Optimizing the parameters of the Gaussian network model for ATP-binding proteins

Normal Mode Analysis: Theory and Applications to Biological and Chemical Systems

Volumn , Issue , 2005, Pages 171-186

  Sen, Taner Z ^a   Jernigan, Robert L ^a  

^a IOWA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 78049283691     PISSN: None     EISSN: None     Source Type: Book    
DOI: None     Document Type: Chapter

References (17)

1. Kundu, S., Melton, J.S., Sorensen, D.C., and Phillips, G.N., Dynamics of proteins in crystals: Comparison of experiment with simple models, Biophys.,83,723-732, 2002.
2. Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., and Bourne, P.E., The protein data bank, Nucleic Acids Res.,28, 235-242, 2000.
3. Orengo, C.A., Michie, A.D., Jones, S., Jones, D.T., Swindells, M.B., and Thornton, J.M., CATH — a hierarchic classification of protein domain structures, Structure, 5,1093-1108,1997.
4. Pearl, F.M.G., Lee, D., Bray, J.E., Sillitoe, I., Todd, A.E., Harrison, A.P., Thornton, J.M., and Orengo, C.A., Assigning genomic sequences to CATH, Nucleic Acids Res,28, 277-282, 2000.
5. Schulze-Gahmen, U., Brandsen, J., Jones, H.D., Morgan, D.O., Meijer, L., Vesely, J., and Kim, S.H., Multiple-modes of ligand recognition — crystal-structures of cyclin-dependent protein-kinase-2 in complex with ATP and 2 inhibitors, olomoucine and isopentenyladenine, Proteins,22, 378-391,1995.
6. Schulze-Gahmen, U., DeBondt, H.L., and Kim, S.H., High-resolution crystal structures of human cyclin-dependent kinase 2 with and without ATP: bound waters and natural ligand as guides for inhibitor design, J. Med. Chem., 39, 4540-4546,1996.
7. Knofel, T. and Strater, N., X-ray structure of the Escherichia coli periplasmic 5;-nucleotidase containing a dimetal catalytic site, Nat. Struct. Biol.,6,448-453,1999.
8. Knofel, T. and Strater, N., Mechanism of hydrolysis of phosphate esters by the dimetal center of 5’-nucleotidase based on crystal structures, J. Mol. Biol.,309, 239-254,2001.
9. Walker, E.H., Pacold, M.E., Perisic, O., Stephens, L., Hawkins, P.T., Wymann, M.P., and Williams, R.L., Structural determinants of phosphoinositide 3-kinase inhibition by wortmannin, LY294002, quercetin, myricetin, and staurosporine, Mol. Cell,6, 909-919,2000.
10. Sobolev, V., Sorokine, A., Prilusky, J., Abola, E.E., and Edelman, M., Automated analysis of interatomic contacts in proteins, Bioinformatics,15, 327-332,1999.
11. Mclachlan, A.D., Rapid comparison of protein structures, Acta Crystallogr., A38, 871-873,1982.
12. Bahar, I., Atilgan, A.R., and Erman, B., Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential, Fold. Des.2, 173-181, 1997.
13. Haliloglu, T., Bahar, I., and Erman, B., Gaussian dynamics of folded proteins, Phys. Rev. Lett.,79, 3090-3093, 1997.
14. Sluis-Cremer, N., Temiz, N.A., and Bahar, I., Conformational changes in HIV-1 reverse transcriptase induced by nonnucleoside reverse transcriptase inhibitor binding, Curr. HIV Res.,2, 323-332, 2004.
15. Temiz, N.A. and Bahar, I., Inhibitor binding alters the directions of domain motions in HIV-1 reverse transcriptase, Proteins,49, 61-70,2002.
16. Hinsen, K., Analysis of domain motions by approximate normal mode calculations, Proteins,33, 417-429,1998.
17. Press, W.H., Flannery, B.P., Teukolsky, S.A., and Vetterling, W.T., Numerical Recipes in Fortran.Cambridge University Press, Cambridge, UK, 1992.