Protein Engineering Protocols - Mycobacteriology research center

18 Kono et al.the heat capacity, C v(59). Sequence properties that are robust with respect to smallstructural fluctuations (1 Å root mean square deviation) occur at values of E cat orabove this heat capacity peak.3. In performing the constrained optimization of the entropy, we find that root-findingmethods using these equations perform as well as constrained minimization algorithms(62).4. The calculated probabilities of amino acids can also be used to evaluate structuraltolerance to mutation. Such mutations are most likely to accumulate in an in vitrodirected protein evolution experiment (72) at sites that have a broad distribution ofamino acids, i.e., sites at which many amino acids have probabilities comparableto the most probable amino acid.References1. Go, N. (1983) Theoretical studies of protein folding. Annu. Rev. Biophys. Bioeng.12, 183–210.2. Shea, J. E. and Brooks, C. L. 3rd. (2001) From folding theories to folding proteins:a review and assessment of simulation studies of protein folding andunfolding. Annu. Rev. Phys. Chem. 52, 499–535.3. Brooks, C. L. 3rd. (2002) Protein and peptide folding explored with molecularsimulations. Acc. Chem. Res. 35, 447–454.4. Kraemer-Pecore, C. M., Wollacott, A. M., and Desjarlais, J. R. (2001) Computationalprotein design. Curr. Opin. Chem. Biol. 5, 690–695.5. Bryson, J. W., Betz, S. F., Lu, H. S., et al. (1995) Protein design: a hierarchicapproach. Science 270, 935–941.6. Dunbrack, R. (2002) Rotamer libraries. Curr. Opin. Struct. Biol. 12, 431–440.7. Shakhnovich, E. I. and Gutin, A. M. (1993) A new approach to the design of stableproteins. Protein Eng. 6, 793–800.8. Jones, D. T. (1994) De novo protein design using pairwise potentials and agenetic algorithm. Protein Sci. 3, 567–574.9. Hellinga, H. W. and Richards, F. M. (1994) Optimal sequence selection in proteinsof known structure by simulated evolution. Proc. Natl. Acad. Sci. USA 91,5803–5807.10. Desjarlais, J. R. and Handel, T. M. (1995) De-novo design of the hydrophobiccores of proteins. Protein Sci. 4, 2006–2018.11. Johnson, E. C., Lazar, G. A., Desjarlais, J. R., and Handel, T. M. (1999) Solutionstructure and dynamics of a designed hydrophobic core variant of ubiquitin.Struct. Fold. Des. 7, 967–976.12. Jiang, X., Farid, H., Pistor, E., and Farid, R. S. (2000) A new approach to thedesign of uniquely folded thermally stable proteins. Protein Sci. 9, 403–416.13. Jiang, X., Bishop, E. J., and Farid, R. S. (1997) A de novo designed protein withproperties that characterize natural hyperthermophilic proteins. J. Am. Chem. Soc.119, 838, 839.14. Bryson, J. W., Desjarlais, J. R., Handel, T. M., and DeGrado, W. F. (1998) Fromcoiled coils to small globular proteins: design of a native-like three-helix bundle.Protein Sci. 7, 1404–1414.