Comparing folding codes for proteins and polymers

Proteins: Structure, Function and Genetics

Volumn 24, Issue 3, 1996, Pages 335-344

  Chan, Hue Sun ^a   Dill, Ken A ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

energy matrix; protein design; sequence degeneracy; structural encodability; synthetic heteropolymer design

Indexed keywords

ARTICLE; CALCULATION; ENERGY; MATHEMATICAL MODEL; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FOLDING; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

MODELS, CHEMICAL; MOLECULAR CONFORMATION; MOLECULAR STRUCTURE; POLYMERS; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEINS; THERMODYNAMICS;

EID: 0003155594     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(199603)24:3<335::AID-PROT6>3.0.CO;2-F     Document Type: Article

References (47)

1. Lau, K.F., Dill, K.A. A lattice statistical mechanical model of the conformational and sequence spaces of proteins. Macromolecules 22:3986-3997, 1989.
2. Chan, H.S., Dill, K.A. Polymer principles in protein structure and stability. Annu. Rev. Biophys. Biophys. Chem. 20:447-490, 1991.
3. Chan, H.S., Dill, K.A. "Sequence space soup" of proteins and copolymers. J. Chem. Phys. 95:3775-3787, 1991.
4. Yue, K., Dill, K.A. Inverse protein folding problem: Designing polymer sequences. Proc. Natl. Acad. Sci. USA 89: 4163-4167, 1992.
5. Yue, K., Dill, K.A. Sequence structure relationship of proteins and copolymers. Phys. Rev. E 48:2267-2278, 1993.
6. Chan, H.S., Dill, K.A. Transition states and folding dynamics of proteins and heteropolymers. J. Chem. Phys. 100:9238-9257, 1994.
7. Yue, K., Dill, K.A. Forces of tertiary structural organization of globular proteins. Proc. Natl. Acad. Sci. USA 92: 146-150, 1995.
8. Yue, K., Fiebig, K.M., Thomas, P.D., Chan, H.S., Shakhnovich, E.I., Dill, K.A. A test of lattice protein folding algorithms. Proc. Natl. Acad. Sci. USA 92:325-329, 1995.
9. Dill, K.A., Bromberg, S., Yue, K., Fiebig, K.M., Yee, D.P., Thomas, P.D., Chan, H.S. Principles of protein folding - a perspective from simple exact models. Protein Sci. 4:561-602, 1995.
10. Shakhnovich, E.I., Gutin, A.M. Enumeration of all compact conformations of copolymers with random sequence of links. J. Chem. Phys. 93:5967-5971, 1990.
11. Shakhnovich, E.I., Gutin, A.M. Implications of thermodynamics of protein folding for evolution of primary sequences. Nature 346:773-775, 1990.
12. Shakhnovich, E., Farztdinov, G., Gutin, A.M., Karplus, M. Protein folding bottlenecks: A lattice Monte Carlo simulation. Phys. Rev. Lett. 67:1665-1668, 1991.
13. Leopold, P.E., Montai, M., Onuchic, J.N. Protein folding funnels: A kinetic approach to the sequence-structure relationship. Proc. Natl. Acad. Sci. USA 89:8721-8725, 1992.
14. O'Toole, E.M., Panagiotopoulos, A.Z. Monte Carlo simulation of folding transitions of simple model proteins using a chain growth algorithm. J. Chem. Phys. 97:8644-8652, 1992.
15. Camacho, C.J., Thirumalai, D. Minimum energy compact structures of random sequences of heteropolymers. Phys. Rev. Lett. 71:2505-2508, 1993.
16. Shakhnovich, E.I., Gutin, A.M. Engineering of stable and fast-folding sequences of model proteins. Proc. Natl. Acad. Sci. USA 90:7195-7199, 1993.
17. Shakhnovich, E.I., Gutin, A.M. A new approach to the design of stable proteins. Protein Eng. 6:793-800, 1993.
18. Gutin, A.M., Shakhnovich, E.I. Ground state of random copolymers and the discrete random energy model. J. Chem. Phys. 98:8174-8177, 1993.
19. Šali, A., Shakhnovich, E., Karplus, M. Kinetics of protein folding: A lattice model study of the requirements for folding to the native state. J. Mol. Biol. 235:1614-1636, 1994.
20. Šali, A., Shakhnovich, E., Karplus, M. How does a protein fold? Nature 369:248-251, 1994.
21. Socci, N.D., Onuchic, J.N. Folding kinetics of protein-like heteropolymers. J. Chem. Phys. 101:1519-1528.
