A software tool for the prediction of Xaa-Pro peptide bond conformations in proteins based on 13C chemical shift statistics.
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.
Schubert
Mario
M
Forschungs Institut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, D- 13125 Berlin, Germany.
Labudde
Dirk
D
Oschkinat
Hartmut
H
Schmieder
Peter
P
D000596:Amino Acids / Q000737:chemistry*; D002247:Carbon Isotopes / Q000737:chemistry*; D019295:Computational Biology / Q000379:methods; D006860:Hydrogen Bonding; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods; D010455:Peptides / Q000737:chemistry*; D011392:Proline / Q000737:chemistry*; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012984:Software / Q000706:statistics & numerical data*; D013237:Stereoisomerism; D013816:Thermodynamics
D000596:Amino Acids; D002247:Carbon Isotopes; D010455:Peptides; D011506:Proteins; D011392:Proline