Absolute free energy of binding of avidin/biotin, revisited

Journal of Physical Chemistry B

Volumn 116, Issue 23, 2012, Pages 6628-6636

  General, Ignacio J ^a   Dragomirova, Ralitsa ^a   Meirovitch, Hagai ^a  

^a UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FREE ENERGY; GLYCOPROTEINS; MOLECULAR DYNAMICS;

BOUNDARY POTENTIALS; COMPUTATIONAL STUDIES; DECOUPLING METHODS; EXPERIMENTAL VALUES; FREE ENERGY OF BINDING; GENERALIZED SOLVENT BOUNDARY POTENTIALS; LIGAND BINDING; PARTICLE MESH EWALD; PERIODIC BOUNDARY CONDITIONS; STATISTICAL MECHANICAL METHODS; THERMODYNAMIC INTEGRATION;

COENZYMES;

EID: 84862271828     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp212276m     Document Type: Article

References (72)

1. Green, N. M. Adv. Protein Chem. 1975, 29, 85-133
2. Wilchek, M.; Bayer, E. A. Trends Biochem. Sci. 1989, 14, 408-412
3. Green, N. M. Avidin and streptavidin. In Methods in Enzymology; Wilchek, M.; Bayer, E. A., Eds.; Academic Press: London, 1990; Vol. 184, pp 51-67.
4. Bayer, E. A.; Wilcheck, M. Methods Biochem. Anal. 1980, 26, 1-45
5. Pugliese, L.; Coda, A.; Malcovati, M.; Bolognesi, M. J. Mol. Biol. 1993, 231, 698-710
6. Livnah, O.; Bayer, E. A.; Wilchek, M.; Sussman, J. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 5076-5080
7. Pugliese, L.; Malcovati, M.; Coda, A.; Bolognesi, M. J. Mol. Biol. 1994, 235, 42-46
8. Nardone, E.; Rosano, C.; Santambrogio, P.; Curnis, F.; Corti, A.; Magni, F.; Siccardi, A. G.; Paganelli, G.; Losso, R.; Apreda, B. Eur. J. Biochem. 1998, 256, 453-460
9. Repo, S.; Paldanius, T. A.; Hytönen, V. P.; Nyholm, T. K. M.; Halling, K. K.; Huuskonen, J.; Pentikäinen, O. T.; Rissanen, K.; Peter Slotte, J.; Airenne, T. T Chem. Biol. 2006, 13, 1029-1039
10. Chu, V.; Freitag, S.; Trong, I. L.; Stenkamp, R. E.; Stayton, P. S. Protein Sci. 1998, 7, 848-859
11. General, I. J.; Dragomirova, R.; Meirovitch, H. J. Phys. Chem. B 2011, 115, 168-175
12. Hermans, J.; Shankar, S. Isr. J. Chem. 1986, 27, 225-227
13. Jorgensen, W. L.; Buckner, J. K.; Boudon, S.; Tirado-Rives, J. J. Chem. Phys. 1988, 89, 3742-3746
14. Miyamoto, S.; Kollman, P. A. Proteins 1993, 16, 226-245
15. Gilson, M. K.; Given, J. A.; Bush, B. L.; McCammon, J. A. Biophys. J. 1997, 72, 1047-1069
16. Boresch, S.; Tettinger, F.; Leitgeb, M.; Karplus, M. J. Phys. Chem. B 2003, 107, 9535-9551
17. Zhou, H.-X.; Gilson, M. K. Chem. Rev. 2009, 109, 4092-4107
18. 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
19. 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, 084108-5
20. Deng, Y.; Roux, B. J. Phys. Chem. B 2009, 113, 2234-2246
21. Singh, N.; Warshel, A. Proteins 2010, 78, 1724-1735
22. Singh, N.; Warshel, A. Proteins 2010, 78, 1705-1723
23. Fujitani, H.; Tanida, Y.; Matsuura, A. Phys. Rev. E 2009, 79, 021914-12
24. Jayachandran, G.; Shirts, M. R.; Park, S.; Pande, V. S. J. Chem. Phys. 2006, 125, 084901-12
25. Hamelberg, D.; McCammon, J. A. J. Am. Chem. Soc. 2004, 126, 7683-7689
26. Mobley, D. L.; Chodera, J. D.; Dill, K. A. J. Chem. Theory Comput. 2007, 3, 1231-1235
27. Pohorille, A.; Jarzynski, C.; Chipot, C. J. Phys. Chem. B 2010, 114, 10235-10253
28. Mobley, D. L.; Dill, K. A. Structure 2009, 17, 489-498
29. Roux, B.; Nina, M.; Pomes, R.; Smith, J.C. Biophys. J. 1996, 71, 670-681
30. Hermans, J.; Wang, L. J. Am. Chem. Soc. 1997, 119, 2707-2714
31. Deng, Y.; Roux, B. J. Chem. Theory Comput. 2006, 2, 1255-1273
32. Chen, P.; Kuyucak, S. Biophys. J. 2009, 96, 2577-2588
