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Journal of Biomolecular NMR

, Volume 30, Issue 3, pp 233–244 | Cite as

Secondary structural effects on protein NMR chemical shifts

  • Yunjun Wang
Article

Abstract

For an amino acid in protein, its chemical shift, δ(ϕ, ψ)s, is expressed as a function of its backbone torsion angles (ϕ and ψ) and secondary state (s): δ(ϕ, ψ)s=δϕ, ψ)_coil+Δδ(ϕ, ψ)_s, where δ(ϕ, ψ)coil represents its chemical shift at coil state (s=coil); Δ δ(ϕ, ψ)s (s=sheet or helix) is herein defined as secondary structural effect correction factor, which are quantitatively determined from Residue-specific Secondary Structure Shielding Surface (RSS) for 13CO, 13Cα, 13Cβ,1Hα, 15N, and 1HN nuclei. The secondary structural effect correction factors defined in this study differ from those in earlier investigations by separating out the backbone conformational effects. As a consequence, their magnitudes are significantly smaller than those earlier reported. The present Δ δ(ϕ, ψ)sheet and Δ δ(ϕ, ψ)helix were found varying little with backbone conformation and the 20 amino acids, specifically for 13CO, 13Cα, and 1Hα nuclei. This study also carries out some useful investigations on other chemical shift prediction approaches – the traditional shielding surfaces, SHIFTS, SHIFTX, PROSHIFT, and identifies some unexpected shortcomings with these methods. It provides some useful insights into understanding protein chemical shifts and suggests a new route to improving chemical shifts prediction. The RSS surfaces were incorporated into the program PRSI [Wang and Jardetzky, J. Biomol. NMR, 28: 327–340 (2004)], which is available for academic users at http://www.pronmr.com or by sending email to the author (yunjunwang@yahoo.com).

Keywords

chemical shift prediction NMR protein chemical shift secondary structural effects 

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References

  1. Aurora, R., Rose, G.D. 1998Protein Sci.72138Google Scholar
  2. Beger, R.D., Bolton, P.H. 1997J. Biomol. NMR10129142Google Scholar
  3. Celda, B., Biamonti, C., Arnau, M.J., Tejero, R., Montelione, G.T. 1995J. Biomol. NMR5161172Google Scholar
  4. Cornilescu, G., Delaglio, F., Bax, A. 1999J. Biomol. NMR13289302CrossRefGoogle Scholar
  5. Dios, A.C., Pearson, J.G., Oldfield, E. 1993Science26014911495Google Scholar
  6. Iwadate, M., Asakura, T., Williamson, M.P. 1999J. Biomol. NMR13199211Google Scholar
  7. Kuszewski, J., Gronenborn, A.M., Clore, G.M. 1995J. Magn. Reson.B107293297Google Scholar
  8. Le, H., Oldfield, E. 1994J. Biomol. NMR4341348Google Scholar
  9. Markley, J.L., Meadows, D.H., Jardetzky, O. 1967J. Mol. Biol.272540Google Scholar
  10. Meiler, J. 2003J. Biomol. NMR262537Google Scholar
  11. Nakamura, A., Jardetzky, O. 1968Biochemistry712261230Google Scholar
  12. Neal, S., Nip, A.M., Zhang, H., Wishart, D.S. 2003J. Biomol. NMR26215240Google Scholar
  13. Oldfield, E. 1995J. Biomol. NMR5217225Google Scholar
  14. Osapay, K., Case, D.A. 1994J. Biomol. NMR4215230Google Scholar
  15. Roberts, G.C., Jardetzky, O. 1970Adv. Protein Chem.24447545Google Scholar
  16. Spera, S., Bax, A. 1991J. Am. Chem. Soc.11354905492Google Scholar
  17. Szilagyi, L., Jardetzky, O. 1989J. Magn. Reson.83441449Google Scholar
  18. Wang, Y., Jardetzky, O. 2002aProtein Sci.11852861Google Scholar
  19. Wang, Y., Jardetzky, O. 2002bJ. Am. Chem. Soc.1241407514084Google Scholar
  20. Wang, Y., Jardetzky, O. 2004J. Biomol. NMR28327340Google Scholar
  21. Willard, L., Ranjan, A., Zhang, H., Monzavi, H., Boyko, R.F., Sykes, B.D., Wishart, D.S. 2003Nucl. Acids Res.3133163319Google Scholar
  22. Williamson, M.P., Kikuchi, J., Asakura, T. 1995J. Mol. Biol.247541546Google Scholar
  23. Wishart, D.S., Case, D.A. 2001Meth. Enzymol.338334Google Scholar
  24. Wishart, D.S., Nip, A.M. 1998Biochem. Cell Biol.76110Google Scholar
  25. Wishart, D.S., Sykes, B.D. 1994J. Biomol. NMR4171180Google Scholar
  26. Wishart, D.S., Bigam, C.G., Holm, A., Hodges, R.S., Sykes, B.D. 1995J. Biomol. NMR56781Google Scholar
  27. Wishart, D.S., Sykes, B.D., Richards, F.M. 1991J. Mol. Biol.222311333Google Scholar
  28. Wishart, D.S., Sykes, B.D., Richards, F.M. 1992Biochemistry3116471651Google Scholar
  29. Xu, X-P., Case, D.A. 2001J. Biomol. NMR21321333Google Scholar
  30. Xu, X-P., Case, D.A. 2002Biopolmers65215240Google Scholar
  31. Zhang, H., Neal, S., Wishart, D.S. 2003J. Biomol. NMR25173195Google Scholar

Copyright information

© Kluwer Academic Publishers 2004

Authors and Affiliations

  1. 1.Mesolight, LLCFayettevilleU.S.A

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