SpringerProtocols: Abstract: 6. Conformational Entropy in Protein Folding: A Guide to Estimating Conformational Entropy via Modeling and Computation

6. Conformational Entropy in Protein Folding: A Guide to Estimating Conformational Entropy via Modeling and Computation

By: Trevor P. Creamer²

Abstract

Full Text

Download PDF (162K)

This chapter outlines methods to estimate, through calculation and modeling, a major destabilizing contributor to protein stability—conformational entropy. This is not a comprehensive review of all published calculations of conformational entropy, but rather serves as a guide for those interested in performing such calculations. The methods outlined in this chapter provide an opportunity to estimate some of the entropic contributions to protein stability. Such methods are currently limited to estimating conformational entropy for relatively small parts of proteins, such as side chains or small pep-tides. Yet these calculations can provide much insight into the role of conformational entropy in protein stability.

Affiliation(s): (2) Kentucky Center for Structural Biology and Department of Biochemistry, University of Kentucky, Lexington, KY

Book Title: Protein Structure, Stability, and Folding

Series: Methods in Molecular Biology | Volume: 168 | Pub. Date: Apr-01-2001 | Page Range: 117-132 | DOI: 10.1385/1-59259-193-0:117

Subject: Protein Science

References

Download References

1.	Aurora, R., Creamer, T. P., Srinivasan, R., and Rose, G. D. (1997) Local interactions in protein folding: lessons from the a-helix. J. Biol. Chem. 272, 1413–1416.

2.	Creamer, T. P. and Rose, G. D. (1992) Side-chain entropy opposes α-helix formation but rationalizes experimentally determined helix-forming propensities. Proc. Natl. Acad. Sci. USA 89, 5937–5941.

3.	Creamer, T. P. and Rose, G. D. (1994) α-Helix-forming propensities in peptides and proteins. Proteins 19, 85–97.

4.	Lee, K. H., Xie, D., Freire, E., and Amzel, L. M. (1994) Estimation of changes in side chain configurational entropy in binding and folding: general methods and application to helix formation. Proteins 20, 68–84.

5.	Blaber, M., Zhang, X. J., Lindstrom, J. D., Pepoit, S. D., Baase, W. A., and Matthews, B. W. (1994) Determination of a-helix propensity within the context of a folded protein: sites 44 and 131 in bacterioph-age T4 lysozyme. J. Mol. Biol. 235, 600–624.

6.	Abagyan, R. and Totrov, M. (1994) Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. J. Mol. Biol. 235, 983–1002.

7.	Pickett, S. D. and Sternberg, M. J. E. (1993) Empirical scale of side-chain conformational entropy in protein folding. J. Mol. Biol. 231, 825–839.

8.	Creamer, T. P. and Rose, G. D. (1995) Interactions between hydro-phobic side chains within α-helices. Protein Sci. 4, 1305–1314.

9.	D’Aquino, J. A., Gomez, J., Hilser, V. J., Lee, K. H., Amzel, L. M., and Freire, E. (1996) The magnitude of the backbone conformational entropy change in protein folding. Proteins 25, 143–156.

10.	Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, Jr., E. F., Brice, M. D., Rodgers, J. R., et al. (1997) The Protein Data Bank: A computer-based archival file for macromolecular structures. J. Mol. Biol. 112, 535–542.

11.	Hobohm, U., Scharf, M., Schneider, R., and Sander, C. (1992) Selection of representative protein data sets. Protein Sci. 1, 409–417.

12.	Hobohm, U. and Sander, C. (1994) Enlarged representative set of protein structures. Protein Sci. 3, 522–524.

13.	Koehl, P. and Delarue, M. (1994) Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy. J. Mol. Biol. 239, 249–275.

14.	Metropolis, N., Rosenbluth, A. W., Rosenbluth, M. N., Teller, A. H., and Teller, E. (1953) Equation of state calculations by fast computing machines. J. Chem. Phys. 21, 1087–1092.

15.	Allen, M. P. and Tildesley, D. J. (1992) ‘Computer Simulation of Liquids,’ Oxford University Press, Oxford, UK, pp. 1–385.

16.	Smith, E. B. and Wells, B. H. (1984) Estimating errors in molecular simulation calculations. Mol. Phys. 52, 701–704.

17.	Creamer, T. P. and Rose, G. D. (1995) Simple force field for study of peptide and protein conformational properties. Meth. Enzymol. 259, 576–589.

18.	Kolafa, J. (1986) Autocorrelations and subseries averages in Monte Carlo simulations. Mol. Phys. 59, 1035–1042.

19.	Cornell, W. D., Cieplak, P., Bayley, C. I., Gould, I. R., Merz, Jr., K. M., Ferguson, D. M., et al. (1995) A second generation force field for the simulation of proteins and nucleic acids. J. Am. Chem. Soc. 117, 5179–5197.

20.	Maple, J. R., Hwang, M. J., Stockfish, T. P., Dinur, U., Waldman, M., Ewig, C. S., et al. (1994) Derivation of class II force fields. I. Methodology and quantum force field for the alkyl functional group and alkane molecules. J. Comp. Chem. 15, 162–182.

21.	Still, W. C., Tempczyk, A., Hawley, R. C., and Hendrickson, T. (1990) Semianalytical treatment of solvation for molecular mechanics and dynamics. J. Am. Chem. Soc. 112, 6127–6129.

22.	Sternberg, M. J. E. and Chickos, J. S. (1994) Protein side-chain conformational entropy derived from fusion data-comparison with other empirical scales. Protein Eng. 7, 149–155.

Comments (Loading...)

Post comment/View all comments