Absolute binding free energies: A quantitative approach for their calculation

Journal of Physical Chemistry B

Volumn 107, Issue 35, 2003, Pages 9535-9551

  Boresch, Stefan ^a   Tettinger, Franz ^a   Leitgeb, Martin ^a   Karplus, Martin ^b,c  

^a UNIVERSITY OF VIENNA   (Austria)

^b UNIVERSITÉ LOUIS PASTEUR   (France)

^c HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BENZENE; CALCULATIONS; COMPUTER SIMULATION; CONVERGENCE OF NUMERICAL METHODS; ENTROPY; FREE ENERGY; MOLECULAR DYNAMICS; PHASE COMPOSITION;

ABSOLUTE BINDING AFFINITIES; HARMONIC RESTRAINTS; LIGAND-RECEPTOR INTERACTIONS; ROTATIONAL ENTROPY; THERMODYNAMIC CYCLE; TRANSLATIONAL ENTROPY;

BINDING ENERGY;

EID: 0141682863     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp0217839     Document Type: Article

References (82)

1. Kollman, P. Chem. Rev. 1993, 93, 2395-2417.
2. Simonson, T.; Archontis, G.; Karplus, M. Acc. Chem. Res. 2002, 35, 430-437.
3. Kollman, P. A. Acc. Chem. Res. 1996, 29, 461-469.
4. Straatsma, T. P. Free Energy by Molecular Simulation. In Reviews in Computational Chemistry, Vol. 9; Lipkowitz, K. B., Boyd, D. B., Eds.; VCH: New York, 1996.
5. Henchman, R. H.; Essex, J. W. J. Comput. Chem. 1998, 20, 499-510.
6. Miller, J. L.; Kollman, P. A. J. Phys. Chem. 1996, 100, 8587-8594.
7. Lau, F. T. K.; Karplus, M. J. Mol. Biol. 1994, 236, 1049-1066.
8. Lamb, M. L.; Jorgensen, W. L. J. Med. Chem. 1998, 41, 3928-3939.
9. Archontis, G.; Simonson, T.; Karplus, M. J. Mol. Biol. 2001, 306, 307-327.
10. Koichi, T.; Shimizu, K. J. Phys. Chem. B 1998, 102, 6419-6424.
11. Tembe, B. L.; McCammon, J. A. Comput. Chem. 1984, 8, 281-283.
12. Boyer, P. D. Annu. Rev. Biochem. 1997, 66, 717-749.
13. Abrahams, J. P.; Leslie, A. G. W.; Lutter, R.; Walker, J. E. Nature 1994, 370, 621-648.
14. Yang, W.; et al. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 874-879.
15. Pranata, J.; Jorgensen, W. L. Tetrahedron 1991, 47, 2491-2501.
16. Jorgensen, W. L.; Buckner, J. K.; Boudon, S.; Tirado-Rives, J. J. Chem. Phys. 1988, 89, 3742-3746.
17. Merz, K. M., Jr. J. Am. Chem. Soc. 1991, 113, 406-411.
18. Miyamoto, S.; Kollman, P. A. J. Am. Chem. Soc. 1992, 114, 3668-3674.
19. Sneddon, S. F.; Tobias, D. J.; Brooks, C. L., III. J. Mol. Biol. 1989, 209, 817-820.
20. Miyamoto, S.; Kollman, P. A. Proteins: Struct., Funct., Genet. 1993, 16, 226-245.
21. Miyamoto, S.; Kollman, P. A. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 8402-8406.
22. Helms, V.; Wade, R. C. Biophys. J. 1995, 69, 810-824.
23. Sun, Y.; Kollman, P. A. J. Am. Chem. Soc. 1995, 117, 3599-3604.
24. Mordasini Denti, T. Z.; van Gunsteren, W. F.; Diederich, F. J. Am. Chem. Soc. 1996, 118, 6044-6051.
25. Dixit, S. B.; Chipot, C. J. Phys. Chem. A 2001, 105, 9795-9799.
26. Roux, B.; Nina, M.; Pomes, R.; Smith, J. C. Biophys. J. 1996, 71, 670-681.
27. Gilson, M. K.; Given, J. A.; Bush, B. L.; McCammon, J. A. Biophys. J. 1997, 72, 1047-1069.
28. Hermanns, J.; Wang, L. J. Am. Chem. Soc. 1997, 119, 2707-2714.
29. Göpel, W.; Wiemhöfer, H.-D. Statistische Thermodynamik; Spektrum; Heidelberg, Berlin, 2000.
30. Boresch, S.; Karplus, M. J. Chem. Phys. 1996, 105, 5145-5154.
31. Boresch, S.; Karplus, M. J. Phys. Chem. A 1999, 103, 103-118.
32. Hermans, J.; Shankar, S. Isr. J. Chem. 1986, 27, 225-227.
33. Zhang, L.; Hermans, J. Proteins: Struct., Funct., Genet. 1996, 24, 433-438.
34. Mann, G.; Hermans, J. J. Mol. Biol. 2000, 302, 979-989.
35. Hermans, J.; Yun, R. H.; Anderson, A. G. J. Comput. Chem. 1992, 13, 429-442.
36. Helms, V.; Wade, R. C. Proteins: Struct., Funct., Genet. 1998, 32, 381-396.
37. Morton, A.; Baase, W. A.; Matthews, B. W. Biochemistry 1995, 34, 8564-8575.
