allows statistically robust identification and quantification of >4,000 proteins in mammalian cell lysates.
  14. pmc The Protein Data Bank
    H M Berman
    Research Collaboratory for Structural Bioinformatics RCSB, Rutgers University, Piscataway, NJ 08854 8087, USA
    Nucleic Acids Res 28:235-42. 2000
    ..This paper describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information, and near-term plans for the future development of the resource...
  15. pmc I-TASSER: a unified platform for automated protein structure and function prediction
    Ambrish Roy
    Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
    Nat Protoc 5:725-38. 2010
    ..The function of the protein is then inferred by structurally matching the 3D models with other known proteins. The output from a typical server run contains full-length secondary and tertiary structure predictions, and ..
  16. ncbi Initial sequencing and analysis of the human genome
    E S Lander
    Whitehead Institute for Biomedical Research, Center for Genome Research, Cambridge, Massachusetts 02142, USA
    Nature 409:860-921. 2001
    ..We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence...
  17. pmc The RCSB Protein Data Bank: redesigned web site and web services
    Peter W Rose
    San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093 0743, USA
    Nucleic Acids Res 39:D392-401. 2011
    ..These improvements enable a range of new possibilities to analyze and understand structure data. The next generation of the RCSB PDB web site, as described here, provides a rich resource for research and education...
  18. pmc NCBI Reference Sequences: current status, policy and new initiatives
    Kim D Pruitt
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Rm 4As 47B, 45 Center Drive, Bethesda, MD, USA
    Nucleic Acids Res 37:D32-6. 2009
    ..nlm.nih.gov/RefSeq/) is a curated non-redundant collection of sequences representing genomes, transcripts and proteins. RefSeq records integrate information from multiple sources and represent a current description of the sequence, ..
  19. pmc Cre reporter strains produced by targeted insertion of EYFP and ECFP into the ROSA26 locus
    S Srinivas
    Department of Genetics and Development, Columbia University, New York, USA
    BMC Dev Biol 1:4. 2001
    ....
  20. ncbi Protein homology detection by HMM-HMM comparison
    Johannes Söding
    Department of Protein Evolution, Max Planck Institute for Developmental Biology Spemannstrasse 35, D 72076 Tubingen, Germany
    Bioinformatics 21:951-60. 2005
    ..Protein homology detection and sequence alignment are at the basis of protein structure prediction, function prediction and evolution...
  21. pmc CDD: a Conserved Domain Database for the functional annotation of proteins
    Aron Marchler-Bauer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 39:D225-9. 2011
    ..Pre-computed domain annotation is available for proteins in the Entrez/Protein dataset, and a novel interface, Batch CD-Search, allows the computation and download of ..
  22. pmc InParanoid 7: new algorithms and tools for eukaryotic orthology analysis
    Gabriel Ostlund
    Department of Biochemistry and Biophysics, Stockholm Bioinformatics Centre, AlbaNova University Centre, Stockholm University, SE 10691 Stockholm, Sweden
    Nucleic Acids Res 38:D196-203. 2010
    ..3 million proteins organized into 42.7 million pairwise ortholog groups...
  23. pmc CHARMM: the biomolecular simulation program
    B R Brooks
    Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Comput Chem 30:1545-614. 2009
    ..been developed over the last three decades with a primary focus on molecules of biological interest, including proteins, peptides, lipids, nucleic acids, carbohydrates, and small molecule ligands, as they occur in solution, crystals, ..
  24. doi Identification of host proteins required for HIV infection through a functional genomic screen
    Abraham L Brass
    Department of Genetics, Center for Genetics and Genomics, Brigham and Women s Hospital, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
    Science 319:921-6. 2008
    HIV-1 exploits multiple host proteins during infection. We performed a large-scale small interfering RNA screen to identify host factors required by HIV-1 and identified more than 250 HIV-dependency factors (HDFs)...
  25. pmc I-TASSER server for protein 3D structure prediction
    Yang Zhang
    Center for Bioinformatics and Department of Molecular Bioscience, University of Kansas, 2030 Becker Dr, Lawrence, KS 66047, USA
    BMC Bioinformatics 9:40. 2008
    ..Our laboratory has since then received numerous requests about the public availability of the I-TASSER algorithm and the usage of the I-TASSER predictions...
  26. pmc DrugBank: a knowledgebase for drugs, drug actions and drug targets
    David S Wishart
    Department of Computing Science, University of Alberta, Edmonton, AB, Canada T6G 2E8
    Nucleic Acids Res 36:D901-6. 2008
    ..DrugBank has also significantly improved the power and simplicity of its structure query and text query searches. DrugBank is available at http://www.drugbank.ca...
  27. ncbi Isolation of a human gene that inhibits HIV-1 infection and is suppressed by the viral Vif protein
    Ann M Sheehy
    Department of Microbiology, The Children s Hospital of Philadelphia, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
    Nature 418:646-50. 2002
    ..The Vif (virion infectivity factor) proteins are encoded by primate immunodeficiency viruses, most notably human immunodeficiency virus-1 (HIV-1)...
  28. pmc PANTHER: a library of protein families and subfamilies indexed by function
    Paul D Thomas
    Protein Informatics, Celera Genomics, Foster City, California 94404, USA
    Genome Res 13:2129-41. 2003
    In the genomic era, one of the fundamental goals is to characterize the function of proteins on a large scale...
  29. ncbi mTOR interacts with raptor to form a nutrient-sensitive complex that signals to the cell growth machinery
    Do Hyung Kim
    Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA
    Cell 110:163-75. 2002
    ..We propose that raptor is a missing component of the mTOR pathway that through its association with mTOR regulates cell size in response to nutrient levels...
  30. pmc The GOA database in 2009--an integrated Gene Ontology Annotation resource
    Daniel Barrell
    Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 37:D396-403. 2009
    ..ebi.ac.uk/QuickGO), which allows users to precisely tailor their annotation set...
  31. pmc STRING 8--a global view on proteins and their functional interactions in 630 organisms
    Lars J Jensen
    European Molecular Biology Laboratory, Heidelberg, Germany
    Nucleic Acids Res 37:D412-6. 2009
    Functional partnerships between proteins are at the core of complex cellular phenotypes, and the networks formed by interacting proteins provide researchers with crucial scaffolds for modeling, data reduction and annotation...
  32. pmc The Amber biomolecular simulation programs
    David A Case
    Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Raod, TPC15, La Jolla, CA 92037, USA
    J Comput Chem 26:1668-88. 2005
    ..with Energy Refinement, and now contains a group of programs embodying a number of powerful tools of modern computational chemistry, focused on molecular dynamics and free energy calculations of proteins, nucleic acids, and carbohydrates.
  33. ncbi In-gel digestion for mass spectrometric characterization of proteins and proteomes
    Andrej Shevchenko
    Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
    Nat Protoc 1:2856-60. 2006
    In-gel digestion of proteins isolated by gel electrophoresis is a cornerstone of mass spectrometry (MS)-driven proteomics. The 10-year-old recipe by Shevchenko et al. has been optimized to increase the speed and sensitivity of analysis...
  34. ncbi ProtTest: selection of best-fit models of protein evolution
    Federico Abascal
    Department of Biochemistry, Genetics and Immunology, Universidad de Vigo, Spain
    Bioinformatics 21:2104-5. 2005
    ..We have built a tool for the selection of the best-fit model of evolution, among a set of candidate models, for a given protein sequence alignment...
