NMR Studies of Biomolecular Dynamics and Structural Plasticity Using Residual Dipolar Couplings

Annual Reports on NMR Spectroscopy

Volumn 51, Issue , 2003, Pages 105-166

  TOLMAN, JOEL R ^a   AL HASHIMI, HASHIM M ^b  

^a JOHNS HOPKINS UNIVERSITY   (United States)

^b UNIVERSITY OF MICHIGAN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 1842596288     PISSN: 00664103     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0066-4103(03)51003-1     Document Type: Review

References (193)

1. J. Skolnick J.S. Fetrow Trends Biotechnol. 18 2000 34 39
2. A. Sali Nat. Struct. Biol. 5 1998 1029 1032
3. O. Jardetzky J.F. Lefevre FEBS Lett. 338 1994 246 250
4. O. Jardetzky Prog. Biophys. Mol. Biol. 65 1996 171
5. M.F. Perutz F.S. Mathews J. Mol. Biol. 21 1966 199
6. M. Brunori Biophys. Chem. 86 2000 221 230
7. I.E. Iben D. Braunstein W. Doster H. Frauenfelder M.K. Hong J.B. Johnson S. Luck P. Ormos A. Schulte P.J. Steinbach A.H. Xie R.D. Young Phys. Rev. Lett. 62 1989 1916 1919
8. P.J. Steinbach B.R. Brooks Proc. Natl. Acad. Sci. USA 93 1996 55 59
9. H. Frauenfelder S.G. Sligar P.G. Wolynes Science 254 1991 1598 1603
10. M. Ferrand A.J. Dianoux W. Petry G. Zaccai Proc. Natl. Acad. Sci. USA 90 1993 9668 9672
11. B.F. Rasmussen A.M. Stock D. Ringe G.A. Petsko Nature 357 1992 423 424
12. L.E. Kay Nat. Struct. Biol. 5 1998 513 517
13. R. Ishima D.A. Torchia Nat. Struct. Biol. 7 2000 740 743
14. A.G. Palmer 3rd, C.D. Kroenke J.P. Loria Methods Enzymol. 339 2001 204 238
15. A.J. Wand Nat. Struct. Biol. 8 2001 926 931
16. M. Akke Curr. Opin. Struct. Biol. 12 2002 642 647
17. D.A. Case Acc. Chem. Res. 35 2002 325 331
18. R. Bruschweiler Curr. Opin. Struct. Biol. 13 2003 175 183
19. J.H. Prestegard J.R. Tolman H.M. Al-Hashimi M. Andrec N.R. Krishna L.J. Berliner Biological Magnetic Resonance 17 1999 Plenum New York 311 355
20. J.H. Prestegard H.M. Al-Hashimi J.R. Tolman Q. Rev. Biophys. 33 2000 371 424
21. N. Tjandra Struct. Fold. Des. 7 1999 R205 R211
22. E.T. Mollova M.R. Hansen A. Pardi J. Am. Chem. Soc. 122 2000 11561 11562
23. A. Bax G. Kontaxis N. Tjandra Methods Enzymol. 339 2001 127 174
24. J.R. Tolman Curr. Opin. Struct. Biol. 11 2001 532 539
25. H.M. Al-Hashimi D.J. Patel J. Biomol. NMR 22 2002 1 8
26. B. Simon M. Sattler Angew. Chem. Int. Ed. Engl. 41 2002 437 440
27. A.M. Gronenborn CR Biol. 325 2002 957 966
28. G.M. Clore C.D. Schwieters Curr. Opin. Struct. Biol. 12 2002 146 153
29. A. Bax Protein Sci. 12 2003 1 16
30. E.W. Bastiaan C. Maclean P.C.M. Van Zilj A.A. Bothner-by Ann. Rep. NMR Spec. 19 1987 35 77
