- 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...
- 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...
- 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...
- 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...
- 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
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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
- 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...
- 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...
- 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
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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
- 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...
- 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
- 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...
- 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
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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?..
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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
- 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)...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- A conformational analysis of Walker motif A [GXXXXGKT (S)] in nucleotide-binding and other proteins
Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
Protein Eng 15:783-98. 2002
- The value of position-specific priors in motif discovery using MEME
Timothy L Bailey
Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Queensland, Australia
BMC Bioinformatics 11:179. 2010
- 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...
- The c3-v4 region is a major target of autologous neutralizing antibodies in human immunodeficiency virus type 1 subtype C infection
Penny L Moore
National Institute for Communicable Diseases, Private Bag X4, Sandringham 2131, Johannesburg, South Africa
J Virol 82:1860-9. 2008
..These data suggest that the C3 and V4 regions combine to form important structural motifs and that epitopes in this region are major targets of the early autologous neutralizing response in HIV-1 subtype C infection...
- 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...
- A general amphipathic alpha-helical motif for sensing membrane curvature
Centre National de la Recherche Scientifique CNRS, Institut de Pharmacologie Moleculaire et Cellulaire, Universite de Nice Sophia Antipolis, 06560 Valbonne, France
Nat Struct Mol Biol 14:138-46. 2007
..In the nucleoporin Nup133, the sensor corresponds to an exposed loop of a beta-propeller structure. Ser/Thr-rich amphipathic helices thus define a general motif used by proteins of various functions for sensing membrane curvature...
- 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...
- A structural-alphabet-based strategy for finding structural motifs across protein families
Chih Yuan Wu
Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan
Nucleic Acids Res 38:e150. 2010
..Furthermore, DNA-specific motifs present 'only' in DBPs were discovered. The motifs found can provide useful guidelines in detecting binding sites and computational protein redesign...
- Topological orientation of acyl-CoA:diacylglycerol acyltransferase-1 (DGAT1) and identification of a putative active site histidine and the role of the n terminus in dimer/tetramer formation
Pamela J McFie
Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
J Biol Chem 285:37377-87. 2010
..Finally, we show that the N-terminal domain of DGAT1 is not required for the catalytic activity of DGAT1 but, instead, may be involved in regulating enzyme activity and dimer/tetramer formation...
- Analysis of the PDZ binding specificities of Influenza A virus NS1 proteins
International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34012 Trieste, Italy
Virol J 8:25. 2011
..In this study we analyse the effect of these differences upon the binding of Influenza A virus NS1 protein to a range of cellular proteins involved in polarity and signal transduction...
- LysM, a widely distributed protein motif for binding to (peptido)glycans
Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
Mol Microbiol 68:838-47. 2008
..This interaction is triggered by chitin-like compounds that are secreted by the symbiotic bacteria or released from fungi, demonstrating an important sensing function of LysMs...
- Large-scale discovery and characterization of protein regulatory motifs in eukaryotes
Daniel S Lieber
Department of Molecular Biology, Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
PLoS ONE 5:e14444. 2010
..These predicted motifs, many of which display preferential association with specific biological pathways and non-random positioning in the linear protein sequence, provide focused hypotheses for experimental validation...
- PML isoforms I and II participate in PML-dependent restriction of HSV-1 replication
MRC University of Glasgow Centre for Virus Research, Church Street, Glasgow G11 5JR, Scotland, UK
J Cell Sci 124:280-91. 2011
..Our observations suggest that complete functionality of PML is dependent on isoform-specific C-terminal sequences acting in concert...
- The GAPs, GEFs, and GDIs of heterotrimeric G-protein alpha subunits
David P Siderovski
Department of Pharmacology, UNC Lineberger Comprehensive Cancer Center, and UNC Neuroscience Center, The University of North Carolina at Chapel Hill, CB 7365, 1106 M E Jones Building, Chapel Hill, NC 27599 7365 USA
Int J Biol Sci 1:51-66. 2005
..Discovery of these novel GAP, GDI, and GEF activities have helped to illuminate a new role for Galpha subunit GDP/GTP cycling required for microtubule force generation and mitotic spindle function in chromosomal segregation...
- Identification of multiple proteins expressed in murine embryos as binding partners for the WW domains of the ubiquitin-protein ligase Nedd4
C N Jolliffe
Hanson Centre for Cancer Research, Institute of Medical and Veterinary Science, P O Box 14, Rundle Mall, Adelaide, SA 5000, Australia
Biochem J 351:557-65. 2000
..These results provide evidence that Nedd4 can potentially interact with multiple proteins, possibly simultaneously, through its WW domains...
- CLEC-2 activates Syk through dimerization
Craig E Hughes
Centre for Cardiovascular Sciences, Institute for Biomedical Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
Blood 115:2947-55. 2010
..This is a unique mode of activation of Syk by a single YxxL-containing receptor...
- Plasmepsin V licenses Plasmodium proteins for export into the host erythrocyte
Howard Hughes Medical Institute, Washington University School of Medicine, Department of Molecular Microbiology, St Louis, Missouri 63110, USA
Nature 463:632-6. 2010
..This enzyme is essential for parasite viability and ER residence is essential for its function. We propose that plasmepsin V is the PEXEL protease and is an attractive enzyme for antimalarial drug development...
- Src is the kinase of the Helicobacter pylori CagA protein in vitro and in vivo
Max Planck Institut für Infektionsbiologie, Abt Molekulare Biologie, Schumannstrasse 20 21, D 10117 Berlin, Germany
J Biol Chem 277:6775-8. 2002
- Tung tree DGAT1 and DGAT2 have nonredundant functions in triacylglycerol biosynthesis and are localized to different subdomains of the endoplasmic reticulum
Jay M Shockey
U S Department of Agriculture, Agricultural Research Service, Southern Regional Research Center, New Orleans, Louisiana 70124, USA
Plant Cell 18:2294-313. 2006
..These data suggest that DGAT1 and DGAT2 have nonredundant functions in plants and that the production of storage oils, including those containing unusual fatty acids, occurs in distinct ER subdomains...
