Solvation: How to obtain microscopic energies from partitioning and solvation experiments

Annual Review of Biophysics and Biomolecular Structure

Volumn 26, Issue , 1997, Pages 425-459

  Chan, Hue Sun ^a   Dill, Ken A ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Flory Huggins; Hydrophobic effect; Partition coefficient; Polymer; Solvation parameter; Transfer experiment

Indexed keywords

ALKANE; BENZENE; CYCLOHEXANE; HEXADECANE; OCTANOL; OIL; POLYMER; SOLVENT; WATER;

ENTROPY; HYDROPHOBICITY; MOLECULAR INTERACTION; MOLECULAR MODEL; PARTITION COEFFICIENT; PRIORITY JOURNAL; REVIEW; SOLUBILITY; SOLVATION;

MOLECULAR CONFORMATION; OILS; POLYMERS; SOLUBILITY; SOLVENTS; THERMODYNAMICS; WATER;

EID: 0343274684     PISSN: 10568700     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.biophys.26.1.425     Document Type: Review

References (122)

1. Abraham MH, Sakellariou P. 1994. The Honig-Flory-Huggins combinatorial entropy correction - Is it valid for aqueous solutions? J. Chem. Soc. Perkin Trans. 2:405-6
2. Baker D, Chan HS, Dill KA. 1993. Coordinate-space formulation of polymer lattice cluster theory. J. Chem. Phys. 98:9951-62
3. Barbe M, Patterson D. 1978. Orientational order and excess entropies of alkane mixtures. J. Phys. Chem. 82:40-46
4. Barbe M, Patterson D. 1980. Thermodynamics of mixtures of hexane and heptane isomers with normal and branched hexadecane. J. Solut. Chem. 9:753-69
5. Bawendi MG, Freed KF. 1988. Systematic corrections to Flory-Huggins theory: polymer-solvent-void systems and binary blend-void systems. J. Chem. Phys. 88:2741-56
6. Bawendi MG, Freed KF, Mohanty U. 1986. A lattice model for self-avoiding polymers with controlled length distributions. II. Corrections to Flory-Huggins mean field. J. Chem. Phys. 84:7036-47
7. Ben-Naim A. 1978. Standard thermodynamics of transfer. Uses and misuses. J. Phys. Chem. 82:792-803
8. Ben-Naim A. 1979. Reply to C. Tanford's comments concerning standard states in the thermodynamics of transfer. J. Phys. Chem. 83:1803
9. Ben-Naim A. 1987. Solvation Thermodynamics. New York: Plenum
10. Ben-Naim A. 1992. Statistical Thermodynamics for Chemists and Biochemists, pp. 440-44. New York: Plenum
11. Ben-Naim A. 1994. Solvation: from small to macro molecules. Curr. Opin. Struct. Biol. 4:264-68
12. Ben-Naim A. 1994. Solvation of large molecules: some exact results on the dependence on volume and surface area of the solute. Biophys. Chem. 51:203-16
13. Ben-Naim A, Marcus Y. 1984. Solubility and thermodynamics of solution of xenon in liquid n-alkanes. J. Chem. Phys. 80:4438-40
14. Ben-Naim A, Marcus Y. 1984. Solvation thermodynamics of nonionic solutes. J. Chem. Phys. 81:2016-27
15. Ben-Naim A, Mazo RM. 1993. Size dependence of the solvation free energies of large solutes. J. Phys. Chem. 97:10829-34
16. Bothorel P. 1968. Determination of molecular optical anisotropy in solutions and liquids by depolarized light scattering. Applications to the study of n-alkanes. J. Colloid Interface Sci. 27:529-41
17. Brandts JF. 1964. The thermodynamics of protein denaturation. II. A model of reversible denaturation and interpretations regarding the stability of chymotrypsinogen. J. Am. Chem. Soc. 86:4302-14
18. Chan HS, Dill KA. 1991. Polymer principles in protein structure and stability. Annu. Rev. Biophys. Biophys. Chem. 20:447-90
19. Chan HS, Dill KA. 1994. Solvation: effects of molecular size and shape. J. Chem. Phys. 101:7007-26
