Skip to main content
PMC home page
Protein Science : A Publication of the Protein Society logoLink to Protein Science : A Publication of the Protein Society
. 1996 Jun;5(6):1067–1080. doi: 10.1002/pro.5560050609

Improving the quality of NMR and crystallographic protein structures by means of a conformational database potential derived from structure databases.

J Kuszewski 1, A M Gronenborn 1, G M Clore 1
PMCID: PMC2143426  PMID: 8762138

Abstract

A new conformational database potential involving dihedral angle relationships in databases of high-resolution highly refined protein crystal structures is presented as a method for improving the quality of structures generated from NMR data. The rationale for this procedure is based on the observation that uncertainties in the description of the nonbonded contacts present a key limiting factor in the attainable accuracy of protein NMR structures and that the nonbonded interaction terms presently used have poor discriminatory power between high- and low-probability local conformations. The idea behind the conformational database potential is to restrict sampling during simulated annealing refinement to conformations that are likely to be energetically possible by effectively limiting the choices of dihedral angles to those that are known to be physically realizable. In this manner, the variability in the structures produced by this method is primarily a function of the experimental restraints, rather than an artifact of a poor nonbonded interaction model. We tested this approach with the experimental NMR data (comprising an average of about 30 restraints per residue and consisting of interproton distances, torsion angles, 3JHN alpha coupling constants, and 13C chemical shifts) used previously to calculate the solution structure of reduced human thioredoxin (Qin J, Clore GM, Gronenborn AM, 1994, Structure 2:503-522). Incorporation of the conformational database potential into the target function used for refinement (which also includes terms for the experimental restraints, covalent geometry, and nonbonded interactions in the form of either a repulsive, repulsive-attractive, or 6-12 Lennard-Jones potential) results in a significant improvement in various quantitative measures of quality (Ramachandran plot, side-chain torsion angles, overall packing). This is achieved without compromising the agreement with the experimental restraints and the deviations from idealized covalent geometry that remain within experimental error, and the agreement between calculated and observed 1H chemical shifts that provides an independent NMR parameter of accuracy. The method is equally applicable to crystallographic refinement, and should be particular useful during the early stages of either an NMR or crystallographic structure determination and in cases where relatively few experimental restraints can be derived from the measured data (due, for example, to broad lines in the NMR spectra or to poorly diffracting crystals).

