Computation of entropy contribution to protein-ligand binding free energy

Biochemistry (Moscow)

Volumn 72, Issue 7, 2007, Pages 785-792

  Grigoriev, F V ^a   Luschekina, S V ^b   Romanov, A N ^a   Sulimov, V B ^a   Nikitina, E A ^c  

^a MOSCOW STATE UNIVERSITY   (Russian Federation)

^b INSTITUTE OF BIOMEDICAL CHEMISTRY   (Russian Federation)

^c INSTITUTE OF APPLIED MECHANICS   (Russian Federation)

Author keywords

Binding free energy; Covariance matrix; Protein ligand complex; Vibration entropy

Indexed keywords

COVARIANCE MATRIX; DEGREES OF FREEDOM (MECHANICS); ENTROPY; FREE ENERGY; HYDROPHOBICITY; LIGANDS;

BINDING FREE ENERGY; INHARMONIC EFFECTS; PROTEIN-LIGAND COMPLEX; VIBRATION ENTROPY;

PROTEINS;

BENZAMIDINE; BENZAMIDINE DERIVATIVE; LIGAND; STREPTAVIDIN; TRYPSIN;

ARTICLE; BIOLOGICAL MODEL; CHEMISTRY; ENTROPY; PROTEIN BINDING; PROTEIN CONFORMATION;

BENZAMIDINES; ENTROPY; LIGANDS; MODELS, BIOLOGICAL; PROTEIN BINDING; PROTEIN CONFORMATION; STREPTAVIDIN; TRYPSIN;

EID: 34547221883     PISSN: 00062979     EISSN: 16083040     Source Type: Journal    
DOI: 10.1134/S0006297907070140     Document Type: Article

References (34)

1. Chang, C. A., Chen, W., and Gilson, M. K. (2007) Proc. Natl. Acad. Sci. USA, 104, 1534-1539.
2. Chang, C. A., and Gilson, M. K. (2003) J. Comput. Chem., 24, 1987-1998.
3. Woo, H. J., and Roux, B. (2005) PNAS, 102, 6825-6830.
4. Carlsson, J., and Aquist, J. (2006) Phys. Chem. Chem. Phys., 8, 5385-5395.
5. Tudor, B., and Karplus, M. (1994) J. Mol. Biol., 238, 405-415.
6. Schwarzl, S. M., Tschopp, T. B., Smith, J. C., and Fischer, S. (2002) J. Comput. Chem., 23, 1143-1149.
7. Karplus, M., and Kushik, J. N. (1981) Macromolecules, 14, 325-332.
8. Schlitter, J. (1993) Chem. Phys. Let., 215, 617-621.
9. Andricioaei, I., and Karplus, M. (2001) J. Chem. Phys., 115, 6289-6292.
10. Schafer, H., Mark, A. E., and Gunsteren, W. F. (2000) J. Chem. Phys., 113, 7809-7817.
11. Luo, H., and Sharp, K. (2002) PNAS, 99, 10399-10404.
12. Schafer, H., Daura, X., Mark, A. E., and Gunsteren, W. F. (2001) Proteins: Struct. Funct. Genet., 43, 45-56.
13. Schafer, H., Smith, L. J., Mark, A. E., and Gunsteren, W. F. (2002) Proteins: Struct. Funct. Genet., 46, 215-224.
14. Hsu, S. D., Peter, C., Gunsteren, W. F., and Bonvin, A. M. J. J. (2005) Biophys. J., 88, 15-24.
15. Carlsson, J., and Aquist, J. (2005) J. Phys. Chem. B., 109, 6448-6456.
16. Dixit, S. B., and Chipot, C. (2001) J. Phys. Chem. A, 105, 9795-9799.
17. Dominy, B., and Brooks, C. L. (1999) J. Phys. Chem., 103, 3765-3773.
18. Brooks, B. R., Bruccoleri, R., Olafson, B., States, D., Swaninathan, S., and Karplus, M. (1983) J. Comput. Chem., 4, 187-217.
19. Halgren, T. A. (1996) J. Comput. Chem., 17, 490-519.
20. Landau, L. D., and Lifshiz, E. M. (2002) Theoretical Physics [in Russian], Vol. 5, Fizmatlit, Moscow.
21. Morris, G. M., Goodsell, D. S., Halliday, R. S., Huey, R., Hart, W. E., Belew, R. K., and Olson, A. J. (1998) J. Comp. Chem., 19, 1639-1662.
22. Tomasi, J., and Persico, M. (1994) Chem. Rev., 94, 2027.
23. Alexandrovsky, V. V., Basilevsky, M. V., Leontyev, I. V., Mazo, M. A., and Sulimov, V. B. (2004) J. Phys. Chem. B, 108, 15830.
24. Basilevsky, M. V., Grigoriev, F. V., Leontyev, I. V., and Sulimov, V. B. (2005) J. Phys. Chem. A, 109, 6939.
25. Huang, D. M., Geissler, P. L., and Chandler, D. (2001) J. Phys. Chem. B, 105, 6704-6709.
26. Grigoriev, I. S., and Meilikhov, E. Z. (eds.) (1991) Physical Values [in Russian], Energoatomizdat.
27. Meissner, T., and Wentz, F. J. (2004) IEEE Trans. Geosci. Remote Sensing, 42, 1836-1849.
28. Klotz, I. M. (1997) Ligand-Receptor Energetics, Jonh Wiley & Sons Inc., N. Y.
29. Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., and Bourne, P. E. (2000) Nucleic Acids Res., 28, 235-242.
30. Word, J. M. (1999) J. Mol. Biol., 285, 1735-1747.
31. Dullwebwr, F., Stubbs, M. T., Musil, D., Sturzebecher, J., and Klebe, G. (2001) J. Mol. Biol., 313, 593-614.
32. Nikitina, E. A., Sulimov, V. B., Zayets, V., and Zaitseva, N. (2004) Int. J. Quantum Chem., 97, 747-763.
33. Eckert, H., and Bajorath, J. (2007) Drug Discovery Today, 12, 225-233.
34. Nikitina, E. A., Sulimov, V. B., Grigoriev, F. V., Kondakova, O. A., and Luschekina, S. V. (2006) Int. J. Quantum Chem., 106, 1943-1963.