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

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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.

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Authors and Affiliations

  1. Institute of Bioinformatics, National Chiao Tung University, HsinChu, 30050, Taiwan, ROC

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

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  1. Shao-Wei Huang
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  2. Chien-Hua Shih
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  3. Chih-Peng Lin
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  4. Jenn-Kang Hwang
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Correspondence to Shao-Wei Huang.

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Huang, SW., Shih, CH., Lin, CP. et al. Prediction of NMR order parameters in proteins using weighted protein contact-number model. Theor Chem Account 121, 197–200 (2008). https://doi.org/10.1007/s00214-008-0465-0

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  • DOI: https://doi.org/10.1007/s00214-008-0465-0

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