Prediction of methyl-side Chain Dynamics in Proteins

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• 作者：Dengming Ming and Rafael Brüschweiler
• 关键词：methyl group dynamics ; NMR relaxation ; prediction of protein mobility ; protein backbone dynamics ; S2 order parameters ; side ; chain dynamics
• 刊名：Journal of Biomolecular NMR
• 出版年：2004
• 出版时间：2004
• 年：2004
• 卷：29
• 期：3
• 页码：363-368
• 全文大小：126 KB
• 刊物类别：Physics and Astronomy
• 刊物主题：Physics
  Biophysics and Biomedical Physics
  Polymer Sciences
  Biochemistry
  
• 出版者：Springer Netherlands
• ISSN：1573-5001

文摘

A simple analytical model is presented for the prediction of methyl-side chain dynamics in comparison with S2 order parameters obtained by NMR relaxation spectroscopy. The model, which is an extension of the local contact model for backbone order parameter prediction, uses a static 3D protein structure as input. It expresses the methyl-group S2 order parameters as a function of local contacts of the methyl carbon with respect to the neighboring atoms in combination with the number of consecutive mobile dihedral angles between the methyl group and the protein backbone. For six out of seven proteins the prediction results are good when compared with experimentally determined methyl-group S2 values with an average correlation coefficient [`(r)]\bar r=0.65±0.14. For the unusually rigid cytochrome c₂ no significant correlation between prediction and experiment is found. The presented model provides independent support for the reliability of current side-chain relaxation methods along with their interpretation by the model-free formalism.