Residual dipolar couplings report on the active conformation of rhodopsin-Bound protein fragments

Topics in Current Chemistry

Volumn 272, Issue , 2007, Pages 187-215

  Koenig, Bernd W ^a,b  

^a FORSCHUNGSZENTRUM JÜLICH   (Germany)

^b HEINRICH HEINE UNIVERSITY   (Germany)

Author keywords

Ligand; Membrane protein; NMR; Residual dipolar couplings; Transient binding

Indexed keywords

EID: 68249104938     PISSN: 03401022     EISSN: None     Source Type: Book Series    
DOI: 10.1007/128-2006-088     Document Type: Article

References (150)

1. Clore GM, Gronenborn AM (1998) Proc Natl Acad Sci USA 95:5891
2. Tolman JR, Flanagan JM, Kennedy MA, Prestegard JH (1995) Proc Natl Acad Sci USA 92:9279
3. Tjandra N, Bax A (1997) Science 278:1111
4. Pervushin K, Riek R, Wider G, Wuthrich K (1997) Proc Natl Acad Sci USA 94:12366
5. Saupe A (1968) Angew Chem Int Ed Engl 7:97
6. Losonczi JA, Andrec M, Fischer MW, Prestegard JH (1999) J Magn Reson 138:334
7. Emsley JW, Lindon JC (1975) NMR spectroscopy using liquid crystal solvents. Pergamon Press, Oxford
8. Clore GM, Gronenborn AM, Bax A (1998) J Magn Reson 133:216
9. Bax A (2003) Protein Sci 12:1
10. Ramirez BE, Bax A (1998) J Am Chem Soc 120:9106
11. Clore GM, Starich MR, Gronenborn AM (1998) J Am Chem Soc 120:10571
12. Lipari G, Szabo A (1982) J Am Chem Soc 104:4546
13. Tjandra N, Omichinski JG, Gronenborn AM, Clore GM, Bax A (1997) Nat Struct Biol 4:732
14. Blackledge M (2005) Prog Nucl Magn Reson Spectrosc 46:23
15. Gayathri C, Bothner-By AA, Van Zijl PCM, Maclean C (1982) Chem Phys Lett 87: 192
16. Beger RD, Marathias VM, Volkman BF, Bolton PH (1998) J Magn Reson 135:256
17. Contreras MA, Ubach J, Millet O, Rizo J, Pons M (1999) J Am Chem Soc 121:8947
18. Bertini I, Felli IC, Luchinat C (2000) J Biomol NMR 18:347
19. Pintacuda G, Keniry MA, Huber T, Park AY, Dixon NE, Otting G (2004) J Am Chem Soc 126:2963
20. Ma C, Opella SJ (2000) J Magn Reson 146:381
21. Feeny J, Birdsall B, Bradbury AF, Biekofsky RR, Bayley PM (2001) J Biomol NMR 21:41
22. Wohnert J, Franz KJ, Nitz M, Imperiali B, Schwalbe H (2003) J Am Chem Soc 125:13338
23. Ikegami T, Verdier L, Sakhaii P, Grimme S, Pescatore B, Saxena K, Fiebig KM, Griesinger C (2004) J Biomol NMR 29:339
24. Tjandra N, Grzesiek S, Bax A (1996) J Am Chem Soc 118:6264
25. Worcester DL (1978) Proc Natl Acad Sci USA 75:5475
26. Kung HC, Wang KY, Goljer I, Bolton PH (1995) J Magn Reson B 109:323
27. Sanders CR, Schwonek JP (1992) Biochemistry 31:8898
28. Sternin E, Nizza D, Gawrisch K (2001) Langmuir 17:2610
29. Gaemers S, Bax A (2001) J Am Chem Soc 123:12343
30. Nieh MP, Glinka CJ, Krueger S, Prosser RS, Katsaras J (2002) Biophys J 82:2487
31. Ottiger M, Bax A (1998) J Biomol NMR 12:361
32. Bax A, Tjandra N (1997) J Biomol NMR 10:289
33. Rückert M, Otting G (2000) J Am Chem Soc 122:7793
34. Hansen MR, Rance M, Pardi A (1998) J Am Chem Soc 120:11210
