Convergent evolution in structural elements of proteins investigated using cross profile analysis

BMC Bioinformatics

Volumn 13, Issue 1, 2012, Pages

  Tomii, Kentaro ^a   Sawada, Yoshito ^a   Honda, Shinya ^a  

^a NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

CONFORMATIONAL ANALYSIS; CONVERGENT EVOLUTION; EVOLUTIONARY INFORMATION; PROFILE-PROFILE COMPARISONS; STRUCTURAL CLASSIFICATION; STRUCTURAL ELEMENTS; STRUCTURAL SIMILARITY; STRUCTURE COMPARISONS;

AMINO ACIDS; CONFORMATIONS; PROTEIN FOLDING;

PEPTIDES;

PEPTIDE; PROTEIN;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; GENETICS; HUMAN; MOLECULAR EVOLUTION; PROTEIN CONFORMATION; PROTEIN FOLDING;

EVOLUTION, MOLECULAR; HUMANS; MODELS, MOLECULAR; PEPTIDES; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEINS;

EID: 84855813563     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-13-11     Document Type: Article

References (62)

1. 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 relics of an ancient peptide world?. J Struct Biol 2001, 134(2-3):191-203. 10.1006/jsbi.2001.4393, 11551179.
2. Gribskov M, McLachlan AD, Eisenberg D. Profile analysis: detection of distantly related proteins. Proc Natl Acad Sci USA 1987, 84(13):4355-4358. 10.1073/pnas.84.13.4355, 305087, 3474607.
3. 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. 10.1002/prot.20184, 15326603.
4. 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. 2144550, 10716175.
5. Panchenko AR. Finding weak similarities between proteins by sequence profile comparison. Nucleic Acids Res 2003, 31(2):683-689. 10.1093/nar/gkg154, 140518, 12527777.
6. Jaroszewski L, Rychlewski L, Li Z, Li W, Godzik A. FFAS03: a server for profile-profile sequence alignments. Nucleic Acids Res 2005, (33 Web Server):W284-288. 1160179, 15980471.
7. Friedberg I, Godzik A. Connecting the protein structure universe by using sparse recurring fragments. Structure 2005, 13(8):1213-1224. 10.1016/j.str.2005.05.009, 16084393.
8. Theobald DL, Wuttke DS. Divergent evolution within protein superfolds inferred from profile-based phylogenetics. J Mol Biol 2005, 354(3):722-737. 10.1016/j.jmb.2005.08.071, 1769326, 16266719.
9. Xie L, Bourne PE. Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments. Proc Natl Acad Sci USA 2008, 105(14):5441-5446. 10.1073/pnas.0704422105, 2291117, 18385384.
10. Remmert M, Biegert A, Linke D, Lupas AN, Soding J. Evolution of outer membrane beta-barrels from an ancestral beta beta hairpin. Mol Biol Evol 2010, 27(6):1348-1358. 10.1093/molbev/msq017, 20106904.
11. Dunbrack RL. Sequence comparison and protein structure prediction. Curr Opin Struct Biol 2006, 16(3):374-384. 10.1016/j.sbi.2006.05.006, 16713709.
12. Taylor WR. Pattern matching methods in protein sequence comparison and structure prediction. Protein Eng 1988, 2(2):77-86. 10.1093/protein/2.2.77, 3072565.
13. Bystroff C, Baker D. Prediction of local structure in proteins using a library of sequence-structure motifs. J Mol Biol 1998, 281(3):565-577. 10.1006/jmbi.1998.1943, 9698570.
14. de Brevern AG, Benros C, Gautier R, Valadie H, Hazout S, Etchebest C. Local backbone structure prediction of proteins. In Silico Biol 2004, 4(3):381-386. 1995003, 15724288.
15. Ikeda K, Tomii K, Yokomizo T, Mitomo D, Maruyama K, Suzuki S, Higo J. Visualization of conformational distribution of short to medium size segments in globular proteins and identification of local structural motifs. Protein Sci 2005, 14(5):1253-1265. 10.1110/ps.04956305, 2253271, 15802651.
16. Sawada Y, Honda S. Structural diversity of protein segments follows a power-law distribution. Biophys J 2006, 91(4):1213-1223. 10.1529/biophysj.105.076661, 1518648, 16731566.
17. Fetrow JS, Palumbo MJ, Berg G. Patterns, structures, and amino acid frequencies in structural building blocks, a protein secondary structure classification scheme. Proteins 1997, 27(2):249-271. 10.1002/(SICI)1097-0134(199702)27:2<249::AID-PROT11>3.0.CO;2-M, 9061789.
