- 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...
- Structural basis for the interaction between focal adhesion kinase and CD4
Marie Line Garron
INSERM, UMR554, 34090 Montpellier, France
J Mol Biol 375:1320-8. 2008
..In infected cells, HIV-1 Nef may displace FAK from CD4 to protect the cells from apoptosis...
- 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...
- 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...
- 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...
- 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
- 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...
- 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...
- 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?..
- 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...
- 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...
- 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...
- 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...
- 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
- 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 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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
- 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...
- 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
- 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...
- Src is the kinase of the Helicobacter pylori CagA protein in vitro and in vivo
, Abt. Molekulare Biologie, Schumannstrasse 20/21, D-10117 Berlin, Germany
J Biol Chem 277:6775-8. 2002
- 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...
- 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...
- 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...
- 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
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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
- 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...
- 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...
- 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...
- 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
, , 1 rue Michel Servet, 1211, , 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...
- 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...
- 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
- Survey on the PABC recognition motif PAM2
Max Planck Institute for Informatics, Stuhlsatzenhausweg 85, Saarbrucken 66123, Germany
Biochem Biophys Res Commun 316:129-38. 2004
..It is also striking that the PAM2 motif appears to occur solely outside globular protein domains...
- 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...
- 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...
- 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...
- Discovery of phosphorylation motif mixtures in phosphoproteomics data
Department of Computer Science, Brown University, Toyota Technological Institute at Chicago, Chicago, IL, USA
Bioinformatics 25:14-21. 2009
..Modification of proteins via phosphorylation is a primary mechanism for signal transduction in cells. Phosphorylation sites on proteins are determined in part through particular patterns, or motifs, present in the amino acid sequence...
- Temperature and pH effects on biophysical and morphological properties of self-assembling peptide RADA16-I
Institute for Nanobiomedical Technology and Membrane Biology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
J Pept Sci 14:152-62. 2008
..These results also help understand the pathogenesis of the beta-sheet-mediated neuronal diseases such as Alzheimer's disease and the mechanism of hemostasis...
- Mutations in the highly conserved SLQYLA motif of Vif in a simian-human immunodeficiency virus result in a less pathogenic virus and are associated with G-to-A mutations in the viral genome
Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, Kansas 66160, USA
Virology 383:362-72. 2009
- Modulation of retroviral restriction and proteasome inhibitor-resistant turnover by changes in the TRIM5alpha B-box 2 domain
Department of Cancer Immunology and AIDS, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
J Virol 81:10362-78. 2007
..However, testing of an array of mutants revealed that the rapid turnover and retroviral restriction functions of this B-box 2 region are separable...
- Inhibition of GSK3 phosphorylation of beta-catenin via phosphorylated PPPSPXS motifs of Wnt coreceptor LRP6
F M Kirby Neurobiology Center, Children s Hospital Boston, Harvard Medical School, Boston, MA, USA
PLoS ONE 4:e4926. 2009
..This model provides a possible mechanism to account, in part, for inhibition of beta-catenin phosphorylation by Wnt-activated LRP6...
- Phage display can select over-hydrophobic sequences that may impair prediction of natural domain-peptide interactions
Oncoproteins, Unité CNRS UDS UMR 7242, Ecole Superieure de Biotechnologie de Strasbourg, Illkirch, France
Bioinformatics 27:899-902. 2011
..Here, we investigated to which extent phage display data that were recently published for 54 human PDZ domains can be applied to the prediction of human PDZ-peptide interactions...
- Germline and somatic cancer-associated mutations in the ATP-binding motifs of PTEN influence its subcellular localization and tumor suppressive function
Glenn P Lobo
Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
Hum Mol Genet 18:2851-62. 2009
..Manipulation of ATP may represent novel therapies in tumors with such PTEN alterations...
- Towards a structural classification of phosphate binding sites in protein-nucleotide complexes: an automated all-against-all structural comparison using geometric matching
Department of Biochemistry and Molecular Biology, University College London, Gower Street, London, England
Proteins 56:250-60. 2004
..Similar classification schemes for nucleotide binding proteins have also been arrived at independently by others using different methods...
- The SPRY domain of SSB-2 adopts a novel fold that presents conserved Par-4-binding residues
Seth L Masters
The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3050, Victoria, Australia
Nat Struct Mol Biol 13:77-84. 2006
..Our findings provide a template for SPRY-domain structure and an insight into the mechanism of SPRY-protein interaction...
