Structure and function predictions of the Msa protein in Staphylococcus aureus

BMC Bioinformatics

Volumn 8, Issue SUPPL. 7, 2007, Pages

  Nagarajan, Vijayaraj ^a   Elasri, Mohamed O ^a  

^a University of Southern Mississippi   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL TOOLS; LIFE-THREATENING INFECTIONS; PHOSPHORYLATION SITES; PHYSICOCHEMICAL PROPERTY; STAPHYLOCOCCUS AUREUS; STRUCTURE INFORMATION; TERTIARY STRUCTURES; TRANSMEMBRANE REGIONS;

BACTERIA; BIOLOGICAL MEMBRANES; GENE EXPRESSION; PROTEINS; SIGNAL TRANSDUCTION;

FORECASTING;

MEMBRANE PROTEIN; MODULATOR OF STAPHYLOCOCCAL ACCESSORY REGULATOR A PROTEIN; TRANSCRIPTION FACTOR;

ACCURACY; ALGORITHM; AMINO ACID SEQUENCE; BACTERIAL GENETICS; BINDING SITE; BIOINFORMATICS; CELLULAR DISTRIBUTION; CONFERENCE PAPER; CONSENSUS SEQUENCE; CONTROLLED STUDY; CRYSTALLIZATION; HYPOTHESIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYSICAL CHEMISTRY; PREDICTION; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN MOTIF; PROTEIN PHOSPHORYLATION; PROTEIN PURIFICATION; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; PROTEIN TERTIARY STRUCTURE; SIGNAL TRANSDUCTION; STAPHYLOCOCCUS AUREUS; ARTICLE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; METABOLISM; METHODOLOGY; MOLECULAR GENETICS; PROTEIN BINDING; PROTEIN CONFORMATION; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; STRUCTURE ACTIVITY RELATION;

STAPHYLOCOCCUS AUREUS;

AMINO ACID SEQUENCE; BASE SEQUENCE; BINDING SITES; COMPUTER SIMULATION; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; PROTEIN CONFORMATION; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; STAPHYLOCOCCUS AUREUS; STRUCTURE-ACTIVITY RELATIONSHIP; TRANSCRIPTION FACTORS;

EID: 38549141931     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-S7-S5     Document Type: Conference Paper

References (57)