  35. pmc Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication
    Renate König
    Infectious and Inflammatory Disease Center, Burnham Institute for Medical Research, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
    Cell 135:49-60. 2008
    Human Immunodeficiency Viruses (HIV-1 and HIV-2) rely upon host-encoded proteins to facilitate their replication...
  36. ncbi UniRef: comprehensive and non-redundant UniProt reference clusters
    Baris E Suzek
    Protein Information Resource, Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC 20007, USA
    Bioinformatics 23:1282-8. 2007
    ..Clustering of protein sequence space based on sequence similarity helps organize all sequences into manageable datasets and reduces sampling bias and overrepresentation of sequences...
  37. doi Lysine acetylation targets protein complexes and co-regulates major cellular functions
    Chunaram Choudhary
    Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
    Science 325:834-40. 2009
    Lysine acetylation is a reversible posttranslational modification of proteins and plays a key role in regulating gene expression. Technological limitations have so far prevented a global analysis of lysine acetylation's cellular roles...
  38. ncbi Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions
    E Krissinel
    European Bioinformatics Institute, Genome Campus, Hinxton, Cambridge CB10 1SD, England
    Acta Crystallogr D Biol Crystallogr 60:2256-68. 2004
    ..A new score, balancing the r.m.s.d. and alignment length Nalign, is proposed. It is found that different servers agree reasonably well on the new score, while showing considerable differences in r.m.s.d. and Nalign...
  39. ncbi Imaging intracellular fluorescent proteins at nanometer resolution
    Eric Betzig
    Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, VA 20147, USA
    Science 313:1642-5. 2006
    We introduce a method for optically imaging intracellular proteins at nanometer spatial resolution...
  40. ncbi Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein
    Yasushi Ishihama
    Laboratory of Seeds Finding Technology LSFT, Eisai Co, Ltd, 5 1 3 Tokodai, Tsukuba, Ibaraki 300 2635, Japan
    Mol Cell Proteomics 4:1265-72. 2005
    ..This was also the case for 46 proteins in a mouse whole cell lysate...
  41. pmc Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution
    D Allan Drummond
    FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
    Cell 134:341-52. 2008
    ..and demonstrate using a molecular-level evolutionary simulation, that selection against toxicity of misfolded proteins generated by ribosome errors suffices to create all of the observed covariation...
  42. pmc Dynamics of DNA damage response proteins at DNA breaks: a focus on protein modifications
    Sophie E Polo
    The Gurdon Institute, Department of Biochemistry, University of Cambridge, Cambridge CB21QN, United Kingdom
    Genes Dev 25:409-33. 2011
    ..A common feature of DDR proteins is their mobilization in response to genotoxic stress...
  43. ncbi Comparison of multiple Amber force fields and development of improved protein backbone parameters
    Viktor Hornak
    Center for Structural Biology, Stony Brook University, Stony Brook, New York 11794, USA
    Proteins 65:712-25. 2006
    ..It also accomplishes improved agreement with published experimental data for conformational preferences of short alanine peptides and better accord with experimental NMR relaxation data of test protein systems...
  44. ncbi The cytoplasmic body component TRIM5alpha restricts HIV-1 infection in Old World monkeys
    Matthew Stremlau
    Department of Cancer Immunology and AIDS, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nature 427:848-53. 2004
    ..Our studies identify TRIM5alpha as a species-specific mediator of innate cellular resistance to HIV-1 and reveal host cell components that modulate the uncoating of a retroviral capsid...
  45. ncbi Structure validation by Calpha geometry: phi,psi and Cbeta deviation
    Simon C Lovell
    Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
    Proteins 50:437-50. 2003
    ..smoothing for 81,234 non-Gly, non-Pro, and non-prePro residues with B < 30 from 500 high-resolution proteins shows sharp boundaries at critical edges and clear delineation between large empty areas and regions that are ..
  46. ncbi The Microprocessor complex mediates the genesis of microRNAs
    Richard I Gregory
    The Wistar Institute, 3601 Spruce Street, Philadelphia, Pennsylvania 19104, USA
    Nature 432:235-40. 2004
    ..The larger complex contains multiple classes of RNA-associated proteins including RNA helicases, proteins that bind double-stranded RNA, novel heterogeneous nuclear ribonucleoproteins ..
  47. pmc The KEGG resource for deciphering the genome
    Minoru Kanehisa
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
    Nucleic Acids Res 32:D277-80. 2004
    ..on molecular interaction networks such as pathways and complexes (PATHWAY database), information about genes and proteins generated by genome projects (GENES/SSDB/KO databases) and information about biochemical compounds and reactions (..
  48. ncbi Protein folding and misfolding
    Christopher M Dobson
    University of Cambridge, Department of Chemistry, Lensfield Road, Cambridge CB2 1EW, UK
    Nature 426:884-90. 2003
    ..Folding and unfolding are crucial ways of regulating biological activity and targeting proteins to different cellular locations...
  49. ncbi Improved prediction of signal peptides: SignalP 3.0
    Jannick Dyrløv Bendtsen
    Center for Biological Sequence Analysis, BioCentrum DTU, Building 208, Technical University of Denmark, DK 2800 Lyngby, Denmark
    J Mol Biol 340:783-95. 2004
    We describe improvements of the currently most popular method for prediction of classically secreted proteins, SignalP...
  50. pmc ExPASy: The proteomics server for in-depth protein knowledge and analysis
    Elisabeth Gasteiger
    Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel Servet, 1211 Geneva 4, Switzerland
    Nucleic Acids Res 31:3784-8. 2003
    ..It provides access to a variety of databases and analytical tools dedicated to proteins and proteomics...
  51. pmc Human non-synonymous SNPs: server and survey
    Vasily Ramensky
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 30:3894-900. 2002
    ..We also studied the dependence of selective pressure on the structural and functional properties of proteins. We found that in our dataset the selection pressure against deleterious SNPs depends on the molecular function ..
  52. pmc PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse
    Peter V Hornbeck
    Cell Signaling Technology, 3 Trask Lane, Danvers, MA 01923, USA
    Nucleic Acids Res 40:D261-70. 2012
    ..resource for studying experimentally observed post-translational modifications, primarily of human and mouse proteins. It encompasses 1,30,000 non-redundant modification sites, primarily phosphorylation, ubiquitinylation and ..
  53. ncbi Phosphorylation and regulation of Akt/PKB by the rictor-mTOR complex
    D D Sarbassov
    Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Nine Cambridge Center, Cambridge, MA 02142, USA
    Science 307:1098-101. 2005
    ..Rictor-mTOR may serve as a drug target in tumors that have lost the expression of PTEN, a tumor suppressor that opposes Akt/PKB activation...
  54. pmc The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes
    Andreas Ruepp
    Institute for Bioinformatics MIPS, GSF National Research Center for Environment and Health, Ingolstaedter Landstrasse 1, D 85764 Neuherberg, Germany
    Nucleic Acids Res 32:5539-45. 2004
    ..flexible and scalable controlled classification system enabling the functional description of proteins from any organism. FunCat has been applied for the manual annotation of prokaryotes, fungi, plants and animals...
  55. 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
    ..that (i) improve the performance of HMMs and (ii) determine a good procedure for creating HMMs for sequences of proteins of known structure...
