Protein design: A perspective from simple tractable models

Folding and Design

Volumn 3, Issue 3, 1998, Pages

  Shakhnovich, Eugene I ^a  

^a HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID COMPOSITION; AMINO ACID SEQUENCE; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE; REVIEW; STOCHASTIC MODEL; SYSTEM ANALYSIS; THERMODYNAMICS;

EID: 0031745665     PISSN: 13590278     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1359-0278(98)00021-2     Document Type: Review

References (90)

1. Karplus, M & Shakhnovich, E. (1992). Theoretical studies of thermodynamics and dynamics. In Protein Folding, pp. 127-196. W.H. Freeman and Company, New York.
2. Bryngelson, J., Onuchic, J.N., Socci, N.D. & Wolynes, P. (1995). Funnels, pathways, and the energy landscape of protein folding: a synthesis. Proteins 21, 167-195.
3. Fersht, A. (1997). Nucleation mechanism of protein folding. Curr. Opin. Struct. Biol. 7, 10-14.
4. Shakhnovich, E.I. (1997). Theoretical studies of protein-folding thermodynamics and kinetics. Curr. Opin. Struct. Biol. 7, 29-40.
5. Quinn, T., Tweedy, N., Williams, R., Richardson, J. & Richardson, D. (1994). Betadoublet: de novo design, synthesis and characterization of a β-sandwich protein. Proc. Natl Acad. Sci. USA 91, 8747-8751.
6. Dahiyat, B. & Mayo, S. (1997). De novo design: fully automated sequence selection. Science 278, 82-87.
7. Riddle, N.S., et al., & Baker, D. (1997). Functional rapidly folding proteins from simplified amino acid sequences. Nat. Struct. Biol. 4, 805-809.
8. Goldstein, R., Luthey-Schulten, Z.A. & Wolynes, V. (1992). Optimal protein-folding codes from spin-glass theory. Proc. Natl Acad. Sci. USA 89, 4918-4922.
9. Shakhnovich, E.I. & Gutin, A. (1993). Engineering of stable and fast-folding sequences of model proteins. Proc. Natl Acad. Sci. USA 90, 7195-7199.
10. Sali, A., Shakhnovich, E.I. & Karplus, M. (1994). Kinetics of protein folding. A lattice model study for the requirements for folding to the native state. J. Mol. Biol. 235, 1614-1636.
11. Klimov, D. & Thirumalai, D. (1996). A criterion which determines foldability of proteins. Phys. Rev. Lett. 76, 4070-4073.
12. Anfinsen, C. (1973). Principles that govern the folding of protein chains. Science 181, 223-230.
13. Ueda, Y., Taketomi, H. & Go, N. (1975). Studies on protein folding, unfolding and fluctuations by computer simulation. Int. J. Pept. Protein Res. 7, 445-449.
14. Shakhnovich, E.I. & Gutin, A.M. (1989). Formation of unique structure in polypeptide chains, theoretical investigation with the aid of replica approach. Biophys. Chem. 34, 187-199.
15. Sfatos, C., Gutin, A.M. & Shakhnovich, E.I. (1993). Phase diagram of random copolymers. Phys. Rev. E 48, 465-475.
16. Ramanathan, S. & Shakhnovich, E.I. (1994). Statistical mechanics of proteins with 'evolutionary selected' sequences. Phys. Rev. E 50, 1303-1312.
17. Pande, V., Grosberg, A.Y. & Tanaka, T. (1995). Freezing transition of random heteropolymers consisting of arbitrary sets of monomers. Phys. Rev. E 51, 3381-3393.
18. Shakhnovich, E.I. (1994). Proteins with selected sequences fold to their unique native conformation. Phys. Rev. Lett 72, 3907-3910.
19. Pande, V.S., Grosberg, A.Y. & Tanaka, T. (1997). Statistical mechanics of simple models of protein folding and design. Biophys. J. 73, 3192-3210.
20. Pande, V.S., Grosberg, A.Y. & Tanaka, T. (1994). Folding thermodynamics and kinetics of imprinted renaturable heteropolymers J. Chem. Phys. 101, 8246-8257.
