Introduction

Chemical shifts of nuclei in or attached to a protein backbone are exquisitely sensitive to their local environment. A computer program, SPARTA, is described that uses this correlation with local structure to predict protein backbone chemical shifts, given an input three-dimensional structure, by searching a newly generated database for triplets of adjacent residues that provide the best match in phi/psi/chi(1 )torsion angles and sequence similarity to the query triplet of interest. The database contains (15)N, (1)H(N), (1)H(alpha), (13)C(alpha), (13)C(beta) and (13)C' chemical shifts for 200 proteins for which a high resolution X-ray (< or =2.4 A) structure is available. The relative importance of the weighting factors for the phi/psi/chi(1) angles and sequence similarity was optimized empirically. The weighted, average secondary shifts of the central residues in the 20 best-matching triplets, after inclusion of nearest neighbor, ring current, and hydrogen bonding effects, are used to predict chemical shifts for the protein of known structure. Validation shows good agreement between the SPARTA-predicted and experimental shifts, with standard deviations of 2.52, 0.51, 0.27, 0.98, 1.07 and 1.08 ppm for (15)N, (1)H(N), (1)H(alpha), (13)C(alpha), (13)C(beta) and (13)C', respectively, including outliers.

Publications

  1. Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology.
    Cite this
    Shen Y, Bax A, 2007-08-01 - Journal of biomolecular NMR

Credits

  1. Yang Shen
    Developer

    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, United States of America

  2. Ad Bax
    Investigator

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Summary
AccessionBT000396
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByAd Bax