Function prediction from networks of local evolutionary similarity in protein structure

BMC Bioinformatics

Volumn 14, Issue SUPPL.3, 2013, Pages

  Erdin, Serkan ^a   Venner, Eric ^a   Lisewski, Andreas Martin ^a   Lichtarge, Olivier ^a  

^a BAYLOR COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AREA UNDER THE ROC CURVE; COMPUTATIONAL STRATEGY; EVOLUTIONARY TRACES; FUNCTION PREDICTION; MULTIPLE TEMPLATES; PROTEIN FUNCTIONS; PROTEIN STRUCTURES; STRUCTURAL GENOMICS;

AMINO ACIDS; FORECASTING;

PROTEINS;

ENZYME; PROTEIN;

ALGORITHM; ARTICLE; BIOLOGY; CHEMISTRY; GENETICS; GENOMICS; MOLECULAR EVOLUTION; MOLECULAR GENETICS; PHYSIOLOGY; PROTEIN CONFORMATION; PROTEIN DATABASE;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; ENZYMES; EVOLUTION, MOLECULAR; GENOMICS; MOLECULAR SEQUENCE ANNOTATION; PROTEIN CONFORMATION; PROTEINS;

MLCS; MLOWN;

EID: 84879294955     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-S3-S6     Document Type: Article

References (42)

