Concepts and tools for NMR restraint analysis and validation
Sander B. Nabuurs
Center for Molecular and Biomolecular Informatics, University of Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands
Search for more papers by this authorChris A.E.M. Spronk
Center for Molecular and Biomolecular Informatics, University of Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands
Search for more papers by this authorGert Vriend
Center for Molecular and Biomolecular Informatics, University of Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands
Search for more papers by this authorCorresponding Author
Geerten W. Vuister
Department of Biophysical Chemistry, University of Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands
Department of Biophysical Chemistry, University of Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, The NetherlandsSearch for more papers by this authorSander B. Nabuurs
Center for Molecular and Biomolecular Informatics, University of Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands
Search for more papers by this authorChris A.E.M. Spronk
Center for Molecular and Biomolecular Informatics, University of Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands
Search for more papers by this authorGert Vriend
Center for Molecular and Biomolecular Informatics, University of Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands
Search for more papers by this authorCorresponding Author
Geerten W. Vuister
Department of Biophysical Chemistry, University of Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands
Department of Biophysical Chemistry, University of Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, The NetherlandsSearch for more papers by this authorAbstract
The quality of NMR-derived biomolecular structure models can be assessed by validation on the level of structural characteristics as well as the NMR data used to derive the structure models. Here, an overview is given of the common methods to validate experimental NMR data. These methods provide measures of quality and goodness of fit of the structure to the data. A detailed discussion is given of newly developed methods to assess the information contained in experimental NMR restraints, which provide powerful tools for validation and error analysis in NMR structure determination. © 2004 Wiley Periodicals, Inc. Concepts Magn Reson Part A 22A: 90–105, 2004.
REFERENCES
- 1
Wüthrich K.
1986.
NMR of proteins and nucleic acids.
New York:
Wiley.
10.1051/epn/19861701011 Google Scholar
- 2 Moseley HNB, Montelione GT. 1999. Automated analysis of NMR assignments and structures for proteins. Curr Opin Struct Biol 9(5): 635–642.
- 3 Guntert P. 2003. Automated NMR protein structure calculation. Prog Nucl Magn Reson Spectrosc 43(3–4): 105–125.
- 4 Seavey BR, Farr EA, Westler WM, Markley JL. 1991. A relational database for sequence-specific protein NMR data. J Biomol NMR 1(3): 217–236.
- 5 Bernstein FC, Koetzle TF, Williams GJ, Meyer EF, Jr., Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M. 1977. The protein data bank: a computer-based archival file for macromolecular structures. J Mol Biol 112(3): 535–542.
- 6 Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. 2000. The protein data bank. Nucleic Acids Res 28(1): 235–242.
- 7 Nabuurs SB, Nederveen AJ, Vranken W, Doreleijers JF, Bonvin AMJJ, Vuister GW, Vriend G, Spronk CAEM. 2004. DRESS: a database of refined solution NMR structures. Proteins 55: 483–486.
- 8 Kuszewski J, Gronenborn AM, Clore GM. 1999. Improving the packing and accuracy of NMR structures with a pseudopotential for the radius of gyration. J Am Chem Soc 121(10): 2337–2338.
- 9 Case DA. 1998. The use of chemical shifts and their anisotropies in biomolecular structure determination. Curr Opin Struct Biol 8(5): 624–630.
- 10 Kuszewski J, Gronenborn AM, Clore GM. 1996. Improving the quality of NMR and crystallographic protein structures by means of a conformational database potential derived from structure databases. Protein Sci 5(6): 1067–1080.
- 11 Clore GM, Robien MA, Gronenborn AM. 1993. Exploring the limits of precision and accuracy of protein structures determined by nuclear magnetic resonance spectroscopy. J Mol Biol 231(1): 82–102.
- 12 Jeener J, Meier BH, Bachmann P, Ernst RR. 1979. Investigation of exchange processes by two-dimensional NMR-spectroscopy. J Chem Phys 71(11): 4546–4553.
- 13 Macura S, Ernst RR. 1980. Elucidation of cross relaxation in liquids by two-dimensional NMR-spectroscopy. Mol Phys 41(1): 95–117.
- 14 Kumar A, Ernst RR, Wuthrich K. 1980. A two-dimensional nuclear Overhauser enhancement (2d Noe) experiment for the elucidation of complete proton-proton cross-relaxation networks in biological macromolecules. Biochem Biophys Res Comm 95(1): 1–6.