- Structural and functional insights into the B30.2/SPRY domain
Jae Sung Woo
Division of Molecular and Life Sciences, Department of Life Sciences, Center for Biomolecular Recognition, Pohang University of Science and Technology, Pohang, Kyungbuk, Korea
EMBO J 25:1353-63. 2006
..2/SPRY domains, suggesting that these domains are protein-interacting modules, which recognize a specific individual partner protein rather than a consensus sequence motif...
- The serine-rich domain from Crk-associated substrate (p130cas) is a four-helix bundle
Burnham Institute, 10901 N Torrey Pines Road, La Jolla, CA 92037, USA
J Biol Chem 280:21908-14. 2005
..Mapping the degree of amino acid conservation onto the molecular surface reveals a patch of invariant residues near the C terminus of the bundle, which may represent a previously unidentified site for protein interaction...
- Xyloglucan is recognized by carbohydrate-binding modules that interact with beta-glucan chains
REQUIMTE, Departamento de Quimica, FCT UNL, 2829 516 Caparica, Portugal, CIISA Faculdade de Medicina Veterinaria, Universidade Tecnica de Lisboa, Avenida da Universidade Tecnica, 1300 477 Lisboa, Portugal
J Biol Chem 281:8815-28. 2006
..The mechanism by which these proteins are able to recognize linear and decorated beta-1,4-glucans is discussed based on the structures of CBM44 and the other CBMs that bind single cellulose chains...
- Crystal structures of the Mnk2 kinase domain reveal an inhibitory conformation and a zinc binding site
Max Planck Institut fur biophysikalische Chemie, Abteilung Molekulare Entwicklungsbiologie, Am Fassberg 11, 37077 Gottingen, Germany
Structure 13:1559-68. 2005
..The results suggest that the ATP binding pocket and the activation segment of Mnk2 require conformational switches to provide kinase activity...
- Structural basis for the enhancement of eIF4A helicase activity by eIF4G
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
Genes Dev 19:2212-23. 2005
..This model can explain the cooperativity between all binding partners of eIF4A (eIF4G, RNA, ATP) and stimulation of eIF4A activity in the eIF4F complex...
- Regulation of Smurf2 ubiquitin ligase activity by anchoring the E2 to the HECT domain
Abiodun A Ogunjimi
Programme in Molecular Biology and Cancer, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
Mol Cell 19:297-308. 2005
..Thus, E2 enzyme recognition by an E3 HECT enzyme is not constitutively competent and provides a point of control for regulating the ubiquitin ligase activity through the action of auxiliary proteins...
- Structural analysis of the PP2C phosphatase tPphA from Thermosynechococcus elongatus: a flexible flap subdomain controls access to the catalytic site
Department of Structural Chemistry, Georg August University, Tammannstrasse 4, 37077 Gottingen, Germany
J Mol Biol 376:570-81. 2008
- Structural organization and interactions of transmembrane domains in tetraspanin proteins
Oleg V Kovalenko
Department of Cancer Immunology and AIDS, Dana Farber Cancer Institute, Boston, MA, USA
BMC Struct Biol 5:11. 2005
..While structure and function analysis of the larger extracellular loop has been performed, the organization and role of transmembrane domains have not been systematically assessed...
- The Plasmodium falciparum cysteine protease falcipain-2 captures its substrate, hemoglobin, via a unique motif
Kailash C Pandey
Department of Medicine, San Francisco General Hospital, P O Box 0811, University of California, San Francisco, CA 94143, USA
Proc Natl Acad Sci U S A 102:9138-43. 2005
..Our results indicate that FP2 utilizes an unusual motif for two specific functions, interaction with hemoglobin, its natural substrate, and interaction with the prodomain, its natural inhibitor...
- Differential effects of heterochromatin protein 1 isoforms on mitotic chromosome distribution and growth in Dictyostelium discoideum
Kassel University, FB 18, Abt Genetik, Heinrich Plett Strasse 40, 34132 Kassel, Germany
Eukaryot Cell 5:530-43. 2006
..Interestingly, heterochromatin organization appeared to be independent of functional RNAi...
- The 2.2 A resolution crystal structure of Bacillus cereus Nif3-family protein YqfO reveals a conserved dimetal-binding motif and a regulatory domain
Michael H Godsey
College of Theology, Arts and Sciences, Concordia University, Portland, OR 97211, USA
Protein Sci 16:1285-93. 2007
..Our results suggest that this domain acts as a signal sensor to regulate the still-unknown catalytic activity of the more-conserved domains...
