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A software tool for the prediction of Xaa-Pro peptide bond conformations in proteins based on 13C chemical shift
Mario Schubert1, Dirk Labudde, Hartmut Oschkinat
1Forschungs Institut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, D- 13125 Berlin, Germany.
Abstract:
The chemical shift difference (delta[13C(beta)]-delta[13C(gamma)]) is a reference-independent indicator of the Xaa-Pro peptide bond conformation. Based on a statistical analysis of the 13C chemical shifts of 1,033 prolines from 304 proteins deposited in the BioMagRes database, a software tool was created to predict the probabilities for cis or trans conformations of Xaa-Pro peptide bonds. Using this approach, the conformation at a given Xaa-Pro bond can be identified in a simple NOE-independent way immediately after obtaining its NMR resonance assignments. This will allow subsequent structure calculations to be initiated using the correct polypeptide chain conformation.