1. Huang S. The practical problems of post-genomic biology. Nat Biotechnol 2000, 18(5):471-472. 10.1038/75235, 10802565.
2. Eisenberg D, Marcotte EM, Xenarios I, Yeates TO. Protein function in the post-enomic era. Nature 2000, 405(6788):823-826. 10.1038/35015694, 10866208.
3. Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res 2012, 40(D1):D71-D75. 3245120, 22102590.
4. Rentzsch R, Orengo CA. Protein function prediction-the power of multiplicity. Trends Biotechnol 2009, 27(4):210-219. 10.1016/j.tibtech.2009.01.002, 19251332.
5. Lee D, Redfern O, Orengo C. Predicting protein function from sequence and structure. Nat Rev Mol Cell Biol 2007, 8(12):995-1005. 10.1038/nrm2281, 18037900.
6. Chothia C, Lesk AM. The relation between the divergence of sequence and structure in proteins. Embo J 1986, 5(4):823-826. 1166865, 3709526.
7. Greene LH, Lewis TE, Addou S, Cuff A, Dallman T, Dibley M, Redfern O, Pearl F, Nambudiry R, Reid A, et al. The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution. Nucleic Acids Res 2007, 35(Database):D291-297. 10.1093/nar/gkl959, 1751535, 17135200.
8. 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.
9. Erdin S, Lisewski AM, Lichtarge O. Protein function prediction: towards integration of similarity metrics. Curr Opin Struct Biol 2011, 21(2):180-188. 10.1016/j.sbi.2011.02.001, 3120633, 21353529.
10. Nagano N, Orengo CA, Thornton JM. One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions. J Mol Biol 2002, 321(5):741-765. 10.1016/S0022-2836(02)00649-6, 12206759.
11. Redfern O, Dessailly B, Orengo C. Exploring structure and function paradigm. Curr Op Struct Biol 2008, 18:394-402.
12. Dodson G, Wlodawer A. Catalytic triads and their relatives. Trends Biochem Sci 1998, 23(9):347-352. 10.1016/S0968-0004(98)01254-7, 9787641.
13. Wallace AC, Laskowski RA, Thornton JM. Derivation of 3D coordinate templates for searching structural databases: application to Ser-His-Asp catalytic triads in the serine proteinases and lipases. Protein Sci 1996, 5(6):1001-1013. 2143436, 8762132.
14. Shulman-Peleg A, Nussinov R, Wolfson HJ. Recognition of functional sites in protein structures. J Mol Biol 2004, 339(3):607-633. 10.1016/j.jmb.2004.04.012, 15147845.
15. Polacco BJ, Babbitt PC. Automated discovery of 3D motifs for protein function annotation. Bioinformatics 2006, 22(6):723-730. 10.1093/bioinformatics/btk038, 16410325.
16. Meng EC, Polacco BJ, Babbitt PC, Rigden DJ. 3D Motifs. From Protein Structure to Function with Bioinformatics 2009, 187-216. Springer Netherlands, Rigden DJ.
17. Kristensen DM, Ward RM, Lisewski AM, Erdin S, Chen BY, Fofanov VY, Kimmel M, Kavraki LE, Lichtarge O. Prediction of enzyme function based on 3D templates of evolutionarily important amino acids. BMC Bioinformatics 2008, 9:17. 10.1186/1471-2105-9-17, 2219985, 18190718.
18. Lichtarge O, Bourne HR, Cohen FE. An evolutionary trace method defines binding surfaces common to protein families. J Mol Biol 1996, 257(2):342-358. 10.1006/jmbi.1996.0167, 8609628.
19. Mihalek I, Res I, Lichtarge O. A family of evolution-entropy hybrid methods for ranking protein residues by importance. J Mol Biol 2004, 336(5):1265-1282. 10.1016/j.jmb.2003.12.078, 15037084.
20. Wilkins AD, Lua R, Erdin S, Ward RM, Lichtarge O. Sequence and structure continuity of evolutionary importance improves protein functional site discovery and annotation. Protein Sci 2010, 19(7):1296-1311. 10.1002/pro.406, 2974822, 20506260.
21. Kristensen DM, Chen BY, Fofanov VY, Ward RM, Lisewski AM, Kimmel M, Kavraki LE, Lichtarge O. Recurrent use of evolutionary importance for functional annotation of proteins based on local structural similarity. Protein Sci 2006, 15(6):1530-1536. 10.1110/ps.062152706, 2242527, 16672239.
22. Ward RM, Venner E, Daines B, Murray S, Erdin S, Kristensen DM, Lichtarge O. Evolutionary Trace Annotation Server: automated enzyme function prediction in protein structures using 3D templates. Bioinformatics 2009, 25(11):1426-1427. 10.1093/bioinformatics/btp160, 2682511, 19307237.
23. Ward RM, Erdin S, Tran TA, Kristensen DM, Lisewski AM, Lichtarge O. De-orphaning the structural proteome through reciprocal comparison of evolutionarily important structural features. PLoS ONE 2008, 3(5):e2136. 10.1371/journal.pone.0002136, 2362850, 18461181.
24. Erdin S, Ward RM, Venner E, Lichtarge O. Evolutionary trace annotation of protein function in the structural proteome. J Mol Biol 2010, 396(5):1451-1473. 10.1016/j.jmb.2009.12.037, 2831211, 20036248.
25. International Union of Biochemistry and Molecular Biology. Nomenclature Committee. Webb EC Enzyme nomenclature 1992: recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the nomenclature and classification of enzymes. 1992, San Diego: Academic Press, International Union of Biochemistry and Molecular Biology. Nomenclature Committee. Webb EC.
26. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25(1):25-29. 10.1038/75556, 3037419, 10802651.
27. Venner E, Lisewski AM, Erdin S, Ward RM, Amin SR, Lichtarge O. Accurate protein structure annotation through competitive diffusion of enzymatic functions over a network of local evolutionary similarities. PLoS One 2010, 5(12):e14286. 10.1371/journal.pone.0014286, 3001439, 21179190.
28. Brown SD, Babbitt PC. Inference of Functional Properties from Large-scale Analysis of Enzyme Superfamilies. J Biol Chem 2012, 287(1):35-42. 10.1074/jbc.R111.283408, 3249087, 22069325.
29. Byres E, Alphey MS, Smith TK, Hunter WN. Crystal structures of Trypanosoma brucei and Staphylococcus aureus mevalonate diphosphate decarboxylase inform on the determinants of specificity and reactivity. J Mol Biol 2007, 371(2):540-553. 10.1016/j.jmb.2007.05.094, 17583736.
30. Voynova NE, Fu Z, Battaile KP, Herdendorf TJ, Kim JJ, Miziorko HM. Human mevalonate diphosphate decarboxylase: characterization, investigation of the mevalonate diphosphate binding site, and crystal structure. Arch Biochem Biophys 2008, 480(1):58-67. 10.1016/j.abb.2008.08.024, 2709241, 18823933.
31. Thoden JB, Holden HM, Firestine SM. Structural analysis of the active site geometry of N5-carboxyaminoimidazole ribonucleotide synthetase from Escherichia coli. Biochemistry 2008, 47(50):13346-13353. 10.1021/bi801734z, 2677550, 19053251.
32. Goihberg E, Dym O, Tel-Or S, Levin I, Peretz M, Burstein Y. A single proline substitution is critical for the thermostabilization of Clostridium beijerinckii alcohol dehydrogenase. Proteins 2007, 66(1):196-204.
33. 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.
34. 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 2010, 38(Database):D211-222. 10.1093/nar/gkp985, 2808889, 19920124.
35. Wilkins A, Erdin S, Lua R, Lichtarge O. Evolutionary trace for prediction and redesign of protein functional sites. Methods Mol Biol 2012, 819:29-42. 10.1007/978-1-61779-465-0_3, 22183528.
36. 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. 10.1093/nar/25.17.3389, 146917, 9254694.
37. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007, 23(21):2947-2948. 10.1093/bioinformatics/btm404, 17846036.
38. Waterman M. 2000, London/Boca Raton: Chapman & Hall/CRC.
39. Shannon CE, Weaver W. 1949, Urbana: University of Illinois Press.
40. Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983, 22(12):2577-2637. 10.1002/bip.360221211, 6667333.
41. Shin H, Lisewski AM, Lichtarge O. Graph sharpening plus graph integration: a synergy that improves protein functional classification. Bioinformatics 2007, 23(23):3217-3224. 10.1093/bioinformatics/btm511, 17977886.
42. Bachman BJ, Venner E, Lua RC, Erdin S, Lichtarge O. ETAscape: analyzing protein networks to predict enzymatic function and substrates in Cytoscape. Bioinformatics 2012, 28(16):2186-2188. 10.1093/bioinformatics/bts331, 22689386.