Elucidating the energetics of entropically driven protein-ligand association: Calculations of absolute binding free energy and entropy

Journal of Physical Chemistry B

Volumn 115, Issue 41, 2011, Pages 11902-11910

  Deng, Nan Jie ^a   Zhang, Peng ^b   Cieplak, Piotr ^c   Lai, Luhua ^b  

^a RUTGERS UNIVERSITY   (United States)

^b Peking University   (China)

^c BURNHAM INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ENTROPY; EXPERIMENTS; FREE ENERGY; LIGANDS; MOLECULAR DYNAMICS; PROTEINS;

BINDING FREE ENERGY; CONFORMATIONAL ENTROPY; CONVERGENCE PROBLEMS; DESOLVATION; ENTROPIC CONTRIBUTIONS; ENTROPIC EFFECTS; ENTROPY CHANGES; ENTROPY GAIN; EXPLICIT SOLVENTS; HIV-1 PROTEASE INHIBITORS; MOLECULAR DYNAMICS SIMULATIONS; NET ENTROPY; NON-POLAR; NONPOLAR INTERACTIONS; PROTEIN-LIGAND ASSOCIATION; SOLVENT RELEASE; STATISTICAL ERRORS; TEMPERATURE DEPENDENCE; VIBRATIONAL ENTROPY;

BINDING ENERGY;

EID: 80054680901     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp204047b     Document Type: Article

References (62)

