The magnitude of the backbone conformational entropy change in protein folding

Proteins: Structure, Function and Genetics

Volumn 25, Issue 2, 1996, Pages 143-156

  D'Aquino, J Alejandro ^a   Gómez, Javier ^a   Hilser, Vincent J ^a   Lee, Kon Ho ^a,b   Amzel, L Mario ^b   Freire, Ernesto ^a  

^a JOHNS HOPKINS UNIVERSITY   (United States)

^b JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; CONFORMATIONAL TRANSITION; ENTROPY; GENE MUTATION; MATHEMATICAL ANALYSIS; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STABILITY; SEQUENCE ANALYSIS;

EID: 0029900846     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.1     Document Type: Article

References (43)

1. Privalov, P.L., Khechinashvili, N.N. A thermodynamic approach to the problem of stabilization of globular protein structure: A calorimetric study. J. Mol. Biol. 86:665-684, 1974.
2. Oobatake, M., Ooi, T. Hydration and heat stability effects on protein unfolding. Prog. Biophys. Mol. Biol. 59:237-284, 1992.
3. Murphy, K.P., Bhakuni, V., Xie, D., Freire, E. The molecular basis of co-operativity in protein folding III: Identification of cooperative folding units and folding intermediates. J. Mol. Biol. 227:293-306, 1992.
4. Privalov, P.L., Makhatadze, G.I. Contribution of hydration to protein folding thermodynamics. II. The entropy and Gibbs energy of hydration. J. Mol. Biol. 232:660-679, 1993.
5. Stites, W.E., Pranata, J. Empirical evaluation of the influence of side chains on the conformational entropy of the polypeptide backbone. Proteins 22:132-140, 1995.
6. Creamer, T.P., Rose, G.D. Side-chain entropy opposes α-helix formation but rationalizes experimentally determined helix-forming propensities. Proc. Natl. Acad. Sci. USA 89: 5937-5941, 1992.
7. Pickett, S.D., Sternberg, M J.E. Empirical scale of side-chain conformational entropy in protein folding. J. Mol. Biol. 231:825-839, 1993.
8. Blaber, M., Zhang, X.J., Lindstrom, J.L., Pepsot, S.D., Baase, W.A., and Matthews, B.W. Determination of alpha-helix propensity within the context of a folded protein: Sites 44 and 131 in bacteriophage T4 lysozyme. J. Mol. Biol. 235:600-624, 1994.
9. Lee, K.H., Xie, D., Freire, E., Amzel, L.M. Estimation of changes in side chain configurational entropy in binding and folding: General methods and application to helix formation. Proteins 20:68-84, 1994.
10. Freire, E., Haynie, D.T., Xie, D. Molecular basis of cooperativity in protein folding. IV. CORE: A general cooperative folding model. Proteins 17:111-123, 1993.
11. Murphy, K.P., Xie, D., Thompson, K., Amzel, L.M., Freire, E. Entropy in biological binding processes: Estimation of translational entropy loss. Proteins 18:63-67, 1994.
12. O'Shea, E.K., Klemm, J.D., Kim, P.S., Alber, T. X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel coiled coil. Science 254:539-544, 1991.
13. O'Shea, E.K., Rutkowski, R., Kim, P.S. Evidence that the leucine zipper is a coiled coil. Science 243:538-542, 1989.
14. Oas, T.G., McIntosh, L.P., O'Shea, E.K., Dahlquist, P.W., Kim, P.S. Secondary structure of a leucine zipper determined by nuclear magnetic resonance spectroscopy. Biochemistry 29:2891-2894, 1990.
15. Spolar, R.S., Livingstone, J.R., Record, M.T. Jr. Use of liquid hydrocarbon and amide transfer data to estimate contributions to thermodynamic functions of protein folding from the removal of nonpolar and polar surface from water. Biochemistry 31:3947-3955, 1992.
16. Gomez, J., Hilser, J.V., Xie, D., Freire, E. The heat capacity of proteins. Proteins 22:404-412, 1995.
17. Kenar, K.T. "Thermodynamic Characterization of the Structural Stability of the GCN4 Leucine Zipper Dimer." Baltimore: The Johns Hopkins University Press, 1994.
18. Kenar, K.T., García-Moreno, B., Freire, E. A calorimetric characterization of the salt dependence of the stability of the GCN4 leucine zipper. Protein Sci. 4:1934-1938, 1995.
