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Protein backbone angle restraints from searching a database for chemical shift and sequence homology
Authors:Gabriel Cornilescu  Frank Delaglio  Ad Bax
Institution:(1) Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, U.S.A.
Abstract:Chemical shifts of backbone atoms in proteins are exquisitely sensitive to local conformation, and homologous proteins show quite similar patterns of secondary chemical shifts. The inverse of this relation is used to search a database for triplets of adjacent residues with secondary chemical shifts and sequence similarity which provide the best match to the query triplet of interest. The database contains 13Cagr, 13Cbeta, 13Cprime, 1Hagr and 15N chemical shifts for 20 proteins for which a high resolution X-ray structure is available. The computer program TALOS was developed to search this database for strings of residues with chemical shift and residue type homology. The relative importance of the weighting factors attached to the secondary chemical shifts of the five types of resonances relative to that of sequence similarity was optimized empirically. TALOS yields the 10 triplets which have the closest similarity in secondary chemical shift and amino acid sequence to those of the query sequence. If the central residues in these 10 triplets exhibit similar phgr and PSgr backbone angles, their averages can reliably be used as angular restraints for the protein whose structure is being studied. Tests carried out for proteins of known structure indicate that the root-mean-square difference (rmsd) between the output of TALOS and the X-ray derived backbone angles is about 15°. Approximately 3% of the predictions made by TALOS are found to be in error.
Keywords:phgr angle" target="_blank">gif" alt="phgr" align="MIDDLE" BORDER="0"> angle  PSgr angle" target="_blank">gif" alt="PSgr" align="BASELINE" BORDER="0"> angle  backbone angles  chemical shift  homology of chemical shift  protein structure  sequence homology  TALOS
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