  56. ncbi Generalized lacZ expression with the ROSA26 Cre reporter strain
    P Soriano
    Nat Genet 21:70-1. 1999
  57. ncbi AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR
    R A Laskowski
    Department of Biochemistry and Molecular Biology, University College London, UK
    J Biomol NMR 8:477-86. 1996
    ..They are intended to be of use both to support ongoing NMR structure determination and in the validation of the final results...
  58. pmc Road to ruin: targeting proteins for degradation in the endoplasmic reticulum
    Melanie H Smith
    Department of Cellular and Molecular Pharmacology, Graduate Group in Biophysics and Howard Hughes Medical Institute, University of California San Francisco, CA 94158, USA
    Science 334:1086-90. 2011
    Some nascent proteins that fold within the endoplasmic reticulum (ER) never reach their native state...
  59. doi Drug target identification using side-effect similarity
    Monica Campillos
    European Molecular Biology Laboratory EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Science 321:263-6. 2008
    ..Nine of these were tested and confirmed in cell assays, documenting the feasibility of using phenotypic information to infer molecular interactions and hinting at new uses of marketed drugs...
  60. doi Adapting proteostasis for disease intervention
    William E Balch
    Department of Cell Biology and Institute for Childhood and Neglected Diseases, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    Science 319:916-9. 2008
    ....
  61. ncbi The ubiquitin-proteasome proteolytic pathway: destruction for the sake of construction
    Michael H Glickman
    Faculty of Biology and the Institute for Catalysis Science and Technology, Haifa, Israel
    Physiol Rev 82:373-428. 2002
    ..Although it was known that proteins do turn over, the large extent and high specificity of the process, whereby distinct proteins have half-lives ..
  62. pmc p62/SQSTM1 forms protein aggregates degraded by autophagy and has a protective effect on huntingtin-induced cell death
    Geir Bjørkøy
    Biochemistry Department, Institute of Medical Biology, University of Tromsø, 9037 Tromsø, Norway
    J Cell Biol 171:603-14. 2005
    ..light chain 3 (LC3) colocalized with p62 bodies and co-immunoprecipitated with p62, suggesting that these two proteins participate in the same complexes...
  63. pmc WoLF PSORT: protein localization predictor
    Paul Horton
    Computational Biology Research Center, AIST, Tokyo, Japan
    Nucleic Acids Res 35:W585-7. 2007
    ..Using html, the evidence for each prediction is shown in two ways: (i) a list of proteins of known localization with the most similar localization features to the query, and (ii) tables with detailed ..
  64. pmc The IntAct molecular interaction database in 2010
    B Aranda
    EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 38:D525-31. 2010
    ..Specialized views then allows 'zooming in' on the full annotation of interactions, interactors and their properties. IntAct source code and data are freely available at http://www.ebi.ac.uk/intact...
  65. pmc ExoCarta 2012: database of exosomal proteins, RNA and lipids
    Suresh Mathivanan
    Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
    Nucleic Acids Res 40:D1241-4. 2012
    ..ExoCarta (http://www.exocarta.org) is a manually curated database of exosomal proteins, RNA and lipids. The database catalogs information from both published and unpublished exosomal studies...
  66. pmc iLoc-Euk: a multi-label classifier for predicting the subcellular localization of singleplex and multiplex eukaryotic proteins
    Kuo Chen Chou
    Gordon Life Science Institute, San Diego, California, United States of America
    PLoS ONE 6:e18258. 2011
    Predicting protein subcellular localization is an important and difficult problem, particularly when query proteins may have the multiplex character, i.e...
  67. pmc PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations
    Todd J Dolinsky
    Department of Biochemistry and Molecular Biophysics, Center for Computational Biology, Washington University in St Louis, 700 S Euclid Ave, Campus Box 8036, St Louis, MO 63110, USA
    Nucleic Acids Res 35:W522-5. 2007
    ..These features are available through a new web interface (http://pdb2pqr.sourceforge.net/), which offers users a wide range of options for PDB file conversion, modification and parameterization...
  68. pmc An efficient algorithm for large-scale detection of protein families
    A J Enright
    Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
    Nucleic Acids Res 30:1575-84. 2002
    ..family classification can significantly contribute to the delineation of functional diversity of homologous proteins, the prediction of function based on domain architecture or the presence of sequence motifs as well as ..
  69. 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
    ..Here, we describe the properties of three well-known N-terminal sequence motifs directing proteins to the secretory pathway, mitochondria and chloroplasts, and sketch a brief history of methods to predict ..
  70. pmc The COG database: an updated version includes eukaryotes
    Roman L Tatusov
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
    BMC Bioinformatics 4:41. 2003
    ..Such a classification system based on orthologous relationships between genes appears to be a natural framework for comparative genomics and should facilitate both functional annotation of genomes and large-scale evolutionary studies...
  71. doi 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
    ..Enrichment for disorder in highly connected hub proteins and its correlation with organism complexity hint at the functional importance of disordered regions...
  72. ncbi Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
    W Kabsch
    Biopolymers 22:2577-637. 1983
  73. pmc SIFT: Predicting amino acid changes that affect protein function
    Pauline C Ng
    Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N A1 162, Seattle, WA 98109, USA
    Nucleic Acids Res 31:3812-4. 2003
    ..We have shown that SIFT can distinguish between functionally neutral and deleterious amino acid changes in mutagenesis studies and on human polymorphisms. SIFT is available at http://blocks.fhcrc.org/sift/SIFT.html...
  74. 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...
  75. pmc PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations
    Todd J Dolinsky
    Department of Biochemistry and Molecular Biophysics, Center for Computational Biology, Washington University in St Louis, 700 S Euclid Avenue, Campus Box 8036, St Louis, MO 63110, USA
    Nucleic Acids Res 32:W665-7. 2004
    ....
  76. pmc Expanded GGGGCC hexanucleotide repeat in noncoding region of C9ORF72 causes chromosome 9p-linked FTD and ALS
    Mariely DeJesus-Hernandez
    Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL 32224, USA
    Neuron 72:245-56. 2011
    ..Our findings indicate that repeat expansion in C9ORF72 is a major cause of both FTD and ALS...
  77. ncbi A statistical model for identifying proteins by tandem mass spectrometry
    Alexey I Nesvizhskii
    Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103, USA
    Anal Chem 75:4646-58. 2003
    A statistical model is presented for computing probabilities that proteins are present in a sample on the basis of peptides assigned to tandem mass (MS/MS) spectra acquired from a proteolytic digest of the sample...
  78. pmc An ATP-competitive mammalian target of rapamycin inhibitor reveals rapamycin-resistant functions of mTORC1
    Carson C Thoreen
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    J Biol Chem 284:8023-32. 2009
    ..Our findings challenge the assumption that rapamycin completely inhibits mTORC1 and indicate that direct inhibitors of mTORC1 kinase activity may be more successful than rapamycin at inhibiting tumors that depend on mTORC1...
  79. ncbi Bcl-2 antiapoptotic proteins inhibit Beclin 1-dependent autophagy
    Sophie Pattingre
    Department of Medicine, Columbia University College of Physicians and Surgeons, New York, New York 10032, USA
    Cell 122:927-39. 2005
    ..Here, we show that wild-type Bcl-2 antiapoptotic proteins, but not Beclin 1 binding defective mutants of Bcl-2, inhibit Beclin 1-dependent autophagy in yeast and mammalian ..
