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| secondary protein structureSummarySummary: The level of protein structure in which regular hydrogen-bond interactions within contiguous stretches of polypeptide chain give rise to alpha helices, beta strands (which align to form beta sheets) or other types of coils. This is the first folding level of protein conformation. Top Publications
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Predicting transmembrane protein topology with a hidden Markov model: application to complete genomesA Krogh
Center for Biological Sequence Analysis, Technical University of Denmark, Building 208, 2800 Lyngby, Denmark
J Mol Biol 305:567-80. 2001..We discuss the possible relevance of this finding for our understanding of membrane protein assembly mechanisms. A TMHMM prediction service is available at http://www.cbs.dtu.dk/services/TMHMM/...- ESPript: analysis of multiple sequence alignments in PostScriptP Gouet
Laboratory of Molecular Biophysics, The Rex Richards Building, South Parks Road, Oxford OX1 3QU, UK
Bioinformatics 15:305-8. 1999..It can read secondary structure files (such as that created by the program DSSP) to produce a synthesis of both sequence and structural information... - Mutation in the alpha-synuclein gene identified in families with Parkinson's diseaseM H Polymeropoulos
Laboratory of Genetic Disease Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 1430, USA
Science 276:2045-7. 1997..This finding of a specific molecular alteration associated with PD will facilitate the detailed understanding of the pathophysiology of the disorder... - Atomic structures of the human immunophilin FKBP-12 complexes with FK506 and rapamycinG D Van Duyne
Department of Chemistry, Cornell University Ithaca, NY 14853 1301
J Mol Biol 229:105-24. 1993..The different complexes are active in suppressing different steps of T cell activation, an activity seemingly unconnected with the PPIase activity... - Protein secondary structure prediction based on position-specific scoring matricesD T Jones
Department of Biological Sciences, University of Warwick, Coventry, CV4 7AL, United Kingdom
J Mol Biol 292:195-202. 1999..Given the success of the method in CASP3, it is reasonable to be confident that the evaluation presented here gives a fair indication of the performance of the method in general... - Crystal structure of the extracellular segment of integrin alpha Vbeta3 in complex with an Arg-Gly-Asp ligandJian Ping Xiong
Renal Unit, Leukocyte Biology and Inflammation Program, Structural Biology Program, Massachusetts General Hospital, 149 13th Street, Charlestown, MA 02129, USA
Science 296:151-5. 2002..Ligand binding induces small changes in the orientation of alphaV relative to beta3... - Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensionsE Krissinel
European Bioinformatics Institute, Genome Campus, Hinxton, Cambridge CB10 1SD, England
Acta Crystallogr D Biol Crystallogr 60:2256-68. 2004..A new score, balancing the r.m.s.d. and alignment length Nalign, is proposed. It is found that different servers agree reasonably well on the new score, while showing considerable differences in r.m.s.d. and Nalign... - AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMRR A Laskowski
Department of Biochemistry and Molecular Biology, University College London, UK
J Biomol NMR 8:477-86. 1996..They are intended to be of use both to support ongoing NMR structure determination and in the validation of the final results... 
Statistical potential for assessment and prediction of protein structuresMin Yi Shen
Department of Biopharmaceutical Sciences, Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, California 94158, USA
Protein Sci 15:2507-24. 2006....- High-resolution crystal structure of an engineered human beta2-adrenergic G protein-coupled receptorVadim Cherezov
Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037, USA
Science 318:1258-65. 2007.... 
Biophysical dissection of membrane proteinsStephen H White
Department of Physiology and Biophysics, and Center for Biomembrane Systems, University of California, Irvine, California 92697, USA
Nature 459:344-6. 2009....- Comparison of multiple Amber force fields and development of improved protein backbone parametersViktor Hornak
Center for Structural Biology, Stony Brook University, Stony Brook, New York 11794, USA
Proteins 65:712-25. 2006..It also accomplishes improved agreement with published experimental data for conformational preferences of short alanine peptides and better accord with experimental NMR relaxation data of test protein systems... - The Jpred 3 secondary structure prediction serverChristian Cole
School of Life Sciences Research, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
Nucleic Acids Res 36:W197-201. 2008..A new software pipeline will enable Jnet/Jpred to continue to be updated in sync with major updates to SCOP and UniProt and so ensures that Jpred 3 will maintain high-accuracy predictions... - Prediction of membrane-protein topology from first principlesAndreas Bernsel
Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE 106 91 Stockholm, Sweden
Proc Natl Acad Sci U S A 105:7177-81. 2008..This result suggests that prediction of membrane-protein topology and structure directly from first principles is an attainable goal, given the recently improved understanding of peptide recognition by the translocon... - In vitro generation of infectious scrapie prionsJoaquin Castilla
Department of Neurology, University of Texas Medical Branch, Galveston, Texas 77555, USA
Cell 121:195-206. 2005..These findings demonstrate that prions can be generated in vitro and provide strong evidence in support of the protein-only hypothesis of prion transmission... - A novel GJA8 mutation (p.I31T) causing autosomal dominant congenital cataract in a Chinese familyKaijie Wang
Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology and Visual Sciences Key Lab, Beijing, China
Mol Vis 15:2813-20. 2009..To identify the genetic defect associated with autosomal dominant congenital nuclear cataract in a Chinese family... - REPETITA: detection and discrimination of the periodicity of protein solenoid repeats by discrete Fourier transformLuca Marsella
CECAM, Lyon, France
Bioinformatics 25:i289-95. 2009.... - HIV-1 broadly neutralizing antibody extracts its epitope from a kinked gp41 ectodomain region on the viral membraneZhen Yu J Sun
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
Immunity 28:52-63. 2008.... - Techniques to study amyloid fibril formation in vitroMelanie R Nilsson
Department of Chemistry, McDaniel College, Eaton Hall, 2 College Hill, Westminster, MD 21157, USA
Methods 34:151-60. 2004.... - Passing the baton in class B GPCRs: peptide hormone activation via helix induction?Christoph Parthier
Institut für Biochemie und Biotechnologie, Martin Luther Universitat Halle Wittenberg, Kurt Mothes Strasse 3, D 06120 Halle Saale, Germany
Trends Biochem Sci 34:303-10. 2009..The structures reveal similar modes of ligand binding, with concomitant alpha-helical structuring of the ligand. The latter suggests an attractive mechanical model for class B GPCR activation... - WoLF PSORT: protein localization predictorPaul Horton
Computational Biology Research Center, AIST, Tokyo, Japan
Nucleic Acids Res 35:W585-7. 2007..Taken together, this information allows a user to understand the evidence (or lack thereof) behind the predictions made for particular proteins. WoLF PSORT is available at wolfpsort.org... - CD81 (TAPA-1): a molecule involved in signal transduction and cell adhesion in the immune systemS Levy
Department of Medicine, Stanford University Medical Center, California 94305, USA
Annu Rev Immunol 16:89-109. 1998..Like CD81, several tetraspanins are involved in cell adhesion, motility, and metastasis, as well as cell activation and signal transduction... - A hidden Markov model for predicting transmembrane helices in protein sequencesE L Sonnhammer
National Center for Biotechnology Information, NLM NIH, Bethesda, Maryland 20894, USA
Proc Int Conf Intell Syst Mol Biol 6:175-82. 1998..The same accuracy was achieved on a larger dataset of 160 proteins. These results compare favourably with existing methods... - Length-dependent prediction of protein intrinsic disorderKang Peng
Center for Information Science and Technology, Temple University, Philadelphia, PA 19122, USA
BMC Bioinformatics 7:208. 2006..However, these predictors are less successful on short disordered regions (< or =30 residues). A probable cause is a length-dependent amino acid compositions and sequence properties of disordered regions... - Solving structures of protein complexes by molecular replacement with PhaserAirlie J McCoy
University of Cambridge, Department of Haematology, Cambridge Institute for Medical Research, Wellcome Trust MRC Building, Hills Road, Cambridge CB2 2XY, England
Acta Crystallogr D Biol Crystallogr 63:32-41. 2007..Two case studies are presented to illustrate how Phaser can be used to best advantage in the standard ;automated MR' mode and two case studies are used to show how to modify the automated search strategy for problematic cases... - Specific interactions for ab initio folding of protein terminal regions with secondary structuresYuedong Yang
Indiana University School of Informatics, Indianapolis, Indiana 46202, USA
Proteins 72:793-803. 2008..The result has significant implications on the theoretical and experimental searches for specific interactions involved in protein folding and molecular recognition between proteins and other biologically active molecules... - Fifty years of coiled-coils and alpha-helical bundles: a close relationship between sequence and structureDavid A D Parry
Institute of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North, New Zealand
J Struct Biol 163:258-69. 2008..An important development has been the recognition that the delightful simplicity that exists between sequence and structure, and between structure and function, allows coiled coils with specialized features to be designed de novo... - Mechanisms of specificity in protein phosphorylationJeffrey 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 fold of alpha-synuclein fibrilsMarçal Vilar
The Salk Institute for Biological Studies, North Torrey Pines Road, La Jolla, CA 92037, USA
Proc Natl Acad Sci U S A 105:8637-42. 2008..5 nm. Based on the combination of these data and published structural studies, a fold of alpha-syn in the fibrils is proposed and discussed... - New phosphorylation sites identified in hyperphosphorylated tau (paired helical filament-tau) from Alzheimer's disease brain using nanoelectrospray mass spectrometryD P Hanger
Department of Neuroscience, Institute of Psychiatry, London, England, UK
J Neurochem 71:2465-76. 1998..We identified 22 phosphorylation sites in PHF-tau, including five sites not previously identified. The combination of our new data with previous reports shows that PHF-tau can be phosphorylated on at least 25 different sites... - X-ray structure of recombinant ricin A-chain at 1.8 A resolutionS A Weston
Protein Structure Laboratory, Zeneca Pharmaceuticals, Macclesfield, Cheshire, United Kingdom
J Mol Biol 244:410-22. 1994..The structures suggest that Glu177 is better positioned for the activation of the catalytic water molecule than Arg180... - Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web serverLUKAS KALL