19. Freire, E. Statistical thermodynamic analysis of the heat capacity function associated with protein folding-unfolding transitions. Comments Mol. Cell. Biophys. 6:123-140, 1989.
20. Thompson, K., Vinson, C., Freire, E. Thermodynamic characterization of the structural stability of the coiled-coil region of the bZIP transcription factor GCN4. Biochemistry 32:5491-5496, 1993.
21. Leach, S.J., Nemethy, G., Scheraga, H.A. Computation of the sterically allowed conformations of peptides. Biopolymers 4:369-407, 1966.
22. Fisher, M.E. Effect of excluded volume on phase transitions in biopolymers. J. Chem. Phys. 45:1469-1473, 1966.
23. Baldwin, R.L. Temperature dependence of the hydrophobic interaction in protein folding. Proc. Natl. Acad. Sci. USA 83:8069-8072, 1986.
24. Makhatadze, G.I., Privalov, P.L. Hydration effects in protein unfolding. Biophys. Chem. 51:291-309, 1994.
25. Xie, D., Freire, E. Structure based prediction of protein folding intermediates. J. Mol. Biol. 242:62-80, 1994.
26. Xie, D., Freire, E. Molecular basis of cooperativity in protein folding. V. Thermodynamic and structural conditions for the stabilization of compact denatured states. Proteins 19:291-301, 1994.
27. Gomez, J., Freire, E. Thermodynamic mapping of the inhibitor site of the aspartic protease endothiapepsin. J. Mol. Biol. 252:337-350, 1995.
28. Schwarz, F.P., Tello, D., Goldbaum, F.A., Mariuzza, R.A., Poljak, R.J. Thermodynamics of antigen-antibody binding using specific anti-lysozyme antibodies. Eur. J. Biochem. 228:388-394, 1995.
29. Spolar, R.S., Record, M.T. Coupling of local folding to site specific binding of proteins to DNA. Science 263:777-784, 1994.
30. Cabani, S., Gianni, P., Mollica, V., Lepori, L. Group contributions to the thermodynamic properties of non-ionic organic solutes in dilute aqueous solution. J. Solution Chem. 10:563-595, 1981.
31. Murphy, K.P. Hydration and convergence temperatures: on the use and interpretation of correlation plots. Biophys. Chem. 51:311-326, 1994.
32. Khechinashvili, N.N., Janin, J., Rodier, F. Thermodynamics of the temperature-induced unfolding of globular proteins. Protein Sci. 4:1315-1324, 1995.
33. Vogl, T., Hinz, H.-J., Hedwig, G.K. 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. 54:261-269, 1995.
34. Habermann, S.M., Murphy, K.P. Energetics of hydrogen bonding in proteins: A model compound study. Nature Struct. Biol. 1995 (submitted).
35. Lazaridis, T., Archontis, G., and Karplus, M. Enthalpic contributions to protein stability; Atom-based calculations and statistical mechanics. Adv. Prot. Chem. 47:231-306, 1995.
36. Schellman, J.A. The stability of hydrogen bonded structures in aqueous solution. CR Trav. Carlsburg, Ser. Chim. 29:230-259, 1955.
37. Nemethy, G., Scheraga, H.A. Theoretical determination of sterically allowed conformations of a polypeptide chain by a computer method. Biopolymers 3:155-184, 1965.
38. Klapper, M.H. The independent distribution of amino acid near neighbor pairs into polypeptides. Biochem. Biophys. Res. Commun. 78:1018-1024, 1977.
39. Kent, S.B.H. Chemical synthesis of peptides and proteins. Annu. Rev. Biochem. 57:957-989, 1988.
40. Lee, B., Richards, F.M. The interpretation of protein structures: Estimation of static accessibility. J. Mol. Biol. 55: 379-400, 1971.
41. Chan, H.S., Dill, K.A. Polymer principles in protein structure and stability. Annu. Rev. Biophys. Biophys. Chem. 20:447-490, 1991.
42. Jorgensen, W.L. and Tirado-Rives, J. The OPLS potential function for proteins. Energy minimization for crystals of cyclic peptides and crambin. J. Am. Chem. Soc. 110:1657-1666, 1988.
43. Brunger, A.T. "X-PLOR, version 3-1A. A system for crystallography and NMR," New Haven, Yale University Press 1992.