  80. ncbi SIN1/MIP1 maintains rictor-mTOR complex integrity and regulates Akt phosphorylation and substrate specificity
    Estela Jacinto
    Department of Physiology and Biophysics, UMDNJ Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
    Cell 127:125-37. 2006
    ..Our findings reveal that the SIN1-rictor-mTOR function in Akt-Ser473 phosphorylation is required for TORC2 function in cell survival but is dispensable for TORC1 function...
  81. pmc Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs
    Joshua E Babiarz
    Institute for Regeneration Medicine, Center for Reproductive Sciences, University of California at San Francisco, San Francisco, California 94143, USA
    Genes Dev 22:2773-85. 2008
    ..Our results extend the known diversity of mammalian small RNA-generating pathways and show that mammalian siRNAs exist in cell types other than oocytes...
  82. pmc Infrastructure for the life sciences: design and implementation of the UniProt website
    Eric Jain
    Swiss Prot group, Swiss Institute of Bioinformatics, CMU, 1 Michel Servet, 1211 Geneva 4, Switzerland
    BMC Bioinformatics 10:136. 2009
    ..Following several years of intense development and a year of public beta testing, the http://www.uniprot.org domain was switched to the newly developed site described in this paper in July 2008...
  83. ncbi A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
    Yong Duan
    Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
    J Comput Chem 24:1999-2012. 2003
    Molecular mechanics models have been applied extensively to study the dynamics of proteins and nucleic acids. Here we report the development of a third-generation point-charge all-atom force field for proteins...
  84. pmc The COG database: a tool for genome-scale analysis of protein functions and evolution
    R L Tatusov
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 28:33-6. 2000
    Rational classification of proteins encoded in sequenced genomes is critical for making the genome sequences maximally useful for functional and evolutionary studies...
  85. doi HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment
    Michael Remmert
    Gene Center and Center for Integrated Protein Science Munich, Ludwig Maximilians Universitat Munchen, Munich, Germany
    Nat Methods 9:173-5. 2012
    ..genzentrum.lmu.de/hhblits/). Compared to the sequence-search tool PSI-BLAST, HHblits is faster owing to its discretized-profile prefilter, has 50-100% higher sensitivity and generates more accurate alignments...
  86. pmc Regulation of the mTOR complex 1 pathway by nutrients, growth factors, and stress
    Shomit Sengupta
    Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA
    Mol Cell 40:310-22. 2010
    ..This review focuses on the key components of the mTOR complex 1 pathway and on how various stresses impinge upon them...
  87. pmc The role of dynamic conformational ensembles in biomolecular recognition
    David D Boehr
    Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA
    Nat Chem Biol 5:789-96. 2009
    ....
  88. pmc Interactome networks and human disease
    Marc Vidal
    Center for Cancer Systems Biology and Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA
    Cell 144:986-98. 2011
    ....
  89. ncbi Cytochrome c and dATP-dependent formation of Apaf-1/caspase-9 complex initiates an apoptotic protease cascade
    P Li
    Howard Hughes Medical Institute, and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 75235, USA
    Cell 91:479-89. 1997
    ....
  90. pmc MolProbity: all-atom contacts and structure validation for proteins and nucleic acids
    Ian W Davis
    Department of Biochemistry, Duke University, Durham, NC, USA
    Nucleic Acids Res 35:W375-83. 2007
    MolProbity is a general-purpose web server offering quality validation for 3D structures of proteins, nucleic acids and complexes...
  91. ncbi The evolutionary fate and consequences of duplicate genes
    M Lynch
    Department of Biology, University of Oregon, Eugene, OR 97403, USA
    Science 290:1151-5. 2000
    ..Although duplicate genes may only rarely evolve new functions, the stochastic silencing of such genes may play a significant role in the passive origin of new species...
  92. doi Some remarks on protein attribute prediction and pseudo amino acid composition
    Kuo Chen Chou
    Gordon Life Science Institute, 13784 Torrey Del Mar Drive, San Diego, CA 92130, USA
    J Theor Biol 273:236-47. 2011
    With the accomplishment of human genome sequencing, the number of sequence-known proteins has increased explosively. In contrast, the pace is much slower in determining their biological attributes...
  93. 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
    The Structural Classification of Proteins (SCOP) database is a comprehensive ordering of all proteins of known structure, according to their evolutionary and structural relationships...
  94. pmc AMPK phosphorylation of raptor mediates a metabolic checkpoint
    Dana M Gwinn
    Molecular and Cell Biology Laboratory, Dulbecco Center for Cancer Research, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
    Mol Cell 30:214-26. 2008
    ..These findings uncover a conserved effector of AMPK that mediates its role as a metabolic checkpoint coordinating cell growth with energy status...
  95. pmc Protein 3D structure computed from evolutionary sequence variation
    Debora S Marks
    Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
    PLoS ONE 6:e28766. 2011
    ..We quantify this observation by computing, from sequence alone, all-atom 3D structures of fifteen test proteins from different fold classes, ranging in size from 50 to 260 residues, including a G-protein coupled receptor...
  96. pmc Ragulator-Rag complex targets mTORC1 to the lysosomal surface and is necessary for its activation by amino acids
    Yasemin Sancak
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
    Cell 141:290-303. 2010
    ..We show that amino acids induce the movement of mTORC1 to lysosomal membranes, where the Rag proteins reside...
  97. ncbi HADDOCK: a protein-protein docking approach based on biochemical or biophysical information
    Cyril Dominguez
    Department of NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584CH, Utrecht, The Netherlands
    J Am Chem Soc 125:1731-7. 2003
    ..In all cases, the best structures generated by HADDOCK, that is, the structures with the lowest intermolecular energies, were the closest to the published structure of the respective complexes (within 2.0 A backbone RMSD)...
  98. pmc MINT, the molecular interaction database: 2012 update
    Luana Licata
    Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
    Nucleic Acids Res 40:D857-61. 2012
    ..bio.uniroma2.it/mint/download.do. We report here the growth of the database, the major changes in curation policy and a new algorithm to assign a confidence to each interaction...
  99. ncbi IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content
    Zsuzsanna Dosztanyi
    Institute of Enzymology, BRC, Hungarian Academy of Sciences, PO Box 7, H 1518 Budapest, Hungary
    Bioinformatics 21:3433-4. 2005
    Intrinsically unstructured/disordered proteins and domains (IUPs) lack a well-defined three-dimensional structure under native conditions...
  100. ncbi Predicting subcellular localization of proteins based on their N-terminal amino acid sequence
    O Emanuelsson
    Stockholm Bioinformatics Center, Department of Biochemistry, Stockholm University, Stockholm, S 106 91, Sweden
    J Mol Biol 300:1005-16. 2000
    A neural network-based tool, TargetP, for large-scale subcellular location prediction of newly identified proteins has been developed...
  101. ncbi A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach
    S Whelan
    Department of Zoology, University of Cambridge, Cambridge, England
    Mol Biol Evol 18:691-9. 2001
    ..This suggests that it provides a better overall fit to the evolutionary process in globular proteins and may lead to more accurate phylogenetic tree estimates...

