On the relationship between the protein structure and protein dynamics |
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Authors: | Lu Chih-Hao Huang Shao-Wei Lai Yan-Long Lin Chih-Peng Shih Chien-Hua Huang Cuen-Chao Hsu Wei-Lun Hwang Jenn-Kang |
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Institution: | Institute of Bioinformatics, National Chiao Tung University, HsinChu 30050, Taiwan, Republic of China. |
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Abstract: | Recently, we have developed a method (Shih et al., Proteins: Structure, Function, and Bioinformatics 2007;68: 34-38) to compute correlation of fluctuations of proteins. This method, referred to as the protein fixed-point (PFP) model, is based on the positional vectors of atoms issuing from the fixed point, which is the point of the least fluctuations in proteins. One corollary from this model is that atoms lying on the same shell centered at the fixed point will have the same thermal fluctuations. In practice, this model provides a convenient way to compute the average dynamical properties of proteins directly from the geometrical shapes of proteins without the need of any mechanical models, and hence no trajectory integration or sophisticated matrix operations are needed. As a result, it is more efficient than molecular dynamics simulation or normal mode analysis. Though in the previous study the PFP model has been successfully applied to a number of proteins of various folds, it is not clear to what extent this model will be applied. In this article, we have carried out the comprehensive analysis of the PFP model for a dataset comprising 972 high-resolution X-ray structures with pairwise sequence identity or=0.5. Our result shows that the fixed-point model is indeed quite general and will be a useful tool for high throughput analysis of dynamical properties of proteins. |
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Keywords: | protein dynamics thermal fluctuations molecular dynamics normal mode analysis B‐factors |
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