De novo design and structural characterization of proteins and metalloproteins

Annual Review of Biochemistry

Volumn 68, Issue , 1999, Pages 779-819

  DeGrado, William F ^a   Summa, Christopher M ^a   Pavone, Vincenzo ^b   Nastri, Flavia ^b   Lombardi, Angela ^b  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

^b CNR   (Italy)

Author keywords

Computation; Folding; Metal ligand; Peptide; Protein structure

Indexed keywords

HEME; IRON BINDING PROTEIN; MERCURY; METALLOPROTEIN;

ALGORITHM; GENETIC ENGINEERING; METAL BINDING; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN FOLDING; REVIEW; STRUCTURE ACTIVITY RELATION;

METALLOPROTEINS; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEINS;

EID: 0032835617     PISSN: 00664154     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.biochem.68.1.779     Document Type: Review

References (312)

1. Beasley JR, Hecht MH. 1997. J. Biol. Chem. 272:2031-34
2. Bryson JW, Betz SF, Lu HS, Suich DJ, Zhou HX, et al. 1995. Science 270:935-41
3. Richardson J, Richardson DC, Tweedy NB, Gernert KM, Quinn TP, et al. 1992. Biophys. J. 63:1186-209
4. Baltzer L. 1998. Curr. Opin. Struct. Biol. 8:466-70
5. Balaram P. 1999. J. Pept. Res. In press
6. Kamtekar S, Schiffer JM, Xiong H, Babik JM, Hecht MH. 1993. Science 262:1680-85
7. Kamtekar S, Hecht MH. 1995. FASEB J. 9:1013-22
8. Fezoui Y, Weaver DL, Osterhout JJ. 1994. Proc. Natl. Acad. Sci. USA 91:3675-79
9. Osterhout JJ, Handel T, Na G, Toumadje A, Long RC, et al. 1992. J. Am. Chem. Soc. 114:331-37
10. DeGrado WF, Wasserman ZR, Lear JD. 1989. Science 243:622-28
11. Riddle DS, Santiago JV, Bray-Hall ST, Doshi N, Grantcharova VP, et al. 1997. Nat. Struct. Biol. 4:805-9
12. Desjarlais JR, Clarke ND. 1998. Curr. Opin. Struct. Biol. 8:471-75
13. Hellinga HW. 1998. Fold. Des. 3:R1-8
14. Handel TM, Williams SA, DeGrado WF. 1993. Science 261:879-85
15. Ho SP, DeGrado WF. 1987. J. Am. Chem. Soc. 109:6751-58
16. Richardson JS, Richardson DC. 1989. Trends Biochem. Sci. 14:304-9
17. Yue K, Fiebig KM, Thomas PD, Chan HS, Shakhnovich EI, Dill KA. 1995. Proc. Natl. Acad. Sci. USA 92:325-29
18. Shakhnovich EI. 1998. Fold. Des. 3:R45-58
19. Betz SF, Liebman PA, DeGrado WF. 1997. Biochemistry 36:2450-58
20. Kellis JT Jr, Nyberg K, Sali D, Fersht AR. 1988. Nature 333:784-86
21. Matthews BW. 1995. Adv. Protein Chem. 46:249-78
22. Aurora R, Rose GD. 1998. Protein Sci. 7:21-38
23. Krylov D, Mikhailenko I, Vinson C. 1994. EMBO J. 13:2849-61
24. Lumb KJ, Kim PS. 1995. Science 268:436-39
25. Kenar KT, García-Moreno B, Freire E. 1995. Protein Sci. 4:1934-38
26. Yu Y, Monera OD, Hodges RS, Privalov PL. 1996. J. Mol. Biol. 255:367-72
27. Chou PY, Fasman GD. 1974. Biochemistry 13:211-22
28. McGregor MJ, Islam SA, Sternberg MJ. 1987. J. Mol. Biol. 198:295-310
29. Munoz R, Serrano L. 1994. Proteins 20:301-11
30. Dunbrack RL Jr, Karplus M. 1993. J. Mol. Biol. 230:543-74
