Temperature dependence of three-body hydrophobic interactions: Potential of mean force, enthalpy, entropy, heat capacity, and nonadditivity

Journal of the American Chemical Society

Volumn 127, Issue 1, 2005, Pages 303-316

  Moghaddam, Maria Sabaye ^b   Shimizu, Seishi ^a   Hue, Sun Chan ^b  

^a UNIVERSITY OF YORK   (United Kingdom)

^b NONE

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; ENTHALPY; ENTROPY; METHANE; PRESSURE EFFECTS; PROTEINS; SOLVENTS; SPECIFIC HEAT; THERMAL EFFECTS;

CONFORMATION COMPACTNESS; DESOLVATION BARRIERS; HYDROPHOBIA INTERACTIONS; NONPOLAR SURFACE AREA;

HYDROPHOBICITY;

METHANE; POLYMER; WATER;

ARTICLE; CONFORMATIONAL TRANSITION; ENTHALPY; ENTROPY; FORCE; HEAT; HYDROPHOBICITY; MATHEMATICAL ANALYSIS; PROTEIN FOLDING; TEMPERATURE DEPENDENCE;

ENTROPY; HYDROPHOBICITY; METHANE; PROTEIN FOLDING; TEMPERATURE;

EID: 11844285690     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja040165y     Document Type: Article

References (108)

