Validation of protein structures derived by NMR spectroscopy

Progress in Nuclear Magnetic Resonance Spectroscopy

Volumn 45, Issue 3-4, 2004, Pages 315-337

  Spronk, Chris A E M ^a   Nabuurs, Sander B ^a   Krieger, Elmar ^a   Vriend, Gert ^a   Vuister, Geerten W ^a  

^a RADBOUD UNIVERSITY NIJMEGEN   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

COUPLINGS; DATA REDUCTION; DATABASE SYSTEMS; DNA; ELECTROSTATICS; HYDROGEN BONDS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; NUCLEIC ACIDS; THREE DIMENSIONAL; X RAY DIFFRACTION ANALYSIS;

BIOLOGICAL FUNCTIONS; COLLABORATIVE COMPUTING PROJECT FOR THE NMR COMMUNITY (CCPN); PROTEIN DATA BANK (PDB); PROTON-DENSITIES;

PROTEINS;

EID: 9944221417     PISSN: 00796565     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.pnmrs.2004.08.003     Document Type: Review

References (97)

1. J.D. Watson, F.H.C. Crick, Nature 171 (1953) 737-738.
2. J.C. Kendrew, G. Bodo, H.M. Dintzis, R.G. Parrish, H. Wyckoff, D.C. Phillips, Nature 181 (1958) 662-666.
3. G.J. Kleywegt, T.A. Jones, Structure 10 (2002) 465-472.
4. P.C. Bernstein, T.F. Koetzle, G.J. Williams, E.F. Meyer Jr, M.D. Brice, J.R. Rodgers, O. Kennard, T. Shimanouchi, M. Tasumi, Eur. J. Biochem. 80 (1977) 319-324.
5. H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, P.E. Bourne, Nucl. Acids Res. 28 (2000) 235-242.
6. M.P. Williamson, T.F. Havel, K. Wüthrich, J. Mol. Biol. 182 (1985) 295-315.
7. R. Kaptein, E.R. Zuiderweg, R.M. Scheek, R. Boelens, W.F. van Gunsteren, J. Mol. Biol. 182 (1985) 179-182.
8. R.A. Laskowski, Methods Biochem. Anal. 44 (2003) 273-303.
9. R.W. Hooft, G. Vriend, C. Sander, E. Abola, Nature 381 (1996) 272.
10. G.J. Kleywegt, Acta Crystallogr. D 56 (2000) 249-265.
11. A.J. Dingley, S. Grzesiek, J. Am. Chem. Soc. 120 (1998) 8293-8297.
12. F. Cordier, S. Grzesiek, J. Am. Chem. Soc. 121 (1999) 1601-1602.
13. N. Tjandra, A. Bax, Science 278 (1997) 1111-1114.
14. G. Cornilescu, J.L. Marquardt, M. Ottiger, A. Bax, J. Am. Chem. Soc. 120 (1998) 6836-6837.
15. R. Sprangers, M.J. Bottomley, J.P. Linge, J. Schultz, M. Nilges, M. Sattler, J. Biomol. NMR 16 (2000) 47-58.
16. L. Banci, I. Bertini, G.G. Savellini, A. Romagnoli, P. Turano, M.A. Cremonini, C. Luchinat, H.B. Gray, Proteins 29 (1997) 68-76.
17. L. Banci, I. Bertini, G. Cavallaro, A. Giachetti, C. Luchinat, G. Parigi, J. Biomol. NMR 28 (2004) 249-261.
18. G. Cornilescu, F. Delaglio, A. Bax, J. Biomol. NMR 13 (1999) 289-302.
19. M. Nilges, M.J. Macias, S.I. O'Donoghue, H. Oschkinat, J. Mol. Biol. 269 (1997) 408-422.
20. J.P. Linge, M. Habeck, W. Rieping, M. Nilges, Bioinformatics 19 (2003) 315-316.
21. T. Herrmann, P. Güntert, J. Biomol. NMR 24 (2002) 171-189.
22. T. Herrmann, P. Güntert, K. Wüthrich, J. Mol. Biol. 319 (2002) 209-227.
23. J. Kuszewski, C.D. Schwieters, D.S. Garrett, R.A. Byrd, N. Tjandra, G.M. Clore, J. Am. Chem. Soc. 126 (2004) 6258-6273.
24. A. Grishaev, M. Llinas, Proc. Natl Acad. Sci. USA 99 (2002) 6707-6712.
25. A. Grishaev, M. Llinas, Proc. Natl Acad. Sci. USA 99 (2002) 6713-6718.
26. A. Grishaev, M. Llinas, J. Biomol. NMR 28 (2004) 1-10.
27. J.P. Linge, M.A. Williams, C.A.E.M. Spronk, A.M.J.J. Bonvin, M. Nilges, Proteins 50 (2003) 496-506.
