An Anisotropic Coarse-Grained Model for Proteins Based On Gay-Berne and Electric Multipole Potentials.
An Anisotropic Coarse-Grained Model for Proteins Based On Gay-Berne and Electric Multipole Potentials.
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基于 Gay-Berne 和电多极势的蛋白质各向异性粗粒模型
DOI：
10.1021/ct400974z
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发表时间：
2014-02-10
影响因子：
5.5
通讯作者：
Li G
中科院分区：
文献类型：
--
作者：
Shen H;Li Y;Ren P;Zhang D;Li G
Gay-Berne各向异性势已被广泛应用于描述为椭圆刚体的粗颗粒之间的非粘结相互作用。本文基于各向异性Gay-Berne势和点电多极（EMP）势，提出了一个适用于20种氨基酸和蛋白质的粗粒度模型。我们证明了各向异性粗粒度模型，即GBEMP模型，能够再现从实验蛋白质结构（Dunbrack库）以及原子力场模拟（使用AMOEBA，AMBER和CHARMM力场）观察到的许多关键特征，同时根据具体情况和原子模型将计算成本节省约10-200倍。更重要的是，不同于其他粗粒度的方法，我们的框架是基于基本的分子间力与静电和排斥分散力的明确治疗。因此，粗粒蛋白质模型提出了一个准确的描述非键之间的相互作用（特别是静电成分）的异/同二聚体（如肽-肽，肽-水）。此外，GBEMP和AMOEBA模型在计算肽的偶极矩时具有良好的相关性，反映了该模型令人鼓舞的性能。总之，本文给出的GBEMP模型具有通用性和可移植性，适用于模拟复杂的生物分子体系。
Gay–Berne anisotropic potential has been widely used to evaluate the nonbonded interactions between coarse-grained particles being described as elliptical rigid bodies. In this paper, we are presenting a coarse-grained model for twenty kinds of amino acids and proteins, based on the anisotropic