Polymer principles and protein folding

Protein Science

Volumn 8, Issue 6, 1999, Pages 1166-1180

  Dill, Ken A ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

New view; Polymer; Protein folding; Statistical mechanics

Indexed keywords

PROTEIN;

HUMAN; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN POLYMERIZATION; PROTEIN SECONDARY STRUCTURE; REVIEW; STATISTICAL MODEL;

EID: 0032993447     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.8.6.1166     Document Type: Review

References (103)

1. Alberts B, Bray D, Johnson A, Raff M, Roberts K, Walter P. 1998. Essential cell biology: An introduction to the molecular biology of the cell. New York: Garland.
2. Anfinsen CB, Scheraga HA. 1975. Experimental and theoretical aspects of protein folding. Adv Prot Chem 29:205-300.
3. Aurora R, Creamer TP, Srinivasan R, Rose GD. 1997. Local interactions in protein folding: Lessons from the α-helix. J Biol Chem 272:1413-1416.
4. Baldwin RL. 1994. Protein folding: Matching speed and stability. Nature 369:183-184.
5. Baldwin RL. 1995. The nature of protein folding pathways: The classic versus the new view. J Biomol NMR 5:103-109.
6. Baldwin RL, Rose GD. 1999a. Is protein folding hierarchic? I. Local structure and peptide folding. Trends Biochem Sci 24:26-33.
7. Baldwin RL, Rose GD. 1999b. Is protein folding hierarchic? II. Folding intermediates and transition states. Trends Biochem Sci 24:77-83.
8. Ballew RM, Sabelko J, Gruebele M. 1996a. Direct observation of fast protein folding: The initial collapse of apomyoglobin. Proc Natl Acad Sci USA 95:5759-5754.
9. Ballew RM, Sabelko J, Gruebele M. 1996b. Observation of distinct nanosecond and microsecond protein folding events. Nature Struct Biol 5:923-926.
10. Bowie J, Reidhaar-Olson J, Lim WA, Sauer RT. 1990. Deciphering the messages in protein sequences: Tolerance to amino acid substitutions. Science 247:1306-1310.
11. Branden C, Tooze J. 1999. Introduction to protein structure, 2nd ed. New York: Garland.
12. Bromberg S, Dill KA. 1994. Side chain entropy and packing in proteins. Protein Sci 3:997-1009.
13. Bryngelson J, Onuchic J, Socci ND, Wolynes PG. 1995. Funnels, pathways, and the energy landscape of protein folding: A synthesis. Proteins 21:167-195.
14. Bryngelson J, Wolynes PG. 1987. Spin-glass and the statistical mechanics of protein folding. Proc Natl Acad Sci USA 84:7524-7528.
15. Burton RE, Huang GS, Daugherty MA, Calderone TL, Oas TG. 1997. The energy landscape of a fast-folding protein mapped by ala → gly substitutions. Nature Struct Biol 4:305-310.
16. Callendar RH, Gilmanshin R, Dyer RB, Woodruff WH. 1999. Annu Rev Phys Chem. Forthcoming.
17. Camacho CJ, Thirumalai D. 1993. Kinetics and thermodynamics of folding in model proteins. Proc Natl Acad Sci USA 90:6369-6372.
18. Chan C-K, Hu Y, Takahashi S, Rousseau DL, Eaton WA, Hofrichter J. 1997. Submillisecond protein folding kinetics studied by ultrarapid mixing. Proc Natl Acad Sci USA 94:1779-1784.
19. Chan HS, Dill KA. 1991. "Sequence space soup" of protein and copolymers. J Chem Phys 95:3775-3787.
20. Chan HS, Dill KA. 1994. Transition states and folding dynamics of proteins and heteropolymers. J Chem Phys 100:9238-9257.
21. Chan HS, Dill KA. 1998. Protein folding in the landscape perspective: Chevron plots and non-Arrhenius kinetics. Proteins 30:2-33.
22. Chandler D. 1987. Introduction to modern statistical mechanics. New York: Oxford Press.
23. Dawkins R. 1996. The blind watchmaker: Why the evidence of evolution reveals a universe without design. New York: Norton.
24. Dill KA. 1985. Theory for the folding and stability of globular proteins. Biochemistry 24:1501-1509.
25. Dill KA. 1987. The stabilities of globular proteins. In: Oxender DL, Fox CF, eds. Protein Engineering. Alan R. Liss Inc. pp 187-192.