1. Kauzmann, W. Adv. Protein Chem. 1959, 14, 1-63.
2. Tanford, C. The Hydrophobic Effect: Formation of Micelles and Biological Membranes; Wiley: New York, 1980.
3. Ben-Naim, A. Hydrophobic Interactions; Plenum: Oxford, 1980.
4. Dill, K. A. Biochemistry 1990, 29, 7133-7155.
5. Blokzijl, W.; Engberts, J. B. F. N. Angew. Chem., Int. Ed. Engl. 1993, 32, 1545-1579.
6. Chan, H. S.; Dill, K. A. Annu. Rev. Biophys. Biomol. Struct. 1997, 26, 425-459.
7. Scheraga, H. A. J. Biomol. Struct. Dyn. 1998, 16, 447-460.
8. Hummer, G.; Garde, S.; Garcia, A. E.; Pratt, L. E. Chem. Phys. 2000, 258, 349-370.
9. Southall, N. T.; Dill, K. A.; Haymet, A. D. J. J. Phys. Chem. B 2002, 106, 521-533; 2002, 106, 2812 (correction).
10. Southall, N. T.; Dill, K. A.; Haymet, A. D. J. J. Phys. Chem. B 2002, 106, 521-533; 2002, 106, 2812 (correction).
11. Pratt, L. R. Annu. Rev. Phys. Chem. 2002, 53, 409-436.
12. Widom, B.; Bhimalapuram, P.; Koga, K. Phys. Chem. Chem. Phys. 2003, 5, 3085-3093.
13. Baldwin, R. L. Proc. Natl. Acad. Sci. U.S.A. 1986, 83, 8069-8072.
14. Makhatadze, G. I.; Privalov, P. L. Adv. Protein Chem. 1995, 47, 307-425.
15. Myers, J. K.; Pace, C. N.; Scholtz, J. M. Protein Sci. 1995, 4, 2138-2148.
16. Lee, B.; Richards, F. M. J. Mol. Biol. 1971, 55, 379-400.
17. Richards, F. M. Annu. Rev. Biophys. Bioeng. 1977, 6, 151-176.
18. Roux, B.; Simonson, T. Biophys. Chem. 1999, 78, 1-20 and references therein.
19. Feig, M.; Brooks, C. L., III. Curr. Opin. Struct. Biol. 2004, 14, 217-224 and references therein.
20. De Los Rios, P.; Caldarelli, G. Phys. Rev. E 2000, 62, 8449-8452.
21. Bedeaux, D.; Koper, J. M.; Ispolatov, I.; Widom, B. Physica A 2001, 291, 39-48.
22. Salvi, G.; De Los Rios, P. Phys. Rev. Lett. 2003, 91, 258102.
23. Pratt, L. R.; Chandler, D. J. Chem. Phys. 1977, 67, 3683-3704.
24. Wood, R. H.; Thompson. P. T. Proc. Natl. Acad. Sci. U.S.A. 1990, 87, 946-949.
25. Geiger, A.; Rahman, A.; Stillinger, F. H. J. Chem. Phys. 1979, 70, 263-276.
26. Pangali, C.; Rao, M.; Berne, B. J. J. Chem. Phys. 1979, 71, 2982-2990.
27. Shimizu, S.; Chan, H. S. J. Chem. Phys. 2000, 113, 4683-4700; 2002, 116, 8636 (erratum).
28. Shimizu, S.; Chan, H. S. J. Chem. Phys. 2000, 113, 4683-4700; 2002, 116, 8636 (erratum).
29. Shimizu, S.; Chan, H. S. Proteins 2002, 48, 15-30; 2002, 49, 294 (erratum).
30. Shimizu, S.; Chan, H. S. Proteins 2002, 48, 15-30; 2002, 49, 294 (erratum).
31. Cheung, M. S.; Garcia, A. E.; Onuchic, J. N. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 685-690.
32. Kaya, H.; Chan, H. S. J. Mol. Biol. 2003, 326, 911-931; 2004, 337, 1069 (corrigendum).
33. Kaya, H.; Chan, H. S. J. Mol. Biol. 2003, 326, 911-931; 2004, 337, 1069 (corrigendum).
34. Masunov, A.; Lazaridis, T. J. Am. Chem. Soc. 2003, 125, 1722-1730.
35. Zhou, R. H. Proteins 2003, 53, 148-161.
36. Guo, W.; Lampoudi, S.; Shea, J.-E. Proteins 2004, 55, 395-406.
37. Shimizu S.; Chan, H. S. J. Am. Chem. Soc. 2001, 123, 2083-2084.
38. Shimizu, S.; Chan, H. S. Proteins 2002, 49, 560-566.
39. Chan, H. S. Proteins 2000, 40, 543-571.
40. Chan, H. S.; Shimizu, S.; Kaya, H. Methods Enzymol. 2004, 380, 350-379.
41. Lee, C. Y.; McCammon, J. A.; Rossky, P. J. J. Chem. Phys. 1984, 80, 4448-4455.
42. Lum, K.; Chandler, D.; Weeks, J. D. J. Phys. Chem. B 1999, 103, 4570-4577.