20. Creamer TP, Srinivasan R, Rose GD. 1995. Modeling unfolded states of peptides and proteins. Biochemistry 34:16245-50
21. de Gennes P-G. 1979. Scaling Concepts in Polymer Physics. Ithaca, NY: Cornell Univ. Press
22. De Young LR, Dill KA. 1988. Solute partitioning into lipid bilayer membranes. Biochemistry 27:5281-89
23. De Young LR, Dill KA. 1990. Partitioning of nonpolar solutes into bilayers and amorphous n-alkanes. J. Phys. Chem. 94:801-9
24. Dill KA. 1990. Dominant forces in protein folding. Biochemistry 29:7133-55
25. Dill KA. 1990. The meaning of hydrophobicity. Science 250:297
26. Dill KA. 1997. Additivity principles in biochemistry. J. Biol. Chem. In press
27. Dudowicz J, Freed KF, Madden WG. 1990. Role of molecular structure on the thermodynamic properties of melts, blends, and concentrated polymer solutions. Comparison of Monte Carlo simulations with the cluster theory for the lattice model. Macromolecules 23:4803-19
28. Eisenberg D, McLachlan AD. 1986. Solvation energy in protein folding and binding. Nature 319:199-203
29. Eisenberg D, Wesson M, Yamashita M. 1989. Interpretation of protein folding and binding with atomic solvation parameters. Chem. Scr. 29A:217-21
30. Eriksson AE, Baase WA, Zhang X-J, Heinz DW, Blaber M, et al. 1992. Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect. Science 255:178-83
31. Fauchère J-L, Pliška V. 1983. Hydrophobic parameters Π of amino-acid side chains from the partitioning of N-acetyl-amino-acid amides. Eur. J. Med. Chem.-Chim. Ther. 18:369-75
32. Fersht AR. 1985. Enzyme Structure and Mechanism. New York: Freeman. 2nd ed.
33. Fink BR, ed. 1980. Molecular Mechanisms of Anesthesia, Int. Res. Conf. Mol. Mech. Anesth. 2nd, Seattle, 1979. New York: Raven.
34. Fisher ME. 1961. Statistical mechanics of dimers on a plane lattice. Phys. Rev. 124:1664-72
35. Flory PJ. 1941. Thermodynamics of high polymer solutions. J. Chem. Phys. 9:660-61
36. Flory PJ. 1942. Thermodynamics of high polymer solutions. J. Chem. Phys. 10:51-61
37. Flory PJ. 1953. Principles of Polymer Chemistry. Ithaca, NY: Cornell Univ. Press
38. Flory PJ. 1965. Statistical thermodynamics of liquid mixtures. J. Am. Chem. Soc. 87:1833-38
39. Flory PJ. 1977. Statistical thermodynamics of macromolecular liquids and solutions. Ber. Bunsen-Ges. Phys. Chem. 81:885-91
40. Fowler RH, Rushbrooke GS. 1937. An attempt to extend the statistical theory of perfect solutions. Trans. Faraday Soc. 22:1272-94
41. Freed KF. 1985. New lattice model for interacting, avoiding polymers with controlled length distribution. J. Phys. A 18:871-87
42. Freed KF, Bawendi MG. 1989. Lattice theories of polymer fluids. J. Phys. Chem. 93:2194-203
43. Freed KF, Pesci AI. 1987. Theory of the molecular origins of the entropic portion of the Flory χ parameter for polymer blends. J. Chem. Phys. 87:7342-44
44. Freire E. 1995. Thermodynamics of partly folded intermediates in proteins. Annu. Rev. Biophys. Biomol. Struct. 24:141-65
45. Giesen DJ, Cramer CJ, Truhlar DG. 1994. Entropic contributions to free energies of solvation. J. Phys. Chem. 98:4141-47
46. Gill SJ, Wadsö I. 1976. An equation of state describing hydrophobic interactions. Proc. Natl. Acad. Sci. USA 73:2955-58
47. Guggenheim EA. 1944. Statistical thermodynamics of mixtures with zero energies of mixing. Proc. R. Soc. London Ser. A 183:203-12
48. Habermann SM, Murphy KP. 1996. Energetics of hydrogen bonding in proteins: a model compound study. Protein Sci. 5:1229-39