31. Dunbrack RL Jr, Karplus M. 1994. Nat. Struct. Biol. 1:334-40
32. Thornton JM, Jones DT, MacArthur MW, Orengo CM, Swindells MB. 1995. Philos. Trans. R. Soc. London Ser. B 348:71-79
33. D'Aquino JA, Gomez J, Hilser VJ, Lee KH, Amzel LM, Freire E. 1996. Proteins 25:143-56
34. Dahiyat BI, Mayo SL. 1997. Science 278:82-87
35. Booth D, Sunde M, Bellotti V, Robinson C, Hutchinson W, et al. 1997. Nature 385:787-93
36. Gassner NC, Baase WA, Matthews BW. 1996. Proc. Natl. Acad. Sci. USA 93:12155-58
37. Axe DD, Foster NW, Fersht A. 1996. Proc. Natl. Acad. Sci. USA 93:5590-94
38. Baldwin EP, Matthews BW. 1994. Curr. Opin. Biotechnol. 5:396-402
39. Honig B, Yang AS. 1995. Adv. Protein Chem. 46:27-58
40. Baker EN, Hubbard RE. 1984. Prog. Biophys. Mol. Biol. 44:97-179
41. Barlow DJ, Thornton JM. 1983. J. Mol. Biol. 168:867-85
42. Cordes MHJ, Davidson AR, Sauer RT. 1996. Curr. Opin. Struct. Biol. 6:3-10
43. Yue K, Dill KA. 1992. Proc. Natl. Acad. Sci. USA 89:4163-67
44. Raleigh DP, Betz SF, DeGrado WF. 1995. J. Am. Chem. Soc. 117:7558-59
45. Waldburger CD, Schildbach JF, Sauer RT. 1995. Nat. Struct. Biol. 2:1122-28
46. Marqusce S, Sauer RT. 1994. Protein Sci. 3:2217-25
47. Hendsch ZS, Jonsson T, Sauer RT, Tidor B. 1996. Biochemistry 35:7621-25
48. Harbury PB, Zhang T, Kim PS, Alber T. 1993. Science 262:1401-7
49. Schneider JP, Lear JD, DeGrado WF. 1997. J. Am. Chem. Soc. 119:5742-43
50. O'Shea EK, Lumb KJ, Kim PS. 1993. Curr. Biol. 3:658-67
51. Lumb KJ, Kim PS. 1996. Science 271:1137-38
52. a. Sindelar CV, Hendsch ZS, Tidor B. 1998. Protein Sci. 7:1898-1914
53. Lavigne P, Sönnichsen FD, Kay CM, Hodges RS. 1996. Science 271:1136-37
54. Monera OD, Kay CM, Hodges RS. 1994. Biochemistry 33:3862-71
55. Zhou NE, Kay CM, Hodges RS. 1994. J. Mol. Biol. 237:500-12
56. Lockhart DJ, Kim PS. 1993. Science 260:198-202
57. Betz SF, DeGrado WF. 1996. Biochemistry 35:6955-62
58. Li H, Helling R, Tang C, Wingreen N. 1996. Science 273:666-69
59. Chan HS, Dill KA. 1996. Proteins 24:335-44
60. Farber GK, Petsko GA. 1990. Trends Biochem. Sci. 15:228-34
61. Reardon D, Farber GK. 1995. FASEB J. 9:497-503
62. Schneider JP, Lombardi A, DeGrado WF. 1998. Fold. Des. 3:R29-40
63. Bork P, Holm L, Sander C. 1994. J. Mol. Biol. 242:309-20
64. Eisenberg D, Wilcox W, Eshita SM, Pryciak PM, Ho SP, DeGrado WF. 1986. Proteins 1:16-22
65. Salemme FR. 1983. Prog. Biophys. Mol. Biol. 42:95-133
66. Chou KC, Pottle M, Nemethy G, Ueda Y, Scheraga HA. 1982. J. Mol. Biol. 162:89-112
67. Murzin AG, Lesk AM, Chothia C. 1994. J. Mol. Biol. 236:1369-81
68. Chou KC, Heckel A, Nemethy G, Rumsey S, Carlacci L, Scheraga HA. 1990. Proteins 8:14-22
69. Crick FHC. 1953. Acta Cryst. 6:685-89
70. Harbury PB, Tidor B, Kim PS. 1995. Proc. Natl. Acad. Sci. USA 92:8408-12
71. Jones TA, Thirup S. 1986. EMBO J. 5:819-22
72. Simons KT, Kooperberg C, Huang E, Baker D. 1997. J. Mol. Biol. 268:209-25
