A limited universe of membrane protein families and folds

Protein Science

Volumn 15, Issue 7, 2006, Pages 1723-1734

  Oberai, Amit ^a   Ihm, Yungok ^a   Kim, Sanguk ^b   Bowie, James U ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b Pohang University of Science and Technology (POSTECH)   (South Korea)

Author keywords

Pfam; Protein structure; SCOP; Structural genomics

Indexed keywords

ABC TRANSPORTER; ACYLTRANSFERASE; ADENOSINE TRIPHOSPHATASE; CHOLINERGIC RECEPTOR; CYTOCHROME B; CYTOCHROME C OXIDASE; CYTOCHROME P450; GLUTAMATE RECEPTOR; MEMBRANE PROTEIN; POTASSIUM CHANNEL; RECEPTOR PROTEIN; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE; RHODOPSIN; SERPENTINE;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; NONHUMAN; PRIORITY JOURNAL; PROTEIN FAMILY; PROTEIN FOLDING; PROTEIN STRUCTURE; STRUCTURAL GENOMICS;

ALGORITHMS; CLUSTER ANALYSIS; GENOMICS; HYDROPHOBICITY; MEMBRANE PROTEINS; PROTEIN FOLDING; SEQUENCE ALIGNMENT; SOLUBILITY;

EID: 33745698481     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1110/ps.062109706     Document Type: Article

References (62)

1. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402.
2. Bass, R.B., Strop, P., Barclay, M., and Rees, D.C. 2002. Crystal structure of Escherichia coli MscS, a voltage-modulated and mechanosensitive channel. Science 298: 1582-1587.
3. Bateman, A., Coin, L., Durbin, R., Finn, R.D., Hollich, V., Griffiths-Jones, S., Khanna, A., Marshall, M., Moxon, S., Sonnhammer, E.L., et al. 2004. The Pfam protein families database. Nucleic Acids Res. 32: D138-D141.
4. Berry, E.A., Guergova-Kuras, M., Huang, L.S., and Crofts, A.R. 2000. Structure and function of cytochrome bc complexes. Annu. Rev. Biochem. 69: 1005-1075.
5. Bowie, J.U. 1997a. Helix packing angle preferences. Nat. Struct. Biol. 4: 915-917.
6. _. 1997b. Helix packing in membrane proteins. J. Mol. Biol. 272: 780-789.
7. Boyd, D., Schierle, C., and Beckwith, J. 1998. How many membrane proteins are there? Protein Sci. 7: 201-205.
8. Brenner, S.E. and Levitt, M. 2000. Expectations from structural genomics. Protein Sci. 9: 197-200.
9. Brenner, S.E., Chothia, C., and Hubbard, T.J. 1998. Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships. Proc. Natl. Acad. Sci. 95: 6073-6078.
10. Chamberlain, A.K. and Bowie, J.U. 2004. Analysis of side-chain rotamers in transmembrane proteins. Biophys. J. 87: 3460-3469.
11. Chandonia, J.M., Hon, G., Walker, N.S., Lo Conte, L., Koehl, P., Levitt, M., and Brenner, S.E. 2004. The ASTRAL compendium in 2004. Nucleic Acids Res. 32: D189-D192.
12. Chang, G. 2003. Structure of MsbA from Vibrio cholera: A multidrug resistance ABC transporter homolog in a closed conformation. J. Mol. Biol. 330: 419-430.
13. Chang, G. and Roth, C.B. 2001. Structure of MsbA from E. coli: A homolog of the multidrug resistance ATP binding cassette (ABC) transporters. Science 293: 1793-1800.
14. Chothia, C., Gough, J., Vogel, C., and Teichmann, S.A. 2003. Evolution of the protein repertoire. Science 300: 1701-1703.
15. Chou, K.C. and Elrod, D.W. 2002. Bioinformatical analysis of G-protein-coupled receptors. J. Proteome Res. 1: 429-433.
16. Coulson, A.F. and Moult, J. 2002. A unifold, mesofold, and superfold model of protein fold use. Proteins 46: 61-71.
17. Driessen, A.J., Rosen, B.P., and Konings, W.N. 2000. Diversity of transport mechanisms: Common structural principles. Trends Biochem. Sci. 25: 397-401.
18. Eisenberg, D., Schwarz, E., Komaromy, M., and Wall, R. 1984. Analysis of membrane and surface protein sequences with the hydrophobic moment plot. J. Mol. Biol. 179: 125-142.
19. Enright, A.J. and Ouzounis, C.A. 2000. GeneRAGE: A robust algorithm for sequence clustering and domain detection. Bioinformatics 16: 451-457.
20. Fischer, D. and Eisenberg, D. 1999. Finding families for genomic ORFans. Bioinformatics 15: 759-762.
21. Friedrich, T. and Bottcher, B. 2004. The gross structure of the respiratory complex I: A Lego system. Biochim. Biophys. Acta 1608: 1-9.
22. Gouzy, J., Corpet, F., and Kahn, D. 1999. Whole genome protein domain analysis using a new method for domain clustering. Comput. Chem. 23: 333-340.
23. Govindarajan, S., Recabarren, R., and Goldstein, R.A. 1999. Estimating the total number of protein folds. Proteins 35: 408-414.
24. Harte, R. and Ouzounis, C.A. 2002. Genome-wide detection and family clustering of ion channels. FEBS Lett. 514: 129-134.
25. Heger, A. and Holm, L. 2000. Towards a covering set of protein family profiles. Prog. Biophys. Mol. Biol. 73: 321-337.
26. _. 2001. Picasso: Generating a covering set of protein family profiles. Bioinformatics 17: 272-279.
27. Holm, L. 1998. Unification of protein families. Curr. Opin. Struct. Biol. 8: 372-379.
28. Holm, L. and Sander, C. 1997. Dali/FSSP classification of three-dimensional protein folds. Nucleic Acids Res. 25: 231-234.
29. Hou, J., Sims, G.E., Zhang, C., and Kim, S.H. 2003. A global representation of the protein fold space. Proc. Natl. Acad. Sci. 100: 2386-2390.
30. Iverson, T.M., Luna-Chavez, C., Cecchini, G., and Rees, D.C. 1999. Structure of the Escherichia coli fumarate reductase respiratory complex. Science 284: 1961-1966.
31. Iverson, T.M., Luna-Chavez, C., Croal, L.R., Cecchini, G., and Rees, D.C. 2002. Crystallographic studies of the Escherichia coli quinol-fumarate reductase with inhibitors bound to the quinol-binding site. J. Biol. Chem. 277: 16124-16130.
32. Jayasinghe, S., Hristova, K., and White, S.H. 2001. MPtopo: A database of membrane protein topology. Protein Sci. 10: 455-458.
33. Jiang, Y., Lee, A., Chen, J., Cadene, M., Chait, B.T., and MacKinnon, R. 2002a. Crystal structure and mechanism of a calcium-gated potassium channel. Nature 417: 515-522.