35. Hansen MR, Mueller L, Pardi A (1998) Nat Struct Biol 5:1065
36. Sass HJ, Musco G, Stahl SJ, Wingfield PT, Grzesiek S (2000) J Biomol NMR 18:303
37. Tycko R, Blanco FJ, Ishii Y (2000) J Am Chem Soc 122:9340
38. Meier S, Haussinger D, Grzesiek S (2002) J Biomol NMR 24:351
39. Ulmer TS, Ramirez BE, Delaglio F, Bax A (2003) J Am Chem Soc 125:9179
40. Prestegard JH, Bougault CM, Kishore AI (2004) Chem Rev 104:3519
41. Bax A, Vuister GW, Grzesiek S, Delaglio F, Wang AC, Tschudin R, Zhu G (1994) Methods Enzymol 239:79
42. Billeter M, Neri D, Otting G, Qian YQ, Wuthrich K (1992) J Biomol NMR 2:257
43. Pham TN, Liptaj T, Bromek K, Uhrin D (2002) J Magn Reson 157:200
44. Tolman JR, Prestegard JH (1996) J Magn Reson B 112:245
45. Kontaxis G, Clore GM, Bax A (2000) J Magn Reson 143:184
46. Griesinger C, Sorensen OW, Ernst RR (1986) J Chem Phys 85:6837
47. Meissner A, Duus JO, Sorensen OW (1997) J Biomol NMR 10:89
48. Vander Kooi CW, Kupce E, Zuiderweg ER, Pellecchia M (1999) J Biomol NMR 15:335
49. Sorensen MD, Meissner A, Sorensen OW (1999) J Magn Reson 137:237
50. Meissner A, Duus JO, Sorensen OW (1997) J Magn Reson 128:92
51. Ottiger M, Delaglio F, Bax A (1998) J Magn Reson 131:373
52. Kontaxis G, Bax A (2001) J Biomol NMR 20:77
53. Ding K, Gronenborn AM (2003) J Magn Reson 163:208
54. Andersson P, Annila A, Otting G (1998) J Magn Reson 133:364
55. Cordier F, Dingley AJ, Grzesiek S (1999) J Biomol NMR 13:175
56. Permi P, Annila A (2000) J Biomol NMR 16:221
57. Vallurupalli P, Moor PB (2002) J Biomol NMR 24:63
58. Ding K, Gronenborn AM (2004) J Magn Reson 167:253
59. Yang D, Tolman JR, Goto NK, Kay LE (1998) J Biomol NMR 12:325
60. Ottiger M, Bax A (1998) J Am Chem Soc 120:12334
61. Ottiger M, Delaglio F, Marquardt JL, Tjandra N, Bax A (1998) J Magn Reson 134:365
62. McFeeters RL, Fowler CA, Gaponenko VV, Byrd RA (2005) J Biomol NMR 31:35
63. Wang YX, Marquardt JL, Wingfield P, Stahl SJ, Lee-Huang S, Torchia D, Bax A (1998) J Am Chem Soc 120:7385
64. Yang D, Venters RA, Mueller GA, Choy WY, Kay LE (1999) J Biomol NMR 14:333
65. Chou JJ, Delaglio F, Bax A (2000) J Biomol NMR 18:101
66. Tugarinov V, Kay LE (2003) J Mol Biol 327:1121
67. Jain NU, Noble S, Prestegard JH (2003) J Mol Biol 328:451
68. Luy B, Marino JP (2003) J Magn Reson 163:92
69. Tjandra N, Bax A (1997) J Magn Reson 124:512
70. Carlomagno T, Peti W, Griesinger C (2000) J Biomol NMR 17:99
71. Chou JJ, Bax A (2001) J Am Chem Soc 123:3844
72. Prestegard JH, al Hashimi HM, Tolman JR (2000) Q Rev Biophys 33:371
73. Bax A, Kontaxis G, Tjandra N (2001) Methods Enzymol 339:127
74. Griesinger C, Meiler J, Peti W (2003) Angular restraints from residual dipolar couplings for structure refinement. In: Rama Krishna N, Berliner LJ (eds) Protein NMR for the Millenium. Kluwer Academic/Plenum Publishers, New York, p 163
75. Bryce DL, Bax A (2004) J Biomol NMR 28:273
