Heme Protein Dynamics: Electron Tunneling and Redox Triggered Folding

The Porphyrin Handbook

Volumn 11, Issue , 2003, Pages 51-73

  Gray, Harry B ^a   Winkler, Jay R ^a  

^a CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMISTRY;

HEME PROTEINS;

ELECTRON TUNNELING;

EID: 84940909292     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1016/B978-0-08-092385-7.50008-2     Document Type: Chapter

References (183)

1. De Vault D., Chance B. Biophys. J. 1966, 6:825-846.
2. McGourty J.L., Blough N.V., Hoffman B.M. J. Am. Chem. Soc. 1983, 105:4447-4472.
3. Peterson-Kennedy S.E., McGourty J.L., Kalweit J.A., Hoffman B.M. J. Am. Chem. Soc. 1986, 108:1739-1746.
4. Hoffman B.M., Ratner M.A. J. Am. Chem. Soc. 1987, 109:6237-6243.
5. Hoffman B.M., Ratner M.A., Wallin S.A. Energetics and Dynamics of Gated Reactions 1990, 226:125-146. American Chemical Society, Washington, DC. M. Johnson (Ed.).
6. Nocek J.M., Stemp E.D.A., Finnegan M.G., Koshy T.I., Johnson M.K., Margoliash E., Mauk A.G., Smith M., Hoffman B.M. J. Am. Chem. Soc. 1991, 113:6822-6831.
7. Wallin S.A., Stemp E.D.A., Everest A.M., Nocek J.M., Netzel T.L., Hoffman B.M. J. Am. Chem. Soc. 1991, 113:1842-1844.
8. Everest A.M., Wallin S.A., Stemp E.D.A., Nocek J.M., Mauk A.G., Hoffman B.M. J. Am. Chem. Soc. 1991, 113:4337-4338.
9. Kuila D., Baxter W.W., Natan M.J., Hoffman B.M. J. Phys. Chem. 1991, 95:1-3.
10. King B.C., Hawkridge F.M., Hoffman B.M. J. Am. Chem. Soc. 1992, 114:10603-10608.
11. Simolo K.P., McLendon G.L., Mauk M.R., Mauk A.G. J. Am. Chem. Soc. 1984, 106:5012-5013.
12. McLendon G., Zhang Q., Wallin S.A., Miller R.M., Billstone V., Spears K.G., Hoffman B.M. J. Am. Chem. Soc. 1993, 115:3665-3669.
13. Stemp E.D.A., Hoffman B.M. Biochemistry 1993, 32:10848-10865.
14. Zhou J.S., Hoffman B.M. J. Am. Chem. Soc. 1993, 115:11008-11009.
15. Zhou J.S., Nocek J.M., DeVan M.L., Hoffman B.M. Science 1995, 269:204-207.
16. Nocek J.M., Zhou J.S., DeForest S., Priyadarshy S., Beratan D.N., Onuchic J.N., Hoffman B.M. Chem. Rev. 1996, 96:2459-2489.
17. Dick L.A., Malfant I., Kuila D., Nebolsky S., Nocek J.M., Hoffman B.M., Ratner M.A. J. Am. Chem. Soc. 1998, 120:11401-11407.