- Characterization of recombinant CDR1, an Arabidopsis aspartic proteinase involved in disease resistance
Departamento de Biologia Molecular e Biotecnologia, Centro de Neurociencias e Biologia Celular, Universidade de Coimbra, Apt 3126, Coimbra 3000, Portugal
J Biol Chem 282:31358-65. 2007
..These findings unveil a pattern of unprecedented functional complexity for Arabidopsis CDR1 and are consistent with a highly specific and regulated biological function...
- Retrocyclin RC-101 overcomes cationic mutations on the heptad repeat 2 region of HIV-1 gp41
Christopher A Fuhrman
Molecular Biology and Microbiology, Biomolecular Science Center, Burnett College of Biomedical Sciences at University of Central Florida, Orlando, FL 32816, USA
FEBS J 274:6477-87. 2007
- Structure of the chloroplast signal recognition particle (SRP) receptor: domain arrangement modulates SRP-receptor interaction
Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E California Boulevard, Pasadena, CA 91125, USA
J Mol Biol 375:425-36. 2008
- Solution structure of the PABC domain from wheat poly (A)-binding protein: an insight into RNA metabolic and translational control in plants
Department of Biochemistry, McGill University, 3655 Promenade Sir William Osler, QC H3G 1Y6, Canada
Biochemistry 46:4221-31. 2007
..We show that wPABC binds to the plant PAM-2 motif with high affinity through a conserved mechanism. Overall, our results suggest that plant species have evolved a distinct regulatory mechanism involving novel PABP binding partners...
- Crystal structure and mutational study of a unique SpoU family archaeal methylase that forms 2'-O-methylcytidine at position 56 of tRNA
Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo 113 0033, Japan
J Mol Biol 375:1064-75. 2008
..However, an essential Arg16 residue is located at a novel position within motif I. Biochemical assays showed that aTrm56 prefers the L-shaped tRNA to the lambda form as its substrate...
- Structure of dimeric SecA, the Escherichia coli preprotein translocase motor
Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, PO Box 1385, 71110 Heraklion, Greece
J Mol Biol 366:1545-57. 2007
..The repercussion of these findings on translocase assembly and catalysis is discussed...
- Crystal structure of the central and C-terminal domain of the sigma(54)-activator ZraR
European Molecular Biology Laboratory Hamburg Outstation, c o DESY, Notkestrasse 85, D 22603 Hamburg, Germany
J Struct Biol 151:160-70. 2005
..The dimerisation interface between DNA-binding domains observed in the crystal structure suggests that dodecamers, rather than hexamers, might be the functionally important oligomer...
- AKAP18 contains a phosphoesterase domain that binds AMP
Matthew G Gold
Section of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, UK
J Mol Biol 375:1329-43. 2008
..It may act as a phosphoesterase, although we did not identify a substrate, or as an AMP sensor with the potential to couple intracellular AMP levels to PKA signalling events...
- Conserved themes in target recognition by the PAH1 and PAH2 domains of the Sin3 transcriptional corepressor
Sarata C Sahu
Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, Evanston, IL 60208 3500, USA
J Mol Biol 375:1444-56. 2008
..These studies reveal that even conservative replacements of PAH2 residues with equivalent PAH1 residues are sufficient to alter the affinity and specificity of these protein-protein interactions dramatically...
- Interdomain cooperativity of calmodulin bound to melittin preferentially increases calcium affinity of sites I and II
Rhonda A Newman
Department of Biochemistry, Roy J and Lucille A Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242 1109, USA
Proteins 71:1792-812. 2008
- A novel mutation in murine hepatitis virus nsp5, the viral 3C-like proteinase, causes temperature-sensitive defects in viral growth and protein processing
Jennifer S Sparks
Department of Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
J Virol 82:5999-6008. 2008
..This study identifies novel residues in nsp5 that may be important for regulating substrate specificity and nsp5 proteinase activity...
- Determinants that control the specific interactions between TAB1 and p38alpha
The Key Laboratory of the Ministry of Education for Cell Biology and Tumor Cell Engineering, School of Life Sciences, Xiamen University, Fujian, China
Mol Cell Biol 26:3824-34. 2006
..This suggests that TAB1-induced autophosphorylation of p38alpha results from conformational changes that are similar but unique to those seen in p38alpha interactions with its substrates and activating kinases...
- XPB: An essential helicase involved in both transcription and repair of DNA
Macromolecular Crystallography Group, European Synchrotron Radiation Facility, B.P. 220, 6 rue Jules Horowitz, F-38043, Grenoble-CEDEX 9, France
Mol Cell 22:149-50. 2006
..In a recent issue of Molecular Cell, Fan et al. (2006) revealed the core structure of XPB helicase, a component of transcription factor IIH, and proposed a mechanism for its dual role in transcription and nucleotide excision repair...