49. Hansch C, Leo A. 1979. Substituent Constants for Correlation Analysis in Chemistry and Biology. New York: Wiley
50. Hermann RB. 1972. Theory of hydrophobic bonding. II. The correlation of hydrocarbon solubility in water with solvent cavity surface area. J. Phys. Chem. 76:2754-58
51. Hildebrand JH. 1947. The entropy of solution of molecules of different size. J. Chem. Phys. 15:225-28
52. Hildebrand JH. 1981. A history of solution theory. Annu. Rev. Phys. Chem. 32:1-23
53. Hildebrand JH, Scott RL. 1962. Regular Solutions. Englewood Cliffs, NJ: Prentice-Hall
54. Hilser VJ, Freire E. 1996. Structure-based calculation of the equilibrium folding pathway of proteins. Correlation with hydrogen exchange protection factors. J. Mol. Biol. 262:756-72
55. Holtzer A. 1992. The use of Flory-Huggins theory in interpreting partitioning of solutes between organic liquids and water. Biopolymers 32:711-15
56. Holtzer A. 1994. Does Flory-Huggins theory help in interpreting solute partition experiments? Biopolymers 34:315-20
57. Honig B, Yang A-S. 1995. Free energy balance in protein folding. Adv. Protein Chem. 46:27-58
58. 18 variants of turkey ovomucoid inhibitor third domain complexed with Streptomyces griseus proteinase B. Protein Sci. 4:1985-97
59. Jackson RM, Sternberg MJE. 1994. Application of scaled particle theory to model the hydrophobic effect: implication for molecular association and protein stability. Protein Eng. 7:371-83
60. Jacobsen CF, Linderstrøm-Lang K. 1949. Salt linkages in proteins. Nature 164:411-12
61. Kauzmann W. 1959. Some factors in the interpretation of protein denaturation. Adv. Protein Chem. 14:1-63
62. Kellis JT Jr, Nyberg K, Fersht AR. 1989. Energetics of complementary side-chain packing in a protein hydrophobic core. Biochemistry 28:4914-22
63. Kim K-S, Tao F, Fuchs J, Danishefsky AT, Housset D, et al. 1993. Crevice-forming mutants of bovine pancreatic trypsin inhibitor: stability changes and new hydrophobic surface. Protein Sci. 2:588-96
64. Kniaź K. 1991. Influence of size and shape effects on the solubility of hydrocarbon: the role of combinatorial entropy. Fluid Phase Equilibria 68:35-46
65. Krukowski AE, Chan HS, Dill KA. 1995. An exact lattice model of complex solutions: chemical potentials depend on solute and solvent shape. J. Chem. Phys. 103:10675-88
66. Kumar SK, Szleifer I, Sharp K, Rossky PJ, Friedman R, Honig B. 1995. Size dependence of transfer free energies. 1. Flory-Huggins approach. J. Phys. Chem. 99:8382-91
67. Lacombe RH, Sanchez IC. 1976. Statistical thermodynamics of fluid mixtures. J. Phys. Chem. 80:2568-80
68. Lebowitz JL. 1964. Exact solution of generalized Percus-Yevick equation for a mixture of hard spheres. Phys. Rev. 133:A895-99
69. Lee B. 1993. Estimation of the maximum change in stability of globular proteins upon mutation of a hydrophobic residue to another of smaller size. Protein Sci. 2:733-38
70. Lee B. 1994. Relation between volume correction and the standard state. Biophys. Chem. 51:263-69
71. Lee B, Richards FM. 1971. The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 55:379-400
72. Liu Y, Bolen DW. 1995. The peptide backbone plays a dominant role in protein stabilization by naturally occuring osmolytes. Biochemistry 34:12884-91
73. Makhatadze GI, Privalov PL. 1993. Contribution of hydration to protein folding thermodynamics. I. The enthalpy of hydration. J. Mol. Biol. 232:639-59