1. Novick RP Autoinduction and signal transduction in the regulation of staphylococcal virulence Mol Microbiol 2003 48 6 1429-1449 10.1046/ j.1365-2958.2003.03526.x 12791129
2. Cheung AL Projan SJ Cloning and sequencing of sarA of Staphylococcus aureus, a gene required for the expression of agr J Bacteriol 1994 176 13 4168-4172 205618 8021198
3. Dunman PM Murphy E Haney S Palacios D Tucker-Kellogg G Wu S Brown EL Zagursky RJ Shlaes D Projan SJ Transcription profiling-based identification of Staphylococcus aureus genes regulated by the agr and/ or sarA loci J Bacteriol 2001 183 24 7341-7353 95583 11717293 10.1128/ JB.183.24.7341-7353.2001
4. Blevins JS Elasri MO Allmendinger SD Beenken KE Skinner RA Thomas JR Smeltzer MS Role of sarA in the pathogenesis of Staphylococcus aureus musculoskeletal infection Infect Immun 2003 71 1 516-523 143404 12496203 10.1128/IAI.71.1.516-523.2003
5. Sambanthamoorthy K Smeltzer MS Elasri MO Identification and characterization of msa (SA1233), a gene involved in expression of SarA and several virulence factors in Staphylococcus aureus Microbiology 2006 152 Pt 9 2559-2572 10.1099/mic.0.29071-0 16946251
6. Rost B Review: Protein secondary structure prediction continues to rise J Struct Biol 2001 134 2-3 204-218 10.1006/jsbi.2001.4336 11551180
7. Pandey G Kumar V Steinbach M Computational Approaches for Protein Function Prediction: A Survey Twin Cities: Department of Computer Science and Engineering, University of Minnesota 2006
8. Holden MT Feil EJ Lindsay JA Peacock SJ Day NP Enright MC Foster TJ Moore CE Hurst L Atkin R et al Complete genomes of two clinical Staphylococcus aureus strains: Evidence for the rapid evolution of virulence and drug resistance Proc Natl Acad Sci USA 2004 101 26 9786-9791 470752 15213324 10.1073/pnas.0402521101
9. von Heijne G Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule J Mol Biol 1992 225 2 487-494 10.1016/0022-2836(92)90934-C 1593632
10. Galperin MY A census of membrane-bound and intracellular signal transduction proteins in bacteria: Bacterial IQ, extroverts and introverts BMC Microbiol 2005 5 35 1183210 15955239 10.1186/ 1471-2180-5-35
11. D'Souza M Glass EM Syed MH Zhang Y Rodriguez A Maltsev N Galperin MY Sentra: A database of signal transduction proteins for comparative genome analysis Nucleic Acids Res 2007 35 Database D271-273 1751548 17135204 10.1093/nar/gkl949
12. Watson JD Milner-White EJ A novel main-chain anion-binding site in proteins: The nest. A particular combination of phi, psi values in successive residues gives rise to anion-binding sites that occur commonly and are found often at functionally important regions J Mol Biol 2002 315 2 171-182 10.1006/jmbi.2001.5227 11779237
13. Gasteiger E Hoogland C Gattiker A Duvaud S Wilkins MR Appel RD Bairoch A Protein Identification and Analysis Tools on the ExPASy Server The Proteomics Protocols Handbook Humana Press Walker JM 2005 571-607
14. Brendel V Bucher P Nourbakhsh IR Blaisdell BE Karlin S Methods and algorithms for statistical analysis of protein sequences Proc Natl Acad Sci USA 1992 89 6 2002-2006 48584 1549558 10.1073/pnas.89.6.2002
15. Altschul SF Madden TL Schaffer AA Zhang J Zhang Z Miller W Lipman DJ Gapped BLAST and PSI-BLAST: A new generation of protein database search programs Nucleic Acids Res 1997 25 17 3389-3402 146917 9254694 10.1093/ nar/25.17.3389
16. Geer LY Domrachev M Lipman DJ Bryant SH CDART: Protein homology by domain architecture Genome Res 2002 12 10 1619-1623 187533 12368255 10.1101/gr.278202
17. Jensen LJ Gupta R Staerfeldt HH Brunak S Prediction of human protein function according to Gene Ontology categories Bioinformatics 2003 19 5 635-642 10.1093/bioinformatics/btg036 12651722
18. Nakai K Horton P PSORT: A program for detecting sorting signals in proteins and predicting their subcellular localization Trends Biochem Sci 1999 24 1 34-36 10.1016/S0968-0004(98)01336-X 10087920
19. Softberry http://www.softberry.com
20. Pasquier C Promponas VJ Hamodrakas SJ PRED-CLASS: Cascading neural networks for generalized protein classification and genome-wide applications Proteins 2001 44 3 361-369 10.1002/prot.1101 11455609
21. Cai CZ Han LY Ji ZL Chen X Chen YZ SVM-Prot: Web-based support vector machine software for functional classification of a protein from its primary sequence Nucleic Acids Res 2003 31 13 3692-3697 169006 12824396 10.1093/nar/gkg600
22. Bendtsen JD Nielsen H von Heijne G Brunak S Improved prediction of signal peptides: SignalP 3.0 J Mol Biol 2004 340 4 783-795 10.1016/ j.jmb.2004.05.028 15223320
23. Hiller K Grote A Scheer M Munch R Jahn D PrediSi: Prediction of signal peptides and their cleavage positions Nucleic Acids Res 2004 32 Web Server W375-379 441516 15215414 10.1093/nar/gkh378
24. von Heijne G A new method for predicting signal sequence cleavage sites Nucleic Acids Res 1986 14 11 4683-4690 311474 3714490 10.1093/nar/ 14.11.4683
25. Kall L Krogh A Sonnhammer EL A combined transmembrane topology and signal peptide prediction method J Mol Biol 2004 338 5 1027-1036 10.1016/ j.jmb.2004.03.016 15111065
