Computing free energy of a large-scale allosteric transition in adenylate kinase using all atom explicit solvent simulations

Journal of Physical Chemistry B

Volumn 116, Issue 5, 2012, Pages 1709-1715

  Potoyan, Davit A ^a,b   Zhuravlev, Pavel I ^a   Papoian, Garegin A ^a,b  

^a University of Maryland   (United States)

^b UNIVERSITY OF MARYLAND   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ENZYMES; PROTEINS;

ADENYLATE KINASE; ALLOSTERIC PROTEINS; ALLOSTERIC TRANSITION; CLOSED FORM; COMPUTATIONAL TECHNIQUE; ENERGY LANDSCAPE; ENERGY PROFILE; EXPLICIT SOLVENTS; FREE-ENERGY DIFFERENCE; LOWER DIMENSIONAL MANIFOLDS; NUMERICAL VALUES; PRIOR ESTIMATES; THEORETICAL APPROACH;

FREE ENERGY;

EID: 84856822956     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp209980b     Document Type: Article

References (48)

1. Frauenfelder, H. Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 5129-34
2. Frauenfelder, H.; Sligar, S. G.; Wolynes, P. G. Science 1991, 254, 1598-1603
3. Zhuravlev, P. I.; Papoian, G. A. Curr. Opt. Struct. Biol. 2010, 20, 16-20
4. Henzler-Wildman, K. A. Nature 2007, 450, 913-916
5. Fenimore, P. W.; Frauenfelder, H.; McMahon, B. H.; Young, R. D. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 14408-14413
6. Frauenfelder, H.; Parak, F. G.; Young, R. D. Annu. Rev. Biophys. Biochem. 1988, 17, 451-79
7. Levy, Y.; Cho, S. S.; Onuchic, J. N.; Wolynes, P. G. J. Mol. Biol. 2005, 346, 1121-1145
8. Zhuravlev, P. I.; Materese, C. K.; Papoian, G. A. J. Phys. Chem. B 2009, 113, 8800-12
9. Zhuravlev, P. I.; Papoian, G. A. Q. Rev. Biophys. 2010, 43, 295-332
10. Onuchic, J. N.; Luthey-Schulten, Z.; Wolynes, P. G. Annu. Rev. Phys. Chem. 1997, 48, 545-600
11. Kern, D.; Zuiderweg, E. R. P. Curr. Opt. Struct. Biol. 2003, 13, 748-57
12. Materese, C. K.; Goldmon, C. C.; Papoian, G. A. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 10659-10664
13. Makarov, D. E. Acc. Chem. Res. 2009, 42, 281-9
14. Müller, C. W.; Schulz, G. E. J. Mol. Biol. 1992, 224, 159-77
15. Kern, D.; Eisenmesser, E. Z.; Wolf-Watz, M. Methods Enzymol. 2005, 394, 507-24
16. Müller, C. W.; Schlauderer, G. J.; Reinstein, J.; Schulz, G. E. Structure 1996, 4, 147-56
17. Wolf-Watz, M.; Thai, V.; Henzler-Wildman, K.; Hadjipavlou, G.; Eisenmesser, E. Z.; Kern, D. Nat. Struct. Mol. Biol. 2004, 11, 945-9
18. Shapiro, Y. E.; Kahana, E.; Tugarinov, V.; Liang, Z.; Freed, J. H.; Meirovitch, E. Biochemistry 2002, 41, 6271-81
19. Shapiro, Y. E.; Meirovitch, E. J. Phys. Chem. B 2006, 110, 11519-24
20. Hanson, J. A.; Duderstadt, K.; Watkins, L. P.; Bhattacharyya, S.; Brokaw, J.; Chu, J.-W.; Yang, H. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 18055-60
21. Adén, J.; Wolf-Watz, M. J. Am. Chem. Soc. 2007, 129, 14003-12
22. Olsson, U.; Wolf-Watz, M. Nat. Commun. 2010, 1, 111
23. Miyashita, O.; Onuchic, J. N.; Wolynes, P. G. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 12570-5
24. Lu, Q.; Wang, J. J. Am. Chem. Soc. 2008, 130, 4772-83
25. Whitford, P. C.; Miyashita, O.; Levy, Y.; Onuchic, J. N. J. Mol. Biol. 2007, 366, 1661-71
26. Maragakis, P.; Spichty, M.; Karplus, M. Phys. Rev. Lett. 2006, 96, 100602
27. Daily, M. D.; Phillips, G. N.; Cui, Q. J. Mol. Biol. 2010, 400, 618-31
28. Jana, B.; Adkar, B. V.; Biswas, R.; Bagchi, B. J. Chem. Phys. 2011, 134, 035101
29. Arora, K.; Brooks, C. L. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 18496-501
30. Zhuravlev, P. I.; Wu, S.; Potoyan, D. A.; Rubinstein, M.; Papoian, G. A. Methods 2010, 52, 115-21
31. Banavali, N. K.; Roux, B. J. Am. Chem. Soc. 2005, 127, 6866-6876
32. Kollman, P. A. Acc. Chem. Res. 2000, 33, 889-97
33. Weis, A.; Katebzadeh, K.; Söderhjelm, P.; Nilsson, I.; Ryde, U. J. Med. Chem. 2006, 49, 6596-606
34. Vorobjev, Y. N.; Hermans, J. Protein Sci. 2001, 10, 2498-2506
35. Park, S.; Lau, A. Y.; Roux, B. J. Chem. Phys. 2008, 129, 134102
36. Adkar, B. V.; Jana, B.; Bagchi, B. J. Phys. Chem. A 2011, 115, 3691-7
37. Plotkin, S. S.; Wang,; Wolynes, P. G. Phys. Rev. E 1996, 53, 6271-6296
38. Phillips, J. C. J. Comput. Chem. 2005, 26, 1781-1802
39. MacKerell, A. D.; Banavali, N. K.; Foloppe, N. Biopolymers 2000, 56, 257-265
40. Plimpton, S. J. Comp. Phys. 1995, 117, 1
41. Portman, J.; S Takada, P. G. W. Phys. Rev. Lett. 1998, 23, 5237
42. Roe, D. R.; Okur, A.; Wickstrom, L.; Hornak, V.; Simmerling, C. J. Phys. Chem. B 2007, 111, 1846-57
43. Zhou, H.-X. Q. Rev. Biophys. 2010, 43, 219-93
44. Kubelka, J.; Hofrichter, J.; Eaton, W. A. Curr. Opt. Struct. Biol. 2004, 14, 76-88
45. Henzler-Wildman, K. A. Nature 2007, 450, 838-44
46. Kabsch, W; S., C. Biopolymers 1983, 22, 2577-637
47. Hammond, G. J. Am. Chem. Soc. 1955, 77, 334
48. Matthews, J. M.; Fersht, A. R. Biochemistry 1995, 34, 6805-14