Reliability measures for membrane protein topology prediction algorithms

Journal of Molecular Biology

Volumn 327, Issue 3, 2003, Pages 735-744

  Melén, Karin ^a   Krogh, Anders ^b   Von Heijne, Gunnar ^a  

^a STOCKHOLM UNIVERSITY   (Sweden)

^b UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

Bioinformatics; Membrane protein; Topology prediction

Indexed keywords

BACTERIAL PROTEIN; CELL MEMBRANE PROTEIN;

ALGORITHM; ANALYTIC METHOD; ARTICLE; BACTERIAL GENOME; CAENORHABDITIS ELEGANS; CARBOXY TERMINAL SEQUENCE; ESCHERICHIA COLI; GENE SEQUENCE; GENOME ANALYSIS; INTERMETHOD COMPARISON; PREDICTION; PRIORITY JOURNAL; PROTEIN STRUCTURE; RELIABILITY; SACCHAROMYCES CEREVISIAE;

BACTERIA (MICROORGANISMS); CAENORHABDITIS; CAENORHABDITIS ELEGANS; ESCHERICHIA COLI; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 0344406716     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(03)00182-7     Document Type: Article

References (26)

1. Krogh A., Larsson B., von Heijne G., Sonnhammer E. Predicting transmembrane protein topology with a hidden Markov model. Application to complete genomes. J. Mol. Biol. 305:2001;567-580.
2. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., et al. The Protein Data Bank. Nucl. Acids Res. 28:2000;235-242.
3. Tusnady G.E., Simon I. Principles governing amino acid composition of integral membrane proteins: application to topology prediction. J. Mol. Biol. 283:1998;489-506.
4. Jones D.T., Taylor W.R., Thornton J.M. A model recognition approach to the prediction of all-helical membrane protein structure and topology. Biochemistry. 33:1994;3038-3049.
5. Rost B., Fariselli P., Casadio R. Topology prediction for helical transmembrane proteins at 86% accuracy. Protein Sci. 5:1996;1704-1718.
6. von Heijne G. Membrane protein structure prediction - hydrophobicity analysis and the positive-inside rule. J. Mol. Biol. 225:1992;487-494.
7. Möller S., Croning M., Apweiler R. Evaluations of methods for the predictive evaluation of membrane spanning regions. Bioinformatics. 17:2001;646-653.
8. Ikeda M., Arai M., Lao D., Shimizu T. Transmembrane topology prediction methods: a re-assessment and improvement by a consensus method using a data-set of experimentally characterized transmembrane topologies. In Silico Biol. 2:2001;1-15.
9. Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 215:1990;403-410.
10. O'Donovan C., Martin M.J., Gattiker A., Gasteiger E., Bairoch A., Apweiler R. High-quality protein knowledge resource: SWISS-PROT and TrEMBL. Brief. Bioinformat. 3:2002;275-284.
11. von Heijne G. The distribution of positively charged residues in bacterial inner membrane proteins correlates with the trans-membrane topology. EMBO J. 5:1986;3021-3027.
12. von Heijne G. Control of topology and mode of assembly of a polytopic membrane protein by positively charged residues. Nature. 341:1989;456-458.
13. Käll L., Sonnhammer E. Reliability of transmembrane predictions in whole-genome data. FEBS Letters. 532:2002;415-418.
14. Nilsson J., Persson B., von Heijne G. Prediction of partial membrane protein topologies using a consensus approach. Protein Sci. 11:2002;2974-2980.
15. Blattner F.R., Plunkett G., Bloch C.A., Perna N.T., Burland V., Riley M., et al. The complete genome sequence of Escherichia coli K-12. Science. 277:1997;1453-1462.
16. Goffeau A., Aert R., Agostini-Carbone M., Ahmed A., Aigle M., Alberghina L., et al. The yeast genome directory. Nature. suppl. 387:1997;1-105.
17. Stein L., Sternberg P., Durbin R., Thierry-Mieg J., Spieth J. WormBase: network access to the genome and biology of Caenorhabditis elegans. Nucl. Acids Res. 29:2001;82-86.
18. Bargmann C. Neurobiology of the Caenorhabditis elegans genome. Science. 282:1998;2028-2033.
19. Drew D., Sjöstrand D., Nilsson J., Urbig T., Chin C.N., de Gier J.W., von Heijne G. Rapid topology mapping of Escherichia coli inner-membrane proteins by prediction and PhoA/GFP fusion analysis. Proc. Natl Acad. Sci. USA. 99:2002;2690-2695.
20. Manoil C. Analysis of membrane protein topology using alkaline phosphatase and β-galactosidase gene fusions. Methods Cell. Biol. 34:1991;61-75.
21. Deak R., Wolf D. Membrane topology and function of Der3/Hrd1p as a ubiquitin-protein ligase (E3) involved in endoplasmic reticulum degradation. J. Biol. Chem. 276:2001;10663-10669.
22. Popov M., Tam L.Y., Li J., Reithmeier R.A.F. Mapping the ends of transmembrane segments in a polytopic membrane protein - scanning N-glycosylation mutagenesis of extracytosolic loops in the anion exchanger, Band 3. J. Biol. Chem. 272:1997;18325-18332.
23. Tusnady G.E., Simon I. The HMMTOP transmembrane topology prediction server. Bioinformatics. 17:2001;849-850.
24. Möller S., Kriventseva E., Apweiler R. A collection of well-characterised integral membrane proteins. Bioinformatics. 16:2000;1159-1160.
25. Thompson J.D., Higgins D.G., Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl. Acids Res. 22:1994;4673-4680.
26. Hobohm U., Scharf M., Schneider R., Sander C. Selection of representative protein data sets. Protein Sci. 1:1992;409-417.