18. McLendon G., Miller J.R. J. Am. Chem. Soc. 1985, 107:7811-7816.
19. McLendon G., Pardue K., Bak P. J. Am. Chem. Soc. 1987, 109:7540-7541.
20. McLendon G., Hake R. Chem. Rev. 1992, 92:481-490.
21. Simmons J., McLendon G., Qiao T. J. Am. Chem. Soc. 1993, 115:4889-4890.
22. Isied S.S., Kuehn C., Worosila G. J. Am. Chem. Soc. 1984, 106:1722-1726.
23. Sun J., Wishart J.F., Isied S.S. Inorg. Chem. 1995, 34:3998-4000.
24. Twitchett M.B., Ferrer J.C., Siddarth P., Mauk A.G. J. Am. Chem. Soc. 1997, 119:435-436.
25. Marcus R.A., Sutin N. Biochim. Biophys. Acta 1985, 811:265-322.
26. Beratan D.N., Onuchic J.N., Hopfield J.J. J. Chem. Phys. 1987, 86:4488-4498.
27. Beratan D.N., Onuchic J.N. Photosynth. Res. 1989, 22:173-186.
28. Onuchic J.N., Beratan D.N. J. Chem. Phys. 1990, 92:722-733.
29. Beratan D.N., Betts J.N., Onuchic J.N. Science 1991, 252:1285-1288.
30. Onuchic J.N., Andrade P.C.P., Beratan D.N. J. Chem. Phys. 1991, 95:1131-1138.
31. Beratan D.N., Betts J.N., Onuchic J.N. Science 1991, 252:1285-1288.
32. Betts J.N., Beratan D.N., Onuchic J.N. J. Am. Chem. Soc. 1992, 114:4043-4046.
33. Beratan D.N., Betts J.N., Onuchic J.N. J. Phys. Chem. 1992, 96:2852-2855.
34. Skourtis S.S., Beratan D.N. JBIC 1997, 2:378-386.
35. Skourtis S.S., Beratan D.N. J. Phys. Chem. B 1997, 101:1215-1234.
36. Kumar K., Kurnikov I.V., Beratan D.N., Waldeck D.H., Zimmt M.B. J. Phys. Chem. A 1998, 102:5529-5541.
37. Roitberg A.E., Holden M.J., Mayhew M.P., Kurnikov I.V., Beratan D.N., Vilker V.L. J. Am. Chem. Soc. 1998, 120:8927-8932.
38. Beratan D.N., Skourtis S.S. Curr. Opin. Chem. Biol. 1998, 2:235-243.
39. de Andrade P.C.P., Onuchic J.N. J. Chem. Phys. 1998, 108:4292-4298.
