Structure-guided comparative analysis of proteins: Principles, tools, and applications for predicting function

PLoS Computational Biology

Volumn 4, Issue 9, 2008, Pages

  Mazumder, Raja ^a   Vasudevan, Sona ^a  

^a GEORGETOWN UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOTECHNOLOGY;

COMPARATIVE ANALYZES; CONSERVED PROTEINS; INITIAL PROCESS; OPERON INFORMATION; PATHWAY ANALYSIS; STEPS PROCEDURE; TEN STEPS; TOOLS AND APPLICATIONS;

PROTEINS;

BACTERIAL PROTEIN; PROTEIN;

AMINO ACID SEQUENCE; AQUIFEX AEOLICUS; COMPARATIVE STUDY; COMPUTER PROGRAM; HYPERTHERMOPHILIC BACTERIUM; INTERNET; NONHUMAN; NUCLEOTIDE SEQUENCE; PREDICTION; PROTEIN DATABASE; PROTEIN FUNCTION; PROTEIN STRUCTURE; REVIEW; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS; ARTICLE; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; GENETICS; METHODOLOGY; PHYLOGENY; PHYSIOLOGY; PROTEIN CONFORMATION; PROTEOMICS; SEQUENCE ALIGNMENT; STATISTICS;

COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; MOLECULAR STRUCTURE; PHYLOGENY; PROTEIN CONFORMATION; PROTEINS; PROTEOMICS; SEQUENCE ALIGNMENT;

EID: 52949095745     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1000151     Document Type: Review

References (46)