73. Drexler KE. 1981. Proc. Natl. Acad. Sci. USA 78:5275-78
74. Pabo C. 1983. Nature 301:200
75. Bowie JU, Reidhaar-Olson JF, Lim WA, Sauer RT. 1990. Science 247:1306-10
76. Kauzmann W. 1959. Adv. Protein Chem. 14:1-64
77. DeGrado WF, Lear JD. 1985. J. Am. Chem. Soc. 107:7684
78. Lim VI. 1974. J. Mol. Biol. 88:857-72
79. Efimov A. 1994. Structure 2:999-1002
80. Eisenberg D, Wilcox W, McLachlan AD. 1986. J. Cell. Biochem. 31:11-17
81. Sternberg MJ, Thornton JM, 1977. J. Mol. Biol. 115:1-17
82. Lesk AM, Chothia C. 1980. J. Mol. Biol. 136:225-70
83. Dill KA, Bromberg S, Yue K, Fiebig KM, Yee DP, et al. 1995. Protein Sci. 4:561-602
84. Reidhaar-Olson JF, Bowie JU, Breyer RM, Hu JC, Knight KL, et al. 1991. Methods Enzymol. 208:564-86
85. Roy S, Helmer KJ, Hecht MH. 1997. Fold. Des. 2:89-92
86. Rojas NR, Kamtekar S, Simons CT, McLean JE, Vogel KM, et al. 1997. Protein Sci. 6:2512-24
87. Smith GP, Petrenko VA, 1997. Chem. Rev. 97:391-410
88. O'Neil KT, DeGrado WF, Hoess RH. 1994. Tech. Protein Chem. 5:517-24
89. O'Neil KT, Hoess RH. 1995. Curr. Opin. Struct. Biol. 5:443-49
90. Matthews BW. 1995. Nat. Struct, Biol. 2:85-86
91. Hellinga HW, Richards FM. 1991. J. Mol. Biol. 222:763-85
92. Lee B, Richards FM. 1971. J. Mol. Biol. 55:379-400
93. Ponder JW, Richards FM. 1987. J. Mol. Biol. 193:775-91
94. Dunbrack RL Jr, Cohen FE. 1997. Protein Sci. 6:1661-81
95. Holland JH. 1992. Adaptation in Natural and Artificial Systems. Cambridge, MA: MIT Press
96. Jones DT. 1994. Protein Sci. 3:567-74
97. Desjarlais JR, Handel TM. 1995. Protein Sci. 4:2006-18
98. Lazar GA, Desjarlais JR, Handel TM. 1997. Protein Sci. 6:1167-78
99. Desmet J, De Maeyer M, Hazes B, Lasters I. 1992. Nature 356:539-42
100. Lasters I, De Maeyer M, Desmet J. 1995. Protein Eng. 8:815-22
101. Hart PE, Nilsson NJ, Raphael B. 1968. IEEE Trans. Syst. Sci. Cybern. 4:100-7
102. Dahiyat BI, Mayo SL. 1996. Protein Sci. 5:895-903
103. McQuarrie DA. 1976. In Statistical Mechanics, pp. 236-37. New York: Harper & Row
104. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. 1983. J. Comp. Chem. 4:187-217
105. Weiner SJ, Kollman PA, Case DA, Singh UC, Ghio C, et al. 1984. J. Am. Chem. Soc. 106:765-84
106. Weiner SJ, Kollman PA, Nguyen DT, Case DA. 1986. J. Comp. Chem. 7:230-52
107. Dahiyat BI, Sarisky CA, Mayo SL. 1997. J. Mol. Biol. 273:789-96
108. Dahiyat BI, Gordon DB, Mayo SL. 1997. Protein Sci. 6:1333-37
109. Godzik A, Kolinski A, Skolnick J. 1993. J. Comput. Aided Mol. Des. 7:397-438
110. Miyazawa S, Jernigan RL. 1985. Macromolecules 18:534-52
111. Miyazawa S, Jernigan RL. 1996. J. Mol. Biol. 256:623-44
112. Sippl MJ. 1990. J. Mol. Biol. 213:859-83
113. Sippl MJ, Ortner M, Jaritz M, Lackner P, Flockner H. 1996. Fold. Des. 1:289-98
114. Samudrala R, Moult J. 1998. J. Mol. Biol. 275:895-916
115. Melo F, Feytmans E. 1997. J. Mol. Biol. 267:207-22
116. Dahiyat BI, Mayo SL. 1997. Proc. Natl. Acad. Sci. USA 94:10172-77