38. Fersht, A. R.; Jakes, R. Biochemistry 1975, 14, 3350-3356.
39. Wells, T. N. C.; Knill-Jones, J. W.; Gray, T. E.; Fersht, A. R. Biochemistry 1991, 30, 5151-5156.
40. Doty, P.; Myers, G. Discuss. Faraday Soc. 1953, 13, 51-58.
41. Steinberg, I. Z.; Scheraga, H. A. J. Biol. Chem. 1963, 238, 172-181.
42. Searle, M. S.; Williams, D. H. J. Am. Chem. Soc. 1992, 114, 10690-10697.
43. Horton, N.; Lewis, M. Prot. Sci. 1992, 1, 169-181.
44. Spolar, R. S.; Record, M. T., Jr. Science 1994, 263, 777-784.
45. Tidor, B.; Karplus, M. J. Mol. Biol. 1994, 238, 405-414.
46. Murphy, K.P.; Xie, D.; Thompson, K.S.; Amzel, L. M.; Freire, E. Proteins: Struct., Funct., Genet. 1994, 18, 63-67.
47. Janin, J. Proteins: Struct., Funct., Genet. 1995, 21, 30-39.
48. Holtzer, A. Biopolymers 1995, 35, 595-602.
49. Baginski, M.; Fogolari, F.; Briggs, J. M. J. Mol. Biol. 1997, 274, 253-267.
50. Amzel, L. M. Proteins: Struct., Funct., Genet. 1997, 28, 144-149.
51. Ben-Tal, B.; Honig, B.; Bagdassarian, C. K.; Ben-Shaul, A. Biophys. J. 2000, 79, 1180-118.
52. McQuarrie, D. A. Statistical Mechanics; Harper & Row: New York, 1976.
53. Torrie, G. M.; Valleau, J. P. Statistical Mechanics. Part A: Equilibrium Techniques; Plenum Press: New York, London, 1977.
54. Brooks, C. L., III; Karplus, M.; Pettit, B. M. Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics. In Advances in Chemical Physics, Vol. LXXI; Wiley: New York, 1988.
55. DeVoe, H. Theory of the Conformations of Biological Macromolecules in Solution. In Structure and Stability of Biological Macromolecules; Timascheff, S. N., Fasman, G. D., Eds.; Dekker: New York, 1969.
56. Go, N.; Scheraga, H. A. Macromolecules 1976, 9, 535-542.
57. Herschbach, D. R.; Johnston, H. S.; Rapp, D. J. Chem. Phys. 1959, 31, 1652-1661.
58. Knox, J. H. Molecular Thermodynamics; John Wiley & Sons: New York, 1978.
59. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M., Jr.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J. Am. Chem. Soc. 1995, 117, 5179-5197.
60. MacKerell, A. D., Jr.; et al. J. Phys. Chem. B 1998, 102, 3586-3616.
61. Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. J. Am. Chem. Soc. 1996, 118, 11225-11236.
62. Shobana, S.; Roux, B.; Andersen, O. S. J. Phys. Chem. B 2000, 104, 5179-5190.
63. Boresch, S. Mol. Simul. 2002, 28, 13-37.
64. Boresch, S.; Karplus, M. J. Phys. Chem. A 1999, 103, 119-136.
65. Ben-Naim, A. Statistical Thermodynamics for Chemists and Biochemists; Plenum: New York, 1992.
66. Minton, A. P. Curr. Opin. Struct. Biol. 2000, 10, 34-39.
67. Ellis, R. J. Curr. Opin. Struct. Biol. 2001, 11, 114-119.
68. Moore, W. J. Physical Chemistry, 5 ed.; Longman: London, 1972.
69. Janin, J. Proteins: Struct., Funct., Genet. 1996, 24, i-ii.
70. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187-217.
71. Neria, E.; Fischer, S.; Karplus, M. J. Chem. Phys. 1996, 105, 1902-1921.
72. Lazaridis, T.; Karplus, M. Proteins: Struct., Funct., Genet. 1999, 35, 133-152.
73. Brooks, B. R.; Janežič, D.; Karplus, M. J. Comput. Chem. 1995, 16, 1522-1542.
74. Brooks, C. L., III; Karplus, M. J. Chem. Phys. 1983, 79, 6312-6325.
75. Zacharias, M.; Straatsma, T. P.; McCammon, J. A. J. Chem. Phys. 1994, 100, 9025-9031.
76. Beutler, T. C.; Mark, A. E.; van Schaik, R. C.; Gerber, P. R.; van Gunsteren, W. F. Chem. Phys. Lett. 1994, 222, 529-539.
77. Hoover, W. G. Phys. Rev. 1985, A31, 1695-1697.
78. Head, M. S.; Given, J. A.; Gilson, M. K. J. Phys. Chem. A 1997, 101, 1609-1618.
79. Kolossváry, I. J. Phys. Chem. A 1997, 101, 9900-9905.
80. Tamura, A.; Privalov, P. L. J. Mol. Biol. 1997, 273, 1048-1060.
81. Karplus, M.; Janin, J. Prot. Eng. 1999, 12, 185-186.
82. Kraulis, P. J. J. Appl. Crystallogr. 1991, 24, 946-950.