21. Bryngelson, J.D. & Wolynes, P.G. (1987). Spin glasses and the statistical mechanics of protein folding. Proc. Natl Acad. Sci. USA 84, 7524-7528.
22. Myazawa, S. & Jernigan, R. (1985). Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules 18, 534-552.
23. Kolinski, A., Godzik, A. & Skolnick, J. (1993). The general method for the prediction of the three-dimensional structure and folding pathway of globular proteins: application to designed helical proteins. J. Chem. Phys. 98, 7420-7433.
24. Shakhnovich, E.I., Farztdinov, G.M., Gutin, A.M. & Karplus, M. (1991). Protein folding bottlenecks: a lattice Monte-Carlo simulation. Phys. Rev. Lett. 67, 1665-1667.
25. Socci, N. & Onuchic, J. (1994). Folding kinetics of protein-like heteropolymers. J. Chem. Phys. 101, 1519-1528.
26. Sippl, M. (1990). Calculation of conformational ensemble from potential of mean force. An approach to knowledge-based prediction of local structures in globular proteins. J. Mol. Biol. 213, 859-883.
27. Mirny, L. & Shakhnovich, E.I. (1996). How to determine protein folding potential? A new approach to the old problem. J. Mol. Biol. 264, 1164-1169.
28. Finkelstein, A.V., Gutin, A. & Badretdinov, A. (1993). Why are some protein structures so common? FEBS Lett. 325, 23-28.
29. Shakhnovich, E.I. & Gutin, A.M. (1990). Implications of thermodynamics of protein folding for evolution of primary sequences. Nature 346, 773-775.
30. Gutin, A.M. & Shakhnovich, E.I. (1993). Ground state of random copolymers and the discrete random energy model. J. Chem. Phys. 98, 8174-8177.
31. Mezard, M., Parisi, G., & Virasoro, M. (1998). Spin Glass Theory and Beyond. World Science, Singapore.
32. Gutin, A., Sali, A., Abkevich, V., Karplus, M. & Shakhnovich, E.I. (1998). Temperature dependence of folding in a simple protein like model: search for glass transition. J. Chem. Phys., in press.
33. Yue, K., Fiedig, K., Thomas, P., Chan, U.S., Shakhnovich, E.I. & Dill, K.A. (1995). A test of lattice protein folding algorithms. Proc. Natl Acad. Sci. USA 92, 325-329.
34. O'Toole, E.M. & Panagiotoupoulos, A.Z. (1993). Effect of sequence and intermolecular interactions on the number and nature of low-energy states of simple model proteins. J. Chem. Phys. 98, 3185-3190.
35. Grosberg, A.Y. & Khohlov, A.R. (1994). Statistical Mechanics of Macromolecules. AIP Press, New York.
36. Abkevich, V., Gutin, A. & Shakhnovich, E.I. (1995). Impact of local and non-local interactions on thermodynamics and kinetics of protein folding. J. Mol. Biol. 252, 460-471.
37. Shakhnovich, E.I. & Gutin, A.M. (1989). Frozen states of disordered globular heteropolymers. J. Phys. A22, 1647-1654.
38. Pande, V., Grosberg, A., Joerg, C. & Tanaka, T. (1996). Is heteropolymer freezing well described by the random energy model? Phys. Rev. Lett. 76, 3987-3990.
39. Govindarajan, S. & Goldstein, R. (1995). Searching for foldable protein structures using optimized energy functions. Biopolymers 36, 43-51.
40. Grosberg, A.Y., Nechaev, S.K. & Shakhnovich, El. (1988). The role of topological constraints in the kinetics of collapse of macromolecules. J. Phys. (France) 49, 2095-2100.
41. Shakhnovich, E.I. & Gutin, A. (1993). A novel approach to design of stable proteins. Protein Eng. 6, 793-800.
42. Pande, V., Grosberg, A.Y. & Tanaka, T. (1994). Thermodynamic procedure to synthesize heteropolymers that can renature to recognize a given target molecule. Proc. Natl Acad. Sci. USA 91, 12976-12979.
43. Gutin, A., Abkevich, V. & Shakhnovich, E.I. (1995). Is burst hydrophobic collapse necessary for rapid folding? Biochemistry 34, 3066-3076.
