Prediction of NMR order parameters in proteins using weighted protein contact-number model

Shao-Wei Huang, Chien Hua Shih, Chih-Peng Lin, Jenn-Kang Hwang

Research output: Contribution to journalArticlepeer-review

12 Scopus citations

Abstract

In the NMR experiment, the protein backbone motion can be described by the N-H order parameters. Though protein dynamics is determined by a complex network of atomic interactions, we show that the order parameter of residues can be determined using a very simple method, the weighted protein contact number model. We computed for each C alpha atom the number of neighboring C alpha atoms weighted by the inverse distance squared between them. We show that the weighted contact number of each residue is directly related to its order parameter. Despite the simplicity of this model, it performs better than the other method. Since we can compute the order parameters directly from the topological properties (such as protein contact number) of protein structures, our study underscores a very direct link between protein topological structure and its dynamics.
Original languageEnglish
Pages (from-to)197-200
Number of pages3
JournalTheoretical Chemistry Accounts
Volume121
Issue number3-4
DOIs
StatePublished - Oct 2008

Keywords

  • NMR order parameter; weighted protein contact number; protein dynamics; prediction

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