Research Grants102 found, 100 shown here

  1. Apoptosis and Trophoblast Fusion
    NEAL STEWART ROTE; Fiscal Year: 2010
    ..phospholipids to form a phosphatidylserine (PS)-rich exofacial surface, expression and insertion of fusion proteins into the plasma membrane, and rearrangement of actin cytoskeletal elements...
  2. ADIPOCYTE PROTEIN SECRETION AND INSULIN ACTION
    Harvey Lodish; Fiscal Year: 2007
    ..endo-/exocytotic compartments in 3T3-L1 adipocytes including vesicles which transport membrane associated proteins like GLUT4, secreted proteins where secretion is stimulated by insulin such as ARCP30 (adipocyte complement ..
  3. MECHANISM-BASED DRUG SELECTION AND DESIGN: NUCLEOTIDE SA
    Buddy Ullman; Fiscal Year: 2003
    ..These reagents are expected to permit structure-based discovery of new drug classes that target proteins necessary for parasite survival...
  4. A novel transgenic silkworm system for recombinant glycoprotein production
    Donald L Jarvis; Fiscal Year: 2010
    DESCRIPTION (provided by applicant): Many biomedically significant proteins, including antibodies, cytokines, anticoagulants, blood clotting factors, and others are glycoproteins...
  5. STATISITICAL DESIGN, MONITORING &COORD. OF VISION CLINICAL TRIALS &EPIDEMIOLOGY
    Keri Hammel; Fiscal Year: 2013
    ..It contains B27PD, a small protein fragment, which is similar to proteins in the parts of the eye being attacked by the immune system...
  6. STATISITICAL DESIGN, MONITORING &COORD. OF VISION CLINICAL TRIALS &EPIDEMIOLOGY
    Keri Hammel; Fiscal Year: 2012
    ..It contains B27PD, a small protein fragment, which is similar to proteins in the parts of the eye being attacked by the immune system...
  7. Understanding/ Treating Neuropsychiatric Symptoms of Pediatric Physical Illness
    Eva Szigethy; Fiscal Year: 2009
    ..abstract_text> ..
  8. Discovery metabolite profiling of the prolyl peptidases
    Alan Saghatelian; Fiscal Year: 2009
    ..Researchers have recently developed a number of methods to identify the genes, proteins, and metabolites associated with disease...
  9. Genetic variation and regulatory networks: Mechanisms and complexity
    DANA PE ER; Fiscal Year: 2009
    ..These tools will be made publicly available, including a friendly graphical user interface and visualization. ..
  10. Variation in M. tuberculosis in response to host selection
    Sarah Fortune; Fiscal Year: 2009
    ..In these studies, we expect to provide fundamental insights into the mechanisms and targets of diversifying immune selection in M. tuberculosis. ..
  11. Personalized Clinical Diagnostics and Beyond: Integrated Ring Resonator Arrays
    Ryan Bailey; Fiscal Year: 2009
    ..This technology promises to broadly impact the landscape of the biomedical sciences, both meeting the clinical diagnostic challenges of today and pioneering the paradigm-shifting discoveries of tomorrow. ..
  12. NIH Director's Pioneer Award
    Junying Yuan; Fiscal Year: 2009
    ..No Abstract provided ..
  13. Chymase-Mediated MMP Activation in Ishemia Reperfusion Injury
    LOUIS JOSEPH DELL'ITALIA; Fiscal Year: 2013
    ..I) to Ang II (11,12), mast cell chymase activates interstitial MMPs (13-18) and directly degrades cell surface proteins such as fibronectin (19), resulting in smooth muscle cell (20,21) and cardiomyocyte (22) death...
  14. Transcription factors regulating sensory gene expression and pain pathways
    Eric E Turner; Fiscal Year: 2011
    ..molecules, called transcription factors, which bind to DNA and regulate the expression of the functional proteins that define sensory neurons...
  15. Mice Humanized with Hepatocytes and iPS Cells from Patients with Metabolic Diseas
    Stephen C Strom; Fiscal Year: 2010
    ..performs over 3,000 functions critical to maintaining the organism, ranging from production and secretion of proteins such as albumin, clotting factors and antiproteases, to metabolism and excretion of exogenous compounds such as ..
  16. Optimization of DNA Repair by Abh8
    Lauren Endres; Fiscal Year: 2013
    ..The DDR is a broad cellular response involving a network of proteins that are highly conserved between yeast and mammals [4]...
  17. CFI Pathogen Inactivation Technology
    Trevor P Castor; Fiscal Year: 2010
    ..and pathogenic bacteria;(3) evaluate the potential of applying SFS-CFI enabling technology to human plasma proteins such as fibrinogen and other components;and (4) evaluate compatibility of SFS-CFI with other enabling pathogen ..
  18. Mapping for Specialized Domains for FCeRI Signaling &Internalization
    Bridget S Wilson; Fiscal Year: 2013
    ..Based upon recent evidence, we propose that membrane proteins are concentrated in "protein islands," protein and cholesterol-rich domains separated by expanses of mostly lipid...
  19. Anti-Inflammatory Glycosaminoglycan Ethers for Treatment of Periodontitis
    JUSTIN RODNEY SAVAGE; Fiscal Year: 2011
    ..due to increased exposure to advanced glycation end-products (AGEs), which arise from spontaneous glycation of proteins. AGEs from high blood sugar or from inhalation of AGES from tobacco products amplify inflammation by ligation of ..
  20. Vaccine Development for Falciparum Malaria in Pregnant Women and Their Offspring
    Ian C Michelow; Fiscal Year: 2013
    ..Candidate vaccine proteins will be screened, confirmed and selected for clinical trials using pioneering molecular tools and blood samples ..
  21. Cardiotrophin-Like Cytokine 1, a Candidate Molecule for the FSGS Factor
    Virginia J Savin; Fiscal Year: 2010
    ..The molecular basis for recurrent FSGS is unknown although abnormal podocyte proteins associated with familial FSGS have been identified...
  22. Hypothalamic Orexin Role in Menopause-Associated Hot Flashes and Mood/Sleep Disru
    PHILIP LEE JOHNSON; Fiscal Year: 2013
    ..tracing compounds, and ex vivo functional brain imaging using immunohistochemistry to detect immediate early gene proteins. In 2008 and 2010, I was respectively promoted to Research Assistant Professor, and then to Assistant Professor ..
  23. H1R Signaling and Immune Deviation in EAE
    Cory Teuscher; Fiscal Year: 2013
    ..Since we found no difference in G-protein activation of allelic H1R-Ga fusion proteins, this suggested that H1R signaling may also involve a novel non-G-protein b-arrestin pathway...
  24. Cross-talk Between Coagulation, Inflammation, and Immunity
    Lawrence L Leung; Fiscal Year: 2013
    ..thrombomodulin and in that context, thrombin's function is "modulated'and will activate two other proteins, protein C and procarboxypeptidase B (pCPB)...
  25. Phosphorylation of FGF23 coordinates crosstalk between the skeleton and kidney
    VINCENT SCOTT TAGLIABRACCI; Fiscal Year: 2013
    ..The majority of phosphoproteins are intracellular;however, numerous extracellular proteins are also phosphorylated...
  26. Physiological role of PRDM16 in brown fat development and energy balance
    Patrick Seale; Fiscal Year: 2011
    ..We therefore hypothesize that another closely related member of the PR-domain containing family of proteins may partially compensate for the chronic loss of PRDM16 in BAT development...