40. Regan J.J., Onuchic J.N. Adv. Chem. Phys. 1999, 107:497-553.
41. Stuchebrukhov A.A., Marcus R.A. J. Phys. Chem. 1995, 99:7581-7590.
42. Daizadeh I., Medvedev E.S., Stuchebrukhov A.A. Proc. Natl. Acad. Sci. USA 1997, 94:3703-3708.
43. Daizadeh I., Guo J.-X., Stuchebrukhov A.A. J. Chem. Phys. 1999, 110:8865-8868.
44. Medvedev D.M., Daizadeh I., Stuchebrukhov A.A. J. Am. Chem. Soc. 2000, 122:6571-6582.
45. Moser C.C., Keske J.M., Warncke K., Farid R.S., Dutton P.L. Nature 1992, 355:796-802.
46. Farid R.S., Moser C.C., Dutton P.L. Curr. Opin. Struct. Biol. 1993, 3:225-233.
47. Moser C.C., Page C.C., Chen X., Dutton P.L. JBIC 1997, 2:393-398.
48. Page C.C., Moser C.C., Chen X., Dutton P.L. Nature 1999, 402:47-52.
49. Winkler J.R., Nocera D.G., Yocom K.M., Bordignon E., Gray H.B. J. Am. Chem. Soc. 1982, 104:5798-5800.
50. Nocera D.G., Winkler J.R., Yocom K.M., Bordignon E., Gray H.B. J. Am. Chem. Soc. 1984, 106:5145-5150.
51. Elias H., Chou M.H., Winkler J.R. J. Am. Chem. Soc. 1988, 110:429-434.
52. Crutchley R.J., Ellis W.R., Gray H.B. J. Am. Chem. Soc. 1985, 107:5002-5004.
53. Mayo S.L., Ellis W.R., Crutchley R.J., Gray H.B. Science 1986, 233:948-952.
54. Axup A.W., Albin M., Mayo S.L., Crutchley R.J., Gray H.B. J. Am. Chem. Soc. 1988, 110:435-439.
55. Karas J.L., Lieber C.M., Gray H.B. J. Am. Chem. Soc. 1988, 110:599-600.
56. Meade T.J., Gray H.B., Winkler J.R. J. Am. Chem. Soc. 1989, 111:4353-4356.
57. Bowler B.E., Meade T.J., Mayo S.L., Richards J.H., Gray H.B. J. Am. Chem. Soc. 1989, 111:8757-8759.
58. Gray H.B., Malmström B.G. Biochemistry 1989, 28:7499-7505.
59. Cowan J.A., Gray H.B. Inorg. Chem. 1989, 28:2074-2078.
60. Therien M.J., Selman M.A., Gray H.B., Chang I.-J., Winkler J.R. J. Am. Chem. Soc. 1990, 112:2420-2422.
61. Chang I.-J., Gray H.B., Winkler J.R. J. Am. Chem. Soc. 1991, 113:7056-7057.
62. Therien M.J., Bowler B.E., Selman M.A., Gray H.B., Chang I.-J., Winkler J.R. Long-Range Electron Transfer in Heme Proteins: Porphyrin-Ruthenium Electronic Couplings in Three Ru(His)Zn-Cytochromes c 1991, 228:191-199. American Chemical Society, Washington, DC. J.R. Bolton, N. Mataga, G. McLendon (Eds.).
63. Jacobs B.A., Mauk M.R., Funk W.D., MacGillivray R.T.A., Mauk A.G., Gray H.B. J. Am. Chem. Soc. 1991, 113:4390-4394.
64. Winkler J.R., Gray H.B. Chem. Rev. 1992, 92:369-379.
65. Wuttke D.S., Bjerrum M.J., Winkler J.R., Gray H.B. Science 1992, 256:1007-1009.
66. Onuchic J.N., Beratan D.N., Winkler J.R., Gray H.B. Annu. Rev. Biophys. Biomol. Struct. 1992, 21:349-377.
67. Wuttke D.S., Bjerrum M.J., Chang I.-J., Winkler J.R., Gray H.B. Biochim. Biophys. Acta 1992, 1101:168-170.
68. Winkler J.R., Gray H.B. Pure Appl. Chem. 1992, 64:1257-1262.
69. Casimiro D.R., Wong L.-L., Colón J.L., Zewert T.E., Richards J.H., Chang I.-J., Winkler J.R., Gray H.B. J. Am. Chem. Soc. 1993, 115:1485-1489.
70. Casimiro D.R., Richards J.H., Winkler J.R., Gray H.B. J. Phys. Chem. 1993, 97:13073-13077.
71. Casimiro D.R., Muheim A., Richards J.R., Arnold F.H., Winkler J.R., Gray H.B. J. Inorg. Biochem. 1993, 51:232.
72. Karpishin T.B., Grinstaff M.W., Komar-Panicucci S., McLendon G., Gray H.B. Structure 1994, 2:415-422.
73. Bjerrum M.J., Casimiro D.R., Chang I.-J., Di Bilio A.J., Gray H.B., Hill M.G., Langen R., Mines G.A., Skov L.K., Winkler J.R., Wuttke D.S. J. Bioenerg. Biomemb. 1995, 27:295-302.
74. Gray H.B., Winkler J.R. Annu. Rev. Biochem. 1996, 65:537-561.
75. Mines G.A., Bjerrum M.J., Hill M.G., Casimiro D.R., Chang I.-J., Winkler J.R., Gray H.B. J. Am. Chem. Soc. 1996, 118:1961-1965.
76. Low D.W., Winkler J.R., Gray H.B. J. Am. Chem. Soc. 1996, 118:117-120.
77. Berglund J., Pascher T., Winkler J.R., Gray H.B. J. Am. Chem. Soc. 1997, 119:2464-2469.
78. Winkler J.R., Gray H.B. JBIC 1997, 2:399-404.
79. Winkler J.R., Di Bilio A., Farrow N.A., Richards J.H., Gray H.B. Pure Appl. Chem. 1999, 71:1753-1764.
80. Wilker J.J., Dmochowski I.J., Dawson J.H., Winkler J.R., Gray H.B. Angew. Chem., Int. Ed. Eng. 1999, 38:89-92.
81. Tezcan F.A., Crane B.R., Winkler J.R., Gray H.B. Proc. Natl. Acad. Sci. USA 2001, 98:5002-5006.
82. Pascher T., Chesick J.P., Winkler J.R., Gray H.B. Science 1996, 271:1558-1560.
83. Mines G.A., Pascher T., Lee S.C., Winkler J.R., Gray H.B. Chem. Biol. 1996, 3:491-497.
84. Telford J.R., Wittung-Stafshede P., Gray H.B., Winkler J.R. Acc. Chem. Res. 1998, 31:755-763.
85. Lee J.C., Chang I.-J., Gray H.B., Winkler J.R. J. Mol. Biol. 2002, 320:159-164.
86. Balzani V. Electron Transfer in Chemistry 2001, Wiley-VCH, Weinheim.
87. Gray H.B., Ellis W.R. Electron Transfer 1994, 315-363. University Science Books, Mill Valley, CA. I. Bertini, H.B. Gray, S.J. Lippard, J.S. Valentine (Eds.).
