Remote homology detection of integral membrane proteins using conserved sequence features

Proteins: Structure, Function and Genetics

Volumn 71, Issue 3, 2008, Pages 1387-1399

  Bernsel, Andreas ^a   Viklund, Håkan ^a   Elofsson, Arne ^a  

^a STOCKHOLM UNIVERSITY   (Sweden)

Author keywords

Hidden Markov model; Homology detection; Membrane protein; Membrane topology

Indexed keywords

GLOBULAR PROTEIN; MEMBRANE PROTEIN;

ALGORITHM; AMINO ACID COMPOSITION; ARTICLE; GENE SEQUENCE; GENETIC CONSERVATION; GENETIC VARIABILITY; HYDROPHOBICITY; MOLECULAR EVOLUTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN DOMAIN; PROTEIN STRUCTURE; SEQUENCE ALIGNMENT; STRUCTURAL HOMOLOGY; STRUCTURE ANALYSIS;

CONSERVED SEQUENCE; DATABASES, PROTEIN; HYDROPHOBICITY; MARKOV CHAINS; MEMBRANE PROTEINS; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 42449160596     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21825     Document Type: Article

References (48)

1. Cane D. Back to basics: assigning biochemical function in the post-genomic era. Chem Biol 2004;11(6):741-743.
2. Whisstock J, Lesk A. Prediction of protein function from protein sequence and structure. Q Rev Biophys 2003;36(3):307-340.
3. Wallner B, Fang H, Ohlson T, Frey-Skott J, Elofsson A. Using evolutionary information for the query and target improves fold recognition. Proteins 2004;54(2):342-350.
4. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990;215(3):403-410.
5. 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.
6. Park J, Karplus K, Barrett C, Hughey R, Haussler D, Hubbard T, Chothia C. Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods. J Mol Biol 1998;284(4):1201-1210.
7. Rychlewski L, Jaroszewski L, Li W, Godzik A. Comparison of sequence profiles, strategies for structural predictions using sequence information. Protein Sci 2000;9(2):232-241.
8. Mittelman D, Sadreyev R, Grishin N. Probabilistic scoring measures for profile-profile comparison yield more accurate short seed alignments. Bioinformatics 2003;19(12):1531-1539.
9. Ohlson T, Wallner B, Elofsson A. Profile-profile methods provide improved fold-recognition: a study of different profile-profile alignment methods. Proteins 2004;57(1):188-197.
10. Krogh A, Larsson B, vonHeijne G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 2001;305(3):567-580.
11. Drews J. Genomic sciences and the medicine of tomorrow. Nat Biotechnol 1996;14(11):1516-1518.
12. Tourasse NJ, Li WH. Selective constraints, amino acid composition, and the rate of protein evolution. Mol Biol Evol 2000;17(4):656-664.
13. Fischer D, Eisenberg D. Protein fold recognition using sequence-derived predictions. Protein Sci 1996;5:947-955.
14. Rice D, Eisenberg D. A 3D-1D substitution matrix for protein fold recognition that includes predicted secondary structure of the sequence. J Mol Biol 1997;267:1026-1038.
15. Rost B, Schneider R, Sander C. Protein fold recognition by prediction-based threading. J Mol Biol 1997;270:471-480.
16. Hargbo J, Elofsson A. Hidden markov models that use predicted secondary structures for fold recognition. Proteins 1999;36(1):68-76.
17. Siew N, Elofsson A, Rychlewski L, Fischer D. Maxsub: An automated measure to assess the quality of protein structure predictions. Bionformatics 2000;16:776-785.
18. vonOhsen N, Sommer I, Zimmer R. Profile-profile alignment: a powerful tool for protein structure prediction. In: Altman RB, Dunker AK, Hunter Jung TAL, Klein TE, editors, Pacific Symposium on Biocomputing. 2003:252-263.
19. Yona G, Levitt M. Within the twilight zone: a sensitive profile-profile comparison tool based on information theory. J Mol Biol 2002;315(5):1257-1275.
20. Sadreyev R, Baker D, Grishin N. Profile-profile comparisons by COMPASS predict intricate homologies between protein families. Protein Sci 2003;12(10):2262-2272.
21. Edgar R, Sjolander K. SATCHMO: sequence alignment and tree construction using hidden Markov models. Bioinformatics 2003;19: 1404-1411.