- 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...
- Eukaryotic class 1 translation termination factor eRF1--the NMR structure and dynamics of the middle domain involved in triggering ribosome-dependent peptidyl-tRNA hydrolysis
Elena V Ivanova
Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
FEBS J 274:4223-37. 2007
- The pro-apoptotic function of death-associated protein kinase is controlled by a unique inhibitory autophosphorylation-based mechanism
Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
J Biol Chem 276:47460-7. 2001
..We propose that this unique mechanism of auto-inhibition evolved to impose a locking device, which keeps death-associated protein kinase silent in healthy cells and ensures its activation only in response to apoptotic signals...
- Structural determinants regulating expression of the high affinity leukotriene B4 receptor: involvement of dileucine motifs and alpha-helix VIII
Immunology Division, Department of Pediatrics, Faculty of Medicine, Universite de Sherbrooke, Quebec J1H 5N4, Canada
J Biol Chem 279:10338-45. 2004
- Mutations within the hMLH1 and hPMS2 subunits of the human MutLalpha mismatch repair factor affect its ATPase activity, but not its ability to interact with hMutSalpha
Institute of Medical Radiobiology, August Forel Strasse 7, Zurich 8008, Switzerland
J Biol Chem 277:21810-20. 2002
- The human polymeric immunoglobulin receptor binds to Streptococcus pneumoniae via domains 3 and 4
Center for Immunology and Microbial Disease, Albany Medical College, Albany, New York 12208, USA
J Biol Chem 278:48178-87. 2003
..These results strongly suggest a conformational CbpA-binding motif(s) in the D3/D4 region of human pIgR, which is functionally separated from the IgA-binding site(s)...
- Crystal structure of the intrinsically flexible addiction antidote MazE
Laboratorium voor Ultrastructuur en Vlaams instituut voor Biotechnologie, Vrije Universiteit Brussel, Gebouw E, Pleinlaan 2, 1050 Brussel, Belgium
J Biol Chem 278:28252-7. 2003
..This hydrophobic core consists exclusively of short aliphatic residues. The folded part of MazE contains a novel DNA binding motif. A model for DNA binding that is consistent with the available biochemical data is presented...
- The 8-kDa dynein light chain binds to its targets via a conserved (K/R)XTQT motif
K W Lo
Department of Biochemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, People s Republic of China
J Biol Chem 276:14059-66. 2001
..The role of each conserved amino acid residue in this pentapeptide motif in supporting complex formation with DLC8 was systematically studied using site-directed mutagenesis...
- The zinc finger domain of Tzfp binds to the tbs motif located at the upstream flanking region of the Aie1 (aurora-C) kinase gene
C J Tang
Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, Republic of China
J Biol Chem 276:19631-9. 2001
..Taken together, our results indicate that Tzfp recognizes a sequence-specific motif (tbs) and may play a role in the regulation of the genes carrying the tbs...
- Substitution of a glycogen synthase kinase-3beta phosphorylation site in presenilin 1 separates presenilin function from beta-catenin signaling
Scios Inc, Sunnyvale, California 94086, USA
J Biol Chem 276:7366-75. 2001
..These results argue against a pathologically relevant role for the association between PS1 and beta-catenin in familial Alzheimer's disease...
- Topography for independent binding of alpha-helical and PPII-helical ligands to a peroxisomal SH3 domain
EMBL Hamburg, c o Deutsches Elektronen Synchrotron, Notkestrasse 85, D 22603 Hamburg, Germany
Mol Cell 10:1007-17. 2002
..Mutations in the Pex13p SH3 domain that abolish interactions within the Pex13p-Pex5p interface specifically impair PTS1-dependent protein import into yeast peroxisomes...
- Mechanism of action of RNase T. II. A structural and functional model of the enzyme
Department of Biochemistry and Molecular Biology, University of Miami School of Medicine, Miami, FL 33101 6129, USA
J Biol Chem 277:50160-4. 2002
..These data explain why RNase T must dimerize to function. The model provides a detailed framework on which to explain the mechanism of action of RNase T...
- The betagamma subunit of heterotrimeric G proteins interacts with RACK1 and two other WD repeat proteins
Edward J Dell
Institute for Neuroscience and Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Medical School, Chicago, Illinois 60613, USA
J Biol Chem 277:49888-95. 2002