Fluctuation theory of molecular association and conformational equilibria

Journal of Chemical Physics

Volumn 135, Issue 1, 2011, Pages

  Jiao, Yuanfang ^a   Smith, Paul E ^a  

^a KANSAS STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CONFORMATIONAL EQUILIBRIUM; EQUILIBRIUM PROCESS; FLUCTUATION THEORY; GENERAL EXPRESSION; ISOTHERMAL COMPRESSIBILITY; LOCAL REGION; MOLAR HEAT CAPACITIES; MOLECULAR ASSOCIATIONS; MULTICOMPONENT MIXTURE; PROTEIN ASSOCIATIONS; PROTEIN DENATURATION;

CHEMICAL BONDS; COMPRESSIBILITY; COMPUTATIONAL METHODS; CONFORMATIONS; PROTEINS; SPECIFIC HEAT;

COMPUTER SIMULATION;

SOLVENT;

ARTICLE; CHEMICAL MODEL; CHEMISTRY; OSMOSIS; PRESSURE; SOLUTION AND SOLUBILITY; THERMODYNAMICS;

MODELS, CHEMICAL; OSMOSIS; PRESSURE; SOLUTIONS; SOLVENTS; THERMODYNAMICS;

EID: 79960217835     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3601342     Document Type: Article

References (65)

