Experimentally constrained topology models for 51,208 bacterial inner membrane proteins

Journal of Molecular Biology

Volumn 352, Issue 3, 2005, Pages 489-494

  Granseth, Erik ^a   Daley, Daniel O ^b   Rapp, Mikaela ^b   Melén, Karin ^a   Von Heijne, Gunnar ^a,b  

^a Stockholm Bioinformatics Center   (Sweden)

^b STOCKHOLM UNIVERSITY   (Sweden)

Author keywords

Bioinformatics; Membrane protein; Proteomics; Topology prediction; Transmembrane helix

Indexed keywords

BACTERIAL PROTEIN; MEMBRANE PROTEIN;

ARTICLE; BACTERIAL MEMBRANE; CARBOXY TERMINAL SEQUENCE; ESCHERICHIA COLI; GENOME ANALYSIS; MOLECULAR MODEL; NONHUMAN; OPEN READING FRAME; PRIORITY JOURNAL; PROTEIN LOCALIZATION; SEQUENCE HOMOLOGY;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 24044436844     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2005.07.053     Document Type: Article

References (17)

1. K. Melén, A. Krogh, and G. von Heijne Reliability measures for membrane protein topology prediction algorithms J. Mol. Biol. 327 2003 735 744
2. D.O. Daley, M. Rapp, E. Granseth, K. Melén, D. Drew, and G. von Heijne Global topology analysis of the Escherichia coli inner membrane proteome Science 308 2005 1321 1323
3. E. Sonnhammer, G. von Heijne, and A. Krogh A hidden Markov model for predicting transmembrane helices in protein sequences Intell. Syst. Mol. Biol. 6 1998 175 182
4. D.A. Benson, I. Karsch-Mizrachi, D.J. Lipman, J. Ostell, and D.L. Wheeler GenBank: update Nucl. Acids Res. 32 2004 D23 D26
5. H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, and H. Weissig The Protein Data Bank Nucl. Acids Res. 28 2000 235 242
6. S. Möller, E. Kriventseva, and R. Apweiler A collection of well-characterised integral membrane proteins Bioinformatics 16 2000 1159 1160
7. S. Jayasinghe, K. Hristova, and S.H. White MPtopo: a database of membrane protein topology Protein Sci. 10 2001 455 458
8. S.F. Altschul, W. Gish, W. Miller, E.W. Myers, and D.J. Lipman Basic local alignment search tool J. Mol. Biol. 215 1990 403 410
9. I.T. Paulsen, M.H. Brown, S.J. Dunstan, and R.A. Skurray Molecular characterization of the staphylococcal multidrug resistance export protein QacC J. Bacteriol. 177 1995 2827 2833
10. S. Ninio, Y. Elbaz, and S. Schuldiner The membrane topology of EmrE - a small multidrug transporter from Escherichia coli FEBS Letters 562 2004 193 196
11. I. Ubarretxena-Belandia, J.M. Baldwin, S. Schuldiner, and C.G. Tate Three-dimensional structure of the bacterial multidrug transporter EmrE shows it is an asymmetric homodimer EMBO J. 22 2003 6175 6181
12. I.T. Paulsen, R.A. Skurray, R. Tam, M.H. Saier Jr, R.J. Turner, and J.H. Weiner The SMR family: a novel family of multidrug efflux proteins involved with the efflux of lipophilic drugs Mol. Microbiol. 19 1996 1167 1175
13. A. Krogh, B. Larsson, G. von Heijne, and E. Sonnhammer Predicting transmembrane protein topology with a hidden Markov model. Application to complete genomes J. Mol. Biol. 305 2001 567 580
14. C.P. Chen, and B. Rost Long membrane helices and short loops predicted less accurately Protein Sci. 11 2002 2766 2773
15. C.P. Chen, A. Kernytsky, and B. Rost Transmembrane helix predictions revisited Protein Sci. 11 2002 2774 2791
16. H. Kim, K. Melén, and G. von Heijne Topology models for 37 Saccharomyces cerevisiae membrane proteins based on C-terminal reporter fusions and prediction J. Biol. Chem. 278 2003 10208 10213
17. A. Bernsel, and G. von Heijne Improved membrane protein topology prediction by domain assignments Protein Sci. 14 2005 1723 1728