31. E.W. Bastiaan C. MacLean NMR-Basic Princ. Prog. 25 1990 17 43
32. C. Gayathri A.A. Bothner-By P.C.M. van Zijl C. MacLean Chem. Phys. Lett. 87 1982 192 196
33. P.C.M. van Zijl B.H. Ruessink J. Bulthuis C. MacLean Acc. Chem. Res. 17 1984 172 180
34. I.W. Emsley J.C. Lindon NMR Spectroscopy Using Liquid Crystal Solvents 1975 Pergamon Press Oxford
35. P. Diehl C.L. Khetrapal NMR: Basic Principles and Progress 1 1969 Springer-Verlag New York
36. C.L. Khetrapal, A.C. Kunwar, A.G. Tracey and P. Diehl, eds., Springer-Verlag, Berlin, 1975
37. L.C. Snyder J. Chem. Phys. 43 1965 4041 4050
38. A. Saupe Angew. Chem. Int. Ed. Engl. 7 1968 97 112
39. J.A.B. Lohman C. MacLean Chem. Phys. 35 1978 269 274
40. A.A. Bothner-By D.M. Grant R.K. Harris Encyclopedia of Nuclear Magnetic Resonance 1995 Wiley Chichester 2932 2938
41. A. Abragam Principles of Nuclear Magnetism 1961 Clarendon Press Oxford
42. R.R. Ernst G. Bodenhausen A. Wokaun Principles of Nuclear Magnetic Resonance in One and Two Dimensions 1987 Clarendon Press Oxford
43. D.A. Case J. Biomol. NMR 15 1999 95 102
44. M. Ottiger A. Bax J. Am. Chem. Soc. 120 1998 12334 12341
45. A. Saupe Z. Naturforsh. 19a 1964 161
46. A.R. Edmonds Angular momentum in quantum mechanics 1968 Princeton Univ. Press Princeton, New Jersey
47. J.R. Tolman J.M. Flanagan M.A. Kennedy J.H. Prestegard Nat. Struct. Biol. 4 1997 292 297
48. J.A. Losonczi J.H. Prestegard Biochemistry 37 1998 706 716
49. J.R. Tolman H.M. Al-Hashimi L.E. Kay J.H. Prestegard J. Am. Chem. Soc. 123 2001 1416 1424
50. J.R. Tolman J. Am. Chem. Soc. 124 2002 12020 12030
51. J.R. Tolman J.M. Flanagan M.A. Kennedy J.H. Prestegard Proc. Natl. Acad. Sci. USA 92 1995 9279 9283
52. N. Tjandra A. Bax Science 278 1997 1111 1114
53. M.R. Hansen P. Hanson A. Pardi Method Enzymol. 317 2000 220 240
54. J.H. Prestegard A.I. Kishore Curr. Opin. Chem. Biol. 5 2001 584 590
55. B.E. Ramirez A. Bax J. Am. Chem. Soc. 120 1998 9106 9107
56. H.M. Al-Hashimi H. Valafar M. Terrell E.R. Zartler M.K. Eidsness J.H. Prestegard J. Magn. Reson. 143 2000 402 406
57. J. Meiler J.J. Prompers W. Peti C. Griesinger R. Bruschweiler J. Am. Chem. Soc. 123 2001 6098 6107
58. W. Peti J. Meiler R. Bruschweiler C. Griesinger J. Am. Chem. Soc. 124 2002 5822 5833
59. K. Briggman and J.R. Tolman, J. Am. Chem. Soc. , 2003, 125 , 10164–10165
60. I. Bertini, M.B.L. Janik, L. Gaohua, C. Luchinat and A. Rosato, Biochemistry , 2000, submitted
61. I. Bertini I.C. Felli C. Luchinat J. Biomol. NMR 18 2000 347 355
62. H.M. Al-Hashimi A. Majumdar A. Gorin A. Kettani E. Skripkin D.J. Patel J. Am. Chem. Soc. 123 2001 633 640