1. K. A. Dill, Biochemistry 29, 7133 (1990). 10.1021/bi00483a001 (Pubitemid 20230041)
2. J. F. Brandts, J. Am. Chem. Soc. 86, 4291 (1964). 10.1021/ja01074a013
3. A. Zipp and W. Kauzmann, Biochemistry 12, 4217 (1973). 10.1021/bi00745a028
4. C. Tanford, J. Am. Chem. Soc. 86, 2050 (1964). 10.1021/ja01064a028
5. V. A. Parsegian, R. P. Rand, N. L. Fuller, and D. C. Rau, Methods Enzymol. 127, 400 (1986). 10.1016/0076-6879(86)27032-9
6. F. Meersman, C. M. Dobson, and K. Heremans, Chem. Soc. Rev. 35, 908 (2006). 10.1039/b517761h (Pubitemid 44465576)
7. R. Liu, H. Barkhordarian, S. Emadi, C. B. Park, and M. R. Sierks, Neurobiol. Dis. 20, 74 (2005). 10.1016/j.nbd.2005.02.003 (Pubitemid 41219204)
8. S. Narayanan and B. Reif, Biochemistry 44, 1444 (2005). 10.1021/bi048264b (Pubitemid 40204388)
9. D. K. Klimov, J. E. Straub, and D. Thirumalai, Proc. Natl. Acad. Sci. U.S.A. 101, 14760 (2004). 10.1073/pnas.0404570101 (Pubitemid 39410748)
10. D. R. Canchi, D. Paschek, and A. E. Garcia, J. Am. Chem. Soc. 132, 2338 (2010). 10.1021/ja909348c
11. D. E. Shaw, P. Maragakis, K. Lindorff-Larsen, S. Piana, R. O. Dror, M. P. Eastwood, J. A. Bank, J. M. Jumper, J. K. Salmon, Y. B. Shan, and W. Wriggers, Science 330, 341 (2010). 10.1126/science.1187409
12. P. Setny, R. Baron, and J. A. McCammon, J. Chem. Theory Comput. 6, 2866 (2010). 10.1021/ct1003077
13. L. V. Schafer, D. H. de Jong, A. Holt, A. J. Rzepiela, A. H. de Vries, B. Poolman, J. A. Killian, and S. J. Marrink, Proc. Natl. Acad. Sci. U.S.A. 108, 1343 (2011). 10.1073/pnas.1009362108
14. T. Lazaridis and M. Karplus, Biophys. Chem. 78, 207 (1999). 10.1016/S0301-4622(99)00022-8 (Pubitemid 29206667)
15. N. V. Prabhu and K. A. Sharp, Annu. Rev. Phys. Chem. 56, 521 (2005). 10.1146/annurev.physchem.56.092503.141202 (Pubitemid 41156887)
16. S. W. Rick, J. Phys. Chem. B 104, 6884 (2000). 10.1021/jp000841s
17. C. A. Royer, Biochim. Biophys. Acta-Protein Struct. Mol. Enzymol. 1595, 201 (2002). 10.1016/S0167-4838(01)00344-2 (Pubitemid 34442644)
18. V. M. Dadarlat and C. B. Post, J. Phys. Chem. B 105, 715 (2001). 10.1021/jp0024118 (Pubitemid 32159691)
19. E. Paci, Biochim. Biophys. Acta-Protein Struct. Mol. Enzymol. 1595, 185 (2002). 10.1016/S0167-4838(01)00343-0 (Pubitemid 34442643)
20. V. M. Dadarlat and C. B. Post, Biophys. J. 91, 4544 (2006). 10.1529/biophysj.106.087726 (Pubitemid 44904239)
21. A. Cooper, Proc. Natl. Acad. Sci. U.S.A. 73, 2740 (1976). 10.1073/pnas.73.8.2740
22. C. Scharnagl, M. Reif, and J. Friedrich, Biochim. Biophys. Acta-Proteins Proteomics 1749, 187 (2005). 10.1016/j.bbapap.2005.03.002
23. A. Wallqvist, D. G. Covell, and D. Thirumalai, J. Am. Chem. Soc. 120, 427 (1998). 10.1021/ja972053v (Pubitemid 28062530)
24. B. J. Bennion and V. Daggett, Proc. Natl. Acad. Sci. U.S.A. 100, 5142 (2003). 10.1073/pnas.0930122100 (Pubitemid 36542672)
25. P. J. Rossky, Proc. Natl. Acad. Sci. U.S.A. 105, 16825 (2008). 10.1073/pnas.0809224105
26. L. Hua, R. H. Zhou, D. Thirumalai, and B. J. Berne, Proc. Natl. Acad. Sci. U.S.A. 105, 16928 (2008). 10.1073/pnas.0808427105
27. V. Pierce, M. Kang, M. Aburi, S. Weerasinghe, and P. E. Smith, Cell Biochem. Biophys. 50, 1 (2008). 10.1007/s12013-007-9005-0
28. S. Shimizu, Proc. Natl. Acad. Sci. U.S.A. 101, 1195 (2004). 10.1073/pnas.0305836101 (Pubitemid 38182665)
29. P. E. Smith, J. Phys. Chem. B 108, 18716 (2004). 10.1021/jp0474879
30. I. L. Shulgin and E. Ruckenstein, J. Chem. Phys. 123, 054909 (2005). 10.1063/1.2011388 (Pubitemid 41203940)
31. E. Ruckenstein and I. L. Shulgin, Adv. Colloid Interface Sci. 123, 97 (2006). 10.1016/j.cis.2006.05.018 (Pubitemid 44665823)
32. I. L. Shulgin and E. Ruckenstein, Biophys. J. 90, 704 (2006). 10.1529/biophysj.105.074112
33. J. Rosgen, B. M. Pettitt, and D. W. Bolen, Protein Sci. 16, 733 (2007). 10.1110/ps.062671607 (Pubitemid 46507002)
34. J. G. Kirkwood and F. P. Buff, J. Chem. Phys. 19, 774 (1951). 10.1063/1.1748352
35. J. P. O'Connell, Mol. Phys. 20, 27 (1971). 10.1080/00268977100100031
36. A. Ben-Naim, Molecular Theory of Solutions (Oxford University Press, New York, 2006).
37. E. Matteoli and G. A. Mansoori, Fluctuation Theory of Mixtures (Taylor Francis, New York, 1990).
38. F. P. Buff and R. Brout, J. Chem. Phys. 23, 458 (1955). 10.1063/1.1742010
39. P. G. Debenedetti, J. Chem. Phys. 87, 1256 (1987). 10.1063/1.453308
40. P. G. Debenedetti, J. Chem. Phys. 86, 7126 (1987). 10.1063/1.452362
41. P. G. Debenedetti, J. Chem. Phys. 88, 2681 (1988). 10.1063/1.453996
42. P. G. Debenedetti, Mol. Simul. 2, 33 (1989). 10.1080/08927028908032782
43. E. A. Ploetz and P. E. Smith, Local fluctuations in solution mixtures., J. Chem. Phys. (submitted).
44. S. Shimizu and C. L. Boon, J. Chem. Phys. 121, 9147 (2004). 10.1063/1.1806402
45. M. Aburi and P. E. Smith, J. Chem. Phys. B 108, 7382 (2004). 10.1021/jp036582z
46. R. L. Perry, J. C. Telotte, and J. P. O'Connell, Fluid Phase Equilib. 5, 245 (1981). 10.1016/0378-3812(80)80060-4
47. R. L. Perry and J. P. O'Connell, Mol. Phys. 52, 137 (1984). 10.1080/00268978400101111
48. A. Ben-Naim, J. Chem. Phys. 63, 2064 (1975). 10.1063/1.431544
49. M. B. Gee and P. E. Smith, J. Chem. Phys. 131, 165101 (2009). 10.1063/1.3253299
50. K. E. Newman, Chem. Soc. Rev. 23, 31 (1994). 10.1039/cs9942300031
51. M. Kang and P. E. Smith, J. Chem. Phys. 128, 244511 (2008). 10.1063/1.2943318
52. P. E. Smith, J. Chem. Phys. 129, 124509 (2008). 10.1063/1.2982171
53. D. J. Adams, Mol. Phys. 29, 307 (1975). 10.1080/00268977500100221
54. T. Imai and Y. Sugita, J. Phys. Chem. B 114, 2281 (2010). 10.1021/jp909701j
55. P. E. Smith, J. Phys. Chem. B 110, 2862 (2006). 10.1021/jp056100e (Pubitemid 43342882)
56. R. F. Greene Jr and C. N. Pace, J. Biol. Chem. 249, 5388 (1974).
57. G. I. Makhatadze, J. Phys. Chem. B 103, 4781 (1999). 10.1021/jp990413q
58. P. E. Pjura, M. E. Paulaitis, and A. M. Lenhoff, AIChE J. 41, 1005 (1995). 10.1002/aic.690410431
59. S. Weerasinghe and P. E. Smith (unpublished).
60. H. J. C. Berendsen, J. R. Grigera, and T. P. Straatsma, J. Phys. Chem. 91, 6269 (1987). 10.1021/j100308a038
61. G. I. Makhatadze, G. M. Clore, and A. M. Gronenborn, Nat. Struct. Biol. 2, 852 (1995). 10.1038/nsb1095-852
62. K. E. Prehoda, E. S. Mooberry, and J. L. Markley, Biochemistry 37, 5785 (1998). 10.1021/bi980384u (Pubitemid 28196729)
63. H. Shiio, T. Ogawa, and H. Yoshihashi, J. Am. Chem. Soc. 77, 4980 (1955). 10.1021/ja01624a008
64. K. Gekko and H. Noguchi, J. Phys. Chem. 83, 2706 (1979). 10.1021/j100484a006
65. K. Gekko and Y. Hasegawa, Biochemistry 25, 6563 (1986). 10.1021/bi00369a034