Energetics of cyclic dipeptide crystal packing and solvation

Biophysical Journal

Volumn 72, Issue 2 I, 1997, Pages 913-927

  Brady, G Patrick ^a   Sharp, Kim A ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CRYSTAL STRUCTURE; ENTHALPY; ENTROPY; HYDROPHOBICITY; MATHEMATICAL ANALYSIS; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; PROTEIN ASSEMBLY; PROTEIN CONFORMATION; PROTEIN DEGRADATION;

EID: 0031030835     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(97)78725-3     Document Type: Article

References (37)

1. Ashcroft, N. W., and N. D. Mermin. 1976. Solid State Physics. W. B. Saunders, Philadelphia.
2. Ben-Naim, A., and Y. Marcus. 1984. Solvation thermodynamics of non-ionic solutes. J Chem. Phys. 81:2016-2027.
3. Ben-Shaul, A., N. Ben-Tal, and B. Honig. 1996. Statistical thermodynamic analysis of protein association into lipid membranes. Biophys. J. (in press).
4. Creighton, T. 1991. Stability of folded conformations. Curr. Opin. Struct. Biol. 1:5-16.
5. Degeilh, R., and R. Marsh. 1959. Three dimensional structure of diketopiperazine. Acta Crystallogr. 12:1007.
6. Gilson, M. K., J. A. McCammon, and J. A. Given. 1996. Principles of noncovalent binding. Biophys. J. (in press).
7. Hagler, A. T., E. Huler, and S. Lifson. 1974. Energy functions for peptides and proteins. I. Derivation of a consistent force field including the hydrogen bond from amide crystals. J. Am. Chem. Soc. 96:5319-5327.
8. Hill, T. L. 1985. Cooperativity Theory in Biochemistry. Springer-Verlag, New York.
9. Hill, T. 1986. An Introduction to Statistical Thermodynamics. Dover Books. New York.
10. Holtzer, A. 1995. The "Cratic correction" and related fallacies. Biopolymers. 35:595-602.
11. Horton, N., and M. Lewis. 1992. Calculation of the free energy of association for protein complexes. Protein Sci. 1:169-181.
12. Janin, J., and C. Chothia. 1978. Role of hydrophobicity in the binding of coenzymes. Biochemistry. 17:2943-2948.
13. Lazaridis, T., G. Archontis, and M. Karplus. 1995. Enthalpic contributions to protein stability. Adv. Protein Chem. 47:231-306.
14. Lee, B. K. 1991. Isoenthalpic and isocntropic temperatures and the thermodynamics of protein denaturation. Proc. Natl. Acad. Sci. USA. 88: 5154-5158.
15. Makhatadze, G., and P. Privalov. 1990. I. Partial molar heat capacity of individual amino acid residues in aqueous solution: hydration effect. J. Mol. Biol. 213:375-384.
16. Makhatadze, G., and P. Privalov. 1996. On the entropy of protein folding. Protein Sci. 5:507-510.
17. McQuarrie, D. 1976. Statistical Mechanics. Harper and Row, New York.
18. Murphy, K., and E. Freire. 1992. Thermodynamics of structural stability and cooperative folding behavior in proteins. Adv. Protein Chem. 43: 313-361.
19. Murphy, K., and S. Gill. 1990a. Group additivity thermodynamics for the dissolution of solid cyclic dipeptides into water. Therm. Acta. 172: 11-20.
20. Murphy, K. P., and S. J. Gill. 1990b. Calorimetric measurement of the enthalpy of dissolution of diketopiperazine in water as a function of temperature. Thermochim. Acta. 139:279-290.
21. Murphy, K. P., and S. J. Gill. 1991. Solid model compounds and the thermodynamics of protein unfolding. J. Mol. Biol. 222.
22. Murphy, K. P., P. L. Privalov, and S. J. Gill. 1990. Common features of protein unfolding and dissolution of hydrophobic compounds. Science. 247:559-561.
23. Murphy, K. P., D. Xie, K. Thompson, M. Amzel, and E. Freire. 1994. Entropy loss in biological processes: estimate of translational entropy loss. Proteins. 18:63-67.
24. Peitzsch, R. M., and S. McLaughlin. 1993. Binding of acylated peptides and fatty acids to phospholipid vesicles: pertinence to myristoylated proteins. Biochemistry. 32:10436-10443.
25. Privalov, P. L., and S. J. Gill. 1988. Stability of protein structure and hydrophobic interaction. Adv. Protein Chem. 39:191-234.
26. Privalov, P., and G. Makhatadze. 1993. Contribution of hydration to protein folding thermodynamics. II. The entropy and Gibbs free energy of hydration. J. Mol. Biol. 232:660-679.
27. Seki, S., K. Suzuki, and T. Koide. 1956. Vapor pressure of molecular crystals. Kogyo Kagaku Zasshi. 77:346.
28. Sharp, K. A., A. Jean-Charles, and B. Honig. 1992. A local dielectric-constant model for solvation free energies which accounts for solute polarizability. J. Phys. Chem. 96:3822-3828.
29. Sitkoff, D., K. Sharp, and B. Honig. 1994. Accurate calculation of hydration free energies using macroscopic solvent models. J. Phys. Chem. 98:1978-1988.
30. Sletten, E. 1970. Conformation of cyclic dipeptides. The crystal and molecular structures of cyclo-D-alanyl-L-alanyl and cyclo-L-alanyl-L-alanyl 3,6-dimethylpipererazine-2,5-dione. J. Am. Chem. Soc. 92: 172-177.
31. Spolar, R., J. Livingstone, and M. T. Record. 1992. Use of liquid hydrocarbon and amide transfer data to estimate contributions to protein folding. Biochemisrry. 31:3947-3955.
32. Sridharan, S., A. Nicholls, and B. Honig. 1992. A new vertex algorithm to calculate solvent accessible surface areas. Biophys. J. 61:abstract 995.
33. Steinberg, I., and H. Scheraga. 1963. Entropy changes accompanying association reactions of proteins. J. Biol. Chem. 238:172-181.
34. Tidor, B., and M. Karplus. 1994. The contribution of vibrational entropy to molecular association. J. Mol. Biol. 238:405-414.
35. Weiner, S. J., P. A. Kollman, D. T. Nguyen, and D. A. Case. 1986. An all atom force field for simulations of proteins and nucleic acids. J. Comp. Chem. 7:230-252.
36. Xie, D., and E. Freire. 1994. Structure based prediction of protein folding intermediates. J. Mol. Biol. 242:62-80.
37. Yang. A., K. Sharp, and B. Honig. 1992. Analysis of the heat capacity dependence of protein folding. J. Mol. Biol. 227:889-900.