63. S. Gaemers A. Bax J. Am. Chem. Soc. 123 2001 12343 12352
64. P. Ram J.H. Prestegard Biochim. Biophys. Acta 940 1988 289 294
65. C.R. Sanders B.J. Hare K.P. Howard J.H. Prestegard Prog. Nucl. Magn. Reson. Spectrosc. 26 1994 421 444
66. C.R. Sanders R.S. Prosser Struct. Fold. Des. 6 1998 1227 1234
67. M. Ottiger A. Bax J. Biomol. NMR 12 1998 361 372
68. J.A. Losonczi J.H. Prestegard J. Biomol. NMR 12 1998 447 451
69. M. Ottiger A. Bax J. Biomol. NMR 13 1999 187 191
70. S. Cavagnero H.J. Dyson P.E. Wright J. Biomol. NMR 13 1999 387 391
71. H. Wang M. Eberstadt E.T. Olejniczak R.P. Meadows S.W. Fesik J. Biomol. NMR 12 1998 443 446
72. M.R. Hansen L. Mueller A. Pardi Nat. Struct. Biol. 5 1998 1065 1074
73. G.M. Clore M.R. Starich A.M. Gronenborn J. Am. Chem. Soc. 120 1998 10571 10572
74. M. Zweckstetter A. Bax J. Biomol. NMR 20 2001 365 377
75. J. Sass F. Cordier A. Hoffmann A. Cousin J.G. Omichinski H. Lowen S. Grzesiek J. Am. Chem. Soc. 121 1999 2047 2055
76. B.W. Koenig J.S. Hu M. Ottiger S. Bose R.W. Hendler A. Bax J. Am. Chem. Soc. 121 1999 1385 1386
77. K. Fleming D. Gray S. Prasannan S. Matthews J. Am. Chem. Soc. 122 2000 5224 5225
78. R.S. Prosser J.A. Losonczi I.V. Shiyanovskaya J. Am. Chem. Soc. 120 1998 11010 11011
79. L.G. Barrientos C. Dolan A.M. Gronenborn J. Biomol. NMR 16 2000 329 337
80. L.G. Barrientos K. Gawrisch N. Cheng A.C. Steven A.M. Gronenborn Langmuir 18 2002 3773 3779
81. M. Ruckert G. Otting J. Am. Chem. Soc. 122 2000 7793 7797
82. H.J. Sass G. Musco S.J. Stahl P.T. Wingfield S. Grzesiek J. Biomol. NMR 18 2000 303 309
83. R. Tycko F.J. Blanco Y. Ishii J. Am. Chem. Soc. 122 2000 9340 9341
84. Y. Ishii M.A. Markus R. Tycko J. Biomol. NMR 21 2001 141 151
85. S. Meier D. Haussinger S. Grzesiek J. Biomol. NMR 24 2002 351 356
86. H.-J. Sass G. Musco S.J. Stahl P.T. Wingfield S. Grzesiek J. Biomol. NMR 18 2000 303 309
87. J.F. Trempe F.G. Morin Z.C. Xia R.H. Marchessault K. Gehring J. Biomol. NMR 22 2002 83 87
88. S.A. Riley J.R. Giuliani M.P. Augustine J. Magn. Reson. 159 2002 82 86
89. J.A. Losonczi M. Andrec M.W.F. Fischer J.H. Prestegard J. Magn. Reson. 138 1999 334 342
90. A. Albert Regression and the Moore-Penrose Pseudoinverse 1972 Academic Press New York
91. A. Ben-Israel T.N.E. Greville Generalized Inverses: Theory and Applications 1974 John Wiley & Sons New York
92. W.H. Press S.A. Teukolsky W.T. Vetterling B.P. Flannery Numerical Recepies in C 1992 Cambridge University Press Cambridge
93. N. Tjandra S. Grzesiek A. Bax J. Am. Chem. Soc. 118 1996 6264 6272
94. N. Tjandra J.G. Omichinski A.M. Gronenborn G.M. Clore A. Bax Nat. Struct. Biol. 4 1997 732 738
