Direct estimation of entropy loss due to reduced translational and rotational motions upon molecular binding

Biopolymers

Volumn 79, Issue 5, 2005, Pages 277-285

  Lu, Benzhuo ^a   Wong, Chung F ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF MISSOURI ST LOUIS   (United States)

Author keywords

Bound water; Molecular binding; Reduced Hessian matrix; Translational and rotational entropy loss

Indexed keywords

APPROXIMATION THEORY; DEGREES OF FREEDOM (MECHANICS); MOLECULAR STRUCTURE; MOLECULES; PARAMETER ESTIMATION; WATER;

BOUND WATER; MOLECULAR BINDING; REDUCED HESSIAN MATRIX; TRANSLATIONAL AND ROTATIONAL ENTROPY LOSS;

ENTROPY;

CYCLIC AMP DEPENDENT PROTEIN KINASE; WATER;

ARTICLE; BINDING AFFINITY; CALCULATION; COMPUTER AIDED DESIGN; ENTROPY; ENZYME BINDING; MOLECULAR INTERACTION; PROTEIN BINDING;

ADENOSINE TRIPHOSPHATE; CYCLIC AMP-DEPENDENT PROTEIN KINASES; ENTROPY; HEAT; KINETICS; LIGANDS; MODELS, MOLECULAR; MODELS, STATISTICAL; MOLECULAR CONFORMATION; PEPTIDES; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; THERMODYNAMICS;

EID: 30444451191     PISSN: 00063525     EISSN: 10970282     Source Type: Journal    
DOI: 10.1002/bip.20344     Document Type: Article

References (30)

1. Gilson, M. K.; Given, J. A.; Bush, B. L.; McCammon, J. A. Biophys J 1997, 72, 1047-1069.
2. Doty, P.; Myers, G. Discuss Faraday Soc 1953, 13, 51-58.
3. Page, M. I.; Jencks, W. P. Proc Natl Acad Sci U S A 1971, 68, 1678-1683.
4. Finkelstein, A. V.; Janin, J. Protein Eng 1989, 3, 1-3.
5. Tidor, B.; Karplus, M. J Mol Biol 1994, 238, 405-414.
6. Amzel, L. M. Proteins 1997, 28, 144-149.
7. Yu, Y. B.; Privalov, P. L.; Hodges, R. S. Biophys J 2001, 81, 1632-1642.
8. Lazaridis, T.; Masunov, A.; Gandolfo, F. Proteins 2002, 47, 194-208.
9. Karplus, M.; Janin, J. Protein Eng 1999, 12, 185-186.
10. Levy, R. M.; Karplus, M. Biopolymers 1979, 18, 2465-2495.
11. Brooks, B.; Karplus, M. Proc Natl Acad Sci U S A 1983, 80, 6571-6575.
12. Karplus, M.; Kushick, J. N. Macromolecules 1981, 14, 325-332.
13. Levy, R. M.; Karplus, M.; Kushick, J.; Perahia, D. Macromolecules 1984, 17, 1370-1374.
14. Schlitter, J. Chem Phys Lett 1993, 215, 617-621.
15. Luo, H.; Sharp, K. Proc Natl Acad. Sci U S A 2002, 99, 10399-10404.
16. Schafer, H.; Mark, A. E.; van Gunsteren, W. F. J Chem Phys 2000, 113, 7809-7817.
17. Swanson, J. M.; Henchman, R. H.; McCammon, J. A. Biophys J 2004, 86, 67-74.
18. Andricioaei, I.; Karplus, M. J Chem Phys 2001, 8, 6289-6292.
19. Wong, C. F.; Thacher, T.; Rabitz, H. Rev Comput Chem 1998, 12, 281-326.
20. Wong, C. F.; Zheng, C.; Shen, J.; McCammon, J. A.; Wolynes, P. G. J Phys Chem 1993, 97, 3100-3110.
21. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J Am Chem Soc 1995, 117, 5179-5197.
22. Meagher, K. L.; Redman, L. T.; Carlson, H. A. J Comput Chem 2003, 9, 1016-1025.
23. Shaltiel, S.; Cox, S.; Taylor, S. S. Proc Natl Acad Sci U S A 1998, 95, 484-491.
24. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. J Comput Phys 1977, 23, 327-341.
25. Hunenberger, P. H.; Helms, V.; Narayana, N.; Taylor, S. S.; McCammon, J. A. Biochemistry 1999, 38, 2358-2366.
26. Wong, C. F.; Hunenberger, P. H.; Akamine, P.; Narayana, N.; Diller, T.; McCammon, J. A.; Taylor, S. S.; Xuong, N. J. Med Chem 2001, 44, 1530-1539.
27. Lai, Y. S.; Mendoza, J. S.; Jagdmann, G. E., Jr.; Menaldino, D. S.; Biggers, C. K.; Heerding, J. M.; Wilson, J. W.; Hall, S. E.; Jiang, J. B.; Janzen, W. P.; Ballas, L. M. J Med Chem 1997, 40, 226-235.
28. Dunitz, J. D. Science 1994, 264, 670.
29. Fischer, S.; Smith, J. C.; Verma, C. S. J Phys Chem B 2001, 105, 8050-8055.
30. Yu, Y. H.; Lu, B. Z.; Han, J. G.; Zhang, P. F. J. Comput-Aided Mol Design 2004, 18, 251-260.