  27. Importance of antigen specific immunoglobulin responses in controlling SIV/SHIV i
    Bapi Pahar; Fiscal Year: 2010
    ..mucosal secretions from macaques with different levels of immunity to trimeric recombinant SIV/SHIVgp140 envelope proteins using surface plasmon resonance (SPR) technology (Biacore)...
  28. Prevention of Acute Lung Injury by IL-6 activated STAT3
    Ana Moran; Fiscal Year: 2010
    ..whose expression was altered the greatest by T/HS and normalized by IL-6-activated Stat3 were genes encoding proteins that are known to be expressed by epithelial cells-Glp1r, Pik3r1 and Lcn2-as well as genes encoding proteins- ..
  29. Antiphospholipid antibodies and lupus: new molecular targets for treatment
    Emilio B Gonzalez; Fiscal Year: 2013
    ..specific binding of aPL/a22GPI Abs to DI of 22GPI or by blocking the interaction of 22GPI with the receptor(s) proteins recognized by 22GPI on target cells...
  30. Novel Mitochondrial Mechanisms of Ethanol-Induced Cardiac Injury in Aged Females
    DONNA HOPE KORZICK; Fiscal Year: 2010
    ..Of particular interest are adaptive changes in proteins associated with metabolism, oxidative stress, and cell death...
  31. Targeting Galectin-3 with novel drugs for treatment of eczema
    Fu Tong Liu; Fiscal Year: 2010
    ..Galectins function intracellularly by binding to other proteins through protein-protein interactions...
  32. Gamma-Synuclein-Mediated Regulation of Norepinephrine Transporter
    Anita Sidhu; Fiscal Year: 2010
    ..synuclein [-Syn], a member of the synuclein family of proteins, is expressed in monoaminergic neurons, but its function in the brain is not known. We have shown that ...
  33. Role of SAMe on UBC9 and sumolyation in liver cancer and alcoholic liver injury
    Maria Lauda Tomasi; Fiscal Year: 2012
    DESCRIPTION (provided by applicant): Posttranslational modifications mediated by ubiquitin-like proteins regulate a variety of cellular pathways...
  34. Structure and function of urea transporters
    Ming Zhou; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): Urea transporters (UT) are integral membrane proteins that facilitate transport of urea across cell membrane. UTs are highly expressed in many mammalian tissues, including kidney, liver, and brain...
  35. Reactive (AA)Amyloidosis
    Merrill D Benson; Fiscal Year: 2013
    ..whether acquired or genetic, cause recurrent inflammation resulting in elevated expression of the acute phase proteins of the serum amyloid A (SAA) family...
  36. Discovery of Small Molecule MBT Domain Antagonists
    STEPHEN VERNON FRYE; Fiscal Year: 2010
    ..1] The template upon which the epigenome is written is chromatin - the complex of histone proteins, RNA and DNA that efficiently package the genome in an appropriately accessible state within each cell...
  37. Role of Txnip in adapting fuel metabolism to nutritional state
    SIMON HUI; Fiscal Year: 2013
    ..Cellular antioxidant and ROS defense system will be measured as well as the levels of oxidative modified proteins, DNA and lipids in the mitochondria...
  38. Right ventricular contractile dysfunction after pressure overload
    CLIFFORD RUSSELL GREYSON; Fiscal Year: 2013
    ..depending on the experimental model, contractile dysfunction has been attributed to disruption of structural proteins such as desmin, spectrin, 1-actinin or titin;modification of regulatory proteins such as troponin-I, troponin-T;..
  39. Sphingolipid Metabolism in Drosophila Development
    Julie D Saba; Fiscal Year: 2013
    ..We have observed that mutants in key membrane proteins such as dynamin and dystroglycan phenocopy the Sply myopathy...
  40. Regulation of B Cell Function by Membrane-Cytoskeletal Remodeling
    Neetu Gupta; Fiscal Year: 2012
    ..effectively, B cells need to migrate in the lymphoid tissues for surveillance, and upon binding pathogenic proteins they need to reorganize their surface components for activation...
  41. Regulation of ER stress-induced cell death
    Randal J Kaufman; Fiscal Year: 2013
    ..that islets from Chop-/- mice are protected from oxidative stress that occurs upon accumulation of unfolded proteins in the ER...
  42. The role of Fli1 in T cell function and the pathogenesis of lupus
    Tamara K Nowling; Fiscal Year: 2011
    ..the down-regulation of Fli1 in activated T cells in lupus prone and control mice will be analyzed by identifying proteins binding the endogenous Fli1 promoter using chromatin immunoprecipitation (IP) and analyses of expression levels, ..
  43. REGULATION AND FUNCTION OF STE20-RELATED PROTEIN KINASES
    Melanie H Cobb; Fiscal Year: 2012
    ..WNKs are ubiquitous multipurpose, multifunctional enzymes that have been found in screens to identify proteins required for development and survival, and that affect growth in flies, worms, and mammals...
  44. THE ROLE OF ACETYLATION IN MITOCHONDRIAL FUNCTION
    Gary Cecchini; Fiscal Year: 2013
    ..Numerous studies show that posttranslational modification of proteins can regulate their function...
  45. Lung Lysyl Oxidase Regulation by Metal Ion Homeostasis
    Wande Li; Fiscal Year: 2013
    ..LO mRNA stability-related cis-elements in the 3'-untranslation region and their corresponding binding proteins;and 4) to investigate biological consequences of Cd silencing of the LO gene in cell and animal models by ..
  46. Functional Genomics of the Mitochondrial Proteome
    Dennis R Winge; Fiscal Year: 2011
    ..Mammalian mitochondria harbor ~ 1000 proteins, but of these proteins, the function of ~ 300 remain largely unknown...
  47. T cell regulation by N-glycosylation
    Michael Demetriou; Fiscal Year: 2013
    ..However, virtually all cell surface and secreted proteins in metazoans are modified by the addition of complex carbohydrates in the ER/Golgi secretory pathway...
  48. DNA Damage and Response in the Bladder Microenvironment.
    Bradley P Dixon; Fiscal Year: 2013
    ..activation will be determined by flow cytometry and by western blot for activation of cell cycle checkpoint proteins. Activation of apoptosis will be quantified by western blot, as well as annexin V binding through flow cytometry...
  49. Targeted siRNA nanotechnology for intravesical treatment of urologicaldiseases
    Robert M Weiss; Fiscal Year: 2010
    ..We now plan to: 1) develop and test a number of nanoparticle controlled release systems containing targeting proteins that will stabilize and deliver siRNAs and drugs, to test their physicochemical properties (materials testing), ..
  50. Translational Machinery in Stress Signaling and Tumor Suppression
    THOMAS J contact BEGLEY; Fiscal Year: 2010
    ..based responses have great potential to maintain or quickly increase the levels of important regulatory proteins when cells are experiencing stress1-2...
  51. Patient-Derived Stem Cells for Phosphoproteomic Profiling Neuropsychopathology
    Dieter A Wolf; Fiscal Year: 2011
    ..be particularly well-suited &informative - is a better understanding of changes in the expression of key proteins, particularly their phosphorylation state, at the level of the proteome &phosphoproteome...
  52. IMMUNOGENETICS OF COLLAGEN INDUCED ARTHRITIS IN MICE
    Chella David; Fiscal Year: 2009
    ..by enhancing production of peptidyl arginine deiminase (PAD) enzyme that leads to citrullination of synovial proteins. These citrullinated proteins are presented with greater efficiency by HLA-DR4 leading to an autoreactive T and B ..