43. Southall, N. T.; Dill, K. A. J. Phys. Chem. B 2000, 104, 1326-1331.
44. Southall, N. T.; Dill, K. A. Biophys. Chem. 2002, 101, 295-307.
45. Leung, K.; Luzar, A.; Bratko, D. Phys. Rev. Lett. 2003, 90, 065502.
46. Huang, X.; Margulis, C. J.; Berne, B. J. J. Phys. Chem. B 2003, 107, 11742-11748.
47. Mountain, R. D.; Thirumalai, D. J. Am. Chem. Soc. 2003, 125, 1950-1957.
48. Collet, O.; Chipot, C. J. Am. Chem. Soc. 2003, 125, 6573-6580.
49. Rank, J. A.; Baker, D. Protein Sci. 1997, 6, 347-354.
50. Tsai, J.; Gerstein, M.; Levitt, M. Protein Sci. 1997, 6, 2606-2616.
51. Martorana, V.; Bulone, D.; San Biagio, P. L.; Palma-Vittorelli, M. B.; Palma, M. U. Biophys. J. 1997, 73, 31-37.
52. Czaplewski, C.; Rodziewicz-Motowidlo, S.; Liwo, A.; Ripoll, D. R.; Wawak, R. J.;Scheraga, H. A. Protein Sci. 2000, 9, 1235-1245.
53. Shimizu, S.; Chan, H. S. J. Chem. Phys. 2001, 115, 1414-1421.
54. Raschke, T. M.; Tsai, J.; Levitt, M. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 5965-5969.
55. Czaplewski, C.; Rodziewicz-Motowidlo, S.; Liwo, A.; Ripoll, D. R.; Wawak, R. J.; Scheraga, H. A. J. Chem. Phys. 2002, 116, 2665-2667.
56. Shimizu, S.; Chan, H. S. J. Chem. Phys. 2002, 116, 2668-2669.
57. Czaplewski, C.; Ripoll, D. R.; Liwo, A.; Rodziewicz-Motowidlo, S.; Wawak, R. J.; Scheraga, H. A. Int. J. Quantum Chem. 2002, 88, 41-45.
58. Yang, H. B.; Elcock, A. H. J. Am. Chem. Soc. 2003, 125, 13968-13969.
59. Ghosh, T.; Garcia, A. E.; Garde, S. J. Phys. Chem. B 2003, 107, 612-617.
60. Czaplewski, C.; Rodziewicz-Motowidlo, S.; Dabal, M.; Ripoll, D. R.; Scheraga, H. A. Biophys. Chem. 2003, 105, 339-359.
61. Garcia-Mira, M. M.; Sadqi, M.; Fischer, N.; Sanchez-Ruiz, J. M.; Muñoz, V. Science 2002, 298, 2191-2195.
62. Scalley-Kim, M.; Baker, D. J. Mol. Biol. 2004, 338, 573-583.
63. Plotkin, S. S.; Wang, J.; Wolynes, P. G. J. Chem. Phys. 1997, 106, 2932-2948.
64. Takada, S.; Luthey-Schulten, Z.; Wolynes, P. G. J. Chem. Phys. 1999, 110, 11616-11629.
65. Kaya, H.; Chan, H. S. Proteins 2000, 40, 637-661; 2001, 43, 523 (erratum).
66. Kaya, H.; Chan, H. S. Proteins 2000, 40, 637-661; 2001, 43, 523 (erratum).
67. Kaya, H.; Chan, H. S. Phys. Rev. Lett. 2000, 85, 4823-4826.
68. Eastwood, M. P.; Wolynes, P. G. J. Chem. Phys. 2001, 114, 4702-4716.
69. Pokarowski, P.; Kolinski, A.; Skolnick, J. Biophys. J. 2003, 84, 1518-1526.
70. Widom, B. J. Chem. Phys. 1963, 39, 2808-2812.
71. Forsman, J.; Jönsson, B. J. Chem. Phys. 1994, 101, 5116-5125.
72. Sturtevant, J. M. Proc. Natl. Acad. Sci. U.S.A. 1977, 74, 2236-2240.
73. Privalov, P. L.; Gill, S. J. Adv. Protein Chem. 1988, 39, 191-234.
74. Makhatadze, G. I.; Privalov, P. L. J. Mol. Biol. 1990, 275, 375-384.
75. Murphy, K. P.; Freire, E. Adv. Protein Chem. 1992, 43, 313-361.
76. Spolar, R. S.; Livingstone, J. R.; Record, M. T. Biochemistry 1992, 31, 3947-3955.
77. Gomez, J.; Hilser, V. J.; Xie, D.; Freire, E. Proteins 1995, 22, 404-412.
78. Loladze, V. V.; Ermolenko, D. N.; Makhatadze, G. I. Protein. Sci. 2001, 10, 1343-1352.
79. Rick, S. W. J. Phys. Chem. B 2000, 104, 6884-6888.
80. Ghosh, T.; Garcia, A. E.; Garde, S. J. Chem. Phys. 2002, 116, 2480-2486.
81. Rick, S. W. J. Phys. Chem. B 2003, 107, 9853-9857.
82. Paschek, D. J. Chem. Phys. 2004, 120, 6674-6690.
83. Paschek, D. J. Chem. Phys. 2004, 120, 10605-10617.
