Robust Heterogeneous Anisotropic Elastic Network Model Precisely Reproduces the Experimental B-factors of Biomolecules
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- 作者：Fei Xia ; Dudu Tong ; Lanyuan Lu
- 刊名：Journal of Chemical Theory and Computation
- 出版年：2013
- 出版时间：August 13, 2013
- 年：2013
- 卷：9
- 期：8
- 页码：3704-3714
- 全文大小：564K
- 年卷期：v.9,no.8(August 13, 2013)
- ISSN：1549-9626
文摘
A computational method called the progressive fluctuation matching (PFM) is developed for constructing robust heterogeneous anisotropic network models (HANMs) for biomolecular systems. An HANM derived through the PFM approach consists of harmonic springs with realistic positive force constants, and yields the calculated B-factors that are basically identical to the experimental ones. For the four tested protein systems including crambin, trypsin inhibitor, HIV-1 protease, and lysozyme, the root-mean-square deviations between the experimental and the computed B-factors are only 0.060, 0.095, 0.247, and 0.049 脜2, respectively, and the correlation coefficients are 0.99 for all. By comparing the HANM/ANM normal modes to their counterparts derived from both an atomistic force field and an NMR structure ensemble, it is found that HANM may provide more accurate results on protein dynamics.