26. SIG-Pred: Signal Peptide Prediction http://www.bioinformatics.leeds.ac.uk/prot_analysis/Signal.html
27. Gomi M Sonoyama M Mitaku S High performance system for signal peptide prediction: SOSUIsignal Chem-Bio Informatics Journal 2004 4 4 142-147 10.1273/cbij.4.142
28. Bannai H Tamada Y Maruyama O Nakai K Miyano S Extensive feature detection of N-terminal protein sorting signals Bioinformatics 2002 18 2 298-305 10.1093/bioinformatics/18.2.298 11847077
29. Claros MG von Heijne G TopPred II: An improved software for membrane protein structure predictions Comput Appl Biosci 1994 10 6 685-686 7704669
30. Hofmann K Stoffel W TMBASE - A database of membrane spanning protein segments Biol Chem Hoppe-Seyler 1993 374 166
31. Rost B Casadio R Fariselli P Sander C Transmembrane helices predicted at 95% accuracy Protein Sci 1995 4 3 521-533 7795533
32. Krogh A Larsson B von Heijne G Sonnhammer EL Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes J Mol Biol 2001 305 3 567-580 10.1006/jmbi.2000.4315 11152613
33. Juretic D Zoranic L Zucic D Basic charge clusters and predictions of membrane protein topology J Chem Inf Comput Sci 2002 42 3 620-632 10.1021/ci010263s 12086524
34. Tusnady GE Simon I The HMMTOP transmembrane topology prediction server Bioinformatics 2001 17 9 849-850 10.1093/bioinformatics/17.9.849 11590105
35. Jones DT Taylor WR Thornton JM A model recognition approach to the prediction of all-helical membrane protein structure and topology Biochemistry 1994 33 10 3038-3049 10.1021/bi00176a037 8130217
36. Cserzo M Wallin E Simon I von Heijne G Elofsson A Prediction of transmembrane alpha-helices in prokaryotic membrane proteins: The dense alignment surface method Protein Eng 1997 10 6 673-676 10.1093/protein/ 10.6.673 9278280
37. Kihara D Shimizu T Kanehisa M Prediction of membrane proteins based on classification of transmembrane segments Protein Eng 1998 11 11 961-970 10.1093/protein/11.11.961 9876916
38. Deleage G Blanchet C Geourjon C Protein structure prediction. Implications for the biologist Biochimie 1997 79 11 681-686 10.1016/ S0300-9084(97)83524-9 9479451
39. Letunic I Copley RR Schmidt S Ciccarelli FD Doerks T Schultz J Ponting CP Bork P SMART 4.0: Towards genomic data integration Nucleic Acids Res 2004 32 Database D142-144 308822 14681379 10.1093/nar/gkh088
40. PPSearch http://www.ebi.ac.uk/ppsearch/
41. Solovyev VV Kolchanov NA Search for functional sites using consensus Computer analysis of Genetic macromolecules World Scientific Kolchanov NA, Lim HA 1994 16-21
42. de Castro E Sigrist CJ Gattiker A Bulliard V Langendijk-Genevaux PS Gasteiger E Bairoch A Hulo N ScanProsite: Detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins Nucleic Acids Res 2006 34 Web Server W362-365 1538847 16845026 10.1093/nar/gkl124
43. Hulo N Bairoch A Bulliard V Cerutti L De Castro E Langendijk-Genevaux PS Pagni M Sigrist CJ The PROSITE database Nucleic Acids Res 2006 34 Database D227-230 1347426 16381852 10.1093/nar/gkj063
44. Schwede T Kopp J Guex N Peitsch MC SWISS-MODEL: An automated protein homology-modeling server Nucleic Acids Res 2003 31 13 3381-3385 168927 12824332 10.1093/nar/gkg520
45. Sali A Blundell TL Comparative protein modelling by satisfaction of spatial restraints J Mol Biol 1993 234 3 779-815 10.1006/jmbi.1993.1626 8254673
46. Alexandrov NN Nussinov R Zimmer RM Fast protein fold recognition via sequence to structure alignment and contact capacity potentials Pac Symp Biocomput 1996 53-72 9390223
47. Bryson K McGuffin LJ Marsden RL Ward JJ Sodhi JS Jones DT Protein structure prediction servers at University College London Nucleic Acids Res 2005 33 Web Server W36-38 1160171 15980489 10.1093/nar/gki410
48. Kelley LA MacCallum RM Sternberg MJ Enhanced genome annotation using structural profiles in the program 3D-PSSM J Mol Biol 2000 299 2 499-520 10.1006/jmbi.2000.3741 10860755
49. Vriend G WHAT IF: A molecular modeling and drug design program J Mol Graph 1990 8 1 52 56-29. 10.1016/0263-7855(90)80070-V 2268628
50. Guex N Peitsch MC SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling Electrophoresis 1997 18 15 2714-2723 10.1002/elps.1150181505 9504803
51. Laskowski RA Watson JD Thornton JM ProFunc: A server for predicting protein function from 3D structure Nucleic Acids Res 2005 33 Web Server W89-93 1160175 15980588 10.1093/nar/gki414
52. Laurie AT Jackson RM Q-SiteFinder: An energy-based method for the prediction of protein-ligand binding sites Bioinformatics 2005 21 9 1908-1916 10.1093/bioinformatics/bti315 15701681
53. Liang S Zhang C Liu S Zhou Y Protein binding site prediction using an empirical scoring function Nucleic Acids Res 2006 34 13 3698-3707 1540721 16893954 10.1093/nar/gkl454
54. Jambon M Imberty A Deleage G Geourjon C A new bioinformatic approach to detect common 3D sites in protein structures Proteins 2003 52 2 137-145 10.1002/prot.10339 12833538
55. SCRATCH http://www.ics.uci.edu/%7Ebaldig/scratch/
56. ProSAL http://xray.bmc.uu.se/sbnet/prosal.html
57. MetaPP http://www.predictprotein.org/newwebsite/meta/submit3.php