- 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...
- T-Coffee: A novel method for fast and accurate multiple sequence alignment
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...
- ELM--the database of eukaryotic linear motifs
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...
- A quantitative atlas of mitotic phosphorylation
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...
- 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...
- 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...
- 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...
- Locating proteins in the cell using TargetP, SignalP and related tools
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...
- 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...
- 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...
- 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...
- 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...
- 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
- Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis
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...
- 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...
- An EB1-binding motif acts as a microtubule tip localization signal
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...
- STAMP: a web tool for exploring DNA-binding motif similarities
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...
- 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...
- 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...
- Crystal structure of rhodopsin: A G protein-coupled receptor
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...
- Diversity and complexity in DNA recognition by transcription factors
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...
- 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...
- Structure of a beta-TrCP1-Skp1-beta-catenin complex: destruction motif binding and lysine specificity of the SCF(beta-TrCP1) ubiquitin ligase
Cellular Biochemistry and Biophysics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
Mol Cell 11:1445-56. 2003
- Role of Rpn11 metalloprotease in deubiquitination and degradation by the 26S proteasome
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...
- 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...
- 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...
- Ubiquitin-binding domains in Y-family polymerases regulate translesion synthesis
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...
- Insights into DNA recombination from the structure of a RAD51-BRCA2 complex
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...
- Structure of a beta1-adrenergic G-protein-coupled receptor
MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
Nature 454:486-91. 2008
- Identification of a SUMO-binding motif that recognizes SUMO-modified proteins
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...
- 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...
- Casein kinase 1 gamma couples Wnt receptor activation to cytoplasmic signal transduction
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...
- An iterative statistical approach to the identification of protein phosphorylation motifs from large-scale data sets
Department of Cell Biology, 240 Longwood Ave, Harvard Medical School, Boston, Massachusetts 02115, USA
Nat Biotechnol 23:1391-8. 2005
- SYFPEITHI: database for MHC ligands and peptide motifs
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...
- 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
- SUMO-targeted ubiquitin ligases in genome stability
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...
- Prediction of peroxisomal targeting signal 1 containing proteins from amino acid sequence
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...
- Tumor suppressor LATS1 is a negative regulator of oncogene YAP
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...
- 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...
- Prediction, conservation analysis, and structural characterization of mammalian mucin-type O-glycosylation sites
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...
- Repression domains of class II ERF transcriptional repressors share an essential motif for active repression
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...
- 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...
- The extended PP1 toolkit: designed to create specificity
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...
- Small ubiquitin-like modifier (SUMO) recognition of a SUMO binding motif: a reversal of the bound orientation
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...
- 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...
- 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...
- 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)...
- A dual-kinase mechanism for Wnt co-receptor phosphorylation and activation
Neurobiology Program, Children s Hospital Boston, Department of Neurology, Harvard Medical School, Boston, Massachusetts 02115, USA
Nature 438:873-7. 2005
- 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
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...
- 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...
- Comparative analysis of mRNA targets for human PUF-family proteins suggests extensive interaction with the miRNA regulatory system
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...
- 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...
- Cloning of the Arabidopsis clock gene TOC1, an autoregulatory response regulator homolog
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...
- HIV-1 and Ebola virus encode small peptide motifs that recruit Tsg101 to sites of particle assembly to facilitate egress
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...
- 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...
- Akt-RSK-S6 kinase signaling networks activated by oncogenic receptor tyrosine kinases
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...
- 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...
- Conserved function of RNF4 family proteins in eukaryotes: targeting a ubiquitin ligase to SUMOylated proteins
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...
- 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...
- The leucine-rich repeat as a protein recognition motif
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
- Prediction of lipid posttranslational modifications and localization signals from protein sequences: big-Pi, NMT and PTS1
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...
- HMM Logos for visualization of protein families
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...
- Close encounters of the third kind: disordered domains and the interactions of proteins
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...
- Crystal structure of opsin in its G-protein-interacting conformation
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...
- Defining the specificity space of the human SRC homology 2 domain
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...
- PML protein isoforms and the RBCC/TRIM motif
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...
- 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
- 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...
- 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...
- Cyclin specificity in the phosphorylation of cyclin-dependent kinase substrates
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...
- 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.
- On the detection and refinement of transcription factor binding sites using ChIP-Seq data
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...
- 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...
- Mechanistic insight into pentatricopeptide repeat proteins as sequence-specific RNA-binding proteins for organellar RNAs in plants
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...
- 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...
- 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...
- Prediction of short linear protein binding regions
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...
- 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...
- 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...
- 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...
- 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...
- Identification of sequence motifs that target neuronal nicotinic receptors to dendrites and axons
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...
- Extensive phosphorylation with overlapping specificity by Mycobacterium tuberculosis serine/threonine protein kinases
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...
- Cracking the RNA polymerase II CTD code
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?..
- GlobPlot: Exploring protein sequences for globularity and disorder
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...
- Systematic sequence analysis and identification of tissue-specific or stress-responsive genes of NAC transcription factor family in rice
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...
- FANMOD: a tool for fast network motif detection
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...
- 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...
- 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...
- Somatic diversification of variable lymphocyte receptors in the agnathan sea lamprey
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)...
- Minimotif Miner 3.0: database expansion and significantly improved reduction of false-positive predictions from consensus sequences
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...
- 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
- c-Src and c-Abl kinases control hierarchic phosphorylation and function of the CagA effector protein in Western and East Asian Helicobacter pylori strains
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...
- SUMO pathway dependent recruitment of cellular repressors to herpes simplex virus type 1 genomes
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...
- 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...
- Partitioning of minimotifs based on function with improved prediction accuracy
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...
- Crystal structure of Toll-like receptor adaptor MAL/TIRAP reveals the molecular basis for signal transduction and disease protection
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...
- 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...
- Noxa, a BH3-only member of the Bcl-2 family and candidate mediator of p53-induced apoptosis
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...
- Mining protein loops using a structural alphabet and statistical exceptionality
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...
- 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...