34. _. 2002b. The open pore conformation of potassium channels. Nature 417: 523-526.
35. Krause, A., Stoye, J., and Vingron, M. 2005. Large scale hierarchical clustering of protein sequences. BMC Bioinformatics 6: 15.
36. Kunin, V., Cases, I., Enright, A.J., de Lorenzo, V., and Ouzounis, C.A. 2003. Myriads of protein families, and still counting. Genome Biol. 4: 401.
37. Kunin, V., Teichmann, S.A., Huynen, M.A., and Ouzounis, C.A. 2005. The properties of protein family space depend on experimental design. Bioinformatics 21: 2618-2622.
38. Linial, M., Linial, N., Tishby, N., and Yona, G. 1997. Global self-organization of all known protein sequences reveals inherent biological signatures. J. Mol. Biol. 268: 539-556.
39. Liu, X., Fan, K., and Wang, W. 2004. The number of protein folds and their distribution over families in nature. Proteins 54: 491-499.
40. Liu, Y., Engelman, D.M., and Gerstein, M. 2002. Genomic analysis of membrane protein families: Abundance and conserved motifs. Genome Biol. 3: research0054.1-research0054.12.
41. Liu, Y., Gerstein, M., and Engelman, D.M. 2004. Transmembrane protein domains rarely use covalent domain recombination as an evolutionary mechanism. Proc. Natl. Acad. Sci. 101: 3495-3497.
42. Long, S.B., Campbell, E.B., and Mackinnon, R. 2005. Crystal structure of a mammalian voltage-dependent Shaker family K+ channel. Science 309: 897-903.
43. Mittl, P.R. and Grutter, M.G. 2001. Structural genomics: Opportunities and challenges. Curr. Opin. Chem. Biol. 5: 402-408.
44. Murzin, A.G., Brenner, S.E., Hubbard, T., and Chothia, C. 1995. SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247: 536-540.
45. O'Donovan, C., Martin, M.J., Gattiker, A., Gasteiger, E., Bairoch, A., and Apweiler, R. 2002. High-quality protein knowledge resource: SWISSPROT and TrEMBL. Brief. Bioinform. 3: 275-284.
46. Orengo, C.A., Jones, D.T., and Thornton, J.M. 1994. Protein superfamilies and domain superfolds. Nature 372: 631-634.
47. Orengo, C.A., Michie, A.D., Jones, S., Jones, D.T., Swindells, M.B., and Thornton, J.M. 1997. CATH - A hierarchic classification of protein domain structures. Structure 5: 1093-1108.
48. Park, J. and Teichmann, S.A. 1998. DIVCLUS: An automatic method in the GEANFAMMER package that finds homologous domains in single- and multi-domain proteins. Bioinformatics 14: 144-150.
49. Remm, M. and Sonnhammer, E. 2000. Classification of transmembrane protein families in the Caenorhabditis elegans genome and identification of human orthologs. Genome Res. 10: 1679-1689.
50. Saier Jr., M.H., Beatty, J.T., Goffeau, A., Harley, K.T., Heijne, W.H., Huang, S.C., Jack, D.L., Jahn, P.S., Lew, K., Liu, J., et al. 1999. The major facilitator superfamily. J. Mol. Microbiol. Biotechnol. 1: 257-279.
51. Sansom, M.S., Shrivastava, I.H., Bright, J.N., Tate, J., Capener, C.E., and Biggin, P.C. 2002. Potassium channels: Structures, models, simulations. Biochim. Biophys. Acta 1565: 294-307.
52. Schmitt, L. and Tampe, R. 2002. Structure and mechanism of ABC transporters. Curr. Opin. Struct. Biol. 12: 754-760.
53. Servant, F., Bru, C., Carrere, S., Courcelle, E., Gouzy, J., Peyruc, D., and Kahn, D. 2002. ProDom: Automated clustering of homologous domains. Brief. Bioinform. 3: 246-251.
54. Sonnhammer, E.L. and Kahn, D. 1994. Modular arrangement of proteins as inferred from analysis of homology. Protein Sci. 3: 482-492.
55. Ubarretxena-Belandia, I. and Engelman, D.M. 2001. Helical membrane proteins: Diversity of functions in the context of simple architecture. Curr. Opin. Struct. Biol. 11: 370-376.
56. Vitkup, D., Melamud, E., Moult, J., and Sander, C. 2001. Completeness in structural genomics. Nat. Struct. Biol. 8: 559-566.
57. White, S.H. 2004. The progress of membrane protein structure determination. Protein Sci. 13: 1948-1949.
58. Wolf, Y.I., Grishin, N.V., and Koonin, E.V. 2000. Estimating the number of protein folds and families from complete genome data. J. Mol. Biol. 299: 897-905.
59. Wootton, J.C. and Federhen, S. 1996. Analysis of compositionally biased regions in sequence databases. Methods Enzymol. 266: 554-571.
60. Yan, Y. and Moult, J. 2005. Protein family clustering for structural genomics. J. Mol. Biol. 353: 744-759.
61. Zhang, C. and DeLisi, C. 1998. Estimating the number of protein folds. J. Mol. Biol. 284: 1301-1305.
62. Zhang, C. and Kim, S.H. 2003. Overview of structural genomics: From structure to function. Curr. Opin. Chem. Biol. 7: 28-32.