Reconciling crystallography and mutagenesis: A synthetic approach to the creation of a comprehensive model for proton pumping by bacteriorhodopsin

Biochimica et Biophysica Acta - Bioenergetics

Volumn 1460, Issue 1, 2000, Pages 49-59

  Brown, Leonid S ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Bacteriorhodopsin; Crystallography; Mutagenesis; Protein structure; Proton pathway; Proton pumping

Indexed keywords

BACTERIORHODOPSIN; MEMBRANE PROTEIN; PROTON PUMP;

BACTERIAL MEMBRANE; CRYSTALLOGRAPHY; GENE MUTATION; HYDROGEN BOND; MODEL; MUTAGENESIS; NONHUMAN; PRIORITY JOURNAL; PROTEIN STRUCTURE; REVIEW;

BACTERIORHODOPSINS; CRYSTALLOGRAPHY; MODELS, CHEMICAL; MUTAGENESIS, SITE-DIRECTED; PHENOTYPE; PROTON PUMPS; STRUCTURE-ACTIVITY RELATIONSHIP; X-RAY DIFFRACTION;

BACTERIA (MICROORGANISMS);

EID: 0034734252     PISSN: 00052728     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0005-2728(00)00129-8     Document Type: Review

References (104)

1. Ahl P.L., Stern L.J., Mogi T., Khorana H.G., Rothschild K.J. Biochemistry. 28:1989;10028-10034.
2. Altenbach C., Flitsch S.L., Khorana H.G., Hubbell W.L. Biochemistry. 28:1989;7806-7812.
3. Altenbach C., Marti T., Khorana H.G., Hubbell W.L. Science. 248:1990;1088-1092.
4. Altenbach C., Greenhalgh D.A., Khorana H.G., Hubbell W.L. Proc. Natl. Acad. Sci. USA. 91:1994;1667-1671.
5. Balashov S.P., Govindjee R., Kono M., Imasheva E., Lukashev E., Ebrey T.G., Crouch R.K., Menick D.R., Feng Y. Biochemistry. 32:1993;10331-10343.
6. Balashov S.P. Isr. J. Chem. 35:1995;415-428.
7. Balashov S.P., Govindjee R., Imasheva E.S., Misra S., Ebrey T.G., Feng Y., Crouch R.K., Menick D.R. Biochemistry. 34:1995;8820-8834.
8. Balashov S.P., Imasheva E.S., Govindjee R., Ebrey T.G. Biophys. J. 70:1996;473-481.
9. Balashov S.P., Imasheva E.S., Ebrey T.G., Chen N., Menick D.R., Crouch R.K. Biochemistry. 36:1997;8671-8676.
10. Barnett S.M., Dracheva S., Hendler R.W., Levin I.W. Biochemistry. 35:1996;4558-4567.
11. Behrens W., Alexiev U., Mollaaghababa R., Khorana H.G., Heyn M.P. Biochemistry. 37:1998;10411-10419.
12. Belrhali H., Nollert P., Royant A., Menzel C., Rosenbusch J.P., Landau E.M., Pebay-Peyroula E. Structure. 7:1999;909-917.
13. Braiman M.S., Stern L.J., Chao B.H., Khorana H.G. J. Biol. Chem. 262:1987;9271-9276.
14. Brown L.S., Yamazaki Y., Maeda A., Sun L., Needleman R., Lanyi J.K. J. Mol. Biol. 239:1994;401-414.
15. Brown L.S., Gat Y., Sheves M., Yamazaki Y., Maeda A., Needleman R., Lanyi J.K. Biochemistry. 33:1994;12001-12011.
16. Brown L.S., Sasaki J., Kandori H., Maeda A., Needleman R., Lanyi J.K. J. Biol. Chem. 270:1995;27122-27126.
17. Brown L.S., Váró G., Needleman R., Lanyi J.K. Biophys. J. 69:1995;2103-2111.
18. Brown L.S., Needleman R., Lanyi J.K. Biochemistry. 38:1999;6855-6861.
19. Brown L.S., Needleman R., Lanyi J.K. Biochemistry. 39:2000;938-945.
20. Cao Y., Váró G., Klinger A.L., Czajkowsky D.M., Braiman M.S., Needleman R., Lanyi J.K. Biochemistry. 32:1993;1981-1990.