95. H.M. Al-Hashimi J.R. Tolman A. Majumdar A. Gorin D.J. Patel J. Am. Chem. Soc. 123 2001 5806 5807
96. H.M. Al-Hashimi A. Gorin A. Majumdar D.J. Patel J. Am. Chem. Soc. 123 2001 3179 3180
97. A. Bax N. Tjandra J. Biomol. NMR 10 1997 289 292
98. A. Bax S.E. Ealick Curr. Opin. Struct. Biol. 7 1997 669 671
99. E.E. Burnell C.A. de Lange Chem. Rev. 98 1998 2359 2387
100. M. Zweckstetter A. Bax J. Am. Chem. Soc. 122 2000 3791 3792
101. H.M. Al-Hashimi Y. Gosser A. Gorin W. Hu A. Majumdar D.J. Patel J. Mol. Biol. 315 2002 95 102
102. H.F. Azurmendi C.A. Bush J. Am. Chem. Soc. 124 2002 2426 2427
103. M.X. Fernandes P. Bernado M. Pons J. Garcia de la Torre J. Am. Chem. Soc. 123 2001 12037 12047
104. A. Almond J.B. Axelsen J. Am. Chem. Soc. 124 2002 9986 9987
105. S.A. Teichmann J. Park C. Chothia Proc. Natl. Acad. Sci. USA 95 1998 14658 14663
106. E.V. Koonin L. Aravind A.S. Kondrashov Cell 101 2000 573 576
107. C. Chothia J. Gough C. Vogel S.A. Teichmann Science 300 2003 1701 1703
108. C. Khosla P.B. Harbury Nature 409 2001 247 252
109. N. Tjandra D.S. Garrett A.M. Gronenborn A. Bax G.M. Clore Nat. Struct. Biol. 4 1997 443 449
110. D. Fushman R. Xu D. Cowburn Biochemistry 38 1999 10225 10230
111. L.E. Kay, Nuclear Magnetic Resonance of Biological Macromolecules , Pt B , Vol. 339, 2001, pp. 174–203
112. M.W.F. Fischer J.A. Losonczi J.L. Weaver J.H. Prestegard Biochemistry 38 1999 9013 9022
113. J.L. Weaver J.H. Prestegard Biochemistry 37 1998 116 128
114. D.T. Braddock M. Cai J.L. Baber Y. Huang G.M. Clore J. Am. Chem. Soc. 123 2001 8634 8635
115. D.T. Braddock J.M. Louis J.L. Baber D. Levens G.M. Clore Nature 415 2002 1051 1056
116. L. Yu A.H. Gunasekera J. Mack E.T. Olejniczak L.E. Chovan X. Ruan D.L. Towne C.G. Lerner S.W. Fesik J. Mol. Biol. 311 2001 593 604
117. N.R. Skrynnikov N.K. Goto D. Yang W.Y. Choy J.R. Tolman G.A. Mueller L.E. Kay J. Mol. Biol. 295 2000 1265 1273
118. P.M. Hwang N.R. Skrynnikov L.E. Kay J. Biomol. NMR 20 2001 83 88
119. J. Evenas V. Tugarinov N.R. Skrynnikov N.K. Goto R. Muhandiram L.E. Kay J. Mol. Biol. 309 2001 961 974
120. J.J. Chou S. Li C.B. Klee A. Bax Nat. Struct. Biol. 8 2001 990 997
121. J.A. Lukin G. Kontaxis V. Simplaceanu Y. Yuan A. Bax C. Ho Proc. Natl. Acad. Sci. USA 100 2003 517 520
122. N.U. Jain S. Noble J.H. Prestegard J. Mol. Biol. 328 2003 451 462
123. H.M. Al-Hashimi P.J. Bolon J.H. Prestegard J. Magn. Reson. 142 2000 153 158
124. R. Varadan O. Walker C. Pickart D. Fushman J. Mol. Biol. 324 2002 637 647
125. M. Zweckstetter A. Bax J. Biomol. NMR 23 2002 127 137
