From folding theories to folding proteins: A review and assessment of simulation studies of protein folding and unfolding

Annual Review of Physical Chemistry

Volumn 52, Issue , 2001, Pages 499-535

  Shea, Joan Emma ^a   Brooks III, Charles L ^a  

^a NONE

Author keywords

Atomic models; Folding mechanism; Free energy surfaces; Molecular dynamics; Protein folding unfolding

Indexed keywords

CHEMICAL STRUCTURE; PROTEIN FOLDING; REVIEW;

MODELS, MOLECULAR; PROTEIN FOLDING;

EID: 0034743155     PISSN: 0066426X     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.physchem.52.1.499     Document Type: Article

References (184)

1. Anfinsen CB. 1973. Science 181:223-30
2. Anfinsen CB, Haber E, Sela M, White FH. 1961. Proc. Natl. Acad. Sci. USA 47:1309-14
3. Kim PS, Baldwin RL. 1990. Annu. Rev. Biochem. 59:631-60
4. Karplus M, Weaver DL. 1994. Protein Sci. 3:650-68
5. Cohen FE, Richmond TJ, Richard FM. 1979. J. Mol. Biol. 132:275-88
6. Levinthal C. 1968. J. Chem. Phys. 65:44-45
7. Onuchic JN, Luthey-Schulten Z, Wolynes PG. 1997. Annu. Rev. Phys. Chem. 48:545-600
8. Bryngelson JD, Onuchic JN, Wolynes PG. 1995. Proteins: Struct. Funct. Genet. 21:167-95
9. Dobson CM, Karplus M. 1999. Curr. Opin. Struct. Biol. 9:92-101
10. Dobson CM, Sali A, Karplus M. 1998. Angew. Chem. Int. Ed. 37:868-93
11. Shakhnovich EI. 1997. Curr. Opin. Struct. Biol. 7:29-40
12. Chan HS, Dill KA. 1998. Proteins: Struct. Funct. Genet. 30:2-33
13. Thirumalai D, Klimov D. 1999. Curr. Opin. Struct. Biol. 9:197-207
14. Leopold PE, Montai M, Onuchic JN. 1992. Proc. Natl. Acad. Sci. USA 89:8721-25
15. Bryngelson JD, Wolynes PG. 1987. Proc. Natl. Acad. Sci. USA 84:7524-28
16. Bryngelson JD, Wolynes PG. 1990. Biopolymers 30:177-88
17. Gō N. 1983. Annu. Rev. Biophys. Bioeng. 12:183-210
18. Chan HS, Dill KA. 1997. Proteins: Struct. Funct. Genet. 8:2-33
19. Guo Z, Thirumalai D. 1995. Biopolymers 36:745-57
20. Guo Z, Brooks CL III, Boczko EM. 1997. Proc. Natl. Acad. Sci. USA 94:10161-66
21. Guo Z, Brooks CL III. 1997. Biopolymers 42:745-57
22. Shea J-E, Nochomovitz YD, Guo Z, Brooks CL III. 1998. J. Chem. Phys. 109:2895-903
23. Honeycutt JN, Thirumalai D. 1992. Biopolymers 32:695-709
24. Shea J-E, Onuchic JN, Brooks CL III. 1999. Proc. Natl. Acad. Sci. USA 96: 12512-17
25. Shea J-E, Onuchic JN, Brooks CL III. 2000. J. Chem. Phys. 113:7663-71
26. Rey A, Skolnick J. 1991. Chem. Phys. 158:199-219
27. Boczko EM, Brooks CL III. 1995. Science 269:393-96
28. Brooks CL III. 1998. Curr. Opin. Struct. Biol. 8:222-26
29. Daggett V. 2000. Curr. Opin. Struct. Biol. 10:160-64
30. Daggett V, Levitt M. 1994. Curr. Opin. Struct. Biol. 4:291-95
31. Klimov D, Thirumalai D. 1996. Proteins: Struct. Funct. Genet. 26:411-41
32. Socci ND, Onuchic JN. 1995. J. Chem. Phys. 103:4732-44
