Structure Determination from NMR — Application to Crambin

  • J. A. C. Rullmann
  • A. M. J. J. Bonvin
  • R. Boelens
  • R. Kaptein

Abstract

In the last decade NMR spectroscopy has proven to be an invaluable tool for determining solution structures of medium sized macromolecules. Advances in magnet technology and electronic data processing led to the development of two-dimensional NMR methods, in which all signals are characterized by two resonance frequencies rather than one (Ernst et al., 1987). This made it possible to solve the resonance assignment problem (Wüthrich, 1986). Finally, calculational procedures were developed, or rather adapted, to generate molecular structures that are in agreement with the data derived from the NMR experiment. In our work we mostly use Distance Geometry (Havel et al., 1983; Havel and Wüthrich, 1984, 1985; Braun and Gō, 1985), Distance bounds Driven Dynamics (Kaptein et al., 1988; Scheek et al., 1989) and restrained Molecular Dynamics (van Gunsteren et al., 1983; Clore et al., 1985; Kaptein et al., 1985, 1988; Scheek et al., 1989). Other methods, such as the Ellipsoid Algorithm (Billeter et al., 1987) and Simulated Annealing (Nilges et al., 1988), which is similar to DDD, may be useful as well.

Keywords

Polypeptide Macromolecule Lysozyme Reso Huygens 

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References

  1. Billeter M, Havel TF, Wüthrich K (1987) The ellipsoid algorithm as a method for the determination of polypeptide conformations from experimental distance constraints and energy minimization. J Comp Chem 8: 132–141CrossRefGoogle Scholar
  2. Boelens R, Koning TMG, Kaptein R (1988). Determination of biomolecular structures from proton-proton NOEs using a relaxation matrix approach. J Mol Struct 173: 299–311CrossRefGoogle Scholar
  3. Boelens R, Koning TMG, van der Marel GA, van Boom JH, Kaptein R (1989) Iterative procedure for structure determination from proton-proton NOEs using a full relaxation matrix approach. Application to a DNA octamer. J Magn Reson 82: 290–308CrossRefGoogle Scholar
  4. Borgias BA, Gochin M, Kerwood DJ, James TL (1990) Relaxation matrix analysis of 2D NMR data. Progr NMR Spectrosc 22: 83–100CrossRefGoogle Scholar
  5. Braun W, Gō N (1985) Calculation of protein conformations by proton-proton distance constraints. J Mol Biol 186: 611–626PubMedCrossRefGoogle Scholar
  6. Brünger AT, Clore GM, Gronenborn AM, Karplus M (1986) Three-dimensional structure of proteins determined by molecular dynamics with interproton distance restraints: application to crambin. Proc Natl Acad Sci USA 83: 3801–3805PubMedCrossRefGoogle Scholar
  7. Clore GM, Gronenborn AM, Brünger AT, Karplus M (1985) Solution conformation of a heptadecapeptide comprising the DNA binding helix F of the cyclic AMP receptor protein of Escherichia coli. Combined use of 1H Nuclear Magnetic Resonance and restrained Molecular Dynamics. J Mol Biol 186: 435–455PubMedCrossRefGoogle Scholar
  8. Ernst RR, Bodenhausen G, Wokaun A (1987) Principles of nuclear magnetic resonance in one and two dimensions. Clarendon Press, OxfordGoogle Scholar
  9. Gonzalez C, Rullmann JAC, Bonvin AMJJ, Boelens R, Kaptein R. Towards an NMR R-factor. J Magn Reson, submittedGoogle Scholar
  10. van Gunsteren WF, Kaptein R, Zuiderweg ERP (1983) Use of Molecular Dynamics computer simulations when determining protein structure by 2D-NMR. In: Olson WK (ed) Nucleic acid conformation and dynamics, Report of the NATO/CECAM workshop, Orsay, p. 79–92Google Scholar
  11. van Gunsteren WF, Berendsen HJC (1987) Groningen Molecular Simulation (GROMOS) Library Manual. Biomos BV, Nijenborgh 16, 9747 AG Groningen, the NetherlandsGoogle Scholar
  12. Havel TF, Kuntz ID, Crippen GM (1983) The theory and practice of distance geometry. Bull Math Biol 45: 665–720Google Scholar
  13. Havel TF, Wüthrich K (1984) A distance geometry program for determining the structures of small proteins and other macromolecules from nuclear magnetic resonance measurements of intramolecular 1H-1H proximities in solution. Bull Math Biol 46: 673–698Google Scholar
  14. Havel TF, Wüthrich K (1985) An evaluation of the combined use of nuclear magnetic resonance and distance geometry for the determination of protein conformations in solution. J Mol Biol 182: 281–294PubMedCrossRefGoogle Scholar