76. Clore GM, Gronenborn AM, Tjandra N (1998) J Magn Reson 131:159
77. Valafar H, Prestegard JH (2004) J Magn Reson 167:228
78. Zweckstetter M, Bax A (2000) J Am Chem Soc 122:3791
79. Zweckstetter M, Hummer G, Bax A (2004) Biophys J 86:3444
80. Schwieters CD, Kuszewski JJ, Tjandra N, Clore GM (2003) J Magn Reson 160:65
81. Banci L, Bertini I, Cremonini MA, Gori-Savellini G, Luchinat C, Wuthrich K, Guntert P (1998) J Biomol NMR 12:553
82. Brunger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse-Kunstleve RW, Jiang JS, Kuszewski J, Nilges M, Pannu NS, Read RJ, Rice LM, Simonson T, Warren GL (1998) Acta Crystallogr D Biol Crystallogr 54:905
83. Tsui V, Zhu L, Huang TH, Wright PE, Case DA (2000) J Biomol NMR 16:9
84. Clore GM, Starich MR, Bewley CA, Cai M, Kuszewski J (1999) J Am Chem Soc 121:6513
85. Skrynnikov NR, Goto NK, Yang D, Choy WY, Tolman JR, Mueller GA, Kay LE (2000) J Mol Biol 295:1265
86. Goto NK, Skrynnikov NR, Dahlquist FW, Kay LE (2001) J Mol Biol 308:745
87. Evenas J, Tugarinov V, Skrynnikov NR, Goto NK, Muhandiram R, Kay LE (2001) J Mol Biol 309:961
88. Bewley CA, Clore GM (2000) J Am Chem Soc 122:6009
89. Clore GM, Bewley CA (2002) J Magn Reson 154:329
90. Mal TK, Skrynnikov NR, Yap KL, Kay LE, Ikura M (2002) Biochemistry 41:12899
91. Contessa GM, Orsale M, Melino S, Torre V, Paci M, Desideri A, Cicero DO (2005) J Biomol NMR 31:185
92. Revington M, Zhang Y, Yip GN, Kurochkin AV, Zuiderweg ER (2005) J Mol Biol 349:163
93. Jain NU, Wyckoff TJ, Raetz CR, Prestegard JH (2004) J Mol Biol 343:1379
94. Braddock DT, Cai M, Baber JL, Huang Y, Clore GM (2001) J Am Chem Soc 123:8634
95. Fischer MW, Losonczi JA, Weaver JL, Prestegard JH (1999) Biochemistry 38:9013
96. Bolon PJ, al Hashimi HM, Prestegard JH (1999) J Mol Biol 293:107
97. Hus JC, Marion D, Blackledge M (2001) J Am Chem Soc 123:1541
98. Tian F, Valafar H, Prestegard JH (2001) J Am Chem Soc 123:11791
99. Giesen AW, Homans SW, Brown JM (2003) J Biomol NMR 25:63
100. Valafar H, Mayer KL, Bougault CM, LeBlond PD, Jenney FE Jr, Brereton PS, Adams MW, Prestegard JH (2004) J Struct Funct Genomics 5:241
101. Prestegard JH, Mayer KL, Valafar H, Benison GC (2005) Methods Enzymol 394:175
102. Annila A, Aitio H, Thulin E, Drakenberg T (1999) J Biomol NMR 14:223
103. Delaglio F, Kontaxis G, Bax A (2000) J Am Chem Soc 122:2142
104. Andrec M, Du P, Levy RM (2001) J Am Chem Soc 123:1222
105. Kontaxis G, Delaglio F, Bax A (2005) Methods Enzymol 394:42
106. Meiler J, Peti W, Griesinger C (2000) J Biomol NMR 17:283
107. Rohl CA, Baker D (2002) J Am Chem Soc 124:2723
108. Qu Y, Guo JT, Olman V, Xu Y (2004) Nucleic Acids Res 32:551
109. Meiler J, Baker D (2005) J Magn Reson 173:310
110. Walsh JD, Kuszewski J, Wang YX (2005) J Magn Reson 177:155
111. Ni F (1994) Prog Nucl Magn Reson Spectrosc 26:517
112. Post CB (2003) Curr Opin Struct Biol 13:581