33. Socci ND, Onuchic JN, Wolynes PG. 1996. J. Chem. Phys. 104:5860-68
34. Onuchic JN, Socci ND, Luthey-Schulten Z, Wolynes PG. 1996. Fold. Des. 1:441-50
35. Shakhnovich E, Abkevich V, Ptitsyn O. 1996. Nature 379:96-98
36. Gutin AM, Abkevich VI, Shakhnovich EI. 1998. Fold. Des. 3:183-94
37. Li L, Mirny LA, Shakhnovich EI. 2000. Nat. Struct. Biol. 7:336-42
38. Pande VS, Grosberg AY, Tanaka T, Rokhsar DS. 1998. Curr. Opin. Struct. Biol. 8:68-79
39. Dellago C, Bolhuis PG, Chandler D. 1999. J. Chem. Phys. 110:6617-25
40. Bryant Z, Pande VS, Rokhsar DS. 2000. Biophys. J. 78:584-89
41. Clementi C, Nymeyer H, Onuchic JN. 2000. J. Mol. Biol. 298:937
42. Nymeyer H, Socci ND, Onuchic JN. 2000. Proc. Natl. Acad. Sci. USA 97:634-39
43. Gutin AM, Abkevich VI, Shakhnovich EI. 1998. Fold. Des. 3:183-94
44. Brooks CL III, Karplus M, Pettitt BM. 1988. Proteins: A Theoretical Perspective of Dynamics, Structure and Thermodynamics. New York: Wiley & Sons
45. Allen MP, Tidesley DJ. 1989. Computer Simulation of Liquids. Oxford :Clarendon
46. McCammon JA, Harvey S. 1987. Dynamics of Proteins and Nucleic Acids. Cambridge Univ. Press
47. Demchuk E, Bashford D, Gippert GP, Case DA. 1997. J. Mol. Biol. 270:305-17
48. Demchuk E, Bashford D, Case DA. 1997. Fold. Des. 2:35-46
49. Daura X, Jaun B, Seebach D, van Gunsteren WF, Mark AE. 1998. J. Mol. Biol. 280:925-32
50. Daura X, van Gunsteren WF, Mark AE. 1999. Proteins: Struct. Funct. Genet. 34: 269-80
51. Duan L, Wang L, Kollman PA. 1998. Proc. Natl. Acad. Sci. USA 95:9897-902
52. Duan L, Kollman PA. 1998. Science 282:740-44
53. Bashford D, Case DA. 2000. Annu. Rev. Phys. Chem. 51:129
54. Sugita Y, Okamoto Y. 2000. Prog. Theor. Phys. Suppl. 138:402-3
55. Okamoto Y. 2000. Prog. Theor. Phys. Suppl. 138:301-10
56. Hansmann UHE, Okamoto Y. 1999. J. Chem. Phys. 111:1339
57. Ferrara P, Apostolakis J, Caflisch A. 2000. Proteins: Struct. Funct. Genet. 39:252-60
58. Lazaridis T, Karplus M. 1997. Science 278:1928-31
59. Bursulaya B, Brooks CL III. 1999. J. Am. Chem. Soc. 121:9927
60. Bartels C, Schaefer M, Karplus M. 1999. J. Chem. Phys. 111:8048-67
61. Bartels C, Schaefer M, Karplus M. 1999. Theor. Chem. Acc. 101:62-66
62. Bartels C, Karplus M. 1998. J. Phys. Chem. B 102:865-80
63. Bartels C, Karplus M. 1997. J. Comput. Chem. 18:1450-62
64. Scheraga HA, Hao M-H. 1999. Adv. Chem. Phys. 105:243-72
65. Zaloj V, Elber R. 2000. Comput. Phys. Commun. 128:118-27
66. Elber R, Meller J, Olender R. 1999. J. Phys. Chem. B 103:899-911
67. Olender R, Elber R. 1996. J. Chem. Phys. 105:9299-315
68. Lazaridis T, Karplus M. 2000. Curr. Opin. Struct. Biol. 10:139-45
69. Bursulaya BD, Brooks CL III. 2000. J. Phys. Chem. B 104: In press
70. Kim PS, Baldwin RL. 1982. Annu. Rev. Biochem. 51:459-89
71. Dyson HJ, Rance M, Houghten RA, Wright PE, Lerner RA. 1988. J. Mol. Biol. 201:201-17