28. S.B. Nabuurs, A.J. Nederveen, W. Vranken, J.F. Doreleijers, A.M. Bonvin, G.W. Vuister, G. Vriend, C.A.E.M. Spronk, Proteins 55 (2004) 483-486.
29. P. Güntert, Q. Rev. Biophys. 31 (1998) 145-237.
30. P. Güntert, Prog. NMR Spec. 43 (2003) 105-125.
31. A.T. Brünger, P.D. Adams, G.M. Clore, W.L. Delano, P. Gros, R.W. Grossc-Kunstleve, J.-S. Jiang, I. Kuszewski, M. Nilges, N.S. Pannu, et al., Acta Crystallogr. D 54 (1998) 905-921.
32. A.T. Brünger, Nature 355 (1992) 472-475.
33. C. Gonzalez, J.A.C. Rullmann, A.M.J.J. Bonvin, R. Boelens, R. Kaptein, J. Magn. Reson. 91 (1991) 659-664.
34. T.L. James, Methods Enzymol. 239 (1994) 416-439.
35. W. Gronwald, R. Kirchhofer, A. Gorler, W. Kremer, B. Ganslmeier, K.P. Neidig, H.R. Kalbitzer, J. Biomol. NMR 17 (2000) 137-151.
36. A.M. Gronenborn, G.M. Clore, Crit Rev. Biochem. Mol. Biol. 30 (1995) 351-385.
37. A.T. Brünger, G.M. Clore, A.M. Gronenborn, R. Saffrich, M. Nilges, Science 261 (1993) 328-331.
38. G.M. Clore, D.S. Garrett, J. Am. Chem. Soc. 121 (1999) 9008-9012.
39. J. Meiler, W. Peti, C. Griesinger, J. Biomol. NMR 17 (2000) 283-294.
40. M. Zweckstetter, A. Bax, I. Am. Chem. Soc. 122 (2000) 3791-3792.
41. C.A.E.M. Spronk, J.P. Linge, C.W. Hilbers, G.W. Vuister, J. Biomol. NMR 22 (2002) 281-289.
42. J.F. Doreleijers, M.L. Raves, T. Rullmann, R. Kaplein, J. Biomol. NMR 14 (1999) 123-132.
43. G.J. Kleywegt, T.A. Jones, Structure 4 (1996) 1395-1400.
44. R.W. Hooft, C. Sander, G. Vriend, Comp. Appl. Biosci. 13 (1997) 425-430.
45. R.A. Laskowski, J.A. Rullmannn, M.W. MacArthur, R. Kaptein, J.M. Thornton, J. Biomol. NMR 8 (1996) 477-486.
46. S.B. Nabours, C.A.E.M. Spronk, E. Krieger, H. Maassen, G. Vriend, G.W. Vuister, J. Am. Chem. Soc. 125 (2003) 12026-12034.
47. C.P. Kloks, C-A-E.M. Spronk, E. Lasonder, A. Honmann, G.W. Vuister, S. Grzesiek, C.W. Hilbers, J. Mol. Biol. 316 (2002) 317-326.
48. A.M. Gronenborn, D.R. Filpula, N.Z. Essig, A. Achari, M. Whitlow, P.T. Wingfield, G.M. Clore, Science 253 (1991) 657-661.
49. T. Gallagher, P. Alexander, P. Bryan, G.L. Gilliland, Biochemistry 33 (1994) 4721-4729.
50. J. Kuszewski, A.M. Gronenborn, G.M. Clore, J. Am. Chem. Soc. 121 (1999) 2337-2338.
51. J.C. Hoch, An Amateur Looks at Error Analysis in the Determination of Protein Structure by NMR, Plenum Press, New York, 1991.
52. D. Zhao, O. Jardetzky, J. Mol. Biol. 239 (1994) 601-607.
53. T.F. Havel, K. Wüthrich, J. Mol. Biol. 182 (1985) 281-294.
54. G.M. Clore, M.A. Robien, A.M. Gronenborn, J. Mol. Biol. 231 (1993) 82-102.
55. F.R. Chalaoux, S.I. O'Donoghue, M. Nilges, Proteins 34 ( 1999) 453-463.
56. C.A.E.M. Spronk, S.B. Nabuurs, A.M. Bonvin, E. Krieger, G.W. Vuister, G. Vriend, J. Biomol. NMR 25 (2003) 225-234.
57. R.A. Laskowski, M.W. MacArthur, D.S. Moss, J.M. Thornton, J. Appl. Crystallogr. 26 (1993) 283-291.
58. G. Vriend, J. Mol. Graph. 8 (1990) 52-56.
59. F.H. Allen, O. Kennard, R. Taylor, Acc. Chem. Res. 16 (1983) 146-153.
60. R.A. Engh, R. Huber, Acta Crystallogr. A47 (1991) 392-400.
61. J.F. Dorclrijers, J.A. Rullmann, R. Kaptein, J. Mol. Biol. 281 (1998) 149-164.
62. R.W. Hooft, C. Sander, G. Vriend, J. Appl. Crystallogr. 29 (1996) 714-716.