1. Jorgensen, W. L. Science 2004, 303, 1813-1818
2. Gilson, M. K.; Zhou, H.-X. Annu. Rev. Biophys. Biomol. Struct. 2007, 36, 21-42
3. Jorgensen, W. L.; Buckner, J. K.; Boudon, S.; Tirado-Rives, J. J. Chem. Phys. 1988, 89, 3742
4. Roux, B.; Nina, M.; Pomes, R.; Smith, J. Biophys. J. 1996, 71, 670-681
5. Helms, V.; Wade, R. C. J. Am. Chem. Soc. 1998, 120, 2710-2713
6. Gilson, M.; Given, J.; Bush, B.; Mccammon, J. Biophys. J. 1997, 72, 1047-1069
7. Boresch, S.; Tettinger, F.; Leitgeb, M.; Karplus, M. J. Phys. Chem. B 2003, 107, 9535-9551
8. Hamelberg, D.; McCammon, J. A. J. Am. Chem. Soc. 2004, 126, 7683-7689
9. Fujitani, H.; Tanida, Y.; Ito, M.; Jayachandran, G.; Snow, C. D.; Shirts, M. R.; Sorin, E. J.; Pande, V. S. J. Chem. Phys. 2005, 123, 084108
10. Wang, J.; Deng, Y.; Roux, B. Biophys. J. 2006, 91, 2798-2814
11. Deng, Y.; Roux, B. J. Chem. Theory Comput 2006, 2, 1255-1273
12. Mobley, D. L.; Graves, A. P.; Chodera, J. D.; McReynolds, A. C.; Shoichet, B. K.; Dill, K. A. J. Mol. Biol. 2007, 371, 1118-1134
13. Mobley, D. L.; Chodera, J. D.; Dill, K. A. J. Chem. Phys. 2006, 125, 084902
14. Jiao, D.; Golubkov, P. A.; Darden, T. A.; Ren, P. Proc. Natl. Acad. Sci. 2008, 105, 6290-6295
15. Yu, H.; Rick, S. W. J. Am. Chem. Soc. 2009, 131, 6608-6613
16. Levy, R. M.; Gallicchio, E. Annu. Rev. Phys. Chem. 1998, 49, 531-567
17. Wan, S.; Stote, R. H.; Karplus, M. J. Chem. Phys. 2004, 121, 9539
18. Chang, C.-E.; Gilson, M. K. J. Am. Chem. Soc. 2004, 126, 13156-13164
19. Chen, J.; Brooks, C. L.; Scheraga, H. A. J. Phys. Chem. B 2008, 112, 242-249
20. Gallicchio, E.; Kubo, M. M.; Levy, R. M. J. Am. Chem. Soc. 1998, 120, 4526-4527
21. Kohl, N. Proc. Natl. Acad. Aci. U.S.A. 1988, 85, 4686-4690
22. Turner, B. G.; Summers, M. F. J. Mol. Biol. 1999, 285, 1-32
23. Wlodawer, A.; Vondrasek, J. Annu. Rev. Biophys. Biomol. Struct. 1998, 27, 249-284
24. Wlodawer, A. Annu. Rev. Med. 2002, 53, 595-614
25. Wang, W. Proc. Natl. Acad. Sci. 2001, 98, 14937-14942
26. Zoete, V.; Michielin, O.; Karplus, M. J. Comput. Aided Mol. Des. 2003, 17, 861-880
27. Lepšík, M.; Kříž, Z.; Havlas, Z. Proteins 2004, 57, 279-293
28. Thorsteinsdottir, H. B.; Schwede, T.; Zoete, V.; Meuwly, M. Proteins 2006, 65, 407-423
29. Wittayanarakul, K.; Hannongbua, S.; Feig, M. J. Comput. Chem. 2008, 29, 673-685
30. Kožíšek, M.; Bray, J.; Řezáč ová, P.; Šašková, K.; Brynda, J.; Pokorná, J.; Mammano, F.; Rulíšek, L.; Konvalinka, J. J. Mol. Biol. 2007, 374, 1005-1016
31. Ode, H.; Matsuyama, S.; Hata, M.; Neya, S.; Kakizawa, J.; Sugiura, W.; Hoshino, T. J. Mol. Biol. 2007, 370, 598-607
32. Åqvist, J.; Medina, C.; Samuelsson, J.-E. Protein Eng., Des. Sel. 1994, 7, 385-391
33. Srinivasan, J.; Cheatham, T. E.; Cieplak, P.; Kollman, P. A.; Case, D. A. J. Am. Chem. Soc. 1998, 120, 9401-9409
34. Stoica, I.; Sadiq, S. K.; Coveney, P. V. J. Am. Chem. Soc. 2008, 130, 2639-2648
35. Deng, N.-J.; Cieplak, P. Phys. Chem. Chem. Phys. 2009, 11, 4968
36. Simonson, T. In Computational biochemistry and biophysics; Marcel Dekker: New York, 2000.
37. Deng, Y.; Roux, B. J. Phys. Chem. B 2009, 113, 2234-2246
38. Velazquez-Campoy, A.; Todd, M. J.; Freire, E. Biochemistry 2000, 39, 2201-2207
39. Ohtaka, H.; Schön, A.; Freire, E. Biochemistry 2003, 42, 13659-13666
40. Shuman, C. F.; Hämäläinen, M. D.; Danielson, U. H. J. Mol. Recognit. 2004, 17, 106-119
41. Chang, C.; Chen, W.; Gilson, M. K. Proc. Natl. Acad. Sci. 2007, 104, 1534-1539
42. Carlsson, J.; Aqvist, J. Phys. Chem. Chem. Phys. 2006, 8, 5385
43. Beutler, T. Chem. Phys. Lett. 1994, 222, 529-539
44. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926
45. Case, D. A. AMBER 10; University of California: San Francisco, CA, 2008.
46. Hornak, V.; Abel, R.; Okur, A.; Strockbine, B.; Roitberg, A.; Simmerling, C. Proteins 2006, 65, 712-725
47. Wang, J.; Wolf, R. M.; Caldwell, J. W.; Kollman, P. A.; Case, D. A. J. Comput. Chem. 2004, 25, 1157-1174
48. Jakalian, A.; Bush, B. L.; Jack, D. B.; Bayly, C. I. J. Comput. Chem. 2000, 21, 132-146
49. Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. J. Chem. Theory Comput. 2008, 4, 435-447
50. Amb2gmx.pl; http://chemistry.csulb.edu/ffamber.
51. Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. J. Chem. Phys. 1995, 103, 8577
52. Ryckaert, J.; Ciccotti, G.; Berendsen, H. J. Comput. Phys. 1977, 23, 327-341
53. Mobley, D. L.; Chodera, J. D.; Dill, K. A. J. Chem. Theory Comput. 2007, 3, 1231-1235
54. Deng, N.; Zheng, W.; Gallicchio, E.; Levy, R. M. J. Am. Chem. Soc. 2011, 133, 9387-9394
55. Sadiq, S. K.; De Fabritiis, G. Proteins 2010, 78, 2873-2885
56. Robbins, A. H.; Coman, R. M.; Bracho-Sanchez, E.; Fernandez, M. A.; Gilliland, C. T.; Li, M.; Agbandje-McKenna, M.; Wlodawer, A.; Dunn, B. M.; McKenna, R. Acta Crystallogr. D Biol. Crystallogr. 2010, 66, 233-242
57. Maschera, B.; Darby, G.; Palú, G.; Wright, L. L.; Tisdale, M.; Myers, R.; Blair, E. D.; Furfine, E. S. J. Biol. Chem. 1996, 271, 33231-33235
58. Kaldor, S. W.; Kalish, V. J.; Davies, J. F.; Shetty, B. V.; Fritz, J. E.; Appelt, K.; Burgess, J. A.; Campanale, K. M.; Chirgadze, N. Y.; Clawson, D. K.; Dressman, B. A.; Hatch, S. D.; Khalil, D. A.; Kosa, M. B.; Lubbehusen, P. P.; Muesing, M. A.; Patick, A. K.; Reich, S. H.; Su, K. S.; Tatlock, J. H. J. Med. Chem. 1997, 40, 3979-3985
59. Gallicchio, E.; Kubo, M. M.; Levy, R. M. J. Phys. Chem. B 2000, 104, 6271-6285
60. Chandler, D. Nature 2005, 437, 640-647
61. Lazaridis, T.; Masunov, A.; Gandolfo, F. Proteins 2002, 47, 194-208
62. Swanson, J. M. J.; Henchman, R. H.; McCammon, J. A. Biophys. J. 2004, 86, 67-74