- 15 Markley JL, Bax A, Arata Y, Hilbers CW, Kaptein R, Sykes BD, Wright PE, Wüthrich K. 1998. Recommendations for the presentation of NMR structures of proteins and nucleic acids. J Mol Biol 280(5): 933–952.
- 16 Fletcher CM, Jones DNM, Diamond R, Neuhaus D. 1996. Treatment of NOE constraints involving equivalent or nonstereoassigned protons in calculations of biomacromolecular structures. J Biomol NMR 8(3): 292–310.
- 17 Nilges M. 1995. Calculation of protein structures with ambiguous distance restraints. Automated assignment of ambiguous NOE crosspeaks and disulphide connectivities. J Mol Biol 245(5): 645–660.
- 18 Nilges M. 1997. Ambiguous distance data in the calculation of NMR structures. Fold Des 2(4): S53–57.
- 19 Wagner G, Wüthrich K. 1982. Amide protein exchange and surface conformation of the basic pancreatic trypsin inhibitor in solution. Studies with two-dimensional nuclear magnetic resonance. J Mol Biol 160(2): 343–361.
- 20 Wishart DS, Sykes BD, Richards FM. 1992. The chemical shift index: a fast and simple method for the assignment of protein secondary structure through NMR spectroscopy. Biochemistry 31(6): 1647–1651.
- 21 Juranic N, Ilich PK, Macura S. 1995. Hydrogen bonding networks in proteins as revealed by the amide 1JNC′ coupling constant. J Am Chem Soc 117(1): 405–410.
- 22 Dingley AJ, Grzesiek S. 1998. Direct observation of hydrogen bonds in nucleic acid base pairs by internucleotide (2)J(NN) couplings. J Am Chem Soc 120(33): 8293–8297.
- 23 Cordier F, Grzesiek S. 1999. Direct observation of hydrogen bonds in proteins by interresidue (3h)J(NC′) scalar couplings. J Am Chem Soc 121(7): 1601–1602.
- 24 Cordier F, Rogowski M, Grzesiek S, Bax A. 1999. Observation of through-hydrogen-bond (2h)J(HC′) in a perdeuterated protein. J Magn Reson 140(2): 510–512.
- 25 Karplus M. 1959. Contact electron-spin coupling of nuclear magnetic moments. J Chem Phys 30(1): 11–15.
- 26 Vuister GW, Tessari M, Karimi-Nejad Y, Whitehead B. 1998. Pulse sequences for measuring coupling constants. In: LJ Berliner, NR Krishna, editors. Modern techniques in protein NMR. Vol. 16. New York: Plenum p 195–257.
- 27 Nabuurs SB, Spronk CA, Krieger E, Maassen H, Vriend G, Vuister GW. 2003. Quantitative evaluation of experimental NMR restraints. J Am Chem Soc 125(39): 12026–12034.
- 28 Tjandra N, Omichinski JG, Gronenborn AM, Clore GM, Bax A. 1997. Use of dipolar 1H–15N and 1H–13C couplings in the structure determination of magnetically oriented macromolecules in solution. Nat Struct Biol 4(9): 732–738.
- 29 Tolman JR, Flanagan JM, Kennedy MA, Prestegard JH. 1995. Nuclear magnetic dipole interactions in field-oriented proteins: information for structure determination in solution. Proc Natl Acad Sci USA 92(20): 9279–9283.
- 30 Tjandra N, Bax A. 1997. Direct measurement of distances and angles in biomolecules by NMR in a dilute liquid crystalline medium. Science 278(5340): 1111–1114.
- 31 Clore GM, Starich MR, Bewley CA, Cai ML, Kuszewski J. 1999. Impact of residual dipolar couplings on the accuracy of NMR structures determined from a minimal number of NOE restraints. J Am Chem Soc 121(27): 6513–6514.
- 32 Doreleijers JF, Raves ML, Rullmann T, Kaptein R. 1999. Completeness of NOEs in protein structure: a statistical analysis of NMR. J Biomol NMR 14(2): 123–132.
- 33 Doreleijers JF, Rullmann JA, Kaptein R. 1998. Quality assessment of NMR structures: a statistical survey. J Mol Biol 281(1): 149–164.
- 34 Gonzalez C, Rullmann JAC, Bonvin AMJJ, Boelens R, Kaptein R. 1991. Toward an NMR R factor. J Magn Reson 91: 659–664.