63. A.L. Morris, M.W. Macarthur, E.G. Hutchinson, J.M. Thornton, Proteins 12 (1992) 345-364.
64. P. Schultze, J. Feigon, Nature 387 (1997) 668.
65. J.F. Doreleijers, G. Vriend, M.L. Raves, R. Kaptein, Proteins 37 (1999) 404-416.
66. J. Kuszewski, A.M. Gronenborn, G.M. Clore, Protein Sci. 5 (1996) 1067-1080.
67. J. Kuszcwski, A.M. Gronenborn, G.M. Clore, J. Magn. Reson. 125 (1997) 171-177.
68. J. Kuszewski, G.M. Clore, J. Magn. Reson. 146 (2000) 249-254.
69. J. Kuszewslri, C. Schwieteis, G.M. Clore, J. Am. Chem. Soc. 123 (2001) 3903-3918.
70. I. Bertini, G. Cavallaro, C. Luchinat, I. Poli, J. Biomol. NMR 26 (2003) 355-366.
71. W. Kabsch, C. Sander, Biopolymers 22 (1983) 2577-2637.
72. G.N. Ramachandran, C. Ramakrishnan, V. Sasisekharan, J. Mol. Biol. 7 (1963) 95.
73. M.W. MacArthur, J.M. Thornton, J. Mol. Biol. 264 (1996) 1180-1195.
74. M.S. Weiss, A. Jabs, R. Hilgenfeld, Nat. Struct. Biol. 5 (1998) 676.
75. K.S. Wilson, S. Butterworth, Z. Dauter, V.S. Lamzin, M. Wilsh, S. Wodak, J. Pontius, J. Richelle, A. Vaguine, C. Sander, et al., J. Mol. Biol. 276 (1998) 417-436.
76. B.R- Brooks, R.E. Braccolcri, B.D. Olafson, D.J. States, S. Swaminathan, M. Karplus, I. Contp. Chem. 4 (1983) 187-217.
77. C.-L Branden, I. Tooze, Introduction to Protein Structure, second ed. Garland Publisher, New Yoik, 1999.
78. I.K. Mcdonald, J.M. Thornton, J. Mol. Biol. 238 (1994) 777-793.
79. D.S. Wishart, B.D. Sykes, F.M. Richards, Biochemistry 31 (1992) 1647-1651.
80. D.S. Wishart, B.D. Sykes, J. Biomol. NMR 4 (1994) 171-180.
81. B. Xia, V. Tsui, D.A. Case, H.J. Dyson, P.E. Wright, J. Biomol. NMR 22 (2002) 317-331.
82. M.B. Bass, D.F. Hopkins, W.A.N. Jaquysh, R.L. Ornstein, Proteins 12 (1992) 266-277.
83. I.K. Mcdonald, J.M. Thornton, Protein Eng. 8 (1994) 217-224.
84. R.W.W. Hooft, C. Sander, G. Vriend, Proteins 26 (1996) 363-376.
85. B. Honig, A. Nicholls, Science 268 (1995) 1144-1149.
86. J.E. Nielsen, K.V. Andersen, B. Honig, R.W. Hooft, G. Klebe, G. Vriend, R.C. Wade, Protein Eng. 12 (1999) 657-662.
87. G. Vriend, C. Sander, J. Appl. Crystallogr. 26 (1993) 47-60.
88. G.S. Ratnaparkhi, S. Ramachandran, J.B. Udgaonkar, R. Varadarajan, Biochemistry 37 (1998) 6958-6966.
89. B.S. DeDecker, R. OBrien, P.J. Fleming, J.H. Geiger, S.P. Jackson, P.B. Sigler, J. Mol. Biol. 264 (1996) 1072-1084.
90. H. Fan, A.E. Mark, Proteins 53 (2003) 111-120.
91. M. Billeter, Y.Q. Qian, G. Otting, M. Muller, W. Gehring, K. Wüthrich, J. Mol. Biol. 234 (1993) 1084-1094.
92. J.J. Prompers, R.H.A. Folmer, M. Nilges, P.J.M. Folkers, R.N.H. Konings, C.W. Hilbers, Eur. J. Biochem. 232 (1995) 506-514.
93. J. Kordel, D.A. Pearlman, W.J. Chazin, J. Biomol. NMR 10 (1997) 231-243.
94. J.P. Linge, M. Nilges, J. Biomol. NMR 13 (1999) 51-59.
95. R. Fogh, J. Ionides, E. Ulrich, W. Boucher, W. Vranken, J.P. Linge, M. Habeck, W. Rieping, T.N. Bhat, J. Westbrook. et al., Nat. Struct. Biol. 9 (2002) 416-418.
96. T. Walma, J. Aelen, S.B. Nabuurs, M. Oostendorp, L. van den Berk, W. Hendriks, G.W. Vuister, Structure (Camb) 12 (2004) 11-20.
97. C.D. Schwieters, J.J. Kuszewski, N. Tjandra, G.M. Clore, J. Magn. Res. 160 (2003) 65-73.