Current status of membrane protein structure classification

Proteins: Structure, Function and Bioinformatics

Volumn 78, Issue 7, 2010, Pages 1760-1773

  Neumann, Sindy ^a   Fuchs, Angelika ^a   Mulkidjanian, Armen ^b,c   Frishman, Dmitrij ^a  

^a TECHNICAL UNIVERSITY OF MUNICH   (Germany)

^b UNIVERSITY OF OSNABRÜCK   (Germany)

^c MOSCOW STATE UNIVERSITY   (Russian Federation)

Author keywords

Fold classification; Four helix bundle; Molecular evolution; Protein fold; Structure comparison

Indexed keywords

MEMBRANE PROTEIN;

ARTICLE; CONTROLLED STUDY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN STRUCTURE;

DATABASES, PROTEIN; MEMBRANE PROTEINS; MODELS, MOLECULAR; POTASSIUM CHANNELS; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 77951217658     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22692     Document Type: Article

References (58)

1. Andreeva A, Howorth D, Chandonia JM, Brenner SE, Hubbard TJ, Chothia C, Murzin AG. Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res 2008;36(Database issue):D419-D425.
2. Cuff AL, Sillitoe I, Lewis T, Redfern OC, Garratt R, Thornton. J, Orengo CA. The CATH classification revisited-architectures reviewed and new ways to characterize structural divergence in superfamilies. Nucleic Acids Res 2009;37(.Database issue):D310-D314.
3. Murzin AG, Brenner SE, Hubbard T, Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995;247:536-540.
4. 4. Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM. CATH-a hierarchic classification of protein domain structures. Structure 1997;5:1093-1108. (Pubitemid 27393093)
5. 5. Holm L, Sander C. Touring protein fold space with Dali/FSSP. Nucleic Acids Res .1998;26:316-319. (Pubitemid 28291549)
6. Shindyalov IN, Bourne PE. An alternative view of protein fold space. Proteins 2000;38:247-260.
7. 7. Dietmann S, Park J, Notredame C, Heger A, Lappe M, Holm L. A fully automatic evolutionary classification of protein folds: Dali Domain Dictionary version 3. Nucleic Acids Res 2001;29:55-57. (Pubitemid 32054406)
8. 8. Rogen P, Fain B. Automatic classification of protein structure by using Gauss integrals. Proc Natl Acad Sci USA 2003;100:119-124. (Pubitemid 36082865)
9. 9. Sam V, Tai CH, Gamier J, Gibrat JF, Lee B, Munson PJ. Towards an automatic classification, of protein structural domains based on structural similarity. BMC Bioinformatics 2008;9:74. (Pubitemid 351404983)
10. 10. Hadley C, Jones DT. A systematic comparison of protein structure classifications: SCOP. CATH and FSSP. Structure 1999;7:1099-1112. (Pubitemid 29436507)
11. Day R, Beck DA, Armen RS, Daggett V. A consensus view of fold space: combining SCOP. CATH, and the Dali Domain Dictionary. Protein Sci 2003;12:2150-2160.
12. Pascual-Garcia A, Abia D, Ortiz AR, Bastolla U. Cross-over between discrete and continuous protein structure space: insights into automatic classification and networks of protein structures. PLoS Comput Biol 2009;5:e1000331.
13. Yang AS, Honig B. An integrated approach to the analysis and modeling of protein sequences and structures. I. Protein structural alignment and a quantitative measure for protein, structural distance. J Mol Biol 2000;301:665-678.
14. 14. Kolodny R, Petrey D, Honig B. Protein structure comparison: implications for the nature of 'fold space', and structure and function prediction. Curr Opin Struct Biol 2006;16:393-398. (Pubitemid 43831645)
15. Petrey D, Honig B. Is protein classification necessary? Toward alternative approaches to function annotation. Curr Opin Struct Biol 2009;19:363-368.
16. Lupas AN, Ponting CP, Russell RB. On the evolution of protein folds; are similar motifs in different protein folds the result of convergence, insertion, or relies of an ancient peptide world? J Struct Biol 2001;134:191-203.
17. 17. Grishin NV. Fold change in evolution of protein structures. J Struct Biol 2001;134:167-185. (Pubitemid 33733488)
18. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE, The Protein Data Bank Nucleic Acids Res 2000;28:235-242.
19. Jones DT. Do transmembrane protein superfolds exist? FEBS Lett 1998;423:281-285.
20. Bowie JU. Helix-bundle membrane protein fold templates. Protein Sci 1999;8:2711-2719.
21. Remm M, Sonnhammer E. Classification of transmembrane protein families in the Caenorhabditis elegans genome and identification of human orthoiogs. Genome Res 2000;10:1679-1689.
22. Oberai A, Ihm Y, Kim S, Bowie JU. A limited universe of membrane protein families and folds. Protein Sci 2006;15:1723-1734.
23. 23. Martin-Galiano AJ, Frishman D. Defining the fold space of membrane proteins: the CAMPS database. Proteins 2006;64:906-922. (Pubitemid 44420932)
24. Grisshammer R, Tate CG. Overexpression of integral membrane proteins for structural, studies. Q Rev Biophys 1995;28:315-422.
25. Torres J, Stevens TJ, Samso M. Membrane proteins: the 'Wild West' of structural biology. Trends Biochem Sci 2003;28:137-144.
26. Opella SJ, Marassi FM. Structure determination of membrane proteins by NMR spectroscopy. Chem Rev 2004;104:3587-3606.
