An insight to the dynamics of conserved water molecular triad in impdh ii (human): Recognition of cofactor and substrate to catalytic arg 322

Journal of Biomolecular Structure and Dynamics

Volumn 27, Issue 2, 2009, Pages 149-158

  Bairagya, Hridoy R ^a   Mukhopadhyay, Bishnu P ^a   Sekar, K ^b  

^a NATIONAL INSTITUTE OF TECHNOLOGY   (India)

^b INDIAN INSTITUTE OF SCIENCE   (India)

Author keywords

Arg 322 recognition; Conserved water molecular triad; Human IMPDH II; Water dynamics

Indexed keywords

AMINO ACID SEQUENCE; ARGININE; CRYSTALLOGRAPHY, X-RAY; HUMANS; HYDROGEN BONDING; IMP DEHYDROGENASE; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; MOLECULAR SEQUENCE DATA; PROTEIN STRUCTURE, TERTIARY; WATER;

ARGININE; INOSINATE DEHYDROGENASE; WATER;

ARTICLE; COMPUTER SIMULATION; ENZYME ACTIVE SITE; ENZYME INHIBITOR INTERACTION; ENZYME MECHANISM; HUMAN; MOLECULAR DYNAMICS; MOLECULAR MODEL; MOLECULAR RECOGNITION; NUCLEOTIDE METABOLISM; PRIORITY JOURNAL; PROTEIN DOMAIN;

EID: 67650439243     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.2009.10507304     Document Type: Article

References (32)

1. Hedstrom, L., Gan, L., Schlippe, Y. G., Riera, T., and Seyedsayamdost, M., 2003. Nucleic Acids Research (Supplement no.), 3:97–98.
2. Pankiewicz, K. W., and Goldstein, B. M., 2003. ACS Symposium Serial No., 839
3. Branden, C., and Tooze, J., 1991. Introduction to Protein Structure. New York and London:Garland Publishing.
4. Sintechak, M. D., and Nimmesgern, E., 2000. Immunopharmacology, 47:163–184.
5. Farazi, T., Leichman, J., Harris, T., Cahoon, M., and Hedstrom, L., 1997. Journal of Biological Chemistry, 272:2–965. 961
6. Gan, L., Petsko, G. A., and Hedstrom, L., 2003. Biochemistry, 41:13309–13317.
7. Prosise, G. L., and Luecke, H., 2003. J Mol Biol, 326:517–527.
8. Bairagya, H. R., Mukhopadhyay, B. P., and Sekar, K., 2009. J Biol Mol Struct Dyn, 26 (4):497–508.
9. Colby, T. D., Vanderveen, K., Stricker, M. D., Markham, G. D., and Goldstein, B. M., 1999. Proceeding of the National Academy Sciences—Biochemistry, 96:3531–3536.
10. Berman, H. M., Westbrook, J., Feng, Z., Gilliand, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., and Bourne, P. E., 2003. Nat Struct Biol, 10:980
11. Berman, H. M., Westbrook, J., Feng, Z., Gilliand, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., and Bourne, P. E., 2000. Nucleic Acids Res, 28:235–242.
12. Bernstein, F. C., Koetzle, T. F., Williams, G. J., Jr., Meyer, E. F., Brice, M. D., Rodgers, J. R., Kennard, O., and Shimanouchi, T., 1977. J Mol Biol, 112:535–542.
13. Risal, D., Stricker, M. D., and Goldstein, B. M., 2004. Structure deposited RCSB. To be published
14. Risal, D., Stricker, M. D., and Goldstein, B. M., 2004. Structure deposited RCSB. To be published
15. Guex, N., Diemand, A., Peitsch, M. C., and Schwede, T., 2001. “ The Swiss-PdbView Programme ”. In An environment for comparative protein modeling. Glaxo Smith Kline R & D.
16. Guex, N., and Peitsch, M. C., 1997. Electrophoresis, 18:2714–2723.
17. Fleming, P. J., Nicholas, C., Fitzkee, M. M., Rajgopal, S., and George, D. R., 2005. Protein Sci, 14:111–118.
18. Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S., and Karplus, M., 1983. J Comput Chem, 4:187–217.
19. Humphrey, W., Dalke, A., and Schulten, K., 1996. VMD—Visual Molecular Dynamics. J Mol Graphics, 14:33–38.
20. Saam, J., Ivanove, I., Walther, M., and Holzhutter, H. G., 2007. PNAS, 104:33–13324. 13319
21. 2005. Hyperchem TM Release 7.52 for windows Molecular Modeling System. © © Hypercube, Inc.
22. Grayson, P., Tajkhorshid, E., and Schulten, K., 2003. Biophysical Journal, 85:36–48.
23. Kale, L., Skeel, R., Bhandarkar, M., Brunner, R., Gursoy, A., Krawetz, N., Phillips, J., Shinozaki, A., Varadarajan, K., and Schulten, K., 1999. J Comput Phys, 151:283–312.
24. Nelson, M., Humphrey, W., Gursoy, A., Dalke, A., Kale, L., Skeel, R. D., and Schulten, K., 1996. Int J Supercomput Appl High Perform Comput, 10:251–268.
25. Phillips, J. C., Rosemary, B., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., and Chipot, C., 2005. J Comput Chem, 26:1781–1802.
26. Gullingsrud, J., Kosztin, D., and Schulten, K., 2001. Biophys J, 80:2074–2081.
27. Cerutti, D. S., Jain, T., and McCammon, J. A., 2006. Protein Sci, 15:1579–1596.
28. Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Merz, K. M., Ferguson, D. M., Jr, Spellmeyer, D. C., Fox, T., Caldwell, J. W., and Kollman, P. A., 1995. J Am Chem Soc, 117:5179–5197.
29. Schymkowitz, J., Borg, J., Stricher, F., Rousseau, Nys R.F., and Serrano, L., 2005. Nucleic Acids Research, 33:382–388.
30. Ogata, K., 2002. Protein Engg, 15:697–705.
31. Bera, A. K., Mukhopadhyay, B. P., Pal, A. K., Halder, U., Bhattacharya, S., and Banerjee, A., 1998. J Chem Crystallogr, 28:7–516. 509
32. Jeffrey, G. A., and Saenger, W., 1992. H-bonding in Biological Structures Springer-Verlag.