Journal of Structural and Functional Genomics

, Volume 6, Issue 4, pp 281–285

Estimation of protein secondary structure content directly from NMR spectra using an improved empirical correlation with averaged chemical shift

Article

Abstract

We have recently shown that the averaged chemical shift (ACS) of a nucleus in the protein backbone correlates well empirically to its secondary structure content (SSC). This allows the estimation of SSC directly from the NMR spectrum without the time intensive process of chemical shift assignment. Here, we present an empirical correlation that accounts both for contributions to the relevant protein and chemical shift databases made subsequent to the original analysis, and for missing or inconsistently referenced resonances. Our results affirm that this method provides a significant tool for initial structural prediction from NMR data prior to complete chemical shift assignment.

Keywords

NMR chemical shift proteins secondary structure content 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1.  1.
    Page R., Peti W., Wilson I.A., Stevens R.C. and Wuthrich K. (2005). NMR screening and crystal quality of bacterially expressed prokaryotic and eukaryotic proteins in a structural genomics pipeline. Proc Natl Acad Sci U S A 102(6):1901–1905PubMedCrossRefGoogle Scholar
  2.  2.
    Gutowsky H.S., Saika A., Takeda M. and Woessner D.E. (1957). Proton magnetic resonance studies on natural rubber. II. Line shape and T1 measurements. Journal of Chemical Physics 27: 534–542CrossRefGoogle Scholar
  3.  3.
    Szilagyi L., (1995). Chemical Shifts in Proteins Come of Age. Progress in Nuclear Magnetic Resonance Spectroscopy 27(P4): 325–443CrossRefGoogle Scholar
  4.  4.
    Case D.A., (2000). Interpretation of chemical shifts and coupling constants in macromolecules. Current Opinion in Structural Biology 10(2):197–203PubMedCrossRefGoogle Scholar
  5.  5.
    Ando I., Kuroki S., Kurosu H. and Yamanobe T. (2001). NMR chemical shift calculations and structural characterizations of polymers. Progress in Nuclear Magnetic Resonance Spectroscopy 39(2): 79–133CrossRefGoogle Scholar
  6.  6.
    Wishart D.S. and Case D.A. (2001). Use of chemical shifts in macromolecular structure determination. Methods in Enzymology 338:3–34CrossRefGoogle Scholar
  7.  7.
    Sibley A.B., Cosman M. and Krishnan V.V. (2003). An empirical correlation between secondary structure content and averaged chemical shifts in proteins. Biophys J 84(2 Pt 1): 1223–1227PubMedCrossRefGoogle Scholar
  8.  8.
    Mielke S.P. and Krishnan V.V. (2003). Protein structural class identification directly from NMR spectra using averaged chemical shifts. Bioinformatics 19(16):2054–64PubMedCrossRefGoogle Scholar
  9.  9.
    Seavey B.R., Farr E.A., Westler W.M. and Markley J.L. (1991). A relational database for sequence-specific protein NMR data. Journal of Biomolecular NMR 1(3):217–236PubMedCrossRefGoogle Scholar
  10. 10.
    Zhang H.Y., Neal S. and Wishart D.S. (2003). RefDB: A database of uniformly referenced protein chemical shifts. Journal of Biomolecular NMR 25(3):173–195PubMedCrossRefGoogle Scholar
  11. 11.
    Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N. and Bourne P.E. (2000). The Protein Data Bank. Nucleic Acids Research 28(1):235–242PubMedCrossRefGoogle Scholar
  12. 12.
    Hutchinson E.G. and Thornton J.M. (1996). Promotif - a Program to Identify and Analyze Structural Motifs in Proteins. Protein Science 5(2):212–220PubMedCrossRefGoogle Scholar
  13. 13.
    Atkinson R.A. and Saudek V. (2002). The direct determination of protein structure by NMR without assignment. FEBS Lett 510(1–2):1–4PubMedCrossRefGoogle Scholar
  14. 14.
    Grishaev A. and Llinas M. (2002). CLOUDS a protocol for deriving a molecular proton density via NMR. Proc Natl Acad Sci U S A 99(10):6707–6712PubMedCrossRefGoogle Scholar
  15. 15.
    Grishaev A. and Llinas M. (2002). Protein structure elucidation from NMR proton densities. Proc Natl Acad Sci U S A 99(10): 6713–6718PubMedCrossRefGoogle Scholar
  16. 16.
    Cornilescu G., Delaglio F. and Bax A. (1999). Protein backbone angle restraints from searching a database for chemical shift and sequence homology. Journal of Biomolecular NMR 13(3): 289–302PubMedCrossRefGoogle Scholar
  17. 17.
    Lee M.S. and Cao B. (1996). Nuclear magnetic resonance chemical shift: comparison of estimated secondary structures in peptides by nuclear magnetic resonance and circular dichroism. Protein Eng 9(1):15–25PubMedCrossRefGoogle Scholar
  18. 18.
    Wishart D.S., Sykes B.D. and Richards F.M. (1992). The Chemical Shift Index - a Fast and Simple Method For the Assignment of Protein Secondary Structure Through NMR Spectroscopy. Biochemistry 31(6):1647–1651PubMedCrossRefGoogle Scholar
  19. 19.
    Wishart D.S. and Sykes B.D. (1994). The C-13 Chemical-Shift Index - a Simple Method For the Identification of Protein Secondary Structure Using C-13 Chemical-Shift Data. Journal of Biomolecular NMR 4(2):171–180PubMedCrossRefGoogle Scholar
  20. 20.
    Mielke S.P. and Krishnan V.V. (2004). An evaluation of chemical shift index-based secondary structure determination in proteins: influence of random coil chemical shifts. J Biomol NMR 30(2):143–53PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, Inc. 2005

Authors and Affiliations

  1. 1.Biophysics Graduate GroupUniversity of CaliforniaDavisUSA
  2. 2.L-448 Biosciences Director ate Lawrence Livermore National LaboratoryLivermoreUSA

Personalised recommendations