74. Matsumura M, Becktel WJ, Matthews BW. 1988. Hydrophobic stabilization in T4 lysozyme determined directly by multiple substitutions of Ile 3. Nature 334:406-10
75. McAuliffe C. 1966. Solubility in water of paraffin, cycloparaffin, olefin, acetylene, cycloefin, and aromatic hydrocarbons. J. Phys. Chem. 70:1267-75
76. Murphy KP, Gill SJ. 1991. Solid model compounds and the thermodynamics of protein unfolding. J. Mol. Biol. 222:699-709
77. Nagai K. 1967. Anisotropies of polarizability of n-alkanes. J. Chem. Phys. 47:4690-96
78. Nozaki Y, Tanford C. 1971. The solubility of amino acids and two glycine peptides in aqueous ethanol and dioxane solutions: establishment of a hydrophobicity scale. J. Biol. Chem. 246:2211-17
79. Ooi T, Oobatake M. 1988. Effects of hydrated water on protein unfolding. J. Biochem. 103:114-20. Erratum. 1989. J. Biochem. 106:539
80. Ooi T, Oobatake M, Némethy G, Scheraga HA. 1987. Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides. Proc. Natl. Acad. Sci. USA 84:3086-90. Erratum. 1987. Proc. Natl. Acad. Sci. USA 84:6015
81. Pace CN. 1992. Contribution of the hydrophobic effect to globular protein stability. J. Mol. Biol. 226:29-35
82. Patterson D, Tewari YB, Schreiber HP. 1972. Interpretation of activity coefficients in alkane systems. J. Chem. Soc. Faraday Trans. II 68:885-94
83. Pollack GL. 1991. Why gases dissolve in liquids. Science 251:1323-30
84. Pollack GL, Himm JF. 1982. Solubility of xenon in liquid n-alkanes: temperature dependence and thermodynamic functions. J. Chem. Phys. 77:3221-29
85. Pollack GL, Himm JF, Enyeart JJ. 1984. Solubility of xenon in liquid n-alkanols: thermodynamic functions in simple polar liquids. J. Chem. Phys. 81:3239-46
86. Privalov PL. 1979. Stability of proteins. Small globular proteins. Adv. Protein Chem. 33:167-241
87. Privalov PL, Gill SJ. 1988. Stability of protein structure and hydrophobic interaction. Adv. Protein Chem. 39:191-234
88. Privalov PL, Makhatadze GI. 1992. Contribution of hydration and non-covalent interactions to the heat capacity effect on protein folding. J. Mol. Biol. 224:715-23
89. Privalov PL, Makhatadze GI. 1993. Contribution of hydration to protein folding thermodynamics. II. The entropy and Gibbs energy of hydration. J. Mol. Biol. 232:660-79
90. Radzicka A, Wolfenden R. 1988. Comparing the polarities of the amino acids: side-chain distribution coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral aqueous solution. Biochemistry 27:1664-70
91. Rashin A. 1994. Comments on the paper by D. Sitkoff, K. Sharp and B. Honig. Biophys. Chem. 51:404-5
92. Reynolds JA, Gilbert DB, Tanford C. 1974. Empirical correlation between hydrophobic free energy and aqueous cavity surface area. Proc. Natl. Acad. Sci. USA 71:2925-27
93. Richards FM. 1977. Areas, volumes, packing and protein structure. Annu. Rev. Biophys. Bioeng. 6:151-76
94. Rose GD, Geselowitz AR, Lesser GJ, Lee RH, Zehfus MH. 1985. Hydrophobicity of amino acid residues in globular proteins. Science 229:834-38
95. Sanchez IC, Lacombe RH. 1974. Theory of liquid-liquid and liquid-vapor equilibria. Nature 252:381-83
96. Sanchez IC, Lacombe RH. 1976. An elementary molecular theory of classical fluids. Pure fluids. J Phys. Chem. 80:2352-62
97. Sanchez-Ruiz JM. 1995. An estimate of shape-related contributions to hydrophobic Gibbs energies. J Phys. Chem. 99:12076-80
98. Schellman JA. 1955. The thermodynamics of urea solutions and the heat of formation of the peptide hydrogen bond. C. R. Trav. Lab. Carlsburg Ser. Chim. 29:223-29
