Active site prediction for comparative model structures with thematics

Journal of Bioinformatics and Computational Biology

Volumn 3, Issue 1, 2005, Pages 127-143

  Shehadi, Ihsan A ^a   Abyzov, Alexej ^b   Uzun, Alper ^b   Wei, Ying ^b   Murga, Leonel F ^b   Ilyin, Valentin ^b   Ondrechen, Mary Jo ^b  

^a UNITED ARAB EMIRATES UNIVERSITY   (United Arab Emirates)

^b NORTHEASTERN UNIVERSITY   (United States)

Author keywords

Comparative models; Functional genomics; Protein function; THEMATICS; Titration

Indexed keywords

ALDEHYDE REDUCTASE; ASPARTATE AMINOTRANSFERASE; PHOSPHOTRANSFERASE; TRIOSEPHOSPHATE ISOMERASE;

ARTICLE; COMPARATIVE STUDY; ENZYME ACTIVE SITE; ENZYME ANALYSIS; ENZYME STRUCTURE; HUMAN; IONIZATION; MOLECULAR MODEL; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; PREDICTION; RAT; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS; TITRIMETRY;

ALGORITHMS; BINDING SITES; ENZYME ACTIVATION; ENZYMES; MODELS, CHEMICAL; MODELS, MOLECULAR; PROTEIN BINDING; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE; STRUCTURE-ACTIVITY RELATIONSHIP; TITRIMETRY;

EID: 14544293684     PISSN: 02197200     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0219720005000916     Document Type: Article

References (50)