117. Farinas E, Regan L. 1998. Protein Sci. 7:1939-46
118. Su A, Mayo SL. 1997. Protein Sci. 6:1701-7
119. Muñoz V, Serrano L. 1995. J. Mol. Biol. 245:275-96
120. Muñoz V, Serrano L. 1995. J. Mol. Biol. 245:297-308
121. Muñoz V, Serrano L. 1997. Biopolymers 41:495-509
122. Petukhov M, Muñoz V, Yumoto N, Yoshikawa S, Serrano L. 1998. J. Mol. Biol. 278:279-89
123. Lippard SJ, Berg JM. 1994. Principles of Bioinorganic Chemistry, pp. 1-20. Mill Valley, CA: Univ. Sci. Books
124. Handel T, DeGrado WF. 1990. J. Am. Chem. Soc. 112:6710-11
125. Choma CT, Lear JD, Nelson MJ, Dutton PL, Robertson DE, DeGrado WF. 1994. J. Am. Chem. Soc. 116:856-65
126. Dieckmann GR, McRorie DK, Tierney DL, Utschig LM, Singer CP, et al. 1997. J. Am. Chem. Soc. 119:6195-96
127. Dieckmann GR, McRorie DK, Lear JD, Sharp KA, DeGrado WF, Pecoraro VL. 1998. J. Mol. Biol. 280:897-912
128. Clarke ND, Yuan SM. 1995. Proteins 23:256-63
129. Robertson DE, Farid RS, Moser CC, Urbauer JL, Mulholland SE, et al. 1994. Nature 368:425-32
130. Pinto A, Hellinga HW, Caradonna JP. 1997. Proc. Natl. Acad. Sci. USA 94:5562-67
131. Benson DE, Wisz MS, Liu W, Hellinga HW. 1998. Biochemistry 37:7070-76
132. Kuhlman B, Yang HY, Boice JA, Fairman R, Raleigh DP. 1997. J. Mol. Biol. 270:640-47
133. Blanco FJ, Rivas G, Serrano L. 1994. Nat. Struct. Biol. 1:584-90
134. Aurora R, Crearner TP, Srinivasan R, Rose GD. 1997. J. Biol. Chem. 272:1413-16
135. Scholtz JM, Baldwin RL. 1995. In Peptides: Synthesis, Structures, and Applications, ed. B. Gutte, 1:171-92. San Diego: Academic. 511 pp.
136. O'Neil KT, DeGrado WF. 1990. Science 250:646-51
137. Began L. 1997. Proc. Natl. Acad. Sci. USA 94:2796-97
138. Myers JK, Pace CN, Scholtz JM. 1997. Proc. Natl. Acad. Sci. USA 94:2833-37
139. Myers JK, Pace CN, Scholtz JM. 1997, Biochemistry 36:10923-29
140. Muñoz V, Serrano L. 1994. Nat. Struct. Biol. 1:399-409
141. Hermans J, Anderson AG, Yun RH. 1992. Biochemistry 31:5646-53
142. Creamer TP, Rose GD. 1994. Proteins 19:85-97
143. Padmanabhan S, Baldwin RL. 1994. Protein Sci. 3:1992-97
144. Viguera AR, Serrano L. 1995. Biochemistry 34:8771-79
145. Armstrong KM, Fairman R, Baldwin RL. 1993. J. Mol. Biol. 230:284-91
146. Smith JS, Scholtz JM. 1998. Biochemistry 37:33-40
147. Huyghues-Despointes BMP, Scholtz JM, Baldwin RL. 1993. Protein Sci. 2:80-85
148. Williams S, Causgrove TP, Gilmanshin R, Fang KS, Callender RH, et al. 1996. Biochemistry 35:691-97
149. Thompson PA, Eaton WA, Hofrichter J. 1997. Biochemistry 36:9200-10
150. Eaton WA, Thompson PA, Chan CK, Hagen SJ, Hofrichter J. 1996. Structure 4:1133-39
151. Richardson JS, Richardson DC. 1988, Science 240:1648-52
152. Presta LG, Rose GD. 1988. Science 240:1632-41
153. Dasgupta S, Bell JA. 1993. Int. J. Pept. Protein Res. 41:499-511
154. Muñoz V, Blanco FJ, Serrano L. 1995. Nat. Struct. Biol. 2:380-85
155. Zhou HX, Lyu P, Wemmer DE, Kallenbach NR. 1994. Proteins 18:1-7