88. Hopfield J.J. Proc. Natl. Acad. Sci. USA 1974, 71:3640-3644.
89. Ponce A., Gray H.B., Winkler J.R. J. Am. Chem. Soc. 2000, 122:8187-8191.
90. Millett F., Miller M.A., Geren L., Durham B. J. Bioenerg. Biomemb. 1995, 27:341-351.
91. Davidson V.L. Acc. Chem. Res. 2000, 33:87-93.
92. Andrew S.M., Thomasson K.A., Northrup S.H. J. Am. Chem. Soc. 1993, 115:5516-5521.
93. Newton M.D. J. Phys. Chem. 1988, 92:3049-3056.
94. Wasielewski M.R. Distance Dependencies of Electron-Transfer Reactions 1988, Elsevier, Amsterdam. M.A. Fox, M. Chanon (Eds.).
95. McConnell H.M. J. Chem. Phys. 1961, 35:508-515.
96. Langen R., Colón J.L., Casimiro D.R., Karpishin T.B., Winkler J.R., Gray H.B. JBIC 1996, 1:221-225.
97. Larsson S. J. Phys. Chem. 1984, 88:1321-1323.
98. Miller N.E., Wander M.C., Cave R.J. J. Phys. Chem. A 1999, 103:1084-1093.
99. Benjamin I., Evans D., Nitzan A. J. Chem. Phys. 1997, 106:6647-6654.
100. Smalley J.F., Feldberg S.W., Chidsey C.E.D., Linford M.R., Newton M.D., Liu Y.-P. J. Phys. Chem. 1995, 99:13141-13149.
101. Langen R., Chang I.-J., Germanas J.P., Richards J.H., Winkler J.R., Gray H.B. Science 1995, 268:1733-1735.
102. Winkler J.R. Curr. Opin. Chem. Biol. 2000, 4:192-198.
103. Mei H., Wang K., Peffer N., Weatherly G., Cohen D.S., Miller M., Pielak G., Durham B., Millett F. Biochemistry 1999, 38:6846-6854.
104. Farver O., Pecht I. JBIC 1997, 2:387-392.
105. Daizadeh I., Gehlen J.N., Stuchebrukhov A.A. J. Chem. Phys. 1997, 106:5658-5666.
106. Jortner J., Bixon M., Langenbacher T.L., Michel-Beyerle M.E. Proc. Natl. Acad. Sci. USA 1998, 95:12759-12765.
107. Pletneva E.V., Fulton D.B., Kohzuma T., Kostic N.M. J. Am. Chem. Soc. 2000, 122:1034-1046.
108. Takano T., Dickerson R.E. Proc. Natl. Acad. Sci. USA 1980, 77:6371.
109. Sun J., Su C., Wishart J.F. Inorg. Chem. 1996, 35:5893-5901.
110. Zemel H., Hoffman B.M. J. Am. Chem. Soc. 1981, 103:1192-1201.
111. Lo Conte L., Chothia C., Janin J. J. Mol. Biol. 1999, 285:2177-2198.
112. Pelletier H., Kraut J. Science 1992, 258:1748-1755.
113. de Rege P.J.F., Williams S.A., Therien M.J. Science 1995, 269:1409-1413.
114. Kirby J.P., Roberts J.A., Nocera D.G. J. Am. Chem. Soc. 1997, 119:9230-9236.
115. Yang J., Seneviratne D., Arbatin G., Andersson A.M., Curtis J.C. J. Am. Chem. Soc. 1997, 119:5329-5336.
116. Bryngelson J.D., Onuchic J.N., Wolynes P.G. Proteins: Struct. Func. Gen. 1995, 21:167-195.
117. Dill K.A., Chan H.S. Nature Struct. Biol. 1997, 4:10-19.
118. Shakhnovich E.I. Curr. Opin. Struct. Biol. 1997, 7:29-40.
119. Lazaridis T., Karplus M. Science 1997, 278:1928-1931.
120. Onuchic J.N., Lutheyschulten Z., Wolynes P.G. Annu. Rev. Phys. Chem. 1997, 48:545-600.
121. Chen L.X.-Q., Petrich J.W., Fleming G.R., Perico A. Chem. Phys. Lett. 1987, 139:55-61.
122. Williams S., Causgrove T.P., Gilmanshin R., Fang K.S., Callender R.H., Woodruff W.H., Dyer R.B. Biochemistry 1996, 35:691-697.