26. Dill KA. 1993. Folding proteins: Finding a needle in a haystack. Curr Op Struct Biol 3:99-103.
27. Dill KA, Bromberg S, Yue K, Fiebig KM, Yee DP, Thomas PD, Chan HS. 1995. Principles of protein folding: A perspective from simple exact models. Protein Sci 4:561-602.
28. Dill KA, Chan HS. 1997. From Levinthal to pathways to funnels: The "new view" of protein folding kinetics. Nature Struct Biol 4:10-19.
29. Dill KA, Fiebig KM, Chan HS. 1993. Cooperativity in protein-folding kinetics. Proc Natl Acad Sci USA 90:1942-1946.
30. Dill KA, Phillips, AT, Rosen JB. 1997. Protein structure and energy landscape dependence on sequence using a continuous energy function. J Comp Biol 4:227-239.
31. Doty P, Bradbury JH, Holtzer AM. 1956. The molecular weight, configuration and association of poly-γ-benzyl-L-glutamate in various solvents. J Am Chem Soc 78:947-954.
32. Doty P, Yang JT. 1956. Polypeptides VII. Poly-gamma-benzyl-L-glutamate: The helix-coil transition in solution. J Am Chem Soc 78:498.
33. Eisenberg D, Weiss RM, Terwilliger C. 1984. The hydrophobic moment detects periodicity in protein hydrophobicity. Proc Natl Acad Sci USA 81:140-144.
34. Fiebig KM, Dill KA. 1993. Protein core assembly processes. J Chem Phys 98:3475-3487.
35. Flory PJ. 1953. Principles of polymer chemistry. Ithaca, New York: Cornell University Press. pp 8-19.
36. Frauenfelder H, Sligar SG, Wolynes PG. 1991. The energy landscapes and motions of proteins. Science 254:1598-1603.
37. Gassner NC, Baase WA, Matthews BW. 1992. A test of the jigsaw puzzle model for protein folding by multiple methionine substitutions within the core of T4 lysozyme. Proc Natl Acad Sci USA 93:12155-12158.
38. Gilmanshin R, Callendar RH, Dyer RB. 1998. Fast events in protein folding: The time evolution of primary processes. Nature Struct Biol 5:363-365.
39. Gilmanshin R, Williams S, Callendar RH, Woodruff WH, Dyer RB. 1997a. Fast events in protein folding: Relaxation dynamics of secondary and tertiary structure in native apomyoglobin. Proc Natl Acad Sci USA 94:3709-3713.
40. Gilmanshin R, Williams S, Callendar RH, Woodruff WH, Dyer RB. 1997b. Fast events in protein folding: Relaxation dynamics and structure of the I form of apomyoglobin. Biochemistry 36:15006-15012.
41. Hamada D, Segawa S, Goto Y. 1996. Non-native alpha-helical intermediate in the refolding of beta-lactoglobulin: A predominantly beta-sheet protein. Nature Struct Biol 3:868-873.
42. Harrison SC, Durbin R. 1985. Is there a single pathway for the folding of a polypeptide chain? Proc Natl Acad Sci USA 82:4028-4030.
43. Honig B, Cohen FE. 1996. Adding backbone to protein folding: Why proteins are polypeptides. Folding Design 1:R17-R20.
44. Huang GS, Oas TG. 1995. Submillisecond folding of monomeric λ repressor. Proc Natl Acad Sci USA 92:6878-6882.
45. Kabsch W, Sander C. 1984. On the use of sequence homologies to predict protein structure: Identical pentapeptides can have completely different conformations. Proc Natl Acad Sci USA 81:1075-1078.
46. Kamtekar S, Schiffer JM, Xiong H, Babik JM, Hecht MH. 1993. Protein design by binary patterning of polar and nonpolar amino acids. Science 262:1680-1685.
47. Karplus M. 1997. The Levinthal paradox: Yesterday and today. Folding Design 2:S69-S75.
48. Karplus M, Weaver DL. 1976. Protein-folding dynamics. Nature 260:404-406.
49. Kauzmann W. 1959. Some factors in the interpretation of protein denaturation. Adv Prot Chem 14:1-63.
50. Kendrew JC, Bodo G, Dintzis HM, Parrish RG, Wyckoff H, Phillips DC. 1958. A three-dimensional model of the myoglobin molecule obtained by X-ray analysis. Nature 181:662-666.
51. Kim PS, Baldwin RL. 1982. Specific intermediates in the folding reactions of small proteins and the mechanism of protein folding. Annu Rev Biochem 51:459-489.