1. Watson JD, Todd AE, Bray J, Laskowski RA, Edwards A, et al. (2003) Target selection and determination of function in structural genomics. IUBMB Life 55: 249-255.
2. Blundell TL, Mizuguchi K (2000) Structural genomics: An overview. Prog Biophys Mol Biol 73: 289-295.
3. Galperin MY (2008) The Molecular Biology Database Collection: 2008 update. Nucleic Acids Res 36: D2-D4.
4. Laskowski RA, Watson JD, Thornton JM (2005) ProFunc: A server for predicting protein function from 3D structure. Nucleic Acids Res 33: W89-W93.
5. Shameer K, Sowdhamini R (2007) IWS: Integrated web server for protein sequence and structure analysis. Bioinformation 2: 86-90.
6. Jensen LJ, Ussery DW, Brunak S (2003) Functionality of system components: Conservation of protein function in protein feature space. Genome Res 13: 2444-2449.
7. Wass MN, Sternberg MJ (2008) ConFunc - Functional annotation in the twilight zone. Bioinformatics 24: 798-806.
8. Hawkins T, Luban S, Kihara D (2006) Enhanced automated function prediction using distantly related sequences and contextual association by PFP. Protein Sci 15: 1550-1556.
9. Natale DA, Vinayaka CR, Wu CH (2004) Large-scale, classification-driven, rule-based functional annotation of proteins. Subramaniam S, ed. New York: John Wiley.
10. Friedberg I (2006) Automated protein function prediction - the genomic challenge. Brief Bioinform 7: 225-242.
11. Rost B (2002) Enzyme function less conserved than anticipated. J Mol Biol 318: 595-608.
12. Todd AE, Orengo CA, Thornton JM (2001) Evolution of function in protein superfamilies, from a structural perspective. J Mol Biol 307: 1113-1143.
13. Brenner SE (1999) Errors in genome annotation. Trends Genet 15: 132-133.
14. Keller JP, Smith PM, Benach J, Christendat D, deTitta GT, et al. (2002) The crystal structure of MT0146/CbiT suggests that the putative precorrin-8w decarboxylase is a methyltransferase. Structure 10: 1475-1487.
15. Adams MA, Suits MD, Zheng J, Jia Z (2007) Piecing together the structure-function puzzle: Experiences in structure-based functional annotation of hypothetical proteins. Proteomics 7: 2920-2932.
16. Watson JD, Sanderson S, Ezersky A, Savchenko A, Edwards A, et al. (2007) Towards fully automated structure-based function prediction in structural genomics: A case study. J Mol Biol 367: 1511-1522.
17. Uniprot Consortium (2008) The universal protein resource (UniProt). Nucleic Acids Res 36: D190-D195.
18. Hedges SB (2002) The origin and evolution of model organisms. Nat Rev Genet 3: 838-849.
19. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
20. Eddy SR (1998) Profile hidden Markov models. Bioinformatics 14: 755-763.
21. Dayhoff MO (1976) The origin and evolution of protein superfamilies. Fed Proc 35: 2132-2138.
22. Wu CH, Nikolskaya A, Huang H, Yeh LS, Natale DA, et al. (2004) PIRSF: Family classification system at the Protein Information Resource. Nucleic Acids Res 32: D112-D114.
23. Koonin EV, Fedorova ND, Jackson JD, Jacobs AR, Krylov DM, et al. (2004) A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. Genome Biol 5: R7.
24. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, et al. (2003) The COG database: An updated version includes eukaryotes. BMC Bioinformatics 4: 41.
25. Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, et al. (2008) The Pfam protein families database. Nucleic Acids Res 36: D281-D288.
26. Bartlett GJ, Todd AE, Thornton JM (2003) Inferring protein function from structure. Methods Biochem Anal 44: 387-407.
27. Whisstock JC, Lesk AM (2003) Prediction of protein function from protein sequence and structure. Q Rev Biophys 36: 307-340.
28. Thornton JM, Todd AE, Milburn D, Borkakoti N, Orengo CA (2000) From structure to function: Approaches and limitations. Nat Struct Biol 7 (Supplement). pp 991-994.
29. Rost B (1997) Protein structures sustain evolutionary drift. Fold Des 2: S19-S24.
30. Gibrat JF, Madej T, Bryant SH (1996) Surprising similarities in structure comparison. Curr Opin Struct Biol 6: 377-385.
31. Shindyalov IN, Bourne PE (1998) Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng 11: 739-747.
32. Holm L, Sander C (1997) Dali/FSSP classification of three-dimensional protein folds. Nucleic Acids Res 25: 231-234.
33. Hubbard TJ, Murzin AG, Brenner SE, Chothia C (1997) SCOP: A structural classification of proteins database. Nucleic Acids Res 25: 236-239.
34. Andreeva A, Howorth D, Chandonia JM, Brenner SE, Hubbard TJ, et al. (2008) Data growth and its impact on the SCOP database: New developments. Nucleic Acids Res 36: D419-D425.
35. Greene LH, Lewis TE, Addou S, Cuff A, Dallman T, et al. (2007) The CATH domain structure database: New protocols and classification levels give a more comprehensive resource for exploring evolution. Nucleic Acids Res 35: D291-D297.
36. Laskowski RA, Chistyakov VV, Thornton JM (2005) PDBsum more: New summaries and analyses of the known 3D structures of proteins and nucleic acids. Nucleic Acids Res 33: D266-D268.
37. Sobolev V, Eyal E, Gerzon S, Potapov V, Babor M, et al. (2005) SPACE: A suite of tools for protein structure prediction and analysis based on complementarity and environment. Nucleic Acids Res 33: W39-W43.
38. Hulo N, Bairoch A, Bulliard V, Cerutti L, Cuche BA, et al. (2008) The 20 years of PROSITE. Nucleic Acids Res 36: D245-D249.
39. Porter CT, Bartlett GJ, Thornton JM (2004) The Catalytic Site Atlas: A resource of catalytic sites and residues identified in enzymes using structural data. Nucleic Acids Res 32: D129-D133.
40. Berman HM, Battistuz T, Bhat TN, Bluhm WF, Bourne PE, et al. (2002) The Protein Data Bank. Acta Crystallogr D Biol Crystallogr 58: 899-907.
41. Eustaquio AS, Pojer F, Noel JP, Moore BS (2008) Discovery and characterization of a marine bacterial SAM-dependent chlorinase. Nat Chem Biol 4: 69-74.
42. Dong C, Huang F, Deng H, Schaffrath C, Spencer JB, et al. (2004) Crystal structure and mechanism of a bacterial fluorinating enzyme. Nature 427: 561-565.
43. O'Hagan D, Schaffrath C, Cobb SL, Hamilton JT, Murphy CD (2002) Biochemistry: Biosynthesis of an organofluorine molecule. Nature 416: 279.
44. Deng H, Cobb SL, McEwan AR, McGlinchey RP, Naismith JH, et al. (2006) The fluorinase from Streptomyces cattleya is also a chlorinase. Angew Chem Int Ed Engl 45: 759-762.
45. Zhu X, Robinson DA, McEwan AR, O'Hagan D, Naismith JH (2007) Mechanism of enzymatic fluorination in Streptomyces cattleya. J Am Chem Soc 129: 14597-14604.
46. Deng H, O'Hagan D, Schaffrath C (2004) Fluorometabolite biosynthesis and the fluorinase from Streptomyces cattleya. Nat Prod Rep 21: 773-784.