123. Koide S., Dyson H.J., Wright P.E. Biochemistry 1993, 32:12299-12310.
124. Karplus M., Weaver D.L. Prot. Sci. 1994, 3:650-668.
125. Zwanzig R. Proc. Natl. Acad. Sci. USA 1995, 92:9801-9804.
126. Jones C.M., Henry E.R., Hu Y., Chan C.-K., Luck S.D., Bhuyan A., Roder H., Hofrichter J., Eaton W.A. Proc. Natl. Acad. Sci. USA 1993, 90:11860-11864.
127. Elöve G., Bhuyan A.K., Roder H. Biochemistry 1994, 33:6925-6935.
128. Sosnick T.R., Mayne L., Hiller R., Englander S.W. Nature Struct. Biol. 1994, 1:149-156.
129. Baldwin R.L. BioEssays 1994, 16:207-210.
130. Fersht A.R. Curr. Opin. Struct. Biol. 1995, 5:79-84.
131. Ptitsyn O.B. Adv. Protein Chem. 1995, 47:83-229.
132. Englander S.W., Mayne L. Annu. Rev. Biophys. Biomol. Struct. 1992, 21:243-265.
133. Plaxco K., Dobson C.M. Curr. Opin. Struct. Biol. 1996, 6:630-636.
134. Churg A.K., Warshel A. Biochemistry 1986, 25:1675-1681.
135. Tezcan F.A., Winkler J.R., Gray H.B. J. Am. Chem. Soc. 1998, 120:13383-13388.
136. Tezcan, F. A. Ph.D. Thesis, California Institute of Technology, 2001.
137. Bixler J., Bakker G., McLendon G. J. Am. Chem. Soc. 1992, 114:6938-6939.
138. Chen B.-L., Baase W.A., Nicholson H., Schellman J.A. Biochemistry 1992, 31:1464-1476.
139. Matouschek A., Otzen D.E., Itzhaki L.S., Jackson S.E., Fersht A.R. Biochemistry 1995, 34:13656-13662.
140. Yao M., Bolen D.W. Biochemistry 1995, 34:3771-3781.
141. Winkler J.R., Wittung-Stafshede P., Leckner J., Malmström B.G., Gray H.B. Proc. Natl. Acad. Sci. USA 1997, 94:4246-4249.
142. Mines G.A., Winkler J.R., Gray H.B. Spectroscopic Studies of Ferrocytochrome c Folding 1998, American Chemical Society, Washington DC. E.I. Solomon, K.O. Hodgson (Eds.).
143. Wittung-Stafshede P., Gray H.B., Winkler J.R. J. Am. Chem. Soc. 1997, 119:9562-9563.
144. Wittung-Stafshede P., Malmström B.G., Winkler J.R., Gray H.B. J. Phys. Chem. A 1998, 102:5599-5601.
145. Telford J.R., Tezcan F.A., Gray H.B., Winkler J.R. Biochemistry 1999, 38:1944-1949.
146. Orii Y. Biochemistry 1993, 32:11910-11914.
147. Babul J., Stellwagen E. Biochemistry 1972, 11:1195-1200.
148. Muthukrishnan K., Nall B.T. Biochemistry 1991, 30:4706-4710.
149. Colón W., Wakem L.P., Sherman F., Roder H. Biochemistry 1997, 36:12535-12541.
150. Kita K., Konishi K., Anraku Y. J. Biol. Chem. 1984, 259:3368-3374.
151. Fisher M.T. Biochemistry 1991, 30:10012-10018.
152. Wittung-Stafshede P., Lee J.C., Winkler J.R., Gray H.B. Proc. Natl. Acad. Sci. USA 1999, 96:6587-6590.
153. Meyer T.E., Kamen M.D. Adv. Protein Chem. 1982, 35:105-212.
154. Moore G.R., McClune G.J., Clayden N.J., Williams R.J.P., Alsaadi B.M., Angstrom J., Ambler R.P., van Beeumen J., Tempst P., Bartsch R.G., Meyer T.E., Kamen M.D. Eur. J. Biochem. 1982, 123:73-80.