126. L.C. Wang Y.X. Pang T. Holder J.R. Brender A.V. Kurochkin E.R.P. Zuiderweg Proc. Natl. Acad. Sci. USA 98 2001 7684 7689
127. H.A. Carlson Curr. Opin. Chem. Biol. 6 2002 447 452
128. H.A. Carlson Curr. Pharm. Des. 8 2002 1571 1578
129. B. Reif M. Hennig C. Griesinger Science 276 1997 1230 1233
130. M.L. Cai Y. Huang G.M. Clore J. Am. Chem. Soc. 123 2001 8642 8643
131. N. Sibille B. Bersch J. Coves M. Blackledge B. Brutscher J. Am. Chem. Soc. 124 2002 14616 14625
132. J.J. Chou A. Bax J. Am. Chem. Soc. 123 2001 3844 3845
133. A. Mittermaier L.E. Kay J. Am. Chem. Soc. 123 2001 6892 6903
134. R. Sprangers M.R. Groves I. Sinning M. Sattler J. Mol. Biol. 327 2003 507 520
135. G. Lipari A. Szabo J. Am. Chem. Soc. 104 1982 4546 4559
136. J. Meiler W. Peti C. Griesinger J. Am. Chem. Soc. 125 2003 8072 8073
137. N. Tjandra S.E. Feller R.W. Pastor A. Bax J. Am. Chem. Soc. 117 1995 12562 12566
138. K. Wuthrich, K. Pervushin, R. Riek, M. Salzmann and G. Wider, Abstr. Pap. Am. Chem. Soc. , 2000, 219, 11-PHYS
139. J.C. Hus R. Bruschweiler J. Biomol. NMR 24 2002 123 132
140. J.C. Hus W. Peti C. Griesinger R. Bruschweiler J. Am. Chem. Soc. 125 2003 5596 5597
141. J.R. Williamson Nat. Struct. Biol. 7 2000 834 837
142. N. Leulliot G. Varani Biochemistry 40 2001 7947 7956
143. X. Zhuang H. Kim M.J. Pereira H.P. Babcock N.G. Walter S. Chu Science 296 2002 1473 1476
144. N.G. Walter P.A. Chan K.J. Hampel D.P. Millar J.M. Burke Biochemistry 40 2001 2580 2587
145. M. Menger F. Eckstein D. Porschke Nucleic Acids Res. 28 2000 4428 4434
146. R.E. Dickerson D.S. Goodsell M.L. Kopka P.E. Pjura J. Biomol. Struct. Dyn. 5 1987 557 579
147. C.G. Hoogstraten J.R. Wank A. Pardi Biochemistry 39 2000 9951 9958
148. M. Akke R. Fiala F. Jiang D. Patel A.G. Palmer RNA-Publ. RNA Soc. 3 1997 702 709
149. J.J. Warren P.B. Moore J. Magn. Reson. 149 2001 271 275
150. N. Sibille A. Pardi J.P. Simorre M. Blackledge J. Am. Chem. Soc. 123 2001 12135 12146
151. S.A. McCallum A. Pardi J. Mol. Biol. 326 2003 1037 1050
152. P. Bayer L. Varani G. Varani J. Biomol. NMR 14 1999 149 155
153. N. Tjandra S. Tate A. Ono M. Kainosho A. Bax J. Am. Chem. Soc. 122 2000 6190 6200
154. A. Vermeulen H.J. Zhou A. Pardi J. Am. Chem. Soc. 122 2000 9638 9647
155. L. Trantirek M. Urbasek R. Stefl J. Feigon V. Sklenar J. Am. Chem. Soc. 122 2000 10454 10455
156. D. MacDonald K. Herbert X.L. Zhang T. Polgruto P. Lu J. Mol. Biol. 306 2001 1081 1098
157. P. Padrta R. Stefl L. Kralik L. Zidek V. Sklenar J. Biomol. NMR 24 2002 1 14
158. T. Sprules N. Green M. Featherstone K. Gehring J. Biol. Chem. 278 2003 1053 1058