52. Kuroda Y, Hamada D, Tanaka T, Goto Y. 1996. High helicity of peptide fragments corresponding to beta-strand regions of beta-lactoglobulin observed by 2D-NMR spectroscopy. Folding Design 4:255-263.
53. Lau KF, Dill KA. 1990. Theory for protein mutability and biogenesis. Proc Natl Acad Sci USA 87:638-642.
54. Lazar GA, Desjarlais JR, Handel TM. 1997. De novo design of the hydrophobic core of ubiquitin. Protein Sci 6:1167-1178.
55. Lazaridis T, Karplus M. 1997. "New view" of protein folding reconciled with the old through multiple unfolding simulations. Science 278:1928-1931.
56. Lee S, Bashford D, Karplus M, Weaver DL. 1987. Brownian dynamics simulation of protein folding: A study of the diffusion-collision model. Biopolymers 20:481-509.
57. Levinthal C. 1968. Are there pathways for protein folding? J Chim Phys 65: 44-45.
58. Lim WA, Farrugio DC, Sauer RT. 1992. Structural and energetic consequences of disruptive mutations in a protein core. Biochemistry 31:4324.
59. Lim WA, Sauer RT. 1991. The role of internal packing interactions in determining the structure and stability of a protein. J Mol Biol 219:359-376.
60. Lipman DJ, Wilbur WJ. 1991. Modeling neutral and selective evolution of protein folding. Proc Roy Soc B245:7-11.
61. Maranas DC, Androulakis IP, Floudas CA. 1995. A deterministic global optimization approach for the protein folding problem. DIMACS series in Discrete Mathematics and Theoretical Computer Science 23:133-150.
62. Matthews BW. 1993. Structural and genetic analysis of protein stability. Annu Rev Biochem 62:139-160.
63. Miller DW, Dill KA. 1995. A statistical mechanical model for hydrogen exchange in globular proteins. Protein Sci 4:1860-1873.
64. Miller DW, Dill KA. 1997. Ligand binding to proteins: The binding landscape model. Protein Sci 6:2166-2179.
65. Miller R, Danko CA, Fasolka MJ, Balacz AC, Chan HS, Dill KA. 1992. Folding kinetics of proteins and copolymers. J Chem Phys 96:768-780.
66. Minor DL, Kim PS. 1994. Context is a major determinant of beta-sheet propensity. Nature 371:264-267.
67. Mirsky AE, Pauling L. 1936. On the structure of native, denatured, and coagulated proteins. Proc Natl Acad Sci USA 22:439-447.
68. Morawetz H. 1985. Polymers: The origins and growth of a science. New York: Wiley.
69. Munson M, Balasubramanian S, Fleming KG, Nagi AD, et al. 1996. What makes a protein a protein: Hydrophobic core designs that specify stability and structural properties. Protein Sci 5:1584-1593.
70. Munson M, O'Brien R, Sturtevant JM, Regan L. 1994. Redesigning the hydrophobic core of a four-helix-bundle-protein. Protein Sci 3:2105-2022.
71. Onuchic JN, Luthy-Schulten Z, Wolynes PG. 1997. Theory of protein folding: The energy landscape perspective. Annu Rev Phys Chem 48:545-600.
72. Pande VS, Grosberg AY, Tanaka T, Rokhsar DS. 1998. Pathways for protein folding: Is a new view needed? Curr Op Struc Biol 8:68-79.
73. Pande VS, Rokhsar DS. 1999. Folding pathway of a lattice model for proteins. Proc Natl Acad Sci USA 96:1273-1278.
74. Pascher T, Chesick JP, Winkler JR, Gray HB. 1996. Protein folding triggered by electron transfer. Science 271:1558-1560.
75. Pauling L, Corey RB. 1951a. Atomic coordinates and structure factors for two helical configurations of polypeptide chains. Proc Natl Acad Sci USA 37:235-240.
76. Pauling L, Corey RB. 1951b. The pleated sheet, a new layer configuration of polypeptide chains. Proc Natl Acad Sci USA 37:251-256.
77. Pauling L, Corey RB. 1951c. The structure of fibrous proteins of the collagen-gelatin group. Proc Natl Acad Sci USA 37:272-281.
78. Pauling L, Corey RB. 1951d. Configurations of polypeptide chains with favored orientations around single bonds: Two new pleated sheets. Proc Natl Acad Sci USA 37:729-740.