Center for Genomics and Bioinformatics, Karolinska Institutet, S 17177 Stockholm, Sweden
Nucleic Acids Res 35:W429-32. 2007..We here present a web interface (http://phobius.cgb.ki.se and http://phobius.binf.ku.dk) to access Phobius... - The peripheral membrane subunits of the SAM complex function codependently in mitochondrial outer membrane biogenesisNickie C Chan
Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia
Mol Biol Cell 19:126-36. 2008..Very different environments surround bacteria and mitochondria, and we discuss the role of Sam35 and Sam37 in terms of the problems peculiar to mitochondrial protein substrates... - Structural basis of multiple drug-binding capacity of the AcrB multidrug efflux pumpEdward W Yu
Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720 3202, USA
Science 300:976-80. 2003..Each ligand uses a slightly different subset of AcrB residues for binding. The bound ligand molecules often interact with each other, stabilizing the binding... - A novel lytic peptide composed of DL-amino acids selectively kills cancer cells in culture and in miceNiv Papo
Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, 76100 Israel
J Biol Chem 278:21018-23. 2003.... - Structure of the cytochrome b6f complex of oxygenic photosynthesis: tuning the cavityGenji Kurisu
Department of Biological Sciences, 915 West State Street, Purdue University, West Lafayette, IN 47907 2054, USA
Science 302:1009-14. 2003..The motion of the Rieske iron-sulfur protein extrinsic domain, essential for electron transfer, must also be different in the b6f complex... - DiANNA: a web server for disulfide connectivity predictionF Ferre
Department of Biology, Boston College, Chestnut Hill, MA 02467, USA
Nucleic Acids Res 33:W230-2. 2005..Our novel neural network-based approach achieves results that are comparable and in some cases better than the current state-of-the-art methods... - A conserved trimerization motif controls the topology of short coiled coilsRichard A Kammerer
Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 PT, United Kingdom
Proc Natl Acad Sci U S A 102:13891-6. 2005..In addition to being of particular interest for the biotechnological production of candidate therapeutic proteins, these findings may be of interest for viral drug development strategies... - Solution NMR studies of the A beta(1-40) and A beta(1-42) peptides establish that the Met35 oxidation state affects the mechanism of amyloid formationLiming Hou
Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106-7078, USA
J Am Chem Soc 126:1992-2005. 2004.... - Protein structure prediction servers at University College LondonKevin Bryson
Department of Computer Science, University College London Gower Street, London WC1E 6BT, UK
Nucleic Acids Res 33:W36-8. 2005..More recent servers include DISOPRED for the prediction of protein dynamic disorder and DomPred for domain boundary prediction. These servers are available from our software home page at http://bioinf.cs.ucl.ac.uk/software.html... - Docking of HIV-1 Vpr to the nuclear envelope is mediated by the interaction with the nucleoporin hCG1Erwann Le Rouzic
Institut Cochin, Department of Infectious Diseases, CNRS UMR8104, INSERM U567, , Paris, France
J Biol Chem 277:45091-8. 2002..This association of Vpr with a component of the nuclear pore complex may contribute to the disruption of the nuclear envelope and to the nuclear import of the viral DNA... - The structure of an open form of an E. coli mechanosensitive channel at 3.45 A resolutionWenjian Wang
Centre for Biomolecular Sciences, The North Haugh, University of St Andrews, KY16 9ST, Scotland, UK
Science 321:1179-83. 2008..Support for this mechanism is provided by single-channel analysis of mutants with altered gating characteristics... - Detecting coevolution without phylogenetic trees? Tree-ignorant metrics of coevolution perform as well as tree-aware metricsJ Gregory Caporaso
Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO, USA
BMC Evol Biol 8:327. 2008..We further considered the influence of sequence recoding using reduced-state amino acid alphabets, a common tactic employed in coevolutionary analyses to improve both statistical and computational performance... - The HMMTOP transmembrane topology prediction serverG E Tusnády
Institute of Enzymology, BRC, Hungarian Academy of Sciences, H 1518 Budapest, PO Box 7, Hungary
Bioinformatics 17:849-50. 2001..e. in epitope insertion experiments. Availability: HMMTOP 2.0 is freely available to non-commercial users at http://www.enzim.hu/hmmtop. Source code is also available upon request to academic users... - Solution structure of dengue virus capsid protein reveals another foldLixin Ma
Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA
Proc Natl Acad Sci U S A 101:3414-9. 2004..We propose a model for the interaction of dengue C protein with RNA and the viral membrane that is based on the asymmetric charge distribution of the protein and is consistent with previously reported results... - Structure of bacteriorhodopsin at 1.55 A resolutionH Luecke
Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, 92697, USA
J Mol Biol 291:899-911. 1999..A bilayer of 18 tightly bound lipid chains forms an annulus around the protein in the crystal. Contacts between the trimers in the membrane plane are mediated almost exclusively by lipids... - Structure of a HoxB1-Pbx1 heterodimer bound to DNA: role of the hexapeptide and a fourth homeodomain helix in complex formationD E Piper
Department of Biophysics and Biophysical Chemistry and Howard Hughes Medical Institute, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