18. Micheletti C, Seno F, Maritan A. Recurrent oligomers in proteins: an optimal scheme reconciling accurate and concise backbone representations in automated folding and design studies. Proteins 2000, 40(4):662-674. 10.1002/1097-0134(20000901)40:4<662::AID-PROT90>3.0.CO;2-F, 10899788.
19. Yang AS, Wang LY. Local structure-based sequence profile database for local and global protein structure predictions. Bioinformatics 2002, 18(12):1650-1657. 10.1093/bioinformatics/18.12.1650, 12490450.
20. Pei J, Grishin NV. Combining evolutionary and structural information for local protein structure prediction. Proteins 2004, 56(4):782-794. 10.1002/prot.20158, 15281130.
21. Tomii K, Akiyama Y. FORTE: a profile-profile comparison tool for protein fold recognition. Bioinformatics 2004, 20(4):594-595. 10.1093/bioinformatics/btg474, 14764565.
22. Tomii K, Hirokawa T, Motono C. Protein structure prediction using a variety of profile libraries and 3D verification. Proteins 2005, 61(Suppl 7):114-121.
23. Du P, Andrec M, Levy RM. Have we seen all structures corresponding to short protein fragments in the Protein Data Bank? An update. Protein Eng 2003, 16(6):407-414. 10.1093/protein/gzg052, 12874373.
24. Soding J, Lupas AN. More than the sum of their parts: on the evolution of proteins from peptides. Bioessays 2003, 25(9):837-846. 10.1002/bies.10321, 12938173.
25. Fritz G, Roth A, Schiffer A, Buchert T, Bourenkov G, Bartunik HD, Huber H, Stetter KO, Kroneck PM, Ermler U. Structure of adenylylsulfate reductase from the hyperthermophilic Archaeoglobus fulgidus at 1.6-A resolution. Proc Natl Acad Sci USA 2002, 99(4):1836-1841. 10.1073/pnas.042664399, 122280, 11842205.
26. Arnoux B, Ducruix A, Prange T. Anisotropic behaviour of the C-terminal Kunitz-type domain of the alpha3 chain of human type VI collagen at atomic resolution (0.9 A). Acta Crystallogr D Biol Crystallogr 2002, 58(Pt 7):1252-1254.
27. 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(4):536-540.
28. Hartwig JH. Actin-binding proteins. 1: Spectrin super family. Protein Profile 1995, 2(7):703-800.
29. Djinovic-Carugo K, Gautel M, Ylanne J, Young P. The spectrin repeat: a structural platform for cytoskeletal protein assemblies. FEBS Lett 2002, 513(1):119-123. 10.1016/S0014-5793(01)03304-X, 11911890.
30. Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM. CATH--a hierarchic classification of protein domain structures. Structure 1997, 5(8):1093-1108. 10.1016/S0969-2126(97)00260-8, 9309224.
31. Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, et al. The Pfam protein families database. Nucleic Acids Res 2008, (38 Database):D211-222. 2808889, 19920124.
32. Honda S, Yamasaki K, Sawada Y, Morii H. 10 residue folded peptide designed by segment statistics. Structure 2004, 12(8):1507-1518. 10.1016/j.str.2004.05.022, 15296744.
33. Gibrat JF, Madej T, Bryant SH. Surprising similarities in structure comparison. Curr Opin Struct Biol 1996, 6(3):377-385. 10.1016/S0959-440X(96)80058-3, 8804824.
34. Grishina IB, Woody RW. Contributions of tryptophan side chains to the circular dichroism of globular proteins: exciton couplets and coupled oscillators. Faraday Discuss 1994, (99):245-262.
35. Guvench O, Brooks CL. Tryptophan side chain electrostatic interactions determine edge-to-face vs. parallel-displaced tryptophan side chain geometries in the designed beta-hairpin "trpzip2". J Am Chem Soc 2005, 127(13):4668-4674. 10.1021/ja043492e, 15796532.
36. Honda S, Akiba T, Kato YS, Sawada Y, Sekijima M, Ishimura M, Ooishi A, Watanabe H, Odahara T, Harata K. Crystal structure of a ten-amino acid protein. J Am Chem Soc 2008, 130(46):15327-15331. 10.1021/ja8030533, 18950166.
37. Brown JE, Klee WA. Helix-coil transition of the isolated amino terminus of ribonuclease. Biochemistry 1971, 10(3):470-476. 10.1021/bi00779a019, 5543977.
38. Kuroda Y. Residual helical structure in the C-terminal fragment of cytochrome c. Biochemistry 1993, 32(5):1219-1224. 10.1021/bi00056a004, 8383525.
39. Blanco FJ, Rivas G, Serrano L. A short linear peptide that folds into a native stable beta-hairpin in aqueous solution. Nat Struct Biol 1994, 1(9):584-590. 10.1038/nsb0994-584, 7634098.