21. Cao Y., Brown L.S., Sasaki J., Maeda A., Needleman R., Lanyi J.K. Biophys. J. 68:1995;1518-1530.
22. Checover S., Nachliel E., Dencher N.A., Gutman M. Biochemistry. 36:1997;13919-13928.
23. le Coutre J., Gerwert K. FEBS Lett. 398:1996;333-336.
24. Delaney J.K., Schweiger U., Subramaniam S. Proc. Natl. Acad. Sci. USA. 92:1995;11120-11124.
25. Dioumaev A.K., Richter H.-T., Brown L.S., Tanio M., Tuzi S., Saitô H., Kimura Y., Needleman R., Lanyi J.K. Biochemistry. 37:1998;2496-2506.
26. Dioumaev A.K., Brown L.S., Needleman R., Lanyi J.K. Biochemistry. 37:1998;9889-9893.
27. Drachev L.A., Kaulen A.D., Khorana H.G., Mogi T., Postanogova N.V., Skulachev V.P., Stern L.J. Photochem. Photobiol. 55:1992;741-744.
28. Duñach M., Marti T., Khorana H.G., Rothschild K.J. Proc. Natl. Acad. Sci. USA. 87:1990;9873-9877.
29. Dunn R.J., Hackett N.R., McCoy J.M., Chao B.H., Kimura K., Khorana H.G. J. Biol. Chem. 262:1987;9246-9254.
30. T.G. Ebrey, in: M. Jackson (Ed.), Thermodynamics of Membrane Receptors and Channels, CRC Press, Boca Raton, FL, 1993, pp. 353-387.
31. Edman K., Nollert P., Royant A., Belrhali H., Pebay-Peyroula E., Hajdu J., Neutze R., Landau E.M. Nature. 401:1999;822-826.
32. Essen L.-O., Siegert R., Lehmann W.D., Oesterhelt D. Proc. Natl. Acad. Sci. USA. 95:1998;11673-11678.
33. Feng Y., Menick D.R., Katz B.M., Beischel C.J., Hazard E.S., Misra S., Ebrey T.G., Crouch R.K. Biochemistry. 33:1994;11624-11630.
34. Flitsch S.L., Khorana H.G. Biochemistry. 28:1989;7800-7805.
35. Govindjee R., Kono M., Balashov S.P., Imasheva E., Sheves M., Ebrey T.G. Biochemistry. 34:1995;4828-4838.
36. Govindjee R., Misra S., Balashov S.P., Ebrey T.G., Crouch R.K., Menick D.R. Biophys. J. 71:1996;1011-1023.
37. Govindjee R., Imasheva E.S., Misra S., Balashov S.P., Ebrey T.G., Chen N., Menick D.R., Crouch R.K. Biophys. J. 72:1997;886-898.
38. Greenhalgh D.A., Altenbach C., Hubbell W.L., Khorana H.G. Proc. Natl. Acad. Sci. USA. 88:1991;8626-8630.
39. Greenhalgh D.A., Farrens D.L., Subramaniam S., Khorana H.G. J. Biol. Chem. 268:1993;20305-20311.
40. Grigorieff N., Ceska T.A., Downing K.H., Baldwin J.M., Henderson R. J. Mol. Biol. 259:1996;393-421.
41. Hackett N.R., Stern L.J., Chao B.H., Kronis K.A., Khorana H.G. J. Biol. Chem. 262:1987;9277-9284.
42. Haupts U., Tittor J., Oesterhelt D. Annu. Rev. Biophys. Biomol. Struct. 28:1999;367-399.
43. Heberle J., Büldt G., Koglin E., Rosenbusch J.P., Landau E.M. J. Mol. Biol. 281:1998;587-592.
44. Henderson R., Baldwin J.M., Ceska T.A., Zemlin F., Beckmann E., Downing K.H. J. Mol. Biol. 213:1990;899-929.
45. Imasheva E.S., Balashov S.P., Ebrey T.G., Chen N., Crouch R.K., Menick D.R. Biophys. J. 77:1999;2750-2763.
46. Imasheva E.S., Balashov S.P., Ebrey T.G., Chen Y., Menick D.R., Crouch R.K. Biophys. J. 78:2000;475A.
47. Kamikubo H., Kataoka M., Váró G., Oka T., Tokunaga F., Needleman R., Lanyi J.K. Proc. Natl. Acad. Sci. USA. 93:1996;1386-1390.