155. Moore G.R., Pettigrew G.W. Cytochromes c: Evolutionary, Structural, and Physicochemical Aspects 1990, Springer-Verlag, New York.
156. Ambler R.P., Bartsch R.G., Daniel M., Kamen M.D., McLellan L., Meyer T.E., Beeumen J.V. Proc. Natl. Acad. Sci. USA 1981, 78:6854-6857.
157. Hamada K., Bethge P.H., Mathews F.S. J. Mol. Biol. 1995, 247:947-962.
158. Shibata N., Iba S., Misaki S., Meyer T.E., Bartsch R.G., Cusanovich M.A., Morimoto Y., Higuchi Y., Yasuoka N. J. Mol. Biol. 1998, 284:751-760.
159. Moore G.R., Williams R.J.P., Peterson J., Thomson A.J., Mathews F.S. Biochim. Biophys. Acta 1985, 829:83-96.
160. Klerk H.D., Bartsch R.G., Kamen M.D. Biochim. Biophys. Acta 1965, 97:275-280.
161. Strekas T.C., Spiro T.G. Biochim. Biophys. Acta 1974, 351:237-245.
162. Fujii S., Yoshimura T., Kamada H., Yamaguchi K., Suzuki S., Shidara S., Takakuwa S. BBA Prot. Struct. Molec. Enzym. 1995, 1251:161-169.
163. Clark K., Dugad L.B., Bartsch R.G., Cusanovich M.A., Mar G.N.L. J. Am. Chem. Soc. 1996, 118:4654-4664.
164. Jackson J.T., Mar G.N.L., Bartsch R.G. J. Biol. Chem. 1983, 258:1799-1805.
165. Barakat R., Strekas T.C. Biochim. Biophys. Acta 1982, 679:393-399.
166. Schmid F.X., Mayr L.M., Mücke M., SchoUnbrunner E.R. Adv. Protein Chem. 1993, 44:25-66.
167. Thirumalai D., Klimov D.K., Woodson S.A. Theor. Chem. Acc. 1997, 96:14-22.
168. Thirumalai D., Klimov D.K. Curr. Opin. Struct. Biol. 1999, 9:197-207.
169. Zhou Y., Karplus M. Nature 1999, 401:400-403.
170. Zhou Y., Karplus M. J. Mol. Biol. 1999, 293:917-951.
171. Shea J.-E., Onuchic J.N., Brooks C.L. J. Chem. Phys. 2000, 113:7663-7671.
172. Shea J.-E., Onuchic J.N., Brooks C.L. Proc. Natl. Acad. Sci. USA 1999, 96:12512-12517.
173. Hagen S.J., Hofrichter J., Eaton W.A. J. Phys. Chem. B 1997, 101:2352-2365.
174. Vanderkooi J.M., Landesberg R., Hayden G., Owen C.S. Eur. J. Biochem. 1977, 81:339-347.
175. Shastry M.C.R., Sauder J.M., Roder H. Acc. Chem. Res. 1998, 31:717-725.
176. Englander S.W., Sosnick T.R., Mayne L.C., Shtilerman M., Qi P.X., Bai Y. Acc. Chem. Res. 1998, 31:737-744.
177. Pierce M.M., Nall B.T. Prot. Sci. 1997, 6:618-627.
178. Scheidt W.R., Kastner M.E., Hatano K. Inorg. Chem. 1978, 17:706-710.
179. Sudha B.P., Dixit N., Moy V.T., Vanderkooi J.M. Biochemistry 1984, 23:2103-2107.
180. Wherland S., Gray H.B. Proc. Natl. Acad. Sci. USA 1976, 73:2950-2954.
181. Akiyama S., Takahashi S., Ishimori K., Morishima I. Nature Struct. Biol. 2000, 7:514-520.
182. Sauder J.M., Roder H. Folding & Design 1998, 3:293-301.
183. Mirny L.A., Abkevich V., Shakhnovich E.I. Folding & Design 1996, 1:103-116.