  15. Hendrickson WA, Teeter MM (1981) Structure of the hydrophobic protein crambin determined directly from anomalous scattering of sulfur. Nature 290: 107–113CrossRefGoogle Scholar
  16. Kaptein R, Zuiderweg ERP, Scheek RM, Boelens R, van Gunsteren WF (1985) A protein structure from Nuclear Magnetic Resonance data. J Mol Biol 182: 179–182PubMedCrossRefGoogle Scholar
  17. Kaptein R, Boelens R, Scheek RM, van Gunsteren WF (1988) Protein structures from NMR. Biochemistry 27: 5389–5395PubMedCrossRefGoogle Scholar
  18. Koning MMG (1990) IRMA: Iterative Relaxation Matrix Approach for NMR structure determination. Application to DNA fragments. PhD thesis, University of Utrecht, the NetherlandsGoogle Scholar
  19. Lamerichs RMJN, Berliner LJ, Boelens R, DeMarco A, Llinàs M, Kaptein R (1988) Secondary structure and hydrogen bonding of crambin in solution. Eur J Biochem 171: 307–312PubMedCrossRefGoogle Scholar
  20. Lamerichs RMJN (1989) 2D NMR studies of biomolecules: protein structures and protein-DNA interactions. PhD thesis, University of Utrecht, the NetherlandsGoogle Scholar
  21. Lipari G, Szabo A (1982) Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity. J Am Chem Soc 104:4546–4559CrossRefGoogle Scholar
  22. Macura S, Ernst RR (1980) Elucidation of cross relaxation in liquids by two-dimensional NMR spectroscopy. Molec Phys 41: 95–117CrossRefGoogle Scholar
  23. Neuhaus D, Williamson M (1989) The Nuclear Overhauser Effect in structural and conformational analysis. VCH Publishers, New YorkGoogle Scholar
  24. Nilges M, Clore GM, Gronenborn AM (1988) Determination of three-dimensional structures of proteins from interproton distance data by hybrid distance geometry — dynamical simulated annealing calculations. FEBS Lett 229: 317–324PubMedCrossRefGoogle Scholar
  25. Olejniczak ET, Dobson CM, Karplus M, Levy RM (1984) Motional averaging of proton nuclear Overhauser effects in proteins. Predictions from a Molecular Dynamics simulation of lysozyme. J Am Chem Soc 106:1923–1930CrossRefGoogle Scholar
  26. Rullmann JAC, Lamerichs RMJN, Gonzalez C, Koning TMG, Boelens R, Kaptein R (1990) Structure determination from NMR using a relaxation matrix approach; application to the solution structure of crambin. In: Rivail J-L (ed) Modelling of molecular structures and properties, Studies in Physical and Theoretical Chemistry vol 71, p 703–710. Elsevier, AmsterdamGoogle Scholar
  27. Scheek RM, van Gunsteren WF, Kaptein R (1989) Molecular Dynamics techniques for determination of molecular structures from Nuclear Magnetic Resonance data. In: Oppenheimer NJ, James TL (eds) Nuclear Magnetic Resonance, Methods in enzymology, vol. 177, p. 204–218. Academic, New YorkGoogle Scholar
  28. Teeter MM, Water structure of a hydrophobic protein at atomic resolution: pentagon rings of water molecules in crystals of crambin. Proc Natl Acad Sci USA 81: 6014–6018Google Scholar
  29. Torda AE, Scheek RM, van Gunsteren WF (1990) Time-averaged nuclear Overhauser effect distance restraints applied to tendamistat. J Mol Biol 214: 223–235PubMedCrossRefGoogle Scholar
  30. Tropp J (1980) Dipolar relaxation and nuclear Overhauser effects in nonrigid molecules: The effect of fluctuating internuclear distances. J Chem Phys 72: 6035–6043CrossRefGoogle Scholar
  31. Vermeulen JAWH, Lamerichs RMJN, Berliner LJ, DeMarco A, Llinàs M, Boelens R, Alleman J, Kaptein R (1987) 1H NMR characterization of two crambin species. FEBS Lett 219: 426–430CrossRefGoogle Scholar
  32. de Vlieg J, Boelens R, Scheek RM, Kaptein R, van Gunsteren WF (1986) Restrained Molecular Dynamics procedure for protein tertiary structure determination from NMR data: a lac repressor headpiece structure based on information on J-coupling and from presence and absence of NOEs. Israel J Chem 27:181–188Google Scholar
  33. Wüthrich K (1986) NMR of proteins and nucleic acids. Wiley, New YorkGoogle Scholar
  34. Yip P, Case DA (1989) A new method for refinement of macromolecular structures based on nuclear Overhauser effect spectra. J Magn Reson 83: 643–648CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 1993

Authors and Affiliations

  • J. A. C. Rullmann
    • 1
  • A. M. J. J. Bonvin
    • 1
  • R. Boelens
    • 1
  • R. Kaptein
    • 1
  1. 1.Department of NMR SpectroscopyUniversity of UtrechtUtrechtthe Netherlands

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