Cell 96:587-97. 1999..The structure suggests a model for modulation of Hox DNA binding activity by Pbx1 and related proteins... - Structural basis for high-affinity peptide inhibition of p53 interactions with MDM2 and MDMXMarzena Pazgier
Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
Proc Natl Acad Sci U S A 106:4665-70. 2009.... - Transmembrane protein topology prediction using support vector machinesTimothy Nugent
Bioinformatics Group, Department of Computer Science, University College London, Gower Street, London, WC1E 6BT, UK
BMC Bioinformatics 10:159. 2009..In the absence of structural data, sequence-based prediction methods allow TM protein topology to be investigated... - Crystal structure of the catalytic subunit of protein kinase CK2 from Zea mays at 2.1 A resolutionK Niefind
Universitat zu Koln, Institut fur Biochemie, Zulpicher Strasse 47, D 50674 Köln, Germany
EMBO J 17:2451-62. 1998..This finding explains the observation that CK2, unlike other protein kinases, can use both ATP and GTP as phosphorylating agents... - Self-propagating, molecular-level polymorphism in Alzheimer's beta-amyloid fibrilsAneta T Petkova
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health NIH, Bethesda, MD 20892 0520, USA
Science 307:262-5. 2005..These results have implications for the mechanism of amyloid formation, the phenomenon of strains in prion diseases, the role of amyloid fibrils in amyloid diseases, and the development of amyloid-based nano-materials... - Structure of the cross-beta spine of amyloid-like fibrilsRebecca Nelson
Howard Hughes Medical Institute, UCLA DOE Institute for Genomics and Proteomics, Box 951570, UCLA, Los Angeles, California 90095 1570, USA
Nature 435:773-8. 2005..The structure illuminates the stability of amyloid fibrils, their self-seeding characteristic and their tendency to form polymorphic structures... - MANIFOLD: protein fold recognition based on secondary structure, sequence similarity and enzyme classificationEckart Bindewald
Computer Science V, University of Mannheim B6 26, D-68131 Mannheim, Germany
Protein Eng 16:785-9. 2003..We argue that using functional and secondary structure information can increase the fold recognition beyond sequence similarity... - Analysis and prediction of leucine-rich nuclear export signalsTanja la Cour
Center for Biological Sequence Analysis, BioCentrum-DTU, Technical University of Denmark, Building 208, DK-2800 Lyngby, Denmark
Protein Eng Des Sel 17:527-36. 2004..We employ both neural networks and hidden Markov models in the prediction algorithm and verify the method on the most recently discovered NESs. The NES predictor (NetNES) is made available for general use at http://www.cbs.dtu.dk/... - Structural search and retrieval using a tableau representation of protein folding patternsArun S Konagurthu
Department of Biochemistry and Molecular Biology and The Huck Institute for Genomics, Proteomics and Bioinformatics, The Pennsylvania State University, University Park, PA 16802, USA
Bioinformatics 24:645-51. 2008..AVAILABILITY: A web server implementing the TableauSearch is available from http://hollywood.bx.psu.edu/TabSearch... - Binding of the general anesthetics propofol and halothane to human serum albumin. High resolution crystal structuresA A Bhattacharya
Biophysics Section, The Blackett Laboratory, Imperial College of Science, Technology and Medicine, London SW7 2BW, United Kingdom
J Biol Chem 275:38731-8. 2000..All of the higher affinity anesthetic binding sites are amphiphilic in nature, with both polar and apolar parts, and anesthetic binding causes only minor changes in local structure... - Structure of C8alpha-MACPF reveals mechanism of membrane attack in complement immune defenseMichael A Hadders
Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
Science 317:1552-4. 2007..The size of the MACPF domain is consistent with known C9 pore sizes. These data imply that these mammalian and bacterial cytolytic proteins share a common mechanism of membrane insertion... - Ab initio protein structure prediction: progress and prospectsR Bonneau
Department of Biochemistry, University of Washington, Seattle, Washington, Box 357350, 98195, USA
Annu Rev Biophys Biomol Struct 30:173-89. 2001..In this work, we review the features of current ab initio protocols in an attempt to highlight the foundations of recent progress in the field and suggest promising directions for future work... - The membrane-proximal tryptophan-rich region of the HIV glycoprotein, gp41, forms a well-defined helix in dodecylphosphocholine micellesD J Schibli
Department of Biological Sciences, University of Calgary, Alberta, Canada
Biochemistry 40:9570-8. 2001..This work shows that the Trp-rich membrane-proximal region of HIV and related viruses can bind to the surfaces of zwitterioninc membranes in a "Velcro-like" manner... - Tubulin modifications and their cellular functionsJennetta W Hammond
Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
Curr Opin Cell Biol 20:71-6. 2008.... - Crystal structure of a Src-homology 3 (SH3) domainA Musacchio
European Molecular Biology Laboratory, Heidelberg, Germany
Nature 359:851-5. 1992..We suggest that a protein ligand binds to this conserved surface of SH3... - Ubiquitin binding modulates IAP antagonist-stimulated proteasomal degradation of c-IAP1 and c-IAP2(1)John W Blankenship
Department of Protein Engineering, Genentech, Inc, 1 DNA Way, M S 40, South San Francisco, CA 94080, USA
Biochem J 417:149-60. 2009..These results suggest that ubiquitin binding may be an important mechanism for rapid turnover of auto-ubiquitinated c-IAP1 and c-IAP2... - Molecular modeling and site-directed mutagenesis of plant chloroplast monogalactosyldiacylglycerol synthase reveal critical residues for activityCyrille Botté