27. Caffrey M. Crystallizing membrane proteins for structure determination: use of lipidic mesophases. Annu Rev Biophys 2009;38:29-51.
28. 28. Rees DC, Komiya. H, Yeates TO, Allen JP, Feher G. The bacterial photosynthetic reaction center as a model for membrane proteins. Annu Rev Biochem 1989;58:607-633. (Pubitemid 19172982)
29. 29. Wallin E, Tsukihara T, Yoshikawa S, von Heijne G, Eiofsson A. Architecture of helix bundle membrane proteins: an analysis of cytochrome c oxidase from bovine mitochondria. Protein. Sci 1997; 6:808-815. (Pubitemid 27154807)
30. 30. Weiss MS, Abele U, Weckesser J, Weite W, Schiltz E, Schulz GE. Molecular architecture and electrostatic properties of a bacterial porin. Science 1991;254:1627-1630. (Pubitemid 21917503)
31. Wimley WC, The versatile beta-barrel membrane protein. Curr Opin Struct Biol 2003;13:404-411.
32. Yeagle PL, Bennett M, Lemaitre V, Watts A. Transmembrane helices of membrane proteins may flex to satisfy hydrophobic mismatch. Biochim. Biophys Acta 2007;1768:530-537.
33. 33. Viklund H, Granseth E, Eiofsson A. Structural classification and prediction of reentrant regions in alpha-helical transmembrane proteins: application to complete genomes. J Mol Biol 2006;361:591-603. (Pubitemid 44118335)
34. Tusnady GE, Dosztanyi Z, Simon I. PDB-TM: selection and membrane localization of transmembrane proteins in the protein, data bank. Nucleic Acids Res 2005;33(Database issue):D275-D278.
35. Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics (Oxford England) 2006;22:1658-1659.
36. Michie AD, Orengo CA, Thornton JM. Analysis of domain structural class using an automated class assignment protocol. J Mol Biol 1996;262:168-185.
37. Holm L, Kaariainen S, Rosenstrom P, Schenkel A. Searching protein structure databases with DaliLite v. 3. Bioinformatics (Oxford England) 2008;24:2780-2781.
38. Orengo CA, Taylor WR. SSAP: sequential structure alignment program for protein structure comparison. Methods Enzymol 1996; 266:617-635.
39. Ashbumer M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski. K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000;25:25-29.
40. Caetano-Anolles G, Wang M, Caetano-Anolles D, Mittenthal JE. The origin, evolution and structure of the protein world. Biochem J 2009;417:621-637.
41. Brenner SE, Chothia C, Hubbard TJ. Population statistics of protein structures: lessons from structural classifications. Curr Opin Struct Biol 1997;7:369-376.
42. Gerstein M. How representative are the known structures of the proteins in a complete genome? A comprehensive structural census. Fold Des 1998;3:497-512.
43. Arkin IT, Brunger AT, Engelman DM. Are there dominant membrane protein families with a given, number of helices? Proteins 1997;28:465-466.
44. Gerstein M. A structural census of genomes: comparing bacterial, eukaryotic, and archaeal genomes in terms of protein structure. J Mol Biol 1997;274:562-576.
45. Wallin E, von Heijne G. Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms. Protein Sci 1998;7:1029-1038.
46. 46. 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;305:567-580. (Pubitemid 33032862)
47. Soriano GM, Ponamarev MV, Carrell CJ, Xia D, Smith JL, Cramer WA. Comparison of the cytochrome bc1 complex with the anticipated structure of the cytochrome b6f complex: Le plus ca change Ie plus c'est la meme chose. J Bioenerg Biomembr 1999;31:201-213.
48. Jones S, Stewart M, Michie A, Swindells MB, Orengo C, Thornton JM. Domain assignment for protein structures using a consensus approach: characterization and analysis. Protein Sci 1998;7;233-242.
49. Liu Y, Gerstein M, Engelman DM. Transmembrane protein domains rarely use covaient domain recombination as an evolutionary mechanism. Proc Natl Acad. Sci USA 2004;101:3495-3497.
50. Orengo CA, Martin AM, Hutchinson G, Jones S, Jones DT, Michie AD, Swindells MB, Thornton JM. Classifying a protein in the CATH database of domain structures. Acta Crystallogr 1998;54 (Parto Part 1):1155-1167.
51. Fleishman SJ, Ben-Tal N. Progress in structure prediction of alphahelical membrane proteins. Curr Opin Struct Biol 2006;16:496-504.
52. Eiofsson A, von Heijne G. Membrane protein structure: prediction versus reality. Annu Rev Biochem 2007;76:125-140.
53. Jekely G. Did the last common ancestor have a biological membrane? Biol Direct 2006; 1:35.
54. Mulkidjanian AY, Galperin MY, Koonin EV. Co-evolution of primordial membranes and membrane proteins. Trends Biochem Sci 2009;34:206-215.
55. Meier T, Poizer P, Diederichs K, Weite W, Dimroth P. Structure of the rotor ring of F-Type Na+-ATPase from lyobacter tartaricus. Science 2005;308:659-662.
56. Presnell SR, Cohen FE. Topological distribution of four-alpha-helix bundles. Proc Natl Acad Sci USA 1989;86:6592-6596.
57. Harris NL, Presnell SR, Cohen FE. Four helix bundle diversity in globular proteins. J Mol Biol 1994;236:1356-1368.
58. Kamtekar S, Hecht MH. Protein Motifs. VII, The four-helix bundle: what determines a fold? FASEB J 1995;9:1013-1022.