99. Schwarzenbach RP, Gschwend PM, Imboden DM. 1993. Environmental Organic Chemistry. New York: Wiley
100. Sharp KA, Kumar SK, Rossky PJ, Friedman RA, Honig B. 1996. Size dependence of transfer free energies. 2. Hard sphere models. J. Phys. Chem. 100:14166-77
101. Sharp KA, Nicholls A, Fine RF, Honig B. 1991. Reconciling the magnitude of the microscopic and macroscopic hydrophobic effects. Science 252:106-9
102. Sharp KA, Nicholls A, Friedman R, Honig B. 1991. Extracting hydrophobic free energies from experimental data: relationship to protein folding and theoretical models. Biochemistry 30:9686-97
103. Shinoda K, Hildebrand JH. 1957. The solubility and entropy of solution of iodine in octamethylcyclotetrasiloxane and tetraethoxysilane. J. Phys. Chem. 61:789-91
104. 3. J. Phys. Chem. 62:292-94
105. Shinoda K, Hildebrand JH. 1958. Partial molal volumes of iodine in various complexing and non-complexing solvents. J. Phys. Chem. 62:295-96
106. Shirley BA, Stanssens P, Hahn U, Pace CN. 1992. Contribution of hydrogen bonding to the conformational stability of ribonuclease T1. Biochemistry 31:725-32
107. Shortle D, Stites WE, Meeker AK. 1990. Contributions of the large hydrophobic amino acids to the stability of staphylococcal nuclease. Biochemistry 29:8033-41
108. Sun Y, Spellmeyer D, Pearlman DA, Kollman P. 1992. Simulation of the solvation free energies of methane, ethane, and propane and corresponding amino acid dipeptides: a critical test of the "bond-PMF" correction, a new set of hydrocarbon parameters, and the gas phase-water hydrophobicity scale. J. Am. Chem. Soc. 114:6798-801
109. Tanford C. 1970. Protein denaturation. Part C. Theoretical models for the mechanism of denaturation. Adv. Protein Chem. 24:1-95
110. Tanford C. 1979. Standard states in the thermodynamics of transfer. J. Phys. Chem. 83:1802-3
111. Tanford C. 1980. The Hydrophobic Effect. New York: Wiley. 2nd ed.
112. Tuñón I, Silla E, Pascual-Ahuir JL. 1992. Molecular surface area and hydrophobic effect. Protein Eng. 5:715-16
113. Tuñón I, Silla E, Pascual-Ahuir JL. 1994. Evaluation of transfer free energies. J. Phys. Chem. 98:377-79
114. Vajda S, Weng Z, DeLisi C. 1995. Extracting hydrophobicity parameters from solute partition and protein mutation/unfolding experiments. Protein Eng. 8:1081-92
115. Vogl T, Hinz H-J, Hedwig GR. 1995. Partial molar heat capacities and volumes of Gly-X-Gly tripeptides in aqueous solution: model studies for the rationalization of thermodynamic parameters of proteins. Biophys. Chem. 54: 261-69
116. Wesson L, Eisenberg D. 1992. Atomic solvation parameters applied to molecular dynamics of proteins in solution. Protein Sci. 1:227-35
117. White SH, Wimley WC. 1994. Peptides in lipid bilayers: structural and thermodynamic basis for partitioning and folding. Curr. Opin. Struct. Biol. 4:79-86
118. Widom B. 1963. Some topics in the theory of fluids. J. Chem. Phys. 39:2808-12
119. Wimley WC, Creamer TP, White SH. 1996. Solvation energies of amino acid side chains and backbone in a family of host-guest pentapeptides. Biochemistry 35:5109-24
120. Wolfenden R, Radzicka A. 1994. On the probability of finding a water molecule in a nonpolar cavity. Science 265:936-37
121. Xie D, Freire E. 1994. Structure based prediction of protein folding intermediates. J. Mol. Biol. 242:62-80
122. Yang A-S, Sharp KA, Honig B. 1992. Analysis of the heat capacity dependence of protein folding. J. Mol. Biol. 227:889-900