UMR 5168 CNRS Commissariat à l Energie Atomique Institut National de la Recherche Agronomique, Universite Joseph Fourier, Departement Reponse et Dynamique Cellulaires, 17 rue des Martyrs, Commissariat a l Energie Atomique, 38054 Grenoble Cedex 9, France
J Biol Chem 280:34691-701. 2005..Additionally, the monotopic insertion of MGD in one membrane leaflet of the plastid envelope occurs very likely at the level of hydrophobic amino acids of the N-terminal domain... - Crystal structures of the conserved tRNA-modifying enzyme GidA: implications for its interaction with MnmE and substrateS Meyer
Department of Structural Biology, Max Planck Institute of Molecular Physiology, Otto Hahn Strasse 11, Dortmund 44227, Germany
J Mol Biol 380:532-47. 2008..We propose a model for the interaction between GidA and MnmE, which is supported by site-directed mutagenesis. Our data suggest that this interaction is modulated and potentially regulated by the switch function of the G domain of MnmE... - Structure of a peptide:N-glycanase-Rad23 complex: insight into the deglycosylation for denatured glycoproteinsJung Hoon Lee
National Creative Research Center for Structural Biology and Department of Life Science, Pohang University of Science and Technology, Hyo ja dong, San 31, Pohang, KyungBook, South Korea
Proc Natl Acad Sci U S A 102:9144-9. 2005.... - Crystal structure of acetylcholine-binding protein from Bulinus truncatus reveals the conserved structural scaffold and sites of variation in nicotinic acetylcholine receptorsPatrick H N Celie
Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
J Biol Chem 280:26457-66. 2005..Comparison of these structures will be valuable for improving structure-function studies of ligand-gated ion channel receptors, including signal transduction, homology modeling, and drug design... - Supramodular nature of GRIP1 revealed by the structure of its PDZ12 tandem in complex with the carboxyl tail of Fras1Jiafu Long
Department of Biochemistry, Molecular Neuroscience Center, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
J Mol Biol 375:1457-68. 2008.... - AKAP18 contains a phosphoesterase domain that binds AMPMatthew 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... - The histone fold subunits of Drosophila CHRAC facilitate nucleosome sliding through dynamic DNA interactionsKlaus F Hartlepp
European Molecular Biology Laboratory, Grenoble Outstation, France
Mol Cell Biol 25:9886-96. 2005.... - Essential role of proline isomerization in stefin B tetramer formationSasa Jenko Kokalj
Department of Biochemistry and Molecular Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
J Mol Biol 366:1569-79. 2007..These results are consistent with the hypothesis that isomerization of proline residues can play a decisive role in amyloidogenesis... - Structures of dimeric nonstandard nucleotide triphosphate pyrophosphatase from Pyrococcus horikoshii OT3: functional significance of interprotomer conformational changesNeratur K Lokanath
Advanced Protein Crystallography Research Group, RIKEN SPring 8 Center, Harima Institute, 1 1 1 Kouto, Sayo cho, Sayo gun, Hyogo 679 5148, Japan
J Mol Biol 375:1013-25. 2008..A combination of the exceptional interdomain and interprotomer relocations is most likely the reason for the observed asymmetric IMP binding that might be necessary for PhNTPase to release the reaction product IMP... - Structural basis for interaction between the Ubp3 deubiquitinating enzyme and its Bre5 cofactorKeqin Li
The Wistar Institute, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
J Biol Chem 280:29176-85. 2005..Together, these studies provide novel insights into protein recognition by NTF2-like domains and provide a molecular scaffold for understanding how Ubp3 function is regulated by Bre5 cofactor binding... - A calcium-gated lid and a large beta-roll sandwich are revealed by the crystal structure of extracellular lipase from Serratia marcescensReto Meier
Department of Chemistry and Biochemistry, University Bern Freiestrasse 3, CH 3012 Bern, Switzerland
J Biol Chem 282:31477-83. 2007..The analysis of the properties of the beta-roll domains suggests an intramolecular chaperone function... - Global dynamics of newly constructed oligonucleosomes of conventional and variant H2A.Z histoneAmutha Ramaswamy
Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, USA
BMC Struct Biol 7:76. 2007..Z histone variant using normal mode analysis... - The structure at 1.7 A resolution of the protein product of the At2g17340 gene from Arabidopsis thalianaEduard Bitto
Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin Madison, USA
Acta Crystallogr Sect F Struct Biol Cryst Commun 61:630-5. 2005..The structure of At2g17340 represents a new fold in protein conformational space... - Dynamic association between the catalytic and lectin domains of human UDP-GalNAc:polypeptide alpha-N-acetylgalactosaminyltransferase-2Timothy A Fritz
Section on Biological Chemistry, NIDDK, National Institutes of Health, Bethesda, Maryland 20892, USA
J Biol Chem 281:8613-9. 2006..The structure of the hT2-UDP-EA2 complex also resolves long standing questions regarding ppGalNAcT acceptor substrate specificity... - On the mechanism of sensing unfolded protein in the endoplasmic reticulumJoel J Credle
Howard Hughes Medical Institute, Departments of Biochemistry and Biophysics and Medicine, University of California, San Francisco, CA 94143-2200, USA
Proc Natl Acad Sci U S A 102:18773-84. 2005..The changes in the ER lumen in turn position Ire1 kinase domains in the cytoplasm optimally for autophosphorylation to initiate the UPR... - Crystal structure of human cytochrome P450 2D6Paul Rowland