Full Text

The Full Text of this article is available as a PDF (4.9 MB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Bartik K., Dobson C. M., Redfield C. 1H-NMR analysis of turkey egg-white lysozyme and comparison with hen egg-white lysozyme. Eur J Biochem. 1993 Jul 15;215(2):255–266. doi: 10.1111/j.1432-1033.1993.tb18030.x. [DOI] [PubMed] [Google Scholar]
  2. Braun W. Distance geometry and related methods for protein structure determination from NMR data. Q Rev Biophys. 1987 May;19(3-4):115–157. doi: 10.1017/s0033583500004108. [DOI] [PubMed] [Google Scholar]
  3. Brunne R. M., Liepinsh E., Otting G., Wüthrich K., van Gunsteren W. F. Hydration of proteins. A comparison of experimental residence times of water molecules solvating the bovine pancreatic trypsin inhibitor with theoretical model calculations. J Mol Biol. 1993 Jun 20;231(4):1040–1048. doi: 10.1006/jmbi.1993.1350. [DOI] [PubMed] [Google Scholar]
  4. Brünger A. T., Kuriyan J., Karplus M. Crystallographic R factor refinement by molecular dynamics. Science. 1987 Jan 23;235(4787):458–460. doi: 10.1126/science.235.4787.458. [DOI] [PubMed] [Google Scholar]
  5. Brünger A. T., Nilges M. Computational challenges for macromolecular structure determination by X-ray crystallography and solution NMR-spectroscopy. Q Rev Biophys. 1993 Feb;26(1):49–125. doi: 10.1017/s0033583500003966. [DOI] [PubMed] [Google Scholar]
  6. Chandrasekhar I., Clore G. M., Szabo A., Gronenborn A. M., Brooks B. R. A 500 ps molecular dynamics simulation study of interleukin-1 beta in water. Correlation with nuclear magnetic resonance spectroscopy and crystallography. J Mol Biol. 1992 Jul 5;226(1):239–250. doi: 10.1016/0022-2836(92)90136-8. [DOI] [PubMed] [Google Scholar]
  7. Chinea G., Padron G., Hooft R. W., Sander C., Vriend G. The use of position-specific rotamers in model building by homology. Proteins. 1995 Nov;23(3):415–421. doi: 10.1002/prot.340230315. [DOI] [PubMed] [Google Scholar]
  8. Clore G. M., Ernst J., Clubb R., Omichinski J. G., Kennedy W. M., Sakaguchi K., Appella E., Gronenborn A. M. Refined solution structure of the oligomerization domain of the tumour suppressor p53. Nat Struct Biol. 1995 Apr;2(4):321–333. doi: 10.1038/nsb0495-321. [DOI] [PubMed] [Google Scholar]
  9. Clore G. M., Gronenborn A. M. Comparison of the solution nuclear magnetic resonance and X-ray crystal structures of human recombinant interleukin-1 beta. J Mol Biol. 1991 Sep 5;221(1):47–53. doi: 10.1016/0022-2836(91)80202-6. [DOI] [PubMed] [Google Scholar]
  10. Clore G. M., Gronenborn A. M. Determination of three-dimensional structures of proteins and nucleic acids in solution by nuclear magnetic resonance spectroscopy. Crit Rev Biochem Mol Biol. 1989;24(5):479–564. doi: 10.3109/10409238909086962. [DOI] [PubMed] [Google Scholar]
  11. Clore G. M., Robien M. A., Gronenborn A. M. Exploring the limits of precision and accuracy of protein structures determined by nuclear magnetic resonance spectroscopy. J Mol Biol. 1993 May 5;231(1):82–102. doi: 10.1006/jmbi.1993.1259. [DOI] [PubMed] [Google Scholar]
  12. Dunbrack R. L., Jr, Karplus M. Backbone-dependent rotamer library for proteins. Application to side-chain prediction. J Mol Biol. 1993 Mar 20;230(2):543–574. doi: 10.1006/jmbi.1993.1170. [DOI] [PubMed] [Google Scholar]
  13. Eriksson M. A., Härd T., Nilsson L. Molecular dynamics simulations of the glucocorticoid receptor DNA-binding domain in complex with DNA and free in solution. Biophys J. 1995 Feb;68(2):402–426. doi: 10.1016/S0006-3495(95)80203-1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Evans J. S., Mathiowetz A. M., Chan S. I., Goddard W. A., 3rd De novo prediction of polypeptide conformations using dihedral probability grid Monte Carlo methodology. Protein Sci. 1995 Jun;4(6):1203–1216. doi: 10.1002/pro.5560040618. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Garrett D. S., Kuszewski J., Hancock T. J., Lodi P. J., Vuister G. W., Gronenborn A. M., Clore G. M. The impact of direct refinement against three-bond HN-C alpha H coupling constants on protein structure determination by NMR. J Magn Reson B. 1994 May;104(1):99–103. doi: 10.1006/jmrb.1994.1061. [DOI] [PubMed] [Google Scholar]
  16. Gronenborn A. M., Clore G. M. Structures of protein complexes by multidimensional heteronuclear magnetic resonance spectroscopy. Crit Rev Biochem Mol Biol. 1995;30(5):351–385. doi: 10.3109/10409239509083489. [DOI] [PubMed] [Google Scholar]