48. Kamikubo H., Oka T., Imamoto Y., Tokunaga F., Lanyi J.K., Kataoka M. Biochemistry. 36:1997;12282-12287.
49. Kandori H., Yamazaki Y., Hatanaka M., Needleman R., Brown L.S., Richter H.-T., Lanyi J.K., Maeda A. Biochemistry. 36:1997;5134-5141.
50. Kataoka M., Kamikubo H., Tokunaga F., Brown L.S., Yamazaki Y., Maeda A., Sheves M., Needleman R., Lanyi J.K. J. Mol. Biol. 243:1994;621-638.
51. Kimura Y., Vassylyev D.G., Miyazawa A., Kidera A., Matsushima M., Mitsuoka K., Murata K., Hirai T., Fujiyoshi Y. Nature. 389:1997;206-210.
52. Koch M.H.J., Dencher N.A., Oesterhelt D., Plöhn H.J., Rapp G., Buldt G. EMBO J. 10:1991;521-526.
53. Krebs M.P., Mollaaghababa R., Khorana H.G. Proc. Natl. Acad. Sci. USA. 90:1993;1987-1991.
54. Krebs M.P., Behrens W., Mollaaghababa R., Khorana H.G., Heyn M.P. Biochemistry. 32:1993;12830-12834.
55. Krebs M.P., Khorana H.G. J. Bacteriol. 175:1993;1555-1560.
56. Lanyi J.K. J. Biol. Chem. 272:1997;31209-31212.
57. Lanyi J.K. J. Struct. Biol. 124:1998;164-178.
58. Lu M., Govindjee R., Balashov S.P., Ebrey T.G., Chen Y., Menick D.R., Crouch R.K. Biophys. J. 78:2000;476A.
59. Luecke H., Richter H.-T., Lanyi J.K. Science. 280:1998;1934-1937.
60. Luecke H., Schobert B., Richter H.-T., Cartailler J.-P., Lanyi J.K. J. Mol. Biol. 291:1999;899-911.
61. Luecke H., Schobert B., Richter H.-T., Cartailler J.-P., Lanyi J.K. Science. 286:1999;255-260.
62. Marti T., Otto H., Mogi T., Rosselet S.J., Heyn M.P., Khorana H.G. J. Biol. Chem. 266:1991;6919-6927.
63. Miercke L.J.W., Betlach M.C., Mitra A.K., Shand R.F., Fong S.K., Stroud R.M. Biochemistry. 30:1991;3088-3098.
64. Misra S., Martin C., Kwon O.-H., Ebrey T.G., Chen N., Crouch R.K., Menick D.R. Photochem. Photobiol. 66:1997;774-783.
65. Mitsuoka K., Hirai T., Murata K., Miyazawa A., Kidera A., Kimura Y., Fujiyoshi Y. J. Mol. Biol. 286:1999;861-882.
66. Mogi T., Stern L.J., Marti T., Chao B.H., Khorana H.G. Proc. Natl. Acad. Sci. USA. 85:1988;4148-4152.
67. Moltke S., Krebs M.P., Mollaaghababa R., Khorana H.G., Heyn M.P. Biophys. J. 69:1995;2074-2083.
68. Müller D.J., Sass H.-J., Müller S.A., Büldt G., Engel A. J. Mol. Biol. 285:1999;1903-1909.
69. Mukhopadhyay A.K., Dracheva S., Bose S., Hendler R.W. Biochemistry. 35:1996;9245-9252.
70. Ni B., Chang M., Duschl A., Lanyi J., Needleman R. Gene. 90:1990;169-172.
71. Oka T., Kamikubo H., Tokunaga F., Lanyi J.K., Needleman R., Kataoka M. Photochem. Photobiol. 66:1997;768-773.
72. Oka T., Kamikubo H., Tokunaga F., Lanyi J.K., Needleman R., Kataoka M. Biophys. J. 76:1999;1018-1023.
73. Otto H., Marti T., Holz M., Mogi T., Stern L.J., Engel F., Khorana H.G., Heyn M.P. Proc. Natl. Acad. Sci. USA. 87:1990;1018-1022.
74. Pebay-Peyroula E., Rummel G., Rosenbusch J.P., Landau E.M. Science. 277:1997;1676-1681.
75. Petkova A.T., Hu J.G., Bizounok M., Simpson M., Griffin R.G., Herzfeld J. Biochemistry. 38:1999;1562-1572.