72. Dyson HJ, Rance M, Houghten RA, Lerner RA, Wright PE. 1988. J. Mol. Biol. 201:161-200
73. Wright PE, Dyson HJ, Lerner RA. 1988. Biochemistry 27:7167-75
74. Wright PE, Lerner RA, Dyson HJ. 1989. GBF Monogr. (Adv. Prot. Des.) 12:13-19
75. Wright PE, Dyson HJ, Feher VA, Tennant LL, Waltho JP, et al. 1990. UCLA Symp. Mol. Cell. Biol., New Ser. 109:1-13
76. Waltho JP, Feher VA, Wright PE. 1990. In Current Research in Protein Chemistry, pp. 283-93. New York: Academic
77. Tobias DJ, Mertz E, Brooks CL III. 1991. Biochemistry 30:6054-58
78. Karpen ME, Tobias DJ, Brooks CL III. 1993. Biochemistry 32:412-20
79. Daggett V, Levitt M. 1992. J. Mol. Biol. 223:1121-38
80. DiCapua FM, Swaminathan S, Beveridge DL. 1990. J. Am. Chem. Soc. 112:6768-71
81. DiCapua FM, Swaminathan S, Beveridge DL. 1991. J. Am. Chem. Soc. 113:6145-55
82. Tirado-Rives J, Jorgensen WL. 1991. Biochemistry 30:3864-71
83. Soman KV, Karimi A, Case DA. 1991. Biopolymers 31:1351-61
84. Hirst JD, Brooks CL III. 1995. Biochemistry 34:7614-21
85. Tobias DJ, Brooks CL III. 1987. Chem. Phys. Lett. 142:472-76
86. Tobias DJ, Brooks CL III. 1988. J. Chem. Phys. 89:5115-27
87. Sneddon SF, Tobias DJ, Brooks CL III. 1989. J. Mol. Biol. 209:817-20
88. Tobias DJ, Sneddon SF, Brooks CL III. 1990. J. Mol. Biol. 216:783-96
89. Tobias DJ, Brooks CL III. 1991. Biochemistry 30:6059-70
90. Tobias DJ, Sneddon SF, Brooks CL III. 1992. J. Mol. Biol. 227:1244-52
91. Tobias DJ, Brooks CL III. 1992. J. Phys. Chem. 96:3864-70
92. Brooks CL III, Nilsson L. 1993. J. Am. Chem. Soc. 115:11034-35
93. Young WS, Brooks CL III. 1996. J. Mol. Biol. 259:560-72
94. Sheinerman FB, Brooks CL III. 1995. J. Am. Chem. Soc. 117:10098-103
95. Brooks CL III. 1996. J. Phys. Chem. 100:2546-49
96. Tropsha A, O'Connell T, Wang L, Hermans J. 1996. Book of Abstracts, 212th ACS Natl. Meet., Orlando, FL, August 25-29. ACS Abstr.#COMP-044
97. Wang L, O'Connell T, Tropsha A, Hermans J. 1995. Proc. Natl. Acad. Sci. USA 92:10924-28
98. Zhang L, Hermans J. 1994. J. Am. Chem. Soc. 116:11915-21
99. Yan Y, Tropsha A, Hermans J, Erickson BW. 1993. Proc. Natl. Acad. Sci. USA 90:7898-902
100. Sundaralingam M, Sekharudu YC. 1989. Science 244:1333-37
101. Sundaralingam M, Sekharudu YC. 1990. Struct. Methods, Proc. Conversation Discip. Biomol. Stereodyn., 6th, 2:115-27
102. Muck SM, Martinez GV, Fiori WR, Todd AP, Millhauser GL. 1992. Nature 359:653-55
103. Fiori WR, Muck SM, Millhauser GL. 1993. Biochemistry 32:11957-62
104. Millhauser GL. 1995. Biochemistry 34: 10318
105. Bolin KA, Millhauser GL. 1999. Acc. Chem. Res. 32:1027-33
106. Brooks CL III. 1993. Curr. Opin. Struct. Biol. 3:92-98
107. Daggett V, Levin M. 1992. Proc. Natl. Acad. Sci. USA 89:5142-46
108. Mark AE, van Gunsteren WF. 1992. Biochemistry 31:7745-48