33. Jiang, W.; Roux, B. J. Chem. Theory Comput. 2010, 6, 2559-2565
34. Woo, H-June; Roux, B. Proc. Natl. Acad. Sci USA 2005, 102, 6825-6830
35. Wang, J.; Dixon, R.; Kollman, P. A. Proteins 1999, 34, 69-81
36. Kuhn, B.; Kollman, P. A. J. Med. Chem. 2000, 43, 3786-3791
37. Genheden, S.; Ryde, U. J. Comput. Chem. 2010, 31, 837-846
38. Genheden, S.; Luchko, T.; Gusarov, S.; Kovalenko, A.; Ryde, U. J. Phys. Chem. B 2010, 114, 8505-8516
39. Tong, Y.; Mei, Y.; Li, Y. L.; Ji, C. G.; Zhang, J. Z. H. J. Am. Chem. Soc. 2010, 132, 5137-5142
40. White, R. P.; Meirovitch, H. J. Chem. Phys. 2004, 121, 10889-10904
41. White, R. P.; Meirovitch, H. J. Chem. Phys. 2005, 123, 214908-11
42. Cheluvaraja, S.; Meirovitch, H. J. Chem. Phys. 2005, 122, 054903-14
43. Cheluvaraja, S.; Meirovitch, H. J. Chem. Theory Comp. 2008, 4, 192-208
44. Cheluvaraja, S.; Mihailescu, M.; Meirovitch, H. J. Phys. Chem. B 2008, 112, 9512-9522
45. Mihailescu, M.; Meirovitch, H. J. Phys. Chem. B 2009, 113, 7950-7964
46. General, I. J.; Meirovitch, H. J. Chem. Phys. 2011, 134, 025104-17
47. Meirovitch, H. J. Mol. Recognit. 2010, 23, 153-172
48. General, I. J.; Dragomirova, R.; Meirovitch, H. J. Chem. Theory Comp. 2011, 7, 4196-4207
49. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926-935
50. Cornell, W. D.; Cieplak, P.; Bayly, C. L.; 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
51. Case, D. A.; Darden, T. A.; Cheatham, III, T. E.; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R; Walker, R. C.; Zhang, W.; Merz, K. M.; AMBER 11, University of California, San Francisco, 2010.
52. Darden, T. A.; York, D. M.; Pedersen, L. G. J. Chem. Phys. 1993, 98, 10089-92
53. Beglov, D.; Roux, B. J. Chem. Phys. 1994, 100, 9050-9063
54. Im, W.; Bernéche, S.; Roux, B. J. Chem. Phys. 2001, 114, 2924-2937
55. MacKerell, A. D., Jr.; Bashford, D.; Bellott, M.; Dumbrack, R. L., Jr.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D. J. Phys. Chem. B 1998, 102, 3586-3616
56. Izrailev, S.; Stepaniants, S.; Balsera, M.; Oono, Y.; Schulten, K. Biophys. J. 1997, 72, 1568-1581
57. Lazaridis, T.; Masunov, A.; Gandolfo, F. Proteins 2002, 47, 194-208
58. Donnini, S.; Mark, A. E.; Juffer, A. H.; Villa, A. J. Comput. Chem. 2005, 26, 115-122
59. Dixit, S. B.; Chipot, C. J. Phys. Chem. A 2001, 105, 9795-9799
60. Hnizdo, V.; Darian, E.; Fedorowicz, A.; Demchuk, E.; Li, S.; Singh, H. J. Comput. Chem. 2007, 28, 655-668
61. Killian, B. J.; Kravitz, J. Y.; Gilson, M. K. J. Chem. Phys. 2007, 127, 024107-16
62. Hnizdo, V.; Tan, J.; Killian, B. J.; Gilson, M. K. J. Comput. Chem. 2008, 29, 1605-1614
63. Wang, J.; Wolf, R.M.; Calldwell, J. W.; Kollman, P. A.; Case, D. A. J. Comput. Chem. 2004, 25, 1157-1174
64. Allen, M. P.; Tildesley, D. J. Computer simulation of liquids: Clarenden Press: Oxford, 1987.
65. Zacharias, M.; Straatsma, T. P.; McCammon, J. A. J. Chem. Phys. 1994, 100, 9025-9031
66. Steinbrecher, T.; Mobley, D. L.; Case, A. C. J. Chem. Phys. 2007, 127, 21410813
67. Warshel, A.; Sharma, P. K.; Kato, M.; Parson, W. W. Biochim. Biophys. Acta 2006, 1764, 1647-1676
68. King, E.; Warshel, A. J. Chem. Phys. 1989, 91, 3647-3661
69. Lee, F. S.; Chu, Z. T.; Warshel, A. J. Comput. Chem. 1993, 14, 161-185
70. Vanommeslaeghe, K; Hatcher, E.; Acharya, C.; Kundu, S.; Zhong, S.; Shim, J.; Darian, E.; Guvench, O.; Lopes, P.; Vorobyov, I.; Mackerel, A. D., Jr. J. Comput. Chem. 2010, 31, 671-690
71. Deng, Y.; Roux, B. J. Chem. Phys. 2008, 128, 115103-8
72. Mihailescu, M.; Meirovitch, H. Entropy 2010, 12, 1946-1974