Advertisement

Journal of Biomolecular NMR

, Volume 3, Issue 1, pp 55–66 | Cite as

Structure refinement using time-averaged J-coupling constant restraints

  • Andrew E. Torda
  • Roger M. Brunne
  • Thomas Huber
  • Horst Kessler
  • Wilfred F. van Gunsteren
Research Papers

Summary

We describe a new penalty function for use in restrained molecular dynamics simulations which allows experimental J-coupling information to be enforced as a time-averaged, rather than instantaneous, quantity. The pseudo-energy term has been formulated in terms of a calculated J value (a measured quantity) rather than the relevant dihedral angle (a derived quantity). This accounts for the distinct non-linearity of the coupling constant with respect to either Cartesian coordinates or dihedral angles. Example simulations of the cyclic decapeptide antamanide show the procedure's ability to enforce experimental restraints while exploring a large region of conformational space and producing a relatively small disturbance of the physical force field.

Keywords

J-coupling Time averaging Structure refinement Computer simulation Molecular dynamics 

Abbreviations

MD

molecular dynamics

rms

root-mean-square

NOE

nuclear Overhauser effect

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Berendsen, H.J.C., Postma, J.P.M., vanGunsteren, W.F., DiNola, A. and Haak, J.R. (1984) J. Chem. Phys., 81, 3684–3690.Google Scholar
  2. Braun, W. (1987) Q. Rev. Biophys., 19, 115–157.Google Scholar
  3. Brüschweiler, R., Blackledge, M. and Ernst, R.R. (1991) J. Biomol. NMR, 1, 3–11.Google Scholar
  4. Bystrov, V.F. (1976) Progr. NMR Spectrosc., 10, 41–81.Google Scholar
  5. Clore, G.M., Nilges, M., Sukumaran, D.K., Brünger, A.T., Karplus, M. and Gronenborn, A.M. (1986) EMBO J., 5, 2729–2735.Google Scholar
  6. Clore, G.M., Sukumaran, D.K., Nilges, M. and Gronenborn, A.M. (1987) Biochemistry, 26, 1732–1745.Google Scholar
  7. DeVlieg, J., Boelens, R., Scheek, R.M., Kaptein, R. and vanGunsteren, W.F. (1986) Isr. J. Chem., 27, 181–188.Google Scholar
  8. Driscoll, P.C., Gronenborn, A.M., Beress, L. and Clore, G.M. (1989) Biochemistry, 28, 2188–2198.Google Scholar
  9. Jardetzky, O. (1980) Biochim. Biophys. Acta., 621, 227–232.Google Scholar
  10. Karle, I.L., Wieland, T., Schermer, D. and Ottenheym, H.C.J. (1979) Proc. Natl. Acad. Sci. USA, 76, 1532–1536.Google Scholar
  11. Karplus, M. (1959) J. Chem. Phys., 30, 11–15.Google Scholar
  12. Kessler, H., Griesinger, C., Lautz, J., Müller, A., vanGunsteren, W.F. and Berendsen, H.J.C. (1988) J. Am. Chem. Soc., 110, 3393–3396.Google Scholar
  13. Kessler, H., Bats, J.W., Lautz, J. and Müller, A. (1989) Liebigs Ann. Chem., 913–928.Google Scholar
  14. Kim, Y. and Prestegard, J.H. (1990) Proteins, 8, 377–385.Google Scholar
  15. Ludvigsen, S., Andersen, K.V. and Poulsen, F.M. (1991) J. Mol. Biol., 217, 731–736.Google Scholar
  16. Mierke, D.F. and Kessler, H. (1992) Biopolymers, 32, 1277–1287.Google Scholar
  17. Pardi, A., Billeter, M. and Wüthrich, K. (1984) J. Mol. Biol., 180, 741–751.Google Scholar
  18. Pearlman, D.A. and Kollman, P.A. (1991) J. Mol. Biol., 220, 457–479.Google Scholar
  19. Ryckaert, J.-P., Ciccotti, G. and Berendsen, H.J.C. (1977) J. Comput. Phys., 23, 327–341.Google Scholar
  20. ShiYun-yu, WangLu and vanGunsteren, W.F. (1988) Mol. Sim., 1, 369–388.Google Scholar
  21. Torda, A.E., Scheek, R.M. and vanGunsteren, W.F. (1989) Chem. Phys. Lett., 157, 289–294.Google Scholar
  22. Torda, A.E., Scheek, R.M. and vanGunsteren, W.F. (1990) J. Mol. Biol., 214, 223–235.Google Scholar
  23. VanGunsteren, W.F. and Berendsen, H.J.C. (1987) Groningen Molecular Simulation (GROMOS) Library Manual, Biomos, Groningen, The Netherlands.Google Scholar
  24. VanGunsteren, W.F. and Berendsen, H.J.C. (1988) Mol. Sim., 1, 173–185.Google Scholar
  25. Wagner, G., Braun, W., Havel, T.F., Schaumann, T., Gõ, N. and Wüthrich, K. (1987) J. Mol. Biol., 196, 611–639.Google Scholar

Copyright information

© ESCOM Science Publishers B.V 1993

Authors and Affiliations

  • Andrew E. Torda
    • 1
  • Roger M. Brunne
    • 1
  • Thomas Huber
    • 2
  • Horst Kessler
    • 2
  • Wilfred F. van Gunsteren
    • 1
  1. 1.Physical Chemistry (Computational Chemistry)ETH ZentrumZürichSwitzerland
  2. 2.Organisch-Chemisches InstitutTechnische Universität MünchenGarchingGermany

Personalised recommendations