Efficient recognition of protein fold at low sequence identity by conservative application of Psi-BLAST: Application

Journal of Molecular Recognition

Volumn 18, Issue 2, 2005, Pages 150-157

  Stevens, F J ^a   Kuemmel, C ^a   Babnigg, G ^a   Collart, F R ^a  

^a ARGONNE NATIONAL LABORATORY   (United States)

Author keywords

Evolution; Hypothetical proteins; Organophosphorus compounds; Protein function; Protein homology

Indexed keywords

PROTEIN;

ALGORITHM; AMINO ACID SEQUENCE; ANIMAL; ARTICLE; BINDING SITE; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; COMPARATIVE STUDY; COMPUTER PROGRAM; GENOME; HUMAN; METHODOLOGY; MOLECULAR EVOLUTION; MOLECULAR GENETICS; PROTEIN DATABASE; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY;

ALGORITHMS; AMINO ACID SEQUENCE; ANIMALS; BINDING SITES; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; EVOLUTION, MOLECULAR; GENOME; HUMANS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; SEQUENCE HOMOLOGY, AMINO ACID; SOFTWARE;

EID: 14744298788     PISSN: 09523499     EISSN: None     Source Type: Journal    
DOI: 10.1002/jmr.719     Document Type: Article

References (35)

1. Baxter SM, Fetrow JS. 2001. Sequence- and structure-based protein function prediction from genomic information. Curr. Opin. Drug Discov. Devel. 4: 291-295.
2. Benning MM, Kuo JM, Raushel FM, Holden HM. 1994. Three-dimensional structure of phosphotriesterase: an enzyme capable of detoxifying organophosphate nerve agents. Biochemistry 33: 15001-15007.
3. Betz SF, Baxter SM, Fetrow JS. 2002. Function first: a powerful approach to post-genomic drug discovery. Drug Discov. Today 7: 865-871.
4. Campobasso N, Mathews II, Begley TP, Ealick SE. 2000. Crystal structure of 4-methyl-5-beta-hydroxyethylthiazole kinase from Bacillus subtilis at 1.5 Å resolution. Biochemistry 39: 7868-7877.
5. Chothia C, Lesk AM. 1986. The relation between the divergence of sequence and structure in proteins. Embo J. 5: 823-826.
6. Costa LG, Li WF, Richter RJ, Shih DM, Lusis A, Furlong CE. 1999. The role of paraoxonase (PON1) in the detoxication of organophosphates and its human polymorphism. Chem. Biol. Interact. 119-120: 429-438.
7. Derbyshire DJ, Basu BP, Serpell LC, Joo WS, Date T, Iwabuchi K, Doherty AJ. 2002. Crystal structure of human 53BP1 BRCT domains bound to p53 tumour suppressor. Embo J. 21: 3863-3872.
8. Fetrow JS, Skolnick J. 1998. Method for prediction of protein function from sequence using the sequence-to-structure-to-function paradigm with application to glutaredoxins/thioredoxins and T1 ribonucleases. J. Mol. Biol. 281: 949-968.
9. Fetrow JS, Siew N, Skolnick J. 1999. Structure-based functional motif identifies a potential disulfide oxidoreductase active site in the serine/threonine protein phosphatase-1 subfamily. Faseb J. 13: 1866-1874.
10. Fetrow JS, Siew N, Di Gennaro JA, Martinez-Yamout M, Dyson HJ, Skolnick J. 2001. Genomic-scale comparison of sequence- and structure-based methods of function prediction: does structure provide additional insight? Prot. Sci. 10: 1005-1014.
11. Gilks WR, Audit B, De Angelis D, Tsoka S, Ouzounis CA. 2002. Modeling the percolation of annotation errors in a database of protein sequences. Bioinformatics 18: 1641-1649.
12. Godzik A. 2003. Fold recognition methods. Meth. Biochem. Anal. 44: 525-546.
13. Heinemann U, Hahn M. 1995. Circular permutation of polypeptide chains: implications for protein folding and stability. Prog. Biophys. Mol. Biol. 64: 121-143.
14. Hemmingsen JM, Gernert KM, Richardson JS, Richardson DS. 1994. The tyrosine corner: a feature of most Greek key beta-barrel proteins. Protein Sci. 3: 1927-1933.