- Structural basis for the sequence-specific RNA-recognition mechanism of human CUG-BP1 RRM3
RIKEN Systems and Structural Biology Center, Tsurumi, Japan
Nucleic Acids Res 37:5151-66. 2009
- Crystal structure of a beta-catenin/Tcf complex
T A Graham
Department of Biological Structure University of Washington 98195, Seattle, WA, USA
Cell 103:885-96. 2000
..The structural and mutagenesis data reveal a potential target for molecular drug design studies...
- Human embryonic stem cell phosphoproteome revealed by electron transfer dissociation tandem mass spectrometry
Danielle L Swaney
Department of Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
Proc Natl Acad Sci U S A 106:995-1000. 2009
..8% compared with 29.6%), and sequences whole classes of phosphopeptides previously unobserved...
- HPV E6 and MAGUK protein interactions: determination of the molecular basis for specific protein recognition and degradation
International Centre for Genetic Engineering and Biotechnology, Padriciano 99, I-34012 Trieste, Italy
Oncogene 20:5431-9. 2001
..Finally, in a series of comparative analyses, we show that the degradation of MAGI-1 occurs through a different mechanism from that used by the E6 protein to induce the degradation of Dlg and p53...
- Nuclear retention of fission yeast dicer is a prerequisite for RNAi-mediated heterochromatin assembly
Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH 4058 Basel, Switzerland
Dev Cell 18:102-13. 2010
..Our findings suggest that Dicer proteins are shuttling proteins and that the steady-state subcellular levels can be shifted toward either compartment...
- Impaired degradation of mutant alpha-synuclein by chaperone-mediated autophagy
Ana Maria Cuervo
Department of Anatomy and Structural Biology, Marion Bessin Liver Research Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
Science 305:1292-5. 2004
..These findings may underlie the toxic gain-of-function by the mutants...
- The DEAD-box protein family of RNA helicases
Département de Microbiologie et Médecine Moléculaire, Centre Medical Universitaire, 1 rue Michel Servet, 1211, Geneve 4, Switzerland
Gene 367:17-37. 2006
..This review will focus on the description of the molecular characteristics of members of the DEAD-box protein family and on the enzymatic activities they possess...
- The mechanisms of PML-nuclear body formation
Tian Huai Shen
Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
Mol Cell 24:331-9. 2006
- Quantifying similarity between motifs
Department of Genome Sciences, University of Washington, 1705 NE Pacific Street, Box 355065, Seattle, WA 98195, USA
Genome Biol 8:R24. 2007
..Experimental simulations demonstrate the accuracy of Tomtom's E values and its effectiveness in finding similar motifs...
- Structural basis and functional consequence of Helicobacter pylori CagA multimerization in cells
Division of Molecular Oncology, Institute for Genetic Medicine, Hokkaido University, Kita 15 Nishi 7, Kita ku, Sapporo 060 0815, Japan
J Biol Chem 281:32344-52. 2006
..The present work raises the possibility that inhibition of CagA multimerization abolishes pathophysiological activities of CagA that promote gastric carcinogenesis...
- Structure of FitAB from Neisseria gonorrhoeae bound to DNA reveals a tetramer of toxin-antitoxin heterodimers containing pin domains and ribbon-helix-helix motifs
Department of Biochemistry, Oregon Health and Science University, Portland, Oregon 97239, USA
J Biol Chem 281:37942-51. 2006
..Interactions between two FitB molecules result in the formation of a tetramer of FitAB heterodimers, which binds to the 36-bp DNA fragment and provides an explanation for how FitB enhances the DNA binding affinity of FitA...
- Inactivation of YAP oncoprotein by the Hippo pathway is involved in cell contact inhibition and tissue growth control
Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, USA
Genes Dev 21:2747-61. 2007
..Our observations demonstrate that YAP plays a key role in the Hippo pathway to control cell proliferation in response to cell contact...
- AAA+ ATPases: achieving diversity of function with conserved machinery
Susan Roehl White
Department of Pathology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
Traffic 8:1657-67. 2007
..The importance of this mechanism to human health is demonstrated by the number of genetic diseases caused by mutant AAA+ proteins...
- Mechanisms of specificity in protein phosphorylation
Jeffrey A Ubersax
Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305 5174, USA
Nat Rev Mol Cell Biol 8:530-41. 2007
..The responsibility for the recognition of substrates by protein kinases appears to be distributed among a large number of independent, imperfect specificity mechanisms...
- Isolation and functional analysis of Arabidopsis stress-inducible NAC transcription factors that bind to a drought-responsive cis-element in the early responsive to dehydration stress 1 promoter
Lam Son Phan Tran
Biological Resources Division, Japan International Research Center for Agricultural Sciences, Tsukuba, Ibaraki 305 8686, Japan
Plant Cell 16:2481-98. 2004
..However, erd1 was not upregulated in the transgenic plants. Other interacting factors may be necessary for the induction of erd1 in Arabidopsis under stress conditions...
- eIF4A: the godfather of the DEAD box helicases
George W Rogers
Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106 4935, USA
Prog Nucleic Acid Res Mol Biol 72:307-31. 2002
- The ribosomal exit tunnel functions as a discriminating gate
Institute for Virus Research and CREST, Japan Science and Technology Corporation, Kyoto University, Japan
Cell 108:629-36. 2002
..Thus, we suggest that this region of the exit tunnel interacts with nascent translation products and functions as a discriminating gate...
- 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...