1. Ondrechen MJ, Clifton JG, Ringe D, THEMATICS: A simple computational predictor of enzyme function from structure, Proc Natl Acad Sci (USA) 98:12473-12478, 2001.
2. Shehadi IA, Yang H, Ondrechen MJ, Future directions in protein function prediction, Mol Biol Reports 29:329-335, 2002.
3. Ringe D, Wei Y, Boino KR, Ondrechen MJ, Protein structure to function: Insights from computation, Cellular Molecular Life Sciences 61 387-392, 2004.
4. Bashford D, Karplus M, Multiple-site titration curves of proteins: An analysis of exact and approximate methods for their calculation, J Phys Chem 95:9556-9561, 1991.
5. Bashford D, Gerwert K, Electrostatic calculations of the pKa values of ionizable groups in bacteriorhodopsin, J Mol Biol 224 2):473-486, 1992.
6. Gilson MK, Multiple-site titration and molecular modeling: Two rapid methods for computing energies and forces for ionizable groups in proteins, Proteins 15(3): 266-282, 1993.
7. Yang AS, Gunner MR, Sampogna R, Sharp K, Honig B, On the calculation of pKa's in proteins, Proteins 15(3):252-265, 1993.
8. Sampogna RV, Honig B, Environmental effects on the protonation states of active site residues in bacteriorhodopsin, Biophys J 66 5):1341-1352, 1994.
9. Beroza P, Fredkin DR, Okamura MY, Feher G, Electrostatic calculations of amino acid titration and electron transfer, Q-AQB-QAQ-B, in the reaction center, Biophys J 68(6):2233-2250, 1995.
10. Antosiewicz J, Briggs JM, Elcock AH, Gilson MK, McCammon JA, Computing the ionization states of proteins with a detailed charge model, J Comp Chem 17: 1633-1644, 1996.
11. Carlson HA, Briggs JM, McCammon JA, Calculation of the pKa values for the ligands and side chains of Escherichia coli D-alanine: D-alanine ligase, J Med Chem 42: 109-117, 1999.
12. Madura JD, Briggs JM, Wade RC, Davis ME, Luty BA, Ilin A, Antosiewicz J, Gilson MK, Bagheri B, Scott LR, McCammon JA, Electrostatics and diffusion of molecules in solution - Simulations with the University of Houston Brownian Dynamics program, Comp Phys Commun 91:57-95, 1995.
13. Karshikoff A, A simple algorithm for the calculation of multiple site titration curves, Protein Engineering 8:243-248, 1995.
14. Antosiewicz J, McCammon JA, Gilson MK, The determinants of pKa's in proteins, Biochemistry 35:7819-7833, 1996.
15. Alexov EG, Gunner MR, Incorporating protein conformational flexibility into the calculation of pH-dependent protein properties, Biophys J 72:2075-2093, 1997.
16. Nielsen JE, Andersen KV, Honig B, Hooft RWW, Klebe G, Vriend G, Wade RC, Improving macromolecular electrostatics calculations, Protein Engineering 12: 657-662, 1999.
17. Mehler EL, Guarnieri F, A self-consistent, microenvironment modulated screened Coulomb potential approximation to calculate pH-dependent electrostatic effects in proteins, Biophys J 77:3-22, 1999.
18. Georgescu RE, Alexov EG, Gunner MR, Combining conformational flexibility and continuum electrostatics for calculating pKa's in proteins, Biophys J 83:1731-1748, 2002.
19. Sali A, 100,000 protein structures for the biologist, Nature Struct Biol 5:1929-1932, 1998.
20. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE, The protein data bank, Nucleic Acids Res 28(1):235-242, 2000.
21. Westbrook J, Feng Z, Chen L, Yang H, Berman HM, The protein data bank and structural genomics, Nucleic Acids Res 31:489-491, 2003.
22. Fiser A, Do RK, Sali A, Modeling of loops in protein structures, Protein Sci 9: 1753-1773, 2000.
23. Sali A, Modeling mutations and homologous proteins. Curr Opin Biotechnol 6: 437-451, 1995.
24. Abyzov A, Leslin C, Ilyin V, An integrated analytical front-end application for bioinformatics, Friend, in Computational and Systems Biology Initiative, Cambridge, MA, 2003.
25. Thompson JD, Higgins DG, Gibson TJ, CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucleic Acids Res 22(22):4673-4680, 1994.
26. Sanchez R, Sali A, Comparative protein structure modeling. Introduction and practical examples with modelle, Methods Mol Biol 143:97, 2000.
27. Schwede T, Kopp J, Guex N, Peitsch MC, SWISS-MODEL: An automated protein homology-modeling server, Nucleic Acids Res 31 3381-3385, 2003.
28. Zhang Z, Sugio S, Komives EA, Liu KD, Knowles JR, Petsko GA, Ringe D, Crystal structure of recombinant chicken triosephosphate isomerase-phosphoglycolo-hydroxamate complex at 1.8-A resolution, Biochemistry 33(10):2830-2837, 1994.