109. van Gunsteren WF, Huenenberger PH, Kovacs H, Mark AE, Schiffer CA. 1995. Philos. Trans. R. Soc. London Ser. B 348:49-59
110. Smith LJ, Mark AE, Dobson CM, van Gunsteren WF. 1995. Biochemistry 34:10918-31
111. Tirado-Rives J, Jorgensen WL. 1993. Biochemistry 32:4175-84
112. Caflisch A, Karplus M. 1994. Proc. Natl. Acad. Sci. USA 91:1746-50
113. Caflisch A, Karplus M. 1995. J. Mol. Biol. 252:672-708
114. Brooks CL III. 1992. J. Mol. Biol. 227:375-80
115. Kitchen DB, Reed LH, Levy RM. 1992. Biochemistry 31:10083-93
116. Tirado-Rives J, Orozco M, Jorgensen WL. 1997. Biochemistry 36:7313-29
117. Alonso DOV, Daggett V. 1995. J. Mol. Biol. 247:501-20
118. Alonso DOV, Daggett V. 1998. Protein Sci. 7:860-74
119. Daggett V, Li A, Itzhaki LS, Otzen DE, Fersht AR. 1996. J. Mol. Biol. 257:430-40
120. Tobias DJ, Sneddon SF, Brooks CL III. 1991. In AIP Conf. Proc., pp. 174-99. Obernai, France
121. Ryckaert JP, Ciccotti G, Berendsen HJC. 1977. J. Comput. Phys. 23:327-41
122. York DM, Darden TA, Pedersen LG. 1993. J. Chem. Phys. 99:8345-48
123. Darden T, York D, Pedersen L. 1993. J. Chem. Phys. 98:10089-92
124. Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG. 1995. J. Chem. Phys. 103:8577-93
125. Darden TA, Toukmaji A, Pedersen LG. 1997. J. Chim. Phys. Phys.-Chim. Biol. 94:1346-64
126. Sheinerman FB, Brooks CL III. 1998. Proc. Natl. Acad. Sci. USA 95:1562-67
127. Sheinerman FB, Brooks CL III. 1998. J. Mol. Biol. 278:439-55
128. Hunenberger PH, Mark AE, van Gunsteren WF. 1995. Proteins: Struct. Funct. Genet. 21:196-213
129. Xu S, Kamath MV, Capson DW. 1993. Patt. Recog. Lett. 14:7-15
130. Ward JH Jr. 1963. J. Am. Stat. Assoc. 58:236-44
131. Wesson L, Eisenberg D. 1992. Protein Sci. 1:227-35
132. Brooks CL III. 2000. Work in progress
133. Boczko EM, Brooks CL III. 1993. J. Phys. Chem. 97:4509-13
134. Ferrenberg AM, Swendsen RH. 1989. Phys. Rev. Lett. 63:1195-98
135. Shea J-E, Onuchic JN, Brooks CL III. 2000. J. Mol. Biol. In preparation
136. Plaxco KW, Simons KT, Baker D. 1998. J. Mol. Biol. 277:985-94
137. Tashiro M, Tejero R, Zimmerman DE, Celda B, Nilsson B, Montelione GT. 1997. J. Mol. Biol. 272:573-90
138. Jendeberg L, Tashiro M, Tejero R, Lyons BA, Uhlen M, et al. 1996. Biochemistry 35:22-31
139. Gouda H, Torigoe H, Saito A, Sato M, Arata Y, Shimada I. 1992. Biochemistry 31:9665-72
140. Gouda H, Shiraishi M, Takahashi H, Kato K, Torigoe H, et al. 1998. Biochemistry 37:129-36
141. Bai Y, Karimi A, Dyson HJ, Wright PE. 1997. Protein Sci. 6:1449-57
142. Witte K, Skolnick J, Wong C-H. 1998. J. Am. Chem. Soc. 120:13042-45
143. Zhou Y, Karplus M. 1999. J. Mol. Biol. 293:917-51
144. Zhou Y, Karplus M. 1999. Nature 401:400-3
145. Zhou Y, Karplus M. 1997. Proc. Natl. Acad. Sci. USA 94:14429-32
146. Li R, Woodward C. 1999. Protein Sci. 8:1571-91