22. Karplus, M., Šali, A. Theoretical studies of protein folding and unfolding. Curr. Opin. Struct. Biol. 5:58-73, 1995.
23. Shakhnovich, E.I. Proteins with selected sequences fold into unique native conformation. Phys. Rev. Lett. 72: 3907-3910, 1994.
24. Abkevich, V.I., Gutin, A.M., Shakhnovich, E.I. Free energy landscape of protein folding kinetics: Intermediates, traps, and multiple pathways in theory and lattice model simulations. J. Chem. Phys. 101:6052-6062, 1994.
25. Abkevich, V.I., Gutin, A.M., Shakhnovich, E.I. Specific nucleus as the transition state for protein folding: Evidence from the lattice model. Biochemistry 33:10026-10036, 1994.
26. Thirumalai, D. Theoretical perspectives on in vitro and in vivo protein folding. In: "Statistical Mechanics, Protein Structure, and Protein-Substrate Interactions." Doniach, S. (ed.). New York: Plenum, 1994:115-134.
27. Chan, H.S. Kinetics of protein folding. Nature 373:664-665, 1995.
28. Bryngelson, J.D., Onuchic, J.N., Socci, N.D., Wolynes, P.G. Funnels, pathways and the energy landscape of protein folding: A synthesis. Proteins 21:167-195, 1995.
29. Gutin, A.M., Abkevich, V.I., Shakhnovich, E.I. Is burst hydrophobic collapse necessary for protein folding? Biochemistry 34:3066-3076, 1995.
30. Gutin, A.M., Abkevich, V.I., Shakhnovich, E.I. Evolution-like selection of fast-folding model proteins. Proc. Natl. Acad. Sci. USA 92:1282-1286, 1995.
31. Onuchic, J.N., Wolynes, P.G., Luthey-Schulten, Z., Socci, N.D. Toward an outline of the topography of a realistic protein-folding funnel. Proc. Natl. Acad. Sci. USA 92: 3626-3630, 1995.
32. Abkevich, V.I., Gutin, A.M., Shakhnovich, E.I. Domains in folding of model proteins. Protein Sci. 4:1167-1177, 1995.
33. Govindarajan, S., Goldstein, R.A. Searching for foldable protein structures using optimized energy functions. Biopolymers 36:43-51, 1995.
34. Govindarajan, S., Goldstein, R.A. Optimal local propensities for model proteins. Proteins 22:413-418, 1995.
35. Betancourt, M.R., Onuchic, J.N. Kinetics of proteinlike models: The energy landscape factors that determines folding. J. Chem. Phys. 103:773-787, 1995.
36. Socci, N.D., Onuchic, J.N. Kinetic and thermodynamic analysis of proteinlike heteropolymers: Monte Carlo histogram technique. J. Chem. Phys. 103:4732-4744, 1995.
37. Chan, H.S., Dill, K.A. Compact polymers. Macromolecules 22:4559-4573, 1989.
38. Taketomi, H., Ueda, Y., Gö, N. Studies on protein folding, unfolding and fluctuations by computer simulation. Int. J. Pept. Protein Res. 7:445-459, 1975.
39. Gö, N., Taketomi, H. Respective role of short- and long-range interactions in protein folding. Proc. Natl. Acad. Sci. USA 75:559-563, 1978.
40. Sun, S., Brem, R., Chan, H.S., Dill, K.A. Designing amino acid sequences to fold with good Hydrophobic cores. Protein Eng. 8:1205-1212, 1995.
41. Miyazawa, S., Jernigan, R.L. Estimation of effective inter-residue contact energies from protein crystal structures: Quasi-chemical approximation. Macromolecules 18:534-552, 1985.
42. Camacho, C.J., Thirumalai, D. Kinetics and thermodynamics of folding in model proteins. Proc. Natl. Acad. Sci. USA 90:6369-6372, 1993.
43. Simon, R.J., Kania, R.S., Zuckermann, R.N., Huebner, V.D., Jewell, D.A., Banville, S., Ng, S., Wang, L., Rosenberg, S., Marlowe, C.K., Spellmeyer, D.C., Tan, R., Frankel, A.D., Santi, D.V., Cohen, F.E., Bartlett, P.A. Peptoids: A modular approach to drug discovery. Proc. Natl. Acad. Sci. USA 89:9367-9371, 1992.
44. Cho, C.Y., Moran, E.J., Cherry, S.R., Stephans, J.C., Fodor, S.P., Adams, C.L., Sundaram, A., Jacobs, J.W., Schultz, P.G. An unnatural biopolymer. Science 261:1303-1305, 1993.
45. Kurosky, T., Deutsch, J.M. Design of copolymeric materials. J. Phys. A 28:L387-393, 1995.
46. Deutsch, J.M., Kurosky, T. New algorithm for protein design. Phys. Rev. Lett. 76:323-326, 1996.
47. Thomas, P.D., Dill, K.A. Statistical potentials extracted from protein structures: How accurate are they? J. Mol. Biol. In press.