- 35 Bonvin AM, Boelens R, Kaptein R. 1991. Direct NOE refinement of biomolecular structures using 2D NMR data. J Biomol NMR 1(3): 305–309.
- 36 James TL. 1991. Relaxation matrix analysis of two-dimensional nuclear Overhauser effect spectra. Curr Opin Struct Biol 1(6): 1042–1053.
- 37 Kleywegt GJ, Jones TA. 1995. Where freedom is given, liberties are taken. Structure 3(6): 535–540.
- 38 Brünger AT. 1992. Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 355: 472–475.
- 39 Brünger AT, Clore GM, Gronenborn AM, Saffrich R, Nilges M. 1993. Assessing the quality of solution nuclear magnetic resonance structures by complete cross-validation. Science 261(5119): 328–331.
- 40 Brunger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse-Kunstleve RW, Jiang JS, Kuszewski J, Nilges M, Pannu NS, et al. 1998. Crystallography and NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr 54(Pt 5): 905–921.
- 41 Bonvin AM, Brünger AT. 1996. Do NOE distances contain enough information to assess the relative populations of multi-conformer structures? J Biomol NMR 7(1): 72–76.
- 42 Cornilescu G, Marquardt JL, Ottiger M, Bax A. 1998. Validation of protein structure from anisotropic carbonyl chemical shifts in a dilute liquid crystalline phase. J Am Chem Soc 120(27): 6836–6837.
- 43 Meiler J, Peti W, Griesinger C. 2000. DipoCoup: a versatile program for 3D-structure homology comparison based on residual dipolar couplings and pseudocontact shifts. J Biomol NMR 17(4): 283–294.
- 44 Zweckstetter M, Bax A. 2000. Prediction of sterically induced alignment in a dilute liquid crystalline phase: aid to protein structure determination by NMR. J Am Chem Soc 122(15): 3791–3792.
- 45 Clore GM, Garrett DS. 1999. R-factor, free R, and complete cross-validation for dipolar coupling refinement of NMR structures. J Am Chem Soc 121(39): 9008–9012.
- 46 Spronk CA, Linge JP, Hilbers CW, Vuister GW. 2002. Improving the quality of protein structures derived by NMR spectroscopy. J Biomol NMR 22(3): 281–289.
- 47 Linge JP, Williams MA, Spronk CA, Bonvin AM, Nilges M. 2003. Refinement of protein structures in explicit solvent. Proteins 50(3): 496–506.
- 48 Crippen GM. 1977. A novel approach to the calculation of conformation: distance geometry. J Comp Phys 26: 449–452.
- 49 Havel TF, Kuntz ID, Crippen GM. 1983. The theory and practice of distance geometry. Bull Math Biol 45: 665–720.
- 50
Shannon CE,
Weaver W.
1949.
The mathematical theory of communication.
Urbana, IL:
University of Illinois Press.
10.1890/0012-9658(1998)079[1029:SARTBM]2.0.CO;2 Google Scholar
- 51 Englander SW, Wand AJ. 1987. Main-chain-directed strategy for the assignment of 1H NMR spectra of proteins. Biochemistry 26(19): 5953–5958.
- 52 Herrmann T, Güntert P, Wüthrich K. 2002. Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. J Mol Biol 319(1): 209–227.
- 53 Laskowski RA, Rullmann JA, MacArthur MW, Kaptein R, Thornton JM. 1996. AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J Biomol NMR 8(4): 477–486.
- 54 Linge JP, Habeck M, Rieping W, Nilges M. 2003. ARIA: automated NOE assignment and NMR structure calculation. Bioinformatics 19(2): 315–316.
- 55 Herrmann T, Guntert P, Wuthrich K. 2002. Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. J Mol Biol 319(1): 209–227.
- 56 Gronwald W, Moussa S, Elsner R, Jung A, Ganslmeier B, Trenner J, Kremer W, Neidig KP, Kalbitzer HR. 2002. Automated assignment of NOESY NMR spectra using a knowledge based method (KNOWNOE). J Biomol NMR 23(4): 271–287.
- 57 Gronenborn AM, Filpula DR, Essig NZ, Achari A, Whitlow M, Wingfield PT, Clore GM. 1991. A novel, highly stable fold of the immunoglobulin binding domain of streptococcal protein G. Science 253(5020): 657–661.