Department of Discovery Research, GlaxoSmithKline, New Frontiers Science Park, Third Avenue, Harlow, Essex CM19 5AW, United Kingdom
J Biol Chem 281:7614-22. 2006..The structure has been compared with published homology models and has been used to explain much of the reported site-directed mutagenesis data and help understand the metabolism of several compounds... - Crystal structures of two bacterial 3-hydroxy-3-methylglutaryl-CoA lyases suggest a common catalytic mechanism among a family of TIM barrel metalloenzymes cleaving carbon-carbon bondsFarhad Forouhar
Department of Biological Sciences and Northeast Structural Genomics Consortium, Columbia University, New York, NY 10027, USA
J Biol Chem 281:7533-45. 2006..2006) J. Biol. Chem. 281, 7526-7532). Our model is consistent with extensive mutagenesis results and can guide subsequent studies directed at definitive experimental elucidation of this enzyme's reaction mechanism... - Crystal structure of the S. cerevisiae D-ribose-5-phosphate isomerase: comparison with the archaeal and bacterial enzymesM Graille
Institut de Biochimie et de Biophysique Moleculaire et Cellulaire, CNRS UMR 8619, Universite Paris Sud, Batiment 430, 91405 Orsay, France
Biochimie 87:763-9. 2005..The yeast enzyme associates as a homotetramer similarly to the archaeal protein. The effect of an inactivating mutation (Arg189 to Lys) is discussed in view of the information brought by this structure... - Structure of the p53 tumor suppressor bound to the ankyrin and SH3 domains of 53BP2S Gorina
Cellular Biochemistry and Biophysics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
Science 274:1001-5. 1996..The six most frequently observed p53 mutations disrupt 53BP2 binding in vitro. The structure provides evidence that the 53BP2-p53 complex forms in vivo and may have a critical role in the p53 pathway of tumor suppression... - Crystal structure of a novel regulatory 40-kDa mammary gland protein (MGP-40) secreted during involutionAshok K Mohanty
Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110 029, India
J Biol Chem 278:14451-60. 2003..However, the site and mode of binding of this protein to cell surface receptors are not yet known... - Structure of a cholesterol-binding protein deficient in Niemann-Pick type C2 diseaseNatalia Friedland
Center for Advanced Biotechnology and Medicine, Howard Hughes Medical Institute, University of Medicine and Dentistry of New Jersey Robert Wood Johnson Medical School, 679 Hoes Lane, Piscataway, NJ 08854, USA
Proc Natl Acad Sci U S A 100:2512-7. 2003..We propose that this region represents the incipient cholesterol-binding site that dilates to accommodate an approximately 740-A(3) cholesterol molecule... - A comparative three-dimensional model of the carboxy-terminal domain of the lambda repressor and its use to build intact repressor tetramer models bound to adjacent operator sitesRajagopal Chattopadhyaya
Department of Biochemistry, Bose Institute, P 1 12, C I T Scheme VII M, Calcutta 700054, India
J Struct Biol 141:103-14. 2003..The oligomerization mode observed in the crystal structure of 132-236 may not exist in the intact repressor bound to the operator since it is shown to contradict several published biochemical data on the intact repressor... - Structural basis for ligand-independent activation of the orphan nuclear receptor LRH-1Elena P Sablin
Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94143, USA
Mol Cell 11:1575-85. 2003..These findings illustrate an alternative structural strategy for nuclear receptor stabilization in the absence of ligand binding... - The structure of the receptor-binding domain of the bacteriophage T4 short tail fibre reveals a knitted trimeric metal-binding foldEllen Thomassen
Biophysical Structural Chemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, NL-2333 CC, Leiden, The Netherlands
J Mol Biol 331:361-73. 2003..It reveals a metal-binding site, containing a zinc ion coordinated by six histidine residues in an octahedral conformation. We also suggest an LPS-binding region... - Crystal structure of carbapenam synthetase (CarA)Matthew T Miller
Department of Biochemistry, Northwestern University, Evanston, Illinois 60208, USA
J Biol Chem 278:40996-1002. 2003.... - Enzymatic E-colicins bind to their target receptor BtuB by presentation of a small binding epitope on a coiled-coil scaffoldArun K Mohanty
Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908 0736, USA
J Biol Chem 278:40953-8. 2003..We conclude that the BtuB binding sites for cobalamins and enzymatic E-colicins are overlapping but inequivalent and that the distal loop and (possibly) the short alpha-helical flanking regions are sufficient for high affinity binding... - Gram-positive DsbE proteins function differently from Gram-negative DsbE homologs. A structure to function analysis of DsbE from Mycobacterium tuberculosisCelia W Goulding
Howard Hughes Medical Institute and UCLA Department of Energy Institute of Genomics and Proteomics, Los Angeles, California 90095 1570
J Biol Chem 279:3516-24. 2004..Structural and biochemical analysis implies that Mtb DsbE functions differently from Gram-negative DsbE homologs, and we discuss its possible functional role in the bacterium... - The zinc finger-associated domain of the Drosophila transcription factor grauzone is a novel zinc-coordinating protein-protein interaction moduleRalf Jauch
Max Planck Institut fur biophysikalische Chemie, Abteilung Molekulare Entwicklungsbiologie, Röntgenkristallographie, Am Fassberg 11, D 37077 Gottingen, Germany
Structure 11:1393-402. 2003..The results indicate that ZAD provides a novel protein-protein interaction module that characterizes a large family of insect transcription factors... - The crystal structure of murine CMP-5-N-acetylneuraminic acid synthetaseStephan Krapp