156. Schellman C. 1980. In Protein Folding, ed. R Jaenicke, pp. 53-61. North-Holland/New York: Elsevier
157. Aurora R, Srinivasan R, Rose GD. 1994. Science 264:1126-30
158. Gunasekaran K, Nagarajaram HA, Ramakrishnan C, Balaram P. 1998. J. Mol. Biol. 275:917-32
159. Kumar S, Bansal M. 1998. Proteins 31: 460-76
160. Prieto J, Serrano L. 1997. J. Mol. Biol. 274:276-88
161. Schneider JP, DeGrado WF. 1998. J. Am. Chem. Soc. 120:2764-67
162. Efimov AV. 1993. Curr. Opin. Struct. Biol. 3:379-84
163. Predki PF, Agrawal V, Brunger AT, Regan L. 1996. Nat. Struct. Biol. 3:54-58
164. Rose GD, Gierasch LM, Smith JA. 1985. Adv. Protein Chem. 37:1-110
165. Marraud M, Aubry A. 1996. Biopolymers 40:45-83
166. Stanfield RL, Wilson IA. 1995. Curr. Opin. Struct. Biol. 5:103-13
167. Hynes TR, Kautz RA, Goodman MA, Gill JF, Fox RO. 1989. Nature 339:73-76
168. Dyson HJ, Rance M, Houghten RA, Lerner RA, Wright PE. 1988. J. Mol. Biol. 201:161-200
169. Milburn PJ, Konishi Y, Meiwald YC, Scheraga HA. 1987. J. Am. Chem. Soc. 109:4486-96
170. Garrett JB, Mullins LS, Raushel FM. 1996. Protein Sci. 5:204-11
171. Helms LR, Wetzel R. 1995. Protein Sci. 4:2073-81
172. Brunet AP, Huang ES, Huffine ME, Loeb JE, Weltman RJ, Hecht MH. 1993. Nature 364:355-58
173. Castagnoli L, Vetriani C, Cesareni G. 1994. J. Mol. Biol. 237:378-87
174. Vlassi M, Steif C, Weber P, Tsernoglou D, Wilson KS. et al. 1994. Nat. Struct. Biol. 1:706-16
175. Gu HD, Kim D, Baker D. 1997. J. Mol. Biol. 274:588-96
176. Kiefhaber T, Grunert HP, Hahn U, Schmid FX. 1990. Biochemistry 29:6475-80
177. Viguera AR, Blanco FJ, Serrano L. 1995. J. Mol. Biol. 247:670-81
178. Sibanda BL, Thornton JM. 1985. Nature 316:170-74
179. Pavone V, Gaeta G, Lombardi A, Nastri F, Maglio O, et al. 1996. Biopolymers 38:705-21
180. Gunasekaran K, Ramakrishnan C, Balaram P. 1997. Protein Eng. 10:1131-41
181. Schimmel PR, Flory PJ. 1968. J. Mol. Biol. 34:105-20
182. McDonald DQ, Still WC. 1996. J. Org. Chem. 61:1385-91
183. Chalmers DK, Marshall GR. 1995. J. Am. Chem. Soc. 117:5927-37
184. Takeuchi Y, Marshall GR. 1998. J. Am. Chem. Soc. 120:5363-72
185. Haque TS, Little JC, Gellman SH. 1996. J. Am. Chem. Soc. 118:6975-85
186. Bean JW, Kopple KD, Peishoff CE. 1992. J. Am. Chem. Soc. 114:5328-34
187. Imperiali B, Fisher SL, Moats RA, Prins TJ. 1992. J. Am. Chem. Soc. 114:3182-88
188. Schneider JP, Kelly JW. 1995. Chem. Rev. 95:2169-87
189. Gillespie P, Cicariello J, Olson GL. 1997. Biopolymers 43:191-217
190. Ramirez-Alvarado M, Blanco FJ, Niemann H, Serrano L. 1997. J. Mol. Biol. 273:898-912
191. Chothia C. 1973. J. Mol. Biol. 75:295-302
192. Lifson S, Sander C. 1980. J. Mol. Biol. 139:627-39
193. Smith CK, Regan L. 1995. Science 270:980-82
194. Wouters MA, Curmi PM. 1995. Proteins 22:119-31
195. Minor DL, Kim PS. 1994. Nature 367:660-63
196. Smith CK, Withka JM, Regan L. 1994. Biochemistry 33:5510-17