22. Pei J, Sadreyev R, Grishin N. PCMA: fast and accurate multiple sequence alignment based on profile consistency. Bioinformatics 2003;19(3):427-428.
23. Ng PC, Henikoff JG, Henikoff S. PHAT: a transmembrane-specific substitution matrix. Predicted hydrophobic and transmembrane. Bioinformatics 2000;16(9):760-766.
24. Hedman M, Deloof H, Von Heijne G, Elofsson A. Improved detection of homologous membrane proteins by inclusion of information from topology predictions. Protein Sci 2002;11(3):652-658.
25. Forrest L, Tang C, Honig B. On the accuracy of homology modeling and sequence alignment methods applied to membrane proteins. Biophys J 2006;91:508-517.
26. Hughey R, Krogh A. Hidden Markov models for sequence analysis: extension and analysis of the basic method. Comput Appl Biosci 1996;12(2):95-107.
27. Eddy SR. Profile hidden Markov models. Bioinformatics 1998; 14(9):755-763.
28. Soding J, Biegert A, Lupas AN. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res 2005;33(Web Server issue):244-248.
29. Karplus K, Karchin R, Draper J, Casper J, Mandel-Gutfreund Y, Diekhans M, Hughey R. Combining local-structure, fold-recognition, and new fold methods for protein structure prediction. Proteins 2003;53(Suppl 6):491-496.
30. Bairoch A, Apweiler R, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O'Donovan C, Redaschi N, Yeh L-SL. The Universal Protein Resource (UniProt). Nucleic Acids Res 2005;33(Database issue): 154-159.
31. Engelman DM, Steitz TA, Goldman A. Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins. Annu Rev Biophys Biophys Chem 1986;15:321-353.
32. vonHeijne G. Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule. J Mol Biol 1992;225(2): 487-494.
33. Boeckmann B, Bairoch A, Apweiler R, Blatter M-C, Estreicher A, Gasteiger E, Martin MJ, Michoud K, O'Donovan C, Phan I, Pilbout S, Schneider M. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res 2003;31(1):365-370.
34. Viklund H, Elofsson A. Best α-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information. Protein Sci 2004;13(7):1908-1917.
35. Rabiner LR. A tutorial on hidden markov models and selected applications in speech recognition. Proceedings of the IEEE 1989;77(2):257-285.
36. Elofsson A. A study on protein sequence alignment quality. Proteins 2002;46(3):330-339.
37. Jones D. Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 1999;292(2):195-202.
38. Horn F, Bettler E, Oliveira L, Campagne F, Cohen FE, Vriend G. GPCRDB information system for G protein-coupled receptors. Nucleic Acids Res 2003;31(1):294-297.
39. Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 2006;22(13):1658-1659.
40. Sali A, Blundell T. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 1993;234(3):779-815.
41. Zemla A. LGA: a method for finding 3d similarities in protein structures. Nucleic Acids Res 2003;31(13):3370-3374.
42. Zhang Y, Skolnick J. Scoring function for automated assessment of protein structure template quality. Proteins 2004;57(4):702-710.
43. Lomize A, Pogozheva I, Lomize M, Mosberg H. Positioning of proteins in membranes: a computational approach. Protein Sci 2006;15(6):1318-1333.
44. Gerstein M, Levitt M. Comprehensive assessment of automatic structural alignment against a manual standard, the scop classification of proteins. Protein Sci 1998;7(2):445-456.
45. Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer ELL, Studholme DJ, Yeats C, Eddy SR. The Pfam protein families database. Nucleic Acids Res 2004;32:138-141.
46. Wistrand M, Kall L, Sonnhammer ELL. A general model of G protein-coupled receptor sequences and its application to detect remote homologs. Protein Sci 2006;15(3):509-521.
47. Provost F, Fawcett T. Robust classification for imprecise environments. Mach Learn 2001;42(3):203-231.
48. Kall L, Krogh A, Sonnhammer ELL. An HMM posterior decoder for sequence feature prediction that includes homology information. Bioinformatics 2005;21(Suppl 1):251-257.