Theoretical Chemistry Accounts

, Volume 121, Issue 3, pp 197–200

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

Authors

    • Institute of BioinformaticsNational Chiao Tung University
  • Chien-Hua Shih
    • Institute of BioinformaticsNational Chiao Tung University
  • Chih-Peng Lin
    • Institute of BioinformaticsNational Chiao Tung University
  • Jenn-Kang Hwang
    • Institute of BioinformaticsNational Chiao Tung University
Regular Article

DOI: 10.1007/s00214-008-0465-0

Cite this article as:
Huang, S., Shih, C., Lin, C. et al. Theor Chem Account (2008) 121: 197. doi:10.1007/s00214-008-0465-0

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 Cα atom the number of neighboring Cα 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.

Keywords

NMR order parameterWeighted protein contact numberProtein dynamicsPrediction

Copyright information

© Springer-Verlag 2008