197. Kim CA, Berg JM. 1993. Nature 362:267-70
198. Muñoz V. Thompson PA, Hofrichter J, Eaton WA. 1997. Nature 390:196-99
199. Blanco FJ, Jiménez MA, Herranz J, Rico M, Santoro J, Nieto JL. 1993. J. Am. Chem. Soc. 115:5887-88
200. Friedrichs MS, Stouch TR, Bruccoleri RE, Mueller L, Constantine KL. 1995. J. Am. Chem. Soc. 117:10855-64
201. Constantine KL, Mueller L, Andersen NH, Tong H, Wandler CF, et al. 1995. J. Am. Chem. Soc. 117:10841-54
202. Chan AW, Hutchinson EG, Harris D, Thornton JM. 1993. Protein Sci. 2:1574-90
203. Searle MS, Williams DH, Packman LC. 1995. Nat. Struct. Biol. 2:999-1006
204. de Alba E, Jimenez MA, Rico M, Nieto JL. 1996. Fold. Des. 1:133-44
205. Ramirez-Alvarado M, Blanco FJ, Serrano L. 1996. Nat. Struct. Biol. 3:604-12
206. Schenck HL, Gellman SH. 1998. J. Am. Chem. Soc. 120:4869-70
207. Karle IL, Awasthi SK, Balaram P. 1996. Proc. Natl. Acad. Sci. USA 93:8189-93
208. Das C, Raghothama S, Balaram P. 1998. J. Am. Chem. Soc. 120:5812-13
209. Kortemme T, Ramirez-Alvarado M, Serrano L. 1998. Science 281:253-56
210. Sudol M, Chen HI, Bougeret C, Einbond A, Bork P. 1995. FEBS Lett. 369:67-71
211. Sharman GJ, Searle MS. 1998. J. Am. Client. Soc. 120:5291-300
212. DeGrado WF. 1988. Adv. Protein Chem. 39:51-124
213. Sander C. 1994. Trends Biotechnol. 12:163-67
214. Gibney BR, Rabanal F, Dutton PL. 1997. Curr. Opin. Chem. Biol. 1:537-42
215. Schafmeister CE, Stroud RM. 1998. Curr. Opin. Biotechnol. 9:350-53
216. Tuchscherer G, Scheibler L, Dumy P, Mutter M. 1998. Biopolymers 47:63-73
217. Betz S, Fairman R, O'Neil K, Lear J, DeGrado W. 1995. Philos. R. Soc. London Ser. B 348:81-88
218. Kuwajima K. 1989. Proteins 6:87-103
219. Ptitsyn OB, Pain RH, Semisotnov GV, Zerovnik E, Razgulyaer OL. 1990. FEBS Lett. 262:20-24
220. Wong KB, Daggett V. 1998. Biochemistry 37:11182-92
221. Shortle D. 1996. EASEB J. 10:27-34
222. Betz SF, Raleigh DP, DeGrado WF. 1993. Curr. Opin. Struct. Biol. 3:601-10
223. Myers JK, Pace CN, Scholtz JM. 1995. Protein Sci. 4:2138-48
224. Englander SW, Kallenbach NR. 1983. Q. Rev. Biophys. 16:521-655
225. Englander SW, Mayae L, Bai Y, Sosnick TR. 1997. Protein Sci. 6:1101-9
226. Gonzalez L Jr, Brown RA, Richardson D, Alber T. 1996. Nat. Struct. Biol. 3:1002-9
227. Betz SF, Raleigh DP, DeGrado WF, Lovejoy B, Anderson D, et al. 1996. Fold. Des. 1:57-64
228. Taylor KS, Lou MZ, Chin TM, Yang NC, Garavito RM. 1996. Protein Sci. 5:414-21
229. Schafmeister CE, LaPorte SL, Miercke LW, Stroud RM. 1997. Nat. Struct. Biol. 4:1039-46
230. Fezoui Y, Connolly PJ, Osterhout JJ. 1997. Protein Sci. 6:1869-77
231. Kuroda Y, Nakai T, Ohkubo T. 1994. J. Mol. Biol. 236:862-68
232. Kuroda Y. 1995. Protein Eng. 8:97-101
233. Crick FHC. 1953. Acta Cryst. 6:689-97
234. Harbury PB, Kim PS, Alber T. 1994. Nature 371:80-83
235. Gonzalez L Jr, Plecs JJ, Alber T. 1996. Nat. Struct. Biol. 3:510-15
236. Gonzalez L Jr, Woolfson DN, Alber T. 1996. Nat. Struct. Biol. 3:1011-18