159. E.T. Mollova A. Pardi Curr. Opin. Struct. Biol. 10 2000 298 302
160. L. Zidek R. Stefl V. Sklenar Curr. Opin. Struct. Biol. 11 2001 275 281
161. D. MacDonald P. Lu Curr. Opin. Struct. Biol. 12 2002 337 343
162. J.J. Warren P.B. Moore J. Biomol. NMR 20 2001 311 323
163. M. Zacharias P.J. Hagerman Proc. Natl. Acad. Sci. USA 92 1995 6052 6056
164. F. Aboul-ela J. Karn G. Varani Nucleic Acids Res. 24 1996 3974 3981
165. J.A. Ippolito T.A. Steitz Proc. Natl. Acad. Sci. USA 95 1998 9819 9824
166. H.M. Al-Hashimi S.W. Pitt A. Majumdar W. Xu D.J. Patel J. Mol. Biol. 329 2003 867 873
167. K. Bondensgaard E.T. Mollova A. Pardi Biochemistry 41 2002 11532 11542
168. H.W. Pley K.M. Flaherty D.B. McKay Nature 372 1994 68 74
169. W.G. Scott J.T. Finch A. Klug Cell 81 1995 991 1002
170. W.G. Scott J.B. Murray J.R. Arnold B.L. Stoddard A. Klug Science 274 1996 2065 2069
171. G.S. Bassi N.E. Mollegaard A.I. Murchie E. von Kitzing D.M. Lilley Nat. Struct. Biol. 2 1995 45 55
172. G.S. Bassi A.I. Murchie F. Walter R.M. Clegg D.M. Lilley EMBO J. 16 1997 7481 7489
173. Q. Zhang, R. Throolin, S. Pitt, A. Serganov and H.M. Al-Hashimi, J. Am. Chem. Soc. , 2003, submitted
174. S. Roseman J. Biol. Chem. 276 2001 41527 41542
175. C. Schaffer P. Messner Biochimie 83 2001 591 599
176. C.A. Bush M. Martin-Pastor A. Imberty Annu. Rev. Biophys. Biomol. Struct. 28 1999 269 293
177. R.J. Woods Glycoconj.J. 15 1998 209 216
178. P. Ram L. Mazzola J.H. Prestegard J. Am. Chem. Soc. 111 1989 3176 3182
179. M. Martin-Pastor C.A. Bush Carbohydr. Res. 323 2000 147 155
180. M. Martin-Pastor C.A. Bush Biochemistry 39 2000 4674 4683
181. M. Martin-Pastor A. Canales-Mayordomo J. Jimenez-Barbero J. Biomol. NMR 26 2003 345 353
182. T.N. Pham T. Liptaj K. Bromek D. Uhrin J. Magn. Reson. 157 2002 200 209
183. A. Almond J. Bunkenborg T. Franch C.H. Gotfredsen J.O. Duus J. Am. Chem. Soc. 123 2001 4792 4802
184. B. Stevensson A.V. Komolkin D. Sandstrom A. Maliniak J. Chem. Phys. 114 2001 2332 2339
185. A. Kjellberg S.W. Homans J. Magn. Reson. 151 2001 90 93
186. H.F. Azurmendi M. Martin-Pastor C.A. Bush Biopolymers 63 2002 89 98
187. H.F. Azurmendi C.A. Bush Carbohydr. Res. 337 2002 905 915
188. G.R. Kiddle S.W. Homans FEBS Lett. 436 1998 128 130
189. F. Tian H.M. Al-Hashimi J.L. Craighead J.H. Prestegard J. Am. Chem. Soc. 123 2001 485 492
190. A. Almond J.O. Duus J. Biomol. NMR 20 2001 351 363
191. D.I. Freedberg J. Am. Chem. Soc. 124 2002 2358 2362
192. B. Stevensson C. Landersjo G. Widmalm A. Maliniak J. Am. Chem. Soc. 124 2002 5946 5947
193. P. Dosset J.C. Hus D. Marion M. Blackledge J. Biomol. NMR 20 2001 223 231