84. Jorgensen, W. L. BOSS, Version 4.1; Yale University: New Haven, CT, 1999.
85. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926-935.
86. Leikin, S.; Parsegian, V. A.; Rau, D. C.; Rand, R. P. Annu. Rev. Phys. Chem. 1993, 44, 369-395.
87. For the two-methane PMF calculation we have conducted, wherein snapshots of water configurations were taken every 100 passes, the statistical inefficiency parameter s (see, e.g., Allen, M. P.; Tildesley, D. J. Computer Simulation of Liquids; Oxford University Press: Oxford, 1987) was determined to range from s ≈ 75 for low and intermediate T (below 328 K) to s ≈ 35 for high T (348, 368 K). It follows that, during the course of our simulation, water configuations become uncorrelated after roughly 4000-7000 passes of sampling.
88. 26 in units of kcal/mol, to be 2.11 ± 0.06 (278 K), 2.34 ± 0.05 (298 K), 2.48 ± 0.08 (313 K), 2.56 ± 0.06 (328 K), 2.69 ± 0.06 (348 K), and 2.71 ± 0.06 (368 K).
89. Rettich, T. R.; Handa, Y. P.; Battino, R.; Wilhelm E. J. Phys. Chem. 1981, 85, 3230-3237.
90. 2∂Δ(G/T)/∂T, etc. We have verified that thermodynamic quantities calculated using these two alternate methods from the data of Rettich et al. are consistent with each other.
91. Naghibi, H.; Dec, S. F.; Gill, S. J. J. Phys. Chem. 1986, 90, 4621-4623.
92. Morrison, T. J.; Billett, F. J. Chem. Soc. 1952, 3819-3822.
93. Glew, D. N. J. Phys. Chem. 1962, 66, 605-609.
94. It is clear from Figure 1 that different φ angles define physically different sets of relative positions for the three methanes. It should also be noted that, as in our previous studies, the PMF at a given ξ,φ is defined here by the free energy of insertion at a particular spatial position. By construction, this PMF does not involve entropic free energy associated with the multiplicity of methane spatial positions sharing a given ξ,φ. In other words, the present PMF contains no "cratic" contribution arising from the configurational degrees of freedom of the methane molecules.
95. Segawa, S.-I.; Sugihara, M. Biopolymers 1984, 23, 2473-2488.
96. Jackson, S. E.; Fersht, A. R. Biochemistry 1991, 30, 10428-10435.
97. Schindler, T.; Schmid, F. X. Biochemistry 1996, 35, 16833-16842.
98. Fernandez-Escamilla, A. M.; Cheung, M. S.; Vega, M. C.; Wilmanns, M.; Onuchic, J. N.; Serrano, L. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 2834-2839.
99. Day, R.; Bennion, B. J.; Ham, S.; Daggett, V. J. Mol. Biol. 2002, 322, 189-203.
100. 26,33,34 the feature of a positive two-methane desolvation heat capacity is confirmed.
101. Shortle, D. FASEB J. 1996, 10, 27-34.
102. Sosnick, T. R.; Trewhella, J. Biochemistry 1992, 31, 8329-8335.
103. Seshadri, S.; Oberg, K. A.; Fink, A. L. Biochemistry 1994, 33, 1351-1355.
104. Mok. Y. K.; Kay, C. M.; Kay, L. E.; Forman-Kay, J. J. Mol. Biol. 1999, 289, 619-638.
105. Nishii, I.; Kataoka, M.; Tokunaga, F.; Goto, Y. Biochemistry 1994, 33, 4903-4909.
106. Nishii, I.; Kataoka, M.; Goto, Y. J. Mol. Biol. 1995, 250, 223-238.
107. Hummer, G.; Garde, S.; Garcia, A. E.; Paulaitis, M. E.; Pratt, L. R. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 1552-1555.
108. We note that Ghosh et al.'s reported anti-cooperativity at the contact minimum and cooperativity at the desolvation barrier do not appear to add up to the values summarized in Table 2 above.