  17. Havel T. F. An evaluation of computational strategies for use in the determination of protein structure from distance constraints obtained by nuclear magnetic resonance. Prog Biophys Mol Biol. 1991;56(1):43–78. doi: 10.1016/0079-6107(91)90007-f. [DOI] [PubMed] [Google Scholar]
  18. Hendrickson W. A. Stereochemically restrained refinement of macromolecular structures. Methods Enzymol. 1985;115:252–270. doi: 10.1016/0076-6879(85)15021-4. [DOI] [PubMed] [Google Scholar]
  19. Kabsch W., Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 1983 Dec;22(12):2577–2637. doi: 10.1002/bip.360221211. [DOI] [PubMed] [Google Scholar]
  20. Kuszewski J., Gronenborn A. M., Clore G. M. The impact of direct refinement against proton chemical shifts on protein structure determination by NMR. J Magn Reson B. 1995 Jun;107(3):293–297. doi: 10.1006/jmrb.1995.1093. [DOI] [PubMed] [Google Scholar]
  21. Kuszewski J., Nilges M., Brünger A. T. Sampling and efficiency of metric matrix distance geometry: a novel partial metrization algorithm. J Biomol NMR. 1992 Jan;2(1):33–56. doi: 10.1007/BF02192799. [DOI] [PubMed] [Google Scholar]
  22. Loncharich R. J., Brooks B. R. Temperature dependence of dynamics of hydrated myoglobin. Comparison of force field calculations with neutron scattering data. J Mol Biol. 1990 Oct 5;215(3):439–455. doi: 10.1016/s0022-2836(05)80363-8. [DOI] [PubMed] [Google Scholar]
  23. Mathiowetz A. M., Goddard W. A., 3rd Building proteins from C alpha coordinates using the dihedral probability grid Monte Carlo method. Protein Sci. 1995 Jun;4(6):1217–1232. doi: 10.1002/pro.5560040619. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Morris A. L., MacArthur M. W., Hutchinson E. G., Thornton J. M. Stereochemical quality of protein structure coordinates. Proteins. 1992 Apr;12(4):345–364. doi: 10.1002/prot.340120407. [DOI] [PubMed] [Google Scholar]
  25. Nilges M., Clore G. M., Gronenborn A. M. 1H-NMR stereospecific assignments by conformational data-base searches. Biopolymers. 1990 Mar-Apr;29(4-5):813–822. doi: 10.1002/bip.360290415. [DOI] [PubMed] [Google Scholar]
  26. Nilges M., Clore G. M., Gronenborn A. M. Determination of three-dimensional structures of proteins from interproton distance data by hybrid distance geometry-dynamical simulated annealing calculations. FEBS Lett. 1988 Mar 14;229(2):317–324. doi: 10.1016/0014-5793(88)81148-7. [DOI] [PubMed] [Google Scholar]
  27. Osapay K., Theriault Y., Wright P. E., Case D. A. Solution structure of carbonmonoxy myoglobin determined from nuclear magnetic resonance distance and chemical shift constraints. J Mol Biol. 1994 Nov 25;244(2):183–197. doi: 10.1006/jmbi.1994.1718. [DOI] [PubMed] [Google Scholar]
  28. Qin J., Clore G. M., Gronenborn A. M. The high-resolution three-dimensional solution structures of the oxidized and reduced states of human thioredoxin. Structure. 1994 Jun 15;2(6):503–522. doi: 10.1016/s0969-2126(00)00051-4. [DOI] [PubMed] [Google Scholar]
  29. Ramachandran G. N., Venkatachalam C. M., Krimm S. Stereochemical criteria for polypeptide and protein chain conformations. 3. Helical and hydrogen-bonded polypeptide chains. Biophys J. 1966 Nov;6(6):849–872. doi: 10.1016/s0006-3495(66)86699-7. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Sali A., Blundell T. L. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol. 1993 Dec 5;234(3):779–815. doi: 10.1006/jmbi.1993.1626. [DOI] [PubMed] [Google Scholar]
  31. Swindells M. B., MacArthur M. W., Thornton J. M. Intrinsic phi, psi propensities of amino acids, derived from the coil regions of known structures. Nat Struct Biol. 1995 Jul;2(7):596–603. doi: 10.1038/nsb0795-596. [DOI] [PubMed] [Google Scholar]
  32. Williamson M. P., Kikuchi J., Asakura T. Application of 1H NMR chemical shifts to measure the quality of protein structures. J Mol Biol. 1995 Apr 7;247(4):541–546. doi: 10.1006/jmbi.1995.0160. [DOI] [PubMed] [Google Scholar]
  33. van Gunsteren W. F., Luque F. J., Timms D., Torda A. E. Molecular mechanics in biology: from structure to function, taking account of solvation. Annu Rev Biophys Biomol Struct. 1994;23:847–863. doi: 10.1146/annurev.bb.23.060194.004215. [DOI] [PubMed] [Google Scholar]

Articles from Protein Science : A Publication of the Protein Society are provided here courtesy of The Protein Society

RESOURCES