113. Mayer M, Meyer B (1999) Angew Chem Int Ed Engl 38:1784
114. Blommers MJJ, Stark W, Jones CE, Head D, Owen CE, Jahnke W (1999) J Am Chem Soc 121:1949
115. Carlomagno T, Felli IC, Czech M, Fischer R, Sprinzl M, Griesinger C (1999) J Am Chem Soc 121:1945
116. Carlomagno T (2005) Annu Rev Biophys Biomol Struct 34:245
117. Shimizu H, Donohue-Rolfe A, Homans SW (1999) J Am Chem Soc 121:5815
118. Thompson GS, Shimizu H, Homans SW, Donohue-Rolfe A (2000) Biochemistry 39:13153
119. al Hashimi HM, Bolon PJ, Prestegard JH (2000) J Magn Reson 142:153
120. Sanders CR, Landis GC (1994) J Am Chem Soc 116:6470
121. Rinaldi F, Lin M, Shapiro MJ, Petersheim M (1997) Biophys J 73:3337
122. Zandomeneghi G, Meier BH (2004) J Biomol NMR 30:303
123. Fischer D, Geyer A (2005) Magn Reson Chem 43:893
124. Koenig BW, Gawrisch K (2005) J Phys Chem B 109:7540
125. Chen Z, Reif B (2004) J Biomol NMR 29:525
126. Bloom M, Burnell EE, MacKay AL, Nichol CP, Valic MI, Weeks G (1978) Biochemistry 17:5750
127. Bocian DF, Chan SI (1978) Annu Rev Phys Chem 29:307
128. Koenig BW, Kontaxis G, Mitchell DC, Louis JM, Litman BJ, Bax A (2002) J Mol Biol 322:441
129. Hamm HE, Deretic D, Arendt A, Hargrave PA, Koenig B, Hofmann KP (1988) Science 241:832
130. Palczewski K, Kumasaka T, Hori T, Behnke CA, Motoshima H, Fox BA, Le TI, Teller DC, Okada T, Stenkamp RE, Yamamoto M, Miyano M (2000) Science 289:739
131. Dratz EA, Hargrave PA (1983) Trends Biochem Sci 8:128
132. Hong FT, Mauzerall D, Mauro A (1971) Proc Natl Acad Sci USA 68:1283
133. Neugebauer DC, Blaurock AE (1977) FEBS Lett 78:31
134. Koenig BW, Mitchell DC, König S, Grzesiek S, Litman BJ, Bax A (2000) J Biomol NMR 16:121
135. Goldman M (1984) J Magn Reson 60:437
136. Cone RA (1972) Nat New Biol 236:39
137. Aris L, Gilchrist A, Rens-Domiano S, Meyer C, Schatz PJ, Dratz EA, Hamm HE (2000) J Biol Chem 276:2333
138. Ohnishi S, Shortle D (2003) Proteins 50:546
139. Koenig BW, Rogowski M, Louis JM (2003) J Biomol NMR 26:193
140. Anglister J, Levy R, Scherf T (1989) Biochemistry 28:3360
141. Kisselev OG, Kao J, Ponder JW, Fann YC, Gautam N, Marshall GR (1998) Proc Natl Acad Sci USA 95:4270
142. Lambright DG, Sondek J, Bohm A, Skiba NP, Hamm HE, Sigler PB (1996) Nature 379:311
143. Cai K, Itoh Y, Khorana HG (2001) Proc Natl Acad Sci USA 98:4877
144. Kisselev OG, Downs MA (2003) Structure (Cambridge MA, US) 11:367
145. Chou JJ, Kaufman JD, Stahl SJ, Wingfield PT, Bax A (2002) J Am Chem Soc 124:2450
146. Koenig BW (2002) Chembiochem 3:975
147. Konig B, Arendt A, McDowell JH, Kahlert M, Hargrave PA, Hofmann KP (1989) Proc Natl Acad Sci USA 86:6878
148. Franke RR, Sakmar TP, Graham RM, Khorana HG (1992) J Biol Chem 267:14767
149. Ernst OP, Meyer CK, Marin EP, Henklein P, Fu WY, Sakmar TP, Hofmann KP (2000) J Biol Chem 275:1937
150. Kisselev OG, Ermolaeva MV, Gautam N (1994) J Biol Chem 269:21399