44. Chung, M., Neuwald, A. & Wilbur, W.J. (1998). A free energy analysis by unfolding applied to 125-mers on a cubic lattice. Fold. Des. 3, 51-65.
45. Jones, D. (1995). Theoretical approaches to designing novel sequences to fit a given fold. Curr. Opin. Biotechnol. 6, 452-459.
46. Koehl, P. & Delarue, M. (1996). Mean-field minimisation methods for biological macromolecules. Curr. Opin. Struct. Biol. 6, 222-226.
47. Saven, J. & Wolynes, P. (1997). Statistical mechanics of the combinatorial synthesis and analysis of folding macromolecules. J. Phys. Chem. 101, 8375-8389.
48. Finkelstein, A.V., Gutin, A. & Badretdinov, A. (1995). Why are the same protein folds used to perform different functions? Proteins 23, 142-149.
49. Li, H., Winfreen, N. & Tang, C. (1996). Emergency of preferred structures in a simple model of protein folding. Science 273, 666-669.
50. Shakhnovich, E.I. & Gutin, A.M. (1990). Exhaustive enumeration of all conformations of compact heteropolymers with quenched disordered sequence of links. J. Chem. Phys. 93, 5967-5971.
51. Deutsch, J.M. & Kurosky, T. (1996). New algorithm for protein design. Phys. Rev. Lett. 76, 323-326.
52. Morrissey, M. & Shakhnovich, E.I. (1996). Design of proteins with selected thermal properties. Fold. Des. 1, 391-406.
53. Seno, F., Vendruscolo, M., Maritan, A. & Banavar, J. (1996). Optimal protein design procedure. Phys. Rev. Lett. 77, 1901-1904.
54. Mirny, L., Abkevich, V. & Shakhnovich, El. (1996). Universality and diversity of the protein folding scenarios: a comprehensive analysis with the aid of lattice model. Fold. Des. 1, 103-116.
55. Bowie, J.U., Luthy, R. & Eisenberg, D. (1991). A method to identify protein sequences that fold into a known three-dimensional structure. Science 253, 164-169.
56. Gutin, A., Abkevich, V. & Shakhnovich, E.I. (1996). Chain length scaling of protein folding time. Phys. Rev. Lett. 77, 5433.
57. Shakhnovich, El. (1994). Statistical Mechanics, Protein Structure and Protein-Ligand Interactions. Plenum Press, New York.
58. Sando, G.N. & Hogenkamp, P.C. (1973). Ribonucleotide reductase from thermus x1, a thermophilic organism. Biochemistry 12, 3316-3322.
59. Abkevich, V., Gutin, A. & Shakhnovich, E. (1995). Domains in folding of model proteins. Protein Sci. 4, 1167-1177.
60. Gutin, A., Abkevich, V. & Shakhnovich, E.I. (1998). Cooperativity of protein folding and the random-field Ising model. Phys. Rev. E, in press.
61. Panchenko, A., Luthey-Schulten, Z. & Wolynes, P. (1995). Foldons, protein structural modules and exons. Proc. Natl Acad. Sci. USA 93, 2003-2013.
62. Abkevich, V., Gutin, A. & Shakhnovich, E.I. (1996). Improved design of stable and fast-folding proteins. Fold. Des. 1, 221-232.
63. Gutin, A., Abkevich, V. & Shakhnovich, El. (1995). Evolution-like selection of fast-folding model proteins. Proc. Natl Acad. Sci. USA 92, 1282-1286.
64. Mirny, L., Abkevich, V. & Shakhnovich, E.I. (1998). How evolution makes proteins fold quickly. Proc. Natl Acad. Sci. USA, in press.
65. Abkevich, V., Gutin, A. & Shakhnovich, E.I. (1994). Specific nucleus as the transition state for protein folding: evidence from the lattice model. Biochemistry 33, 10026-10036.
66. Itzhaki, L, Otzen, D. & Fersht, A. (1995). The structure of the transition state for folding of chymotrypsin inhibitor 2 analyzed by protein engineering methods: evidence for a nucleation-condensation mechanism for protein folding. J. Mol. Biol. 254, 260-288.
67. Fersht, A.R. (1995). Optimization of rates of protein folding: the nucleation-condensation mechanism and its implications. Proc. Natl Acad. Sci. USA 92, 10869-10873.
