TMFF—A Two-Bead Multipole Force Field for Coarse-Grained Molecular Dynamics Simulation of Protein

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• 作者：Min Li ; Fengjiao Liu ; John Z. H. Zhang
• 刊名：Journal of Chemical Theory and Computation
• 出版年：2016
• 出版时间：December 13, 2016
• 年：2016
• 卷：12
• 期：12
• 页码：6147-6156
• 全文大小：651K
• ISSN：1549-9626

文摘

Coarse-grained (CG) models are desirable for studying large and complex biological systems. In this paper, we propose a new two-bead multipole force field (TMFF) in which electric multipoles up to the quadrupole are included in the CG force field. The inclusion of electric multipoles in the proposed CG force field enables a more realistic description of the anisotropic electrostatic interactions in the protein system and, thus, provides an improvement over the standard isotropic two-bead CG models. In order to test the accuracy of the new CG force field model, extensive molecular dynamics simulations were carried out for a series of benchmark protein systems. These simulation studies showed that the TMFF model can realistically reproduce the structural and dynamical properties of proteins, as demonstrated by the close agreement of the CG results with those from the corresponding all-atom simulations in terms of root-mean-square deviations (RMSDs) and root-mean-square fluctuations (RMSFs) of the protein backbones. The current two-bead model is highly coarse-grained and is 50-fold more efficient than all-atom method in MD simulation of proteins in explicit water.