29. Liu F, Hu W, Yan Q, Xu X, Zhu Z, Zhang X, Wang J, Sun J, Wang Z, Zeng L et al., The full-length cDNA of S. japonicum genes. EMBL GenBank DDBJ databases, 2003.
30. Paulsen IT, Banerjei L, Myers GSA, Nelson KE, Seshadri R, Read TD, Fouts DE, Eisen JA, Gill SR, Heidelberg JF et al., Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis, Science 299:2071-2074, 2003.
31. Fraser CM, Gocayne JD, White O, Adams MD, Clayton RA, Fleischmann RD, Bult CJ, Kerlavage AR, Sutton G, Kelley JM et al., The minimal gene complement of Mycoplasma genitalium, Science 270:397-403, 1995.
32. Lodi PJ, Knowles JR, Neutral imidazole is the electrophile in the reaction catalyzed by triosephosphate isomerase: Structural origins and catalytic implications, Biochemistry 30:6948-6956, 1991.
33. Xiao B, Shi G, Chen X, Yan H, Ji X, Crystal structure of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, a potential target for the development of novel antimicrobial agents, Structure Fold Des 7:489-496, 1999.
34. Rhee JH, Kim SY, Chung SS, Kim JJ, Moon YH, Jeong H, Choy HE, Complete Genome Sequence of Vibrio Vilnificus, EMBL GenBank DDBJ databases, 2002.
35. Makino K, Oshima K, Kurokawa K, Yokoyama K, Uda T, Tagomori K, Iijima Y, Najima M, Nakano M, Yamashita A et al., Genome sequence of Vibrio parahaemolyticus: A pathogenic mechanism distinct from that of V. cholerae, Lancet 361:743-749, 2003.
36. Stover CK et al., Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen, Nature 406 959-964, 2000.
37. Nelson KE, Weinel C, Paulsen IT, Dodson RJ, Hilbert H, Martins dos Santos VAP, Fouts DE, Gill SR, Pop M, Holmes M et al., Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440, Environ Microbiol 4:799-808, 2002.
38. Stammers DK, Achari A, Somers DO, Bryant PK, Rosemond J, Scott DL, Champness JN, 2.0A X-ray structure of the ternary complex of 7,8-Dihydro-6-Hydroxymethyl-pterinpyrophosphokinase rom E. coli with ATP and a substrate analogue, FEBS Lett 456:49, 1999.
39. Miyahara I, Hirotsu K, Hayashi H, Kagamiyama H, X-ray crystallographic study of pyridoxamine 5′-phosphate-type aspartate aminotransferases from E. coli in three forms, J Biochem (Tokyo) 116:1001, 1994.
40. Heidelberg JF, Eisen JA, Nelson WC, Clayton RA, Gwinn ML, Dodson RJ, Haft DH, Hickey EK, Peterson JD, Umayam LA et al.. DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae, Nature 406 477-483, 2000.
41. Sasaki T, Matsumoto T, Yamamoto K, Oryza sativa nipponbare (GA3) genomic DNA, chromosome 1, PAC clone. EMBL GenBank DDBJ databases, FEB-2001, 2001.
42. Tetelin H, Saunders NJ, Heidelberg J, Jeffries AC, Nelson KE, Eisen JA, Ketchum KA, Hood DW, Peden JF, Dodson RJ et al., Complete genome sequence of Neisseria meningitidis serogroup B strain MC58, Science 287:1809-1815, 2000.
43. Jeffery CJ, Barry T, Doonan S, Petsko GA, Ringe D, Crystal structure of saccharomyces cerevisiae cytosolic aspartate aminotransferase, Protein Sci 7:1380-1387, 1998.
44. Jeffery CJ, Gloss LM, Petsko GA, Ringe D, The role of residues outside the active site: Structural basis for function of C191 mutants of E. coli aspartate aminotransferase, Protein Engineering 13 105-112, 2000.
45. Mizuguchi H, Hayashi H, Okada K, Miyahara I, Hirotsu K, Kagamiyama H, Strain is more important than electrostatic interaction in controlling the pKa of the catalytic group in aspartate aminotransferase, Biochemistry 40:353-360, 2001.
46. Harrison DH, Bohren KM, Ringe D, Petsko GA, Gabbay KH, An anion binding site in human aldose reductase: Mechanistic implications for the binding of citrate, cacodylate and glucose-6-phosphate, Biochemistry 33:2011-2020, 1994.
47. Wermuth B, Omar A, Forster A, di Francesco C, Wolf M, von Wartburg JP, Bullock B, Gabbay KH, Primary structure of aldehyde reductase from human liver, Prog Clin Biol Res 232:297-307, 1987.
48. Stolz A, Hammond L, Lou H, Takikawa H, Ronk M, Shively JE, cDNA cloning and expression of the human hepatic bile-acid binding protein. A member of the monomeric reductase gene family, J Biol Chem 268 10448-10457, 1993.
49. Kondo KH, Kai MH, Setoguchi Y, Eggertsen G, Sjoeblom P, Setoguchi T, Okuda KI, Bjoerkhem I, Cloning and expression of cDNA of human delta 4-3-oxosteroid 5 beta-reductase and substrate specificity of the expressed enzyme, Eur J Biochem 219: 357-363, 1994.
50. Qin KN, New MI, Cheng KC, Molecular cloning of multiple cDNAs encoding human enzymes structurally related to 3 alpha-hydroxysteroid dehydrogenase, J Steroid Biochem Mol Biol 46:673-679, 1993.