15. Kabat EA, Wu TT, Perry HM, Gottesman KS, Foeller C. 1991. Sequences of Proteins of Immunological Interest, 5th edn. Public Health Service, US Department of Health and Human Services, National Instituties of Health: Bethesda, MD.
16. Koonin EV, Tatusov RL, Galperin MY. 1998. Beyond complete genomes: from sequence to structure and function. Curr. Opin. Struct. Biol. 8: 355-363.
17. Marti-Renom MA, Stuart AC, Fiser A, Sanchez R, Melo F, Sali A. 2000. Comparative protein structure modeling of genes and genomes. A. Rev. Biophys. Biomol. Struct. 29: 291-325.
18. Park J, Teichmann SA, Hubbard T, Chothia C. 1997. Intermediate sequences increase the detection of homology between sequences. J. Mol. Biol. 273: 349-354.
19. Pawlowski K, Rychlewski L, Reed JC, Godzik A. 2000. From fold to function predictions: an apoptosis regulator protein BID. Comput. Chem. 24: 511-517.
20. Rost B, Sander C. 1993. Prediction of protein secondary structure at better than 70% accuracy. J. Mol. Biol. 232: 584-589.
21. Rychlewski L, Zhang B, Godzik A. 1999. Functional insights from structural predictions: analysis of the Escherichia coli genome. Prot. Sci. 8: 614-624.
22. Salamov AA, Suwa M, Orengo CA, Swindells MB. 1999. Combining sensitive database searches with multiple intermediates to detect distant homologs. Prot. Eng. 12: 95-100.
23. Scharff EI, Koepke J, Fritzsch G, Lucke C, Ruterjans H. 2001. Crystal structure of diisopropylfluorophosphatase from Loligo vulgaris. Structure (Camb) 9: 493-502.
24. Skolnick J, Fetrow JS, Kolinski A. 2000. Structural genomics and its importance for gene function analysis. Nat. Biotechnol. 18: 283-287.
25. Stevens FJ. 2004a. Hypothetical structure of human serum amyloid A protein. Amyloid 11: 71-80.
26. Stevens FJ. 2004b. Efficient recognition of protein fold at low sequence identity by conservative application of Psi-BLAST: validation. J. Mol. Recognit. in press.
27. Tuovinen K, Kaliste-Korhoner E, Raushel FM, Hanninen O. 1999. Success of pyridostigmine, physostigmine, eptastigmine and phosphotriestrase treatments in acute sarin intoxication. Toxicology 134: 169-178.
28. Vaidehi N, Floriano WB, Trabanino R, Hall SE, Freddolino P, Choi EJ, Zamanakos G, Goddard WA 3rd. 2002. Prediction of structure and function of G protein-coupled receptors. Proc. Natl. Acad. Sci. USA 99: 12622-12627.
29. Vanhooke JL, Benning MM, Raushel FM, Holden HM. 1996. Three-dimensional structure of the zinc-containing phosphotriesterase with the bound substrate analog diethyl 4-methylbenzylphosphonate. Biochemistry35: 6020-6025.
30. Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO. 2004. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304: 66-74.
31. Williams RS, Green R, Glover JN. 2001. Crystal structure of the BRCT repeat region from the breast cancer-associated protein BRCA1. Nat. Struct. Biol. 8: 838-842.
32. Zhang H, Somasundaram K, Peng Y, Tian H, Bi D, Weber BL, El-Deiry WS. 1998. BRCA1 physically associates with p53 and stimulates its transcriptional activity. Oncogene 16: 1713-1721.
33. Zhang B, Rychlewski L, Pawlowski K, Fetrow JS, Skolnick J, Godzik A. 1999. From fold predictions to function predictions: automation of functional site conservation analysis for functional genome predictions. Prot. Sci. 8: 1104-1115.
34. Zhang RG, Grembecka J, Vinokour E, Collart F, Dementieva I, Minor W, Joachimiak A. 2002. Structure of Bacillus subtilis YXKO - a member of the UPF0031 family and a putative kinase. J. Struct. Biol. 139: 161-170.
35. Zheng L, Li S, Boyer TG, Lee W-H. 2000. Lessons learned from BRCA1 and BRCA2. Oncogene 19: 6159-6175.