Hydrophobicity regained

Protein Science

Volumn 6, Issue 6, 1997, Pages 1302-1307

  Karplus, P Andrew ^a  

^a Department of Obstetrics Gynecology   (United States)

Author keywords

Amino acids; Atomic solvation parameters; Hydrophobic effect; Hydrophobicity; Protein folding; Protein stability

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; ENERGY TRANSFER; HYDROGEN BOND; HYDROPHOBICITY; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN STABILITY;

EID: 0031008576     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1002/pro.5560060618     Document Type: Article

References (37)

1. Ben-Naim A. 1994. Solvation: From small to macro molecules. Curr Op Struct Biol 4:264-268.
2. Blokzijl W, Engberts JBFN. 1993. Hydrophobic effects. Opinions and facts. Angew Chem Int Ed Engl 32:1545-1579.
3. Chan HS, Dill KA. 1997. Solvation: How to obtain microscopic energies from partitioning and solvation experiments. Ann Rev Biophys Biomolec Struct 26. Forthcoming.
4. Chothia C. 1974. Hydrophobic bonding and accessible surface area in proteins. Nature 248:338-339.
5. Creighton T. 1994. Proteins: Structures and molecular properties. New York: Freeman Press.
6. Cummings MD, Hart TN, Read RJ. 1995. Atomic solvation parameters in the analysis of protein-protein docking results. Protein Sci 4:2087-2099.
7. Damodaran S, Song KB. 1986. The role of solvent polarity in the free energy of transfer of amino acid side chains from water to organic solvents. J Biol Chem 261:7220-7222.
8. Dill KA. 1990a. Dominant forces in protein folding. Biochemistry 29:7133-7155.
9. Dill KA. 1990b. The meaning of hydrophobicity. Science 250:297.
10. Dill KA. 1997. Additivity principles in biochemistry. J Biol Chem 272:701-704.
11. Eisenberg D, McLachlan AD. 1986. Solvation energy in protein folding and binding. Nature 319:199-203.
12. Eriksson AE, Baase WA, Zhang X-J, Heinz DW, Blaber M, Baldwin EP, Matthews BW. 1992. Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect. Science 255:178-183.
13. Fauchere J-L, Pliska V. 1983. Hydrophobic parameters π of amino acid side chains from the partitioning of N-acetyl-amino-acid amides. Eur J Med Chem 18:369-375.
14. Hermann RB. 1972. Theory of hydrophobic bonding. II. The correlation of hydrocarbon solubility in water with solvent cavity surface area. J Phys Chem 76:2754-2759.
15. Honig B, Yang A-S. 1995. Free energy balance in protein folding. Adv Prot Chem 46:27-55.
16. Horton N, Lewis M. 1992. Calculation of the free energy of association for protein complexes. Protein Sci 1:169-181.
17. Janin J. 1995. Elusive Affinities. Proteins Struct Funct and Genet 21:30-39.
18. Juffer AH, Eisenhaber F, Hubbard SJ, Walther D, Argos P. 1995. Comparison of atomic solvation parametric sets: Applicability and limitations in protein folding and binding. Protein Sci 4:2499-2509.
19. Kauzmann W. 1959. Some factors in the interpretation of protein denaturation. Adv Prot Chem 14:1-63.
20. Lazaridis T, Archontis G, Karplus M. 1995. Enthalpic contribution to protein stability: Insights from atom-based calculations and statistical mechanics. Adv Prot Chem 47:231-296.
21. Lee B. 1995. Analyzing solvent reorganization and hydrophobicity. Meth Enzymol 259:555-576.
22. Lemieux RU. 1996. How water provides the impetus for molecular recognition in aqueous solution. Acc Chem Res 29:373-380.
23. Lesser GJ, Rose GD. 1990. Hydrophobicity of amino acid subgroups in proteins. Proteins Struct Funct Genet 8:6-13.
24. Liu Y, Bolen DW. 1995. The peptide backbone plays a dominant role in protein stabilization by naturally occurring osmolytes. Biochemistry 34:12884-12891.
25. Makhatadze GI, Privalov PI. 1995. Energetics of protein structure. Adv Prot Chem 47:307-417.
26. Nozaki Y, Tanford C. 1971. The solubility of amino acids and two glycine peptides in aqueous ethanol and dioxane solutions. J Biol Chem 246:2211-2217.
27. Pace CN. 1995. Evaluating the contribution of hydrogen bonding and hydrophobic bonding to protein folding. Meth Enzymol 259:538-554.
28. Ponnuswamy PK. 1993. Hydrophobic characteristics of folded proteins. Prog Biophys Molec Biol 59:57-103.
29. 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 27:1664-1670.
30. Reynolds JA, Gilbert DB, Tanford C. 1974. Empirical correlation between hydrophobic free energy and aqueous cavity surface area. Proc Nat Acad Sci USA 71:2925-2927.
31. Rose GD, Wolfenden R. 1993. Hydrogen bonding, hydrophobicity, packing, and protein folding. Ann Rev Biophys Biomol Struct 22:381-415.
32. Roseman MA. 1988. Hydrophobicity of polar amino acid side chains is markedly reduced by flanking peptide bonds. J Mol Biol 200:513-522.
33. Sharp KA, Nicholls A, Fine RF, Honig B. 1991a. Reconciling the magnitude of the microscopic and macroscopic hydrophobic effects. Science 252:106-109.
34. Sharp KA, Nicholls A, Freidman R, Honig B. 1991b. Extracting hydrophobic free energies from experimental data: Relationship to protein folding and theoretical models. Biochemistry 30:9686-9697.
35. Tanford C. 1962. Contribution of hydrophobic interactions to the stability of the globular conformation of proteins. J Am Chem Soc 84:4240-4247.
36. Tanford C. 1964. Isothermal unfolding of globular proteins in aqueous urea solutions. J Am Chem Soc 86:2050-2059.
37. Vajda S, Weng Z, DeLisi C. 1995. Extracting hydrophobicity parameters from solute partition and protein mutation/unfolding experiments. Protein Engineering 8:1081-1092.