  53. Investigating Mechanism of Intracellular Rotational Transport with Optical T
    Jeffrey N Anker; Fiscal Year: 2012
    ..This inflammation and associated overproduction of reactive oxygen species further oxidize RNA/DNA/proteins, leading to fibrosis, mutagenesis and lung cancer...
  54. Targeting Inflammation for the Amelioration of Cisplatin-Hearing Loss
    Vickram Ramkumar; Fiscal Year: 2011
    ..Other treatment approaches target proteins involved in apoptosis which contribute to death of outer hair cells (OHCs)...
  55. MOLECULAR BASIS OF REOVIRUS PATHOGENESIS
    Terence S Dermody; Fiscal Year: 2013
    ..steps in virus-host interaction often depend on selective recognition of cellular receptors and viral replication proteins that operate at distinct sites...
  56. Insulin Signaling and the Heart in Diabetes
    EVAN DALE ABEL; Fiscal Year: 2011
    ..basis of unregulated autophagy, thereby defining an essential role for insulin and IGF-1 signaling acting via IRS proteins in the regulation cardiac autophagy in vivo...
  57. Vitamin D and Estrogen Action in Bone: Concerted Role for hnRNPs in the C Family
    John S Adams; Fiscal Year: 2013
    ..We coined these resistance-causing proteins the vitamin D response element binding protein (VDRE-BP) and estrogen response element binding (ERE-BP) for their ..
  58. Skeletal Muscle. Ca Release Control Inside the Sarcoplasmic Reticulum.
    Eduardo Rios; Fiscal Year: 2013
    ..Ca2+ release from the store, and (2) whether and how calsequestrin and triadin, two strategically located SR proteins, contribute to this control. A technical task, which we call "aim 0", is to image and measure [Ca2+]SR...
  59. Role of IKK in NSCLC: Modulation of SMRT and NF-kappaB
    Marty W Mayo; Fiscal Year: 2012
    ..transcription factors, including Twist, and increases the expression of the polycomb repressive complex (PRC) proteins, which are critical for initiation and maintenance of stem-like phenotypes...
  60. Mitochondrial Dysfunction and Adipose Insulin Resistance
    David A Bernlohr; Fiscal Year: 2013
    ..proteomic, metabolomic and molecular analyses that point toward the covalent modification of mitochondrial proteins with bioactive lipids and the oxidation of mitochondrial thioredoxin as central to the process...
  61. Biology and Pathologies of Type V Collagen
    Daniel S Greenspan; Fiscal Year: 2013
    ..artery disease is, at least partly, an autoimmune disease directed against one of the body's own proteins. If such studies are borne out, the ramifications are huge, with profound implications for understanding, ..
  62. Trichothecene Toxicity and the Ribotoxic Stress Response
    James J Pestka; Fiscal Year: 2012
    ..In Aim 3, we will track DON-induced changes in ribosome-associated proteins in the macrophage relative to composition, kinetics and kinase activites...
  63. Role of JAK2-PAK1 interaction in prolactin-dependent signaling
    Maria Diakonova; Fiscal Year: 2013
    ..Tyrosine (Tyr) kinase JAK2 was identified as a PRLR-bound signaling molecule. Identification of the proteins recruited to the PRLR-JAK2 and dissection of the signaling pathways that are subsequently activated will ..
  64. SUPPORT CONTRACT FOR THE NTP INTERAGENCY CENTER/VALIDATION OF ALT METHODS
    David Allen; Fiscal Year: 2009
    ..components, allergenics, somatic cells, gene therapy, tissues, monoclonal antibodies, and recombinant therapeutic proteins that are used to treat or protect humans or animals...
  65. Structural and molecular basis of drug-induced IKACh reduction
    SAMI FOUAD NOUJAIM; Fiscal Year: 2012
    ..I elucidated the roles of sarcolemmal inward rectifier (Kir2.x) potassium channel proteins in the maintenance of VF, and of the ryanodine receptor type 2 in the initiation of ventricular tachyarrhythmias ..
  66. Rac GTPase signaling during embryonic salivary gland branching morphogenesis
    Sharon Sequeira; Fiscal Year: 2012
    ..hydroxylase;IB, immunoblotting;IF, immunofluorescence;IP, immunoprecipitation;Par, partitioning-defective proteins;PLGA, polylactic-co-glycolic acid polymer;Rac1, Ras-related C3 botulinum substrate 1;SMG, submandibular salivary ..
  67. Structural and molecular basis of drug-induced IKACh reduction
    SAMI FOUAD NOUJAIM; Fiscal Year: 2013
    ..I elucidated the roles of sarcolemmal inward rectifier (Kir2.x) potassium channel proteins in the maintenance of VF, and of the ryanodine receptor type 2 in the initiation of ventricular tachyarrhythmias ..
  68. Molecular Mechanisms of Parvovirus Gene Expression and Replication
    Jianming Qiu; Fiscal Year: 2013
    ..of B19V mRNAs, and generates abundant small viral mRNAs for encoding two small non- structural viral proteins, i.e. 7.5-kDa and 11-kDa...
  69. Metabolic mechanisms of antiestrogen resistance in breast cancer
    UBALDO EMILIO MARTINEZ OUTSCHOORN; Fiscal Year: 2013
    ..I will stain a human tumor microarray (TMA) of patients with ER+ breast cancer treated with tamoxifen for the proteins listed in aim 1...
  70. Analysis of gene regulation of Vibrio cholerae during infection
    Jun Zhu; Fiscal Year: 2013
    ..cholerae proteins and other pathogens. We will first investigate how V...
  71. Role of Peroxidasin in Glomerular Matrix Homeostasis
    Gautam Bhave; Fiscal Year: 2013
    ..HOX are highly reactive and oxidatively halogenate proteins to adversely affect cell function...
  72. Lipid Droplet Metabolism
    Fredric B Kraemer; Fiscal Year: 2013
    ..physical properties of LDs are distinctively altered in quantifiably defined ways by specific droplet-associated proteins and these physical properties contribute to LD size (growth and fusion) and metabolism...
  73. Identification of Proteins Important for Male Osteoporosis
    Hong Wen Deng; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): Identification of Proteins Important for Male Osteoporosis Osteoporosis is a major public health problem, mainly characterized by low bone mineral density (BMD)...
  74. Molecular Mechanisms of Disease Progression in Myeloid Malignancy
    ELIZABETH ANN EKLUND; Fiscal Year: 2013
    ..Stat3, Stat5 and Xiap proteins are also increased in Icsbp-/- cells in a Gas2/calpain-dependent manner...
  75. MECHANISMS OF RADIORESISTANCE AND CELL CYCLE PROGRESSION
    Howard B Lieberman; Fiscal Year: 2013
    ..metastasis, including migration towards fibronectin, invasion, cell adhesion to various extracellular matrix proteins, and metastatic behavior in an in vivo model...
  76. Modifiers of Cyst Progression in Polycystic Kidney Disease
    Phillip Darwin Bell; Fiscal Year: 2013
    ..by applicant): Polycystic kidney disease (PKD) is a "ciliopathic" disease since the loss of cilia or mutations in proteins involved in the function of cilia lead to renal cystic development...