76. Pfeiffer M., Rink T., Gerwert K., Oesterhelt D., Steinhoff H.-J. J. Mol. Biol. 287:1999;163-171.
77. Rammelsberg R., Huhn G., Lubben M., Gerwert K. Biochemistry. 37:1998;5001-5009.
78. Richter H.-T., Brown L.S., Needleman R., Lanyi J.K. Biochemistry. 35:1996;4054-4062.
79. Riesle J., Oesterhelt D., Dencher N.A., Heberle J. Biochemistry. 35:1996;6635-6643.
80. Rink T., Riesle J., Oesterhelt D., Gerwert K., Steinhoff H.-J. Biophys. J. 73:1997;983-993.
81. Sanz C., Lazarova T., Sepulcre F., Gonzalez-Moreno R., Bourdelande J.-L., Querol E., Padrós E. FEBS Lett. 456:1999;191-195.
82. Sass H.-J., Schachowa I.W., Rapp G., Koch M.H.J., Oesterhelt D., Dencher N.A., Büldt G. EMBO J. 16:1997;1484-1491.
83. Sass H.-J., Gessenich R., Koch M.H.J., Oesterhelt D., Dencher N.A., Büldt G., Rapp G. Biophys. J. 75:1998;399-405.
84. Sato H., Takeda K., Tani K., Hino T., Okada T., Nakasako M., Kamiya N., Kouyama T. Acta Crystallogr. D: Biol. Crystallogr. 55:1999;1251-1256.
85. Schertler G.F.X., Lozier R., Michel H., Oesterhelt D. EMBO J. 10:1991;2353-2361.
86. Soppa J., Oesterhelt D. J. Biol. Chem. 264:1989;13043-13048.
87. Soppa J., Otomo J., Straub J., Tittor J., Meessen S., Oesterhelt D. J. Biol. Chem. 264:1989;13049-13056.
88. Steinhoff H.J., Mollaaghababa R., Altenbach C., Hideg K., Krebs M., Khorana H.G., Hubbell W.L. Science. 266:1994;105-107.
89. Stoeckenius W. Protein Sci. 8:1999;447-459.
90. Subramaniam S., Gerstein M., Oesterhelt D., Henderson R. EMBO J. 12:1993;1-8.
91. Subramaniam S., Faruqi A.R., Oesterhelt D., Henderson R. Proc. Natl. Acad. Sci. USA. 94:1997;1767-1772.
92. Subramaniam S., Lindahl M., Bullough P., Faruqi A.R., Tittor J., Oesterhelt D., Brown L., Lanyi J., Henderson R. J. Mol. Biol. 287:1999;145-161.
93. Subramaniam S. Curr. Opin. Struct. Biol. 9:1999;462-468.
94. Szaraz S., Oesterhelt D., Ormos P. Biophys. J. 67:1994;1706-1712.
95. Tanio M., Inoue S., Yokota K., Seki T., Tuzi S., Needleman R., Lanyi J.K., Naito A., Saitô H. Biophys. J. 77:1999;431-442.
96. Tanio M., Tuzi S., Yamaguchi S., Kawaminami R., Naito A., Needleman R., Lanyi J.K., Saitô H. Biophys. J. 77:1999;1577-1584.
97. Thorgeirsson T.E., Xiao W., Brown L.S., Needleman R., Lanyi J.K., Shin Y.-K. J. Mol. Biol. 273:1997;951-957.
98. Váró G., Zimányi L., Chang M., Ni B., Needleman R., Lanyi J.K. Biophys. J. 61:1992;820-826.
99. Vonck J. Biochemistry. 35:1996;5870-5878.
100. Weidlich O., Schalt B., Friedman N., Sheves M., Lanyi J.K., Brown L.S., Siebert F. Biochemistry. 35:1996;10807-10814.
101. Weik M., Zaccai G., Dencher N.A., Oesterhelt D., Hauss T. J. Mol. Biol. 275:1998;625-634.
102. Yamazaki Y., Sasaki J., Hatanaka M., Kandori H., Maeda A., Needleman R., Shinada T., Yoshihara K., Brown L.S., Lanyi J.K. Biochemistry. 34:1995;577-582.
103. Yeates T.O., Fam B.C. Structure. 7:1999;R25-R29.
104. Zscherp C., Schlesinger R., Tittor J., Oesterhelt D., Heberle J. Proc. Natl. Acad. Sci. USA. 96:1999;5498-5503.