68. Shakhnovich, E.I., Abkevich, V. & Ptitsyn, O. (1996). Conserved residues and the mechanism of protein folding. Nature 379, 96-98.
69. Ebeling, M. & Nadler, W. (1995). On constructing folding heteropolymers. Proc. Natl Acad. Sci. USA 92, 8798-8802.
70. Abkevich, V., Gutin, A. & Shakhnovich, E.I. (1994). Free energy landscape for protein folding kinetics. Intermediates, traps and multiple pathways in theory and lattice model simulations. J. Chem. Phys. 101, 6052-6062.
71. Lifshits, E.M. & Pitaevskii, L.P. (1997). Physical Kinetics. Pergamon, Oxford.
72. Guo, Z. & Brooks, C. (1997). Thermodynamics of protein folding: a statistical-mechanical study of a small all beta-protein. Biopolymers 42, 745-757.
73. Socci, N. & Onuchic, J. (1995). Kinetics and thermodynamic analysis of protein like heteropolymer: Monte Carlo histogram technique. J. Chem. Phys. 103, 4732-4744.
74. Privalov, P.L. (1996). Intermediate states in protein folding. J. Mol. Biol. 258, 707-725.
75. Guo, Z. & Thirumalai, D. (1995). Nucleation mechanism for protein folding and theoretical predictions for hydrogen-exchange labelling experiments. Biopolymers 35, 137-139.
76. Guo, Z. & Thirumalai, D. (1997). The nucleation collapse mechanism in protein folding: evidence for the non-uniqueness of the folding nucleus. Fold. Des. 2, 377-391.
77. Kamtekar, M., Schiffer, M., Xiong, H., Babik, J. & Hecht, M. (1993). Protein design by binary patterning of polar and nonpolar amino acids. Science 262, 1680-1685.
78. Holm, L. & Sander, C. (1993). Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233, 123-138.
79. Ladurner, A., Itzhaki, L. & Fersht, A. (1997). Strain in the folding nucleus of chymotrypsin inhibitor 2. Fold. Des. 2, 363-366.
80. Pande, V.S., Grosberg, A.Y., Rokshar, D. & Tanaka, T. (1998). Pathways for protein folding: is a 'new view' needed. Curr. Opin. Struct. Biol. 8, 68-79.
81. Jernigan, R. & Bahar, I. (1996). Structure-derived potentials and folding simulations. Curr. Opin. Struct Biol. 6, 195-209.
82. Jones, D. & Thornton, J. (1996). Potential energy functions for threading. Curr. Opin. Struct. Biol. 6, 210-216.
83. DeWitte, R.S. & Shakhnovich, E.I. (1996). Smog: de novo design method based on simple, fast and accurate free energy estimates. 1. Methodology and supporting evidence. J. Am. Chem. Soc. 118, 11733-11744.
84. Ponder, J. & Richards, F.M. (1994). Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes. J. Mol. Biol. 193, 5803-5807.
85. Lim, W. & Sauer, R. (1991). The role of internal packing interactions in determining the structure and stability of a protein. J. Mol. Biol. 219, 359-376.
86. Lim, W., Hadel, A., Sauer, R.T., & Richards, F.M. (1994). The crystal structure of a mutant protein with altered but improved hydrophobic core packing. Proc. Natl Acad. Sci. USA 91, 423-427.
87. Baldwin, E., Hajiseyedjavadi, O., Baas, W. & Mathews, B. (1993). The role of backbone flexibility in the accommodation of variants that repack the core of 14 lysozyme. Science 262, 1715-1718.
88. Dahiyat, B. & Mayo, S. (1995). Probing the role of packing specificity in protein design. Proc. Natl Acad. Sci. USA 94, 10172-10177.
89. De Maeyer, M., Desmet, J. & Lasters, I. (1997). All in one: a highly detailed rotamer library improves both accuracy and speed in the modelling of sidechains by dead-end elimination. Fold. Des. 2, 53-66.
90. Hellinga, H. & Richards, F. (1994). Optimal sequence selection in proteins of known structure by simulated evolution. Proc. Natl Acad. Sci. USA 91, 5803-5807.