Stability and the Evolvability of Function in a Model Protein

Biophysical Journal

Volumn 86, Issue 5, 2004, Pages 2758-2764

  Bloom, Jesse D ^a   Wilke, Claus O ^a   Arnold, Frances H ^b   Adami, Christoph ^c  

^a CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

^b California Institute of Technology   (United States)

^c CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LIGAND;

ARTICLE; BIOPHYSICS; CALCULATION; LIGAND BINDING; MATHEMATICAL ANALYSIS; MOLECULAR MODEL; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN STABILITY; PROTEIN STRUCTURE;

EID: 1842835981     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(04)74329-5     Document Type: Article

References (37)

1. Anfinsen, C. B. 1973. Principles that govern the folding of protein chains. Science. 181:223-230.
2. Amold, F. H. 1998. Enzyme engineering reaches the boiling point. Proc. Natl. Acad. Sci. USA. 95:2035-2036.
3. Amold, F. H., P. L. Wintrode, K. Miyaszki, and A. Gershenson. 2001. How enzymes adapt: lessons from directed evolution. Trends Biochem. Sci. 25:100-106.
4. Bastolla, U., H. E. Roman, and M. Vendruscolo. 1999. Neutral evolution of model proteins: diffusion in sequence space and overdispersion. J. Theor. Biol. 200:49-64.
5. Bastolla, U., M. Vendruscolo, and H. E. Roman. 2000. Structurally constrained protein evolution: results from a lattice simulation. Eur. Phys. J. B. 15:385-397.
6. Bornberg-Bauer, E., and H. S. Chan. 1999. Modeling evolutionary landscapes: mutational stability, topology, and superfunnels in sequence space. Proc. Natl. Acad. Sci. USA. 96:10689-10694.
7. Broglia, R., G. Tiana, H. Roman, E. Vigezzi, and E. Shakhnovich. 1999. Stability of designed proteins against mutations. Phys. Rev. Lett. 82:4727-1730.
8. Chan, H. S., and E. Bornberg-Bauer. 2002. Perspectives on protein evolution from simple exact models. Applied Bioinformatics. 1:121-144.
9. Cui, Y., W. H. Wong, E. Bornberg-Bauer, and H. S. Chan. 2002. Recombinatoric exploration of novel folded structures: a heteropolymer-based model of protein evolutionary landscapes. Proc. Natl. Acad. Sci. USA. 99:809-814.
10. Davidson, A. R., K. J. Lumb, and R. T. Sauer. 1995. Cooperatively folded proteins in random sequence libraries. Nat. Struct. Biol. 2:856-864.
11. Dill, K. A., S. Bromberg, K. Yue, K. M. Fiebig, D. P. Yee, P. D. Thomas, and H. S. Chan. 1995. Principles of protein folding: a perspective from simple exact models. Protein Sci. 4:561-602.
12. Fersht, A. R. 2002. Structure and Mechanism in Protein Science. W. H. Freeman and Company, New York.
13. Giver, L., A. Gershenson, P. O. Freskgard, and F. H. Arnold. 1998. Directed evolution of a thermostable esterase. Proc. Natl. Acad. Sci. USA. 95:12809-12813.
14. Gutin, A. M., V. I. Abkevich, and E. I. Shakhnovich. 1995. Evolution-like selection of fast-folding model proteins. Proc. Natl. Acad. Sci. USA. 92:1281-1286.
15. Hinds, D. A., and M. Levitt. 1994. Exploring conformational space with a simple lattice model for protein-structure. J. Mol. Biol. 243:668-682.
16. Hirst, J. D. 1999. The evolutionary landscape of functional model proteins. Protein Eng. 12721-726.
17. Keefe, A. D., and J. W. Szostak. 2001. Functional proteins from a random-sequence library. Nature. 410:715-718.
18. Koehl, P., and M. Levitt. 2002. Protein topology and stability define the space of allowed sequences. Proc. Natl. Acad. Sci. USA. 993:1280-1285.
19. Miller, D. W., and K. A. Dill. 1997. Ligand binding to proteins: the binding landscape model. Protein Sci. 6:2166-2179.
20. Mirny, L. A., V. I. Abkevich, and E. I. Shakhnovich. 1998. How evolution makes proteins fold quickly. Proc. Natl. Acad. Sci. USA. 95:4976-4981.
21. Miyazawa, S., and R. L. Jernigan. 1985. Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules. 18:534-552.
22. Press, W. H., S. A. Teukolsky, W. T. Vetterling, and B. P. Flannery, editors 2002. Are two distributions different? In Numerical Recipes in C. Cambridge University Press, Cambridge, UK. 620-628.
23. Rapaport, D. C. 1987. Algorithms for lattice statistics. Comput. Phys. Rep. 5:265-350.
24. Rees, D. C., and M. W. W. Adams. 1995. Hyperthermophiles: taking the heat and loving it. Structure. 3:251-254.
25. Schreiber, G., A. M. Buckle, and A. R. Fersht. 1994. Stability and function: two constraints in the evolution of barstar and other proteins. Structure. 2:945-951.
26. Serrano, L., A. G. Day, and A. R. Fersht. 1993. Step-wise mutation of barnase to binase: a procedure for engineering increased stability of proteins and an experimental analysis of the evolution of protein stability. J. Mol. Biol. 233:305-312.
27. Shakhnovich, E. I. 1998. Protein design: a perspective from simple tractable models. Fold. Des. 3:R45-R58.
28. Shakhnovich, E. I., and A. M. Gutin. 1993. Engineering of stable and fast-folding sequences of model proteins. Proc. Natl. Acad. Sci. USA. 90:7195-7199.
29. Shoichet, B. K., W. A. Baase, R. Kuroki, and B. W. Matthews. 1995. A relationship between protein stability and protein function. Proc. Natl. Acad. Sci. USA. 92:452-456.
30. Socci, N. D., J. N. Onuchic, and P. G. Wolynes. 1998. Protein folding mechanisms and the multidimensional folding funnel. Proteins. 32:136-158.
31. Somero, G. N. 1995. Proteins and temperature. Annu. Rev. Physiol. 57:43-68.
32. Taverna, D. M., and R. A. Goldstein. 2000. The distribution of structures in evolving protein populations. Biopolymers. 53:1-8.
33. Taverna, D. M., and R. A. Goldstein. 2002. Why are proteins marginally stable? Proteins. 46:105-109.
34. Tiana, G., R. Broglia, and E. Shakhnovich. 2000. Hiking in the energy landscape in sequence space: a bumpy road to good folders. Proteins. 39:244-251.
35. Wang, X., G. Minasov, and B. K. Shoichet. 2002. Evolution of an antibiotic resistance enzyme constrained by stability and activity trade-offs. J. Mol. Biol. 320:85-95.
36. Williams, P. D., D. D. Pollock, and R. A. Goldstein. 2001. Evolution of functionality in lattice proteins. J. Mol. Graph. Model. 19:150-156.
37. Xia, Y., and M. Levitt. 2002. Roles of mutation and recombination in the evolution of protein thermodynamics. Proc. Natl. Acad. Sci. USA. 16:10382-10387.