237. Boice JA, Dieckmann GR, DeGrado WF, Fairman R. 1996. Biochemistry 35:14480-85
238. Ogihara NL, Weiss MS, DeGrado WF, Eisenberg D. 1997. Protein. Sci. 6:80-88
239. Lovejoy B, Choe S, Cascio D, McRorie DK, DeGrado WF, Eisenberg D. 1993. Science 259:1288-93
240. Hodges RS. 1996. Biochem. Cell Biol. 74:133-54
241. Betz SF, Bryson JW, DeGrado WF. 1995. Curr. Opin. Struct. Biol. 5:457-63
242. Cohen C, Parry DA. 1990. Proteins 7:1-15
243. Brown JH, Cohen C, Parry DA. 1996. Proteins 26:134-45
244. Talbot JA, Hodges RS. 1982. Acc. Chem. Res. 15:224-30
245. Sikorski A, Kolinski A, Skolnick J. 1998. Biophys. J. 75:92-105
246. Hodges RS. 1996. Biochem. Cell Biol. 74:133-54
247. Chin TM, Berndt KD, Yang NC. 1992. J. Am. Chem. Soc. 114:2279-80
248. Schafmeister CE, Miercke LJW, Stroud RM. 1993. Science 262:734-38
249. Bryson JW, Desjarlais JR, Handel TM, DeGrado WF. 1998. Protein Sci. 7: 1404-14
250. Walsh STR, Cheng H, Bryson JW, Roder H, DeGrado WF. 1999. Proc. Natl. Acad. Sci. USA. In press.
251. Deisenhofer J, Jones TA, Huber R, Sjodahl J, Sjoquist J. 1978. Hoppe Seylers Z. Physiol. Chem. 359:975-85
252. Gouda H, Torigoe H, Saito A, Arata Y, Shimada I. 1992. Biochemistry 31: 9665-72
253. Lombardi A, Bryson JW, Ghirlanda G, DeGrado WF. 1997. J. Am. Chem. Soc. 119:12378-79
254. Ghirlanda G, Lear JD, Lombardi A, DeGrado WF. 1998. J. Mol. Biol. 281: 379-91
255. Hill RB, DeGrado WF. 1998. J. Am. Chem. Soc. 120:1138-45
256. Raleigh DP, DeGrado WF. 1992. J. Am. Chem. Soc. 114:10079-81
257. Broo KS, Nilsson H, Nilsson J, Flodberg A, Baltzer L, 1998. J. Am. Chem. Soc. 120:4063-68
258. Broo KS, Brive L, Sott RS, Baltzer L. 1998. Fold. Des. 3:303-12
259. Broo KS, Brive L, Ahlberg P, Baltzer L. 1997. J. Am. Chem. Soc. 119:11362-72
260. Yan Y, Erickson BW. 1994. Protein Sci. 3:1069-73
261. Quinn TP, Tweedy NB, Williams RW, Richardson JS, Richardson DC. 1994. Proc. Natl. Acad. Sci. USA 91:8747-51
262. Hecht MH. 1994. Proc. Natl. Acad. Sci. USA 91:8729-30
263. Tramontano A, Bianchi E, Venturini S, Martin F, Pessi A, Sollazzo M. 1994. J. Mol. Recognit. 7:9-24
264. Kanmera T, Homandberg GA, Komoriya A, Chaiken IM. 1983. Int. J. Pept. Protein Res. 21:74-83
265. O'Neil KT, Hoess RH, DeGrado WF. 1990. Science 249:774-78
266. Fisher DE, Parent LA, Sharp PA. 1993. Cell 72:467-76
267. Zhang XJ, Baase WA, Matthews BW. 1992. Protein Sci. 1:761-76
268. Mayo KH, Ilyina E, Park H. 1996. Protein Sci. 5:1301-15
269. Ilyina E, Roongta V, Mayo KH. 1997. Biochemistry 36:5245-50
270. Braisted AC, Wells JA. 1996. Proc. Natl. Acad. Sci. USA 93:5688-92
271. Starovasnik MA, Braisted AC, Wells JA. 1997. Proc. Natl. Acad, Sci. USA 94: 10080-85
272. Deisenhofer J. 1981. Biochemistry 20: 2361-70
273. Berg JM, Godwin HA. 1997. Annu. Rev. Biophys. Biomol. Struct. 26:357-71
274. Struthers MD, Cheng RP, Imperiali B. 1996. Science 271:342-45