40. Honda S, Kobayashi N, Munekata E. Thermodynamics of a beta-hairpin structure: evidence for cooperative formation of folding nucleus. J Mol Biol 2000, 295(2):269-278. 10.1006/jmbi.1999.3346, 10623525.
41. Zerella R, Chen PY, Evans PA, Raine A, Williams DH. Structural characterization of a mutant peptide derived from ubiquitin: implications for protein folding. Protein Sci 2000, 9(11):2142-2150. 10.1110/ps.9.11.2142, 2144502, 11152124.
42. Crameri A, Raillard SA, Bermudez E, Stemmer WP. DNA shuffling of a family of genes from diverse species accelerates directed evolution. Nature 1998, 391(6664):288-291. 10.1038/34663, 9440693.
43. Crameri A, Whitehorn EA, Tate E, Stemmer WP. Improved green fluorescent protein by molecular evolution using DNA shuffling. Nat Biotechnol 1996, 14(3):315-319. 10.1038/nbt0396-315, 9630892.
44. Riechmann L, Winter G. Novel folded protein domains generated by combinatorial shuffling of polypeptide segments. Proc Natl Acad Sci USA 2000, 97(18):10068-10073. 27691, 10954734.
45. Shiba K, Schimmel P. Functional assembly of a randomly cleaved protein. Proc Natl Acad Sci USA 1992, 89(5):1880-1884. 10.1073/pnas.89.5.1880, 48557, 1542687.
46. Shiba K, Takahashi Y, Noda T. Creation of libraries with long ORFs by polymerization of a microgene. Proc Natl Acad Sci USA 1997, 94(8):3805-3810. 10.1073/pnas.94.8.3805, 20522, 9108059.
47. Takahashi K, Noguti T, Hojo H, Yamauchi K, Kinoshita M, Aimoto S, Ohkubo T, Go M. A mini-protein designed by removing a module from barnase: molecular modeling and NMR measurements of the conformation. Protein Eng 1999, 12(8):673-680. 10.1093/protein/12.8.673, 10469828.
48. Yanagawa H, Yoshida K, Torigoe C, Park JS, Sato K, Shirai T, Go M. Protein anatomy: functional roles of barnase module. J Biol Chem 1993, 268(8):5861-5865.
49. Han KF, Baker D. Global properties of the mapping between local amino acid sequence and local structure in proteins. Proc Natl Acad Sci USA 1996, 93(12):5814-5818. 10.1073/pnas.93.12.5814, 39144, 8650175.
50. Hobohm U, Scharf M, Schneider R, Sander C. Selection of representative protein data sets. Protein Sci 1992, 1(3):409-417. 2142204, 1304348.
51. Richards JA, Jia X. Remote sensing digital image analysis. 1999, New York: Springer.
52. Sawada Y, Honda S. ProSeg: a database of local structures of protein segments. J Comput Aided Mol Des 2009, 23(3):163-169. 10.1007/s10822-008-9248-x, 18931918.
53. Chandonia JM, Walker NS, Lo Conte L, Koehl P, Levitt M, Brenner SE. ASTRAL compendium enhancements. Nucleic Acids Res 2002, 30(1):260-263. 10.1093/nar/30.1.260, 99063, 11752310.
54. 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(1):235-242. 10.1093/nar/28.1.235, 102472, 10592235.
55. Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, Dicuccio M, Edgar R, Federhen S, et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2008, (36 Database):D13-21. 2238880, 18045790.
56. 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. 10.1093/bioinformatics/btl158, 16731699.
57. Jones DT. Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 1999, 292(2):195-202. 10.1006/jmbi.1999.3091, 10493868.
58. Pearl FM, Lee D, Bray JE, Buchan DW, Shepherd AJ, Orengo CA. The CATH extended protein-family database: providing structural annotations for genome sequences. Protein Sci 2002, 11(2):233-244. 2373435, 11790833.
59. Schaffer AA, Wolf YI, Ponting CP, Koonin EV, Aravind L, Altschul SF. IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices. Bioinformatics 1999, 15(12):1000-1011. 10.1093/bioinformatics/15.12.1000, 10745990.
60. Shiozawa K, Maita N, Tomii K, Seto A, Goda N, Akiyama Y, Shimizu T, Shirakawa M, Hiroaki H. Structure of the N-terminal domain of PEX1 AAA-ATPase. Characterization of a putative adaptor-binding domain. J Biol Chem 2004, 279(48):50060-50068. 10.1074/jbc.M407837200, 15328346.
61. Cai W, Pei J, Grishin NV. Reconstruction of ancestral protein sequences and its applications. BMC Evol Biol 2004, 4:33. 10.1186/1471-2148-4-33, 522809, 15377393.
62. Crooks GE, Hon G, Chandonia JM, Brenner SE. WebLogo: a sequence logo generator. Genome Res 2004, 14(6):1188-1190. 10.1101/gr.849004, 419797, 15173120.