  77. A Novel Thioredoxin Mimetic Prodrug for Prevention of Bronchopulmonary Dysplasia
    Prakash Jagtap; Fiscal Year: 2013
    ..Compounding this increase in superoxide production is the developmental deficiency of anti-oxidant proteins, such as superoxide dismutase and Trx, that are present in insufficient quantity at an early gestational age...
  78. High throughput screen for selective inhibitors of cyclophilin B
    Richard J Bram; Fiscal Year: 2013
    ..improved therapies will be accelerated by the identification of compounds that specifically target novel cellular proteins that contribute to tumr cell survival...
  79. Growth Hormone Regulation of SH2B1
    Christin Carter-Su; Fiscal Year: 2013
    ..ligands, and to gain insight into unrecognized cellular actions of GH;new functions of SH2B1;and how scaffold proteins such as SH2B1 move highly regulated and dynamic complexes from membrane-bound receptors to multiple, often remote,..
  80. RSK-2 regulates integrin-mediated adhesion and migration
    JOE WILLIAM RAMOS; Fiscal Year: 2013
    ..We have found that the proteins PEA-15 and RSK2 may conspire to influence cell adhesion and migration...
  81. Role of Membrane Modifications in the Bioactivities of Conjugated Linoleic Acids
    Papasani V Subbaiah; Fiscal Year: 2013
    ..The effect of CLA on the distribution of raft-associated proteins will be investigated in cultured cells, as well as in primary adipocytes and hepatocytes from mice and rats...
  82. Mechanistic Studies on Prostate Cancer Prevention by Gugulipid
    Dong Xiao; Fiscal Year: 2013
    ..treated with vehicle (control) and GL for assay of apoptosis and levels of apoptosis and autophagy regulating proteins. Innovation and Significance: We trust that our proposal falls under the criteria of innovative research because ..
  83. The PKCepsilon-regulated oncogenic and tumor suppressor roles of ATF2 in melanoma
    ERIC KIRK LAU; Fiscal Year: 2013
    ..In Aim 2, I propose to determine how specifically ATF2 activates Bcl2 proteins and modulates HK1:VDAC1 complexes to promote mitochondrial membrane leakage...
  84. Role of poly (ADP-ribose) polymerase 1 (PARP-1) in experimental colitis
    Claire Larmonier; Fiscal Year: 2013
    ..PARPs) constitute a family of 18 cell signaling enzymes, which are involved in the regulation of DNA-binding proteins and DNA repair...
  85. Hepatitis B virus replication and DDB1
    Betty L Slagle; Fiscal Year: 2013
    ..Additionally, MS data will be mined for evidence that HBV replication induces recruitment of immune regulatory proteins to the Cul4-DDB1 complex...
  86. Mindfulness Based Stress Reduction as an Adjunctive Treatment for Psoriasis
    Jan A Moynihan; Fiscal Year: 2013
    ..Cytokines (small molecular weight messenger proteins) produced by T helper (Th)1 and Th17 lymphocytes, antigen presenting cells, and leukocytes have been implicated ..
  87. Integrating stress MAP kinase signaling with DNA replication origin licensing
    Jeanette Gowen Cook; Fiscal Year: 2013
    ..Our long-term goal is to determine precisely how origin licensing proteins are regulated by intracellular cell cycle cues and by extracellular signaling pathways...
  88. Suppression of Ocular Scarring - Controlled Delivery of an ALK-5 Inhibitor
    Hiroshi Nakamura; Fiscal Year: 2013
    ..In our previous experiments, the ALK-5 inhibitor SB-505124 induced a marked reduction in downstream proteins of TGF-2 in vitro...
  89. Role of Vimentin in Pathogenesis of CNS Inflammation
    Sheng He Huang; Fiscal Year: 2013
    ..Vim has emerged as an organizer of a number of critical proteins involved in cell adhesion/migration and cell signaling...
  90. Regulation of EBV Latency by EBNA1
    Paul M Lieberman; Fiscal Year: 2013
    ..that EBNA1 functions at the viral origin of plasmid DNA replication (OriP) through interactions with several host proteins important for chromosome integrity, including telomere repeat binding factors (TRFs), DNA replication pausing ..
  91. The role of LKB1 in the maintenance of genomic stability.
    Zhi Xiang Xu; Fiscal Year: 2013
    ..We found that LKB1 interacts with ATM, BRCA1, and other DNA damage response (DDR) proteins in vivo...
  92. Identifying underlying mechanisms of intracellular changes in response to caregiv
    MELANIE SARAH FLINT; Fiscal Year: 2013
    ..extensive proteomic profiling revealed that stress can trigger significant changes in several actin regulating proteins important for T cell cytoskeletal rearrangement and cell migration in rodents...
  93. Regulation of Human Papillomavirus Replication via Cell Signaling Pathways
    ANASTACIA GRIEGO; Fiscal Year: 2013
    ..Early proteins E5, E6, And E7 from oncogenic HPV types are known to regulate epidermal growth factor receptor (EGFR) gene ..
  94. THE EFFECT OF DIOXINS ON GLUCOSE HOMEOSTASIS IN MURINE TESTES
    KENAN RIFAT OMURTAG; Fiscal Year: 2013
    ..glucose transporters play a significant role in the testes and on spermatogenesis and that certain cell signaling proteins/receptors play a role in modulating glucose homeostasis in these germ cells at the various stages of ..
  95. Role of Subdiaphragmatic Vagus in Fibromyalgia Syndrome
    JON DAVID LEVINE; Fiscal Year: 2013
    ..mediators involved a switch in coupling of their receptors from predominantly stimulatory to inhibitory G-proteins (Gs to Gi) and for PGE2, in particular, emergence of novel dependence on protein kinase C5 signaling...
  96. CELLULAR REGULATION OF CLATHRIN ASSEMBLY AND FUNCTION
    Frances M Brodsky; Fiscal Year: 2013
    ..Clathrin light chain (CLC) subunits mediate CCV binding to Hip proteins (Hip1 and Hip1R), which can bind actin and cortactin and thereby regulate actin dynamics in the vicinity of the ..
  97. Serotonin transporter-mediated regulation of neuroendocrine exocytosis
    KEVIN P CURRIE; Fiscal Year: 2013
    ..This novel mechanism involves covalent binding of 5HT to cytosolic proteins by transglutaminase-2 (dubbed "serotonylation")...
  98. Triazole hypersensitivity in Candida albicans
    Neeraj Chauhan; Fiscal Year: 2009
    ..Two-component signal transduction proteins have been reported in bacteria and lower eukaryotes...
  99. Functional role of a host metabolic enzyme in viral replication
    Peter Nagy; Fiscal Year: 2010
    ..Due to their small genome sizes, RNA viruses greatly depend on the co-opted host proteins during replication...
  100. Development of an Algae-based Membrane Protein Expression System
    ALEXANDER ARAVANIS; Fiscal Year: 2009
    ..is a biotechnology company developing algae as a scalable low-cost platforms for producing a broad range of proteins with biomedical and biofuels applications...
  101. Clinical Trial of DRibble Vaccine in NSCLC
    Walter Urba; Fiscal Year: 2009
    ..Our novel strategy targets T-cell responses to tumor-derived short-lived proteins by blocking proteasome-dependent protein degradation causing highly immunogenic tumor antigens to accumulate as ..