79. Pauling L, Corey RB, Branson HR. 1951. The structure of proteins: Two hydrogen-bonded helical configurations of the polypeptide chain. Proc Natl Acad Sci USA 37:205-211.
80. Phillips AT, Rosen JB, Walke VH. 1995. Molecular structure determination by convex global underestimation. DIMACS series in Discrete Mathematics and Theoretical Computer Science 23:181.
81. Poland DC, Scheraga HA. 1970. Theory of the helix-coil transition. New York: Academic Press.
82. Predki PF, Agrawal V, Brunger AT, Regan L. 1996. Amino-acid substitutions in a surface turn modulate protein stability. Nature Struct Biol 3:54-58.
83. Ramachandra Shastry MC, Roder H. 1998. Evidence for barrier-limited protein folding kinetics on the microsecond time scale. Nature Struct Biol 5:385-392.
84. Ramachandra Shastry MC, Saunder JM, Roder H. 1998. Kinetic and structural analysis of submillisecond folding events in cytochrome c. Acc Chem Res 31:717-725.
85. Reidhaar-Olson JF, Sauer RT. 1988. Combinatorial cassette mutagenesis as a probe of the informational content of protein sequences. Science 241:53-57.
86. Riddle DS, Santiago JV, BrayHall ST, Doshi N, Grantcharova VP, Yi Q, Baker D. 1997. Functional rapidly folding proteins from simplified amino acid sequences. Nature Struct Biol 4:805-809.
87. Roy S, Ratnaswamy G, Boice JA, Fairman D, McLendon G, Hecht MH. 1997. A protein designed by binary patterning of polar and nonpolar amino acids displays native-like properties. J Am Chem Soc 116:5302-5306.
88. Schafmeister CE, LaPorte SL, Miercke LJW, Stroud RM. 1997. A designed four helix bundle protein with native-like structure. Nature Struct Biol 4:1039-1046.
89. Schellman JA. 1958. The factors affecting the stability of hydrogen-bonded polypeptide structures in solution. J Chem Phys 62:1485.
90. Scholtz JM, Baldwin RL. 1992. The mechanism of α-helix formation by peptides. Annu Rev Biophys Biomol Struct 21:95-118.
91. Shiraki K, Nishikawa K, Goto Y. 1995. Trifluoroethanol-induced stabilization of the α-helical structure of β-lectoglobulin: Implication for non-hierarchical protein folding. J Mol Biol 245:180-194.
92. Smith CK, Regan L. 1995. Guidelines for protein design: The energetics of beta-sheet side chain interactions. Science 270:980-982.
93. Stanley HE. 1971. Introduction to phase transitions and critical phenomena, Oxford: Oxford Press.
94. Tang KES, Dill KA. 1998. Native protein fluctuations: The conformationalmotion temperature and the inverse correlation of protein flexibility with protein stability. J Biomol Struct Dyn 16:397-411.
95. Thomas PD, Dill KA. 1993. Local and nonlocal interactions in globular proteins and mechanisms of alcohol denaturation. Protein Sci 2:2050-2065.
96. Tsai C-J, Kumar S, Ma B, Nussinov R. 1999. Folding funnels, binding funnels, and protein function. Protein Sci 8:1179-1188.
97. Wetlaufer DB. 1973. Nucleation, rapid folding, and globular intrachain regions in proteins. Proc Natl Acad Sci USA 70:697-701.
98. Williams S, Causgrove TP, Gilmanshin R, Fang KS, Callendar RH, Woodruff WH, Dyer RB. 1996. Fast events in protein folding: Helix melting and formation in a small peptide. Biochemistry 35:691-697.
99. Wu LC, Kim PS. 1997. Hydrophobic sequence minimization of the α-lactalbumin molten globule. Proc Natl Acad Sci USA 94:14314-14319.
100. Yapa K, Weaver DL, Karplus M. 1992. β-sheet coil transitions in a simple polypeptide model. Proteins 12:237-265.
101. Yue K, Dill KA. 1995. Forces of tertiary structural organization in globular proteins. Proc Natl Acad Sci USA 92:146-150.
102. Zimm BH, Bragg J. 1959. Theory of the phase transition between helix and random coil in polypeptide chains. J Chem Phys 31:526.
103. Zwanzig R, Szabo A, Bagchi B. 1992. Levinthal's paradox. Proc Natl Acad Sci USA 89:20-22.