147. Woodward C, Li R. 1998. Trends Biochem. Sci. 23:379
148. Barbar E, LiCata VJ, Barany G, Woodward C. 1997. Biophys. Chem. 64:45-57
149. Woodward C. 1993. Trends Biochem. Sci. 18:359-60
150. Gallagher T, Alexander P, Bryan P, Gilliland GL. 1994. Biochemistry 33: 4721-29
151. Clore GM, Gronenborn AM. 1992. J. Mol. Biol. 223:853-56
152. Gronenborn AM, Filpula DR, Essig NZ, Achari A, Whitlow M, et al. 1991. Science 253:657-61
153. Barchi JJ Jr, Grasberger B, Gronenborn AM, Clore GM. 1994. Protein Sci. 3:15-21
154. Sheinerman FB, Brooks CL III. 1997. Proteins: Struct. Funct. Genet. 29:193-202
155. Park SH, O'Neil KT, Roder H. 1997. Biochemistry 36:14277-83
156. Frank MK, Clore GM, Gronenborn AM. 1995. Protein Sci. 4:2605-15
157. Kuszewski J, Clore GM, Gronenborn AM. 1994. Protein Sci. 3:1945-52
158. Leeson DT, Gai F, Rodriguez HM, Gregoret LM, Dyer RB. 2000. Proc. Natl. Acad. Sci. USA 97:2527-32
159. Baker D. 2000. Nature 405:39-42
160. Grantcharova VP, Baker D. 1997. Biochemistry 36:15685-92
161. Grantcharova VP, Riddle DS, Santiago JV, Baker D. 1998. Nat. Struct. Biol. 5:714-20
162. Riddle DS, Grantcharova VP, Santiago JV, Alm E, Ruczinski I, Baker D. 1999. Nat. Struct. Biol. 6:1016-24
163. Tsai J, Levitt M, Baker D. 1999. J. Mol. Biol. 291:215-25
164. Mueller U, Perl D, Schmid FX, Heinemann U. 2000. J. Mol. Biol. 297:975-88
165. Feng W, Tejero R, Zimmerman DE, Inouye M, Montelione GT. 1998. Biochemistry 37:10881-96
166. Schindelin H, Jiang W, Inouye M, Heinemann U. 1994. Proc. Natl. Acad. Sci. USA 91:5119-23
167. Schindler T, Graumann PL, Perl D, Ma S, Schmid FX, Marahiel MA. 1999. J. Biol. Chem. 274:3407-13
168. Schindler T, Herrler M, Marahiel MA, Schmid FX. 1995. Nat. Struct. Biol. 2:663-73
169. Schindler T, Schmid FX. 1996. Biochemistry 35:16833-42
170. Li A, Daggett V. 1994. Proc. Natl. Acad. Sci. USA 9:10430-34
171. Karplus M, Sali A. 1995. Curr. Opin. Struct. Biol. 5:58-73
172. Daggett V, Levitt M. 1992. J. Mol. Biol. 223:1121-38
173. Li A, Daggett V. 1996. J. Mol. Biol. 257:412-29
174. Li A, Daggett V. 1998. J. Mol. Biol. 275:677-94
175. Alonso DO, Daggett V. 2000. Proc. Natl. Acad. Sci. USA 97:133-38
176. Brooks CL III. 2000. Work in progress
177. Itzhaki LS, Otzen DE, Fersht AR. 1995. J. Mol. Biol. 254:260-88
178. Ladurner AG, Itzhaki LS. Daggett V, Fersht AR. 1998. Proc. Natl. Acad. Sci. USA 95:8473-78
179. Fersht AR. 1995. Curr. Opin. Struct. Biol. 5:79-84
180. Reid K, Rodriguez HM, Hillier BJ, Gregoret LM. 1998. Protein Sci. 7:470-79
181. Hillier BJ, Rodriguez HM, Gregoret LM. 1998. Fold. Des. 3:87-93
182. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan DJ, Karplus M. 1982. J. Comp. Chem. 4:187-217
183. Hammond GS. 1955. J. Am. Chem. Soc. 77:334
184. Dinner AR, Karplus M. 1999. J. Mol. Biol. 292:403-19