275. Struthers MD, Cheng RP, Imperiali B. 1996. J. Am. Chem. Soc. 118:3073-81
276. Struthers MD, Ottesen JJ, Imperiali B. 1998. Fold. Des. 3:95-103
277. Regan L. 1995. Trends Biochem. Sci. 20: 280-85
278. Vallee BL, Auld DS. 1990. Proc. Natl. Acad. Sci. USA 87:220-24
279. Christianson DW, Fierke CA. 1996. Acc. Chem. Res. 29:331-39
280. Pessi A, Bianchi E, Crameri S, Venturini S, Tramontano A, Sollazzo M. 1993. Nature 362:367-69
281. Handel TM, Williams SA, Menyhard D, DeGrado WF. 1993. J. Am. Chem. Soc. 115:4457-60
282. Regan L, Clarke ND. 1990. Biochemistry 29:10878-83
283. Klemba M, Regan L. 1995. Biochemistry 34: 10094-100
284. Wisz MS, Garrett CZ, Hellinga HW. 1998. Biochemistry 37:8269-77
285. Wright JG, Tsang HT, Penner-Hahn JE, O'Halloran TV. 1990. J. Am. Chem. Soc. 112:2434-35
286. Stephens PJ, Jollie DR, Warshel A. 1996. Chem. Rev. 96:2491-513
287. Gibney BR, Mulholland SE, Rabanal F, Dutton PL. 1996. Proc. Natl. Acad. Sci. USA 93:15041-46
288. Regan L, DeGrado WF. 1988. Science 241:976-78
289. Scott MP, Biggins J. 1997. Protein Sci. 6:340-46
290. Coldren C, Hellinga HW, Caradonna JP. 1997. Proc. Natl. Acad. Sci. USA 94:6635-40
291. Rabanal F, DeGrado WF, Dutton PL. 1996. J, Am. Chem, Soc. 118:473-74
292. Kalsbeck WA, Robertson DE, Pandey RK, Smith KM, Dutton PL, Bocian DF. 1996. Biochemistry 35:3429-38
293. Gibney BR, Rabanal F, Skalicky JJ, Wand AJ, Dutton PL. 1997. J. Am. Chem. Soc. 119:2323-24
294. Gibney BR, Rabanal F, Reddy KS, Dutton PL. 1998. Biochemistry 37:4635-43
295. Sasaki T, Kaiser ET. 1989. J. Am. Chem. Soc. 111:380-81
296. Sasaki T, Kaiser ET. 1990. Biopolymers 29:79-88
297. Nastri F, Lombardi A, Morelli G, Maglio O, D'Auria G, et al. 1997. Chem. Eur. J. 3:340-49
298. Nastri F, Lombardi A, D'Andrea LD, Sanseverino M, Maglio O, Pavone V. 1998. Biopolymers 47:5-22
299. D'Auria G, Maglio O, Nastri F, Lombardi A, Mazzeo M, et al. 1997. Chem. Eur. J. 3:350-62
300. Lombardi A, Nastri F, Sanseverino M, Maglio O, Pedone C, Pavone V. 1998. Inorg. Chim. Acta 276:301-13
301. Perutz MF, Hasnain SS, Duke PJ, Sessler JL, Hahn JE. 1982. Nature 295:535-38
302. Benson DR, Hart BR, Zhu X, Doughty MB. 1995. J. Am. Chem. Soc. 117: 8502-10
303. Williamson DA, Benson DR. 1998. Chem. Commun. 9:961-62
304. Arnold PA, Shelton WR, Benson DR. 1997. J. Am. Chem. Soc. 119:3181-82
305. Ghadiri MR, Soares C, Choi C, 1992. J. Am. Chem. Soc. 114:825-31
306. Ghadiri MR, Soares C, Choi C. 1992. J. Am. Chem. Soc. 114:4000-2
307. a. Sakamoto S, Sakurai S, Ueno A, Mihara H. 1997. Chem Commun. 13:1221-22
308. b. Sakamoto S, Ueno A, Mihara H. 1998. Chem. Commun. 10:1073-74
309. Mutz MW, McLendon GL, Wishart JF, Gaillard ER, Corin AF. 1996. Proc. Natl. Acad. Sci. USA 93:9521-26
310. Efimov AV. 1991. Protein Eng. 4:245-50
311. Elrod-Erickson M, Rould MA, Nekludova L, Pabo CO. 1996. Structure 4: 1171-80
312. Grobler JA, Essen LO, Williams RL, Hurley JH. 1996. Nat. Struct. Biol. 3: 788-95