Max Planck Institut fur Biochemie, Abteilung für Strukturforschung, Am Klopferspitz 18a, 82152, Martinsried, Germany
J Mol Biol 334:625-37. 2003..In addition, a complex regulation of the enzyme activity is proposed that includes phosphorylation and dephosphorylation... - The crystal structure of cyclin AN R Brown
Laboratory of Molecular Biophysics, Oxford, UK
Structure 3:1235-47. 1995..From the determination of the structure of cyclin A, together with results from biochemical and genetic analyses, we can identify which parts of the cyclin molecular may contribute to cyclin A structure and function... - A novel variant of the immunoglobulin fold in surface adhesins of Staphylococcus aureus: crystal structure of the fibrinogen-binding MSCRAMM, clumping factor AChampion C S Deivanayagam
Center for Biophysical Sciences and Engineering, School of Optometry, 244 CBSE, 1025 18th Street South, University of Alabama at Birmingham, Birmingham, AL 35294 0005, USA
EMBO J 21:6660-72. 2002.... - Structure of human FIH-1 reveals a unique active site pocket and interaction sites for HIF-1 and von Hippel-LindauCheolju Lee
Center for Cellular Switch Protein Structure, Korea Research Institute of Bioscience and Biotechnology, 52 Euh eun dong, Yuseong Gu, Daejeon 305 806, Korea
J Biol Chem 278:7558-63. 2003..The unique environment of the active site and cofactor-binding region revealed in the structure should allow design of selective drugs that can be used in ischemic diseases to promote hypoxia responses... - Crystal structure of trbp111: a structure-specific tRNA-binding proteinM A Swairjo
Skaags Institute for Chemical Biology, Department of Molecular Biology and Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
EMBO J 19:6287-98. 2000..These residues line the inner surfaces of two clefts formed between the ss-barrel of each monomer and the dimer interface. The results are consistent with a proposed model for asymmetrical docking of the convex side of tRNA to the dimer... - A novel all helix fold of the AP180 amino-terminal domain for phosphoinositide binding and clathrin assembly in synaptic vesicle endocytosisY Mao
Structural and Computational Biology and Molecular Biophysics Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA
Cell 104:433-40. 2001..The finding that the clathrin-box motif is mostly buried and lies in a helix indicates a different site and mechanism for binding of the domain to clathrins than previously assumed... - Calcium binding properties of gamma-crystallin: calcium ion binds at the Greek key beta gamma-crystallin foldB Rajini
Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad-500007, India
J Biol Chem 276:38464-71. 2001..These results are of significance in understanding the mechanism of calcium homeostasis in the lens... - Crystallographic and modeling studies of RNase III suggest a mechanism for double-stranded RNA cleavageJ Blaszczyk
Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
Structure 9:1225-36. 2001..The three-dimensional structure of the dsRBD in Escherichia coli RNase III has been elucidated; no structural information is available for the endonuclease domain of any RNase III... - Twists and turns of the cation-dependent mannose 6-phosphate receptor. Ligand-bound versus ligand-free receptorLinda J Olson
Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
J Biol Chem 277:10156-61. 2002..4... - The rhesus rotavirus VP4 sialic acid binding domain has a galectin fold with a novel carbohydrate binding sitePhilip R Dormitzer
Laboratory of Molecular Medicine, Enders 673, Children s Hospital, 320 Longwood Avenue, Boston, MA 02115, USA
EMBO J 21:885-97. 2002..From the fit of the VP8* core into the virion spikes, we propose that VP4 arose from the insertion of a host carbohydrate binding domain into a viral membrane interaction protein... - Structure and backbone dynamics of Apo- and holo-cellular retinol-binding protein in solutionLorella Franzoni
Department of Experimental Medicine, Section of Chemistry and Structural Biochemistry, University of Parma, 43100 Parma, Italy
J Biol Chem 277:21983-97. 2002....
Research Grants
- Cloning of a type 2 diabetes modifier in obese miceRudolph Leibel; Fiscal Year: 2006..4.) computational assessment of effects of coding and non-coding variants on secondary protein structure/function and transcription. 5...
- Probing the cellular Mechanisms of Transthyretin CytotoxicityNatalia Reixach; Fiscal Year: 2010The transthyretin (TTR) amyloidoses are fatal disorders of secondary protein structure characterized by extracellular deposition of aggregates, including amyloid fibrils, derived from the secreted transthyretin protein...
- PHOSPHATE TRANSPORT PATHS WITHIN HOMODIMERIC PTPHartmut Wohlrab; Fiscal Year: 2001..The aim now is to identify transmembrane secondary protein structure elements that line the Pi transport path through PTP and to demonstrate that they undergo Pi-induced ..
- STRUCTURAL ORGANIZATION AND PROTEOMICS OF TBThomas Terwilliger; Fiscal Year: 2005..The structural and functional information obtained in this project is to be placed in the public domain by timely deposition in publicly available databases. ..
- LIGAND BASED STUDIES OF NUCLEAR RECEPTORSThomas Scanlan; Fiscal Year: 2003..Moreover, these selective ligands could be useful as therapeutics for the treatment of human disease associated with thyroid hormone regulation. ..
- CHEMICAL MODELS OF PROTEIN BETA SHEET INTERACTIONSJames Nowick; Fiscal Year: 2002..5) Artificial beta-sheets designed to block beta-amyloid aggregation will be synthesized, and their abilities to block its aggregation and deposition will be studied using in vitro assays. ..
- CELL BIOLOGY OF THE NEURONAL SODIUM CHANNELWilliam A Catterall; Fiscal Year: 2010..This project will use a mouse genetic model of this disease to determine how this gene defect causes epilepsy and to test new drug combinations for control of this intractable epilepsy syndrome. ..
- Factors influencing regulation of the dynamics of the actin filament pointed endAlla S Kostyukova; Fiscal Year: 2010..The information obtained in this study will help us to understand the formation of the capping complex at the pointed end and its function in regulating dynamics of the actin filament in cells and tissues. ..
- Dietary Polyphenols Are Consequential Epigenetic Modulators of Gene ExpressionBAOTING ZHU; Fiscal Year: 2009..It is expected that the outcomes of the proposed studies will have direct clinical utility in the near future and far-reaching human health implications. ..
- Biomolecular Analysis of Proteins in Visual DiseaseESTHER BISWAS FISS; Fiscal Year: 2007....
- Membrane Protein Folding and AssemblyStephen White; Fiscal Year: 2007..The information obtained will help us understand how to predict the topology and structure of unusual membrane proteins, such as the CIC chloride channel. ..
- INTRACELLULAR SIGNALING BY BACTERIAL CHEMORECEPTORSJohn Parkinson; Fiscal Year: 2006..These studies will provide important new perspectives on the issue of receptor clustering, a hallmark of biological signaling systems at every complexity level. ..
- CALCIUM RECEPTOR SIGNAL RECOGNITION AND TRANSDUCTIONEdward M Brown; Fiscal Year: 2006..abstract_text> ..
- Cold Neutrons For Biology And TechnologyStephen White; Fiscal Year: 2005..We foresee a future when computer simulations will allow three-dimensional detail to be inferred routinely from 1- and 2-dimensional neutron and X-ray data. ..
- How Insulin Binds to the Insulin ReceptorMICHAEL AARON WEISS; Fiscal Year: 2010..To demonstrate proof-of- principle, respective application of this enabling technology to the liver and pancreatic p cells of LIRKO and PIRKO mice is planned in collaboration with C. R. Kahn (Joslin Diabetes Center, Boston). ..
- VOLTAGE-SENSITIVE SODIUM CHANNELS IN BRAINWilliam Catterall; Fiscal Year: 1991..These studies will provide essential information to understanding the molecular basis of electrical excitability...
- GENETICS OF CHEMOTACTIC BEHAVIOR IN ESCHERICHIA COLIJohn Parkinson; Fiscal Year: 1991..The DNA sequence changes in selected mutants will be determined in order to delineate functional domains within the proteins. From these studies, structurefunction models will be devised that can be tested by sitespecific mutagenesis...
- MOLECULAR MECHANISM OF RENAL NA+ DEPENDENT COTRANSPORTAna Pajor; Fiscal Year: 2006..abstract_text> ..
- Arg199: key player in electron transfer in NOS enzymeValentin Gogonea; Fiscal Year: 2004..Primary focus is placed on how Arg199 modulates the electron transfer in NOS a role only revealed during the dynamics of the system. ..
- PROTON & ELECTRON TRANSFER & ENERGY COUPLING IN SITE ITomoko Ohnishi; Fiscal Year: 2009..Using this new strategy, we found that both cluster N2 and flavin can generate superoxide. We will solidify this exciting finding and study its relevance to complex I function under physiological and pathological conditions. ..
- INTRACELLULAR SIGNALING BY BACTERIAL CHEMORECEPTORSJohn Parkinson; Fiscal Year: 2007....
- X-ray diffraction analysis of human adenovirusVijay Reddy; Fiscal Year: 2006..et al. Science 309: 1090-1092, 2005). ..
- X-ray diffraction analysis of human adenovirusVijay S Reddy; Fiscal Year: 2010..The proposed studies are aimed at determining the crystal structure of the entire human adenovirus virion at near atomic resolution employing x-ray diffraction methods. ..
- MOLECULAR MECHANISM OF RENAL NA+ DEPENDENT COTRANSPORTAna Pajor; Fiscal Year: 2001..These studies should provide fundamental information on the functional properties of this family of sodium-dependent transporters, and on the physiological role of these transporters in the kidney. ..
- MOLECULAR MECHANISM OF RENAL NA+ DEPENDENT COTRANSPORTAna Pajor; Fiscal Year: 2009..Understanding how NaDC1 and SdcS work will help us to develop treatments for NaDC1-mediated diseases. ..
- PROTON & ELECTRON TRANSFER & ENERGY COUPLING IN SITE ITomoko Ohnishi; Fiscal Year: 2000..The P.I. will collaborate on this project with a multi-disciplinary research team, consisting of renowned experts of molecular biology, mitochondrial disease, biochemistry and biophysics. ..
- MOLECULAR MECHANISM OF RENAL NA+ DEPENDENT COTRANSPORTAna M Pajor; Fiscal Year: 2010..Understanding how NaDC1 and SdcS work will help us to develop treatments for NaDC1-mediated diseases. ..
- PROTON & ELECTRON TRANSFER & ENERGY COUPLING IN SITE ITOMOKO NONE OHNISHI; Fiscal Year: 2010..Using this new strategy, we found that both cluster N2 and flavin can generate superoxide. We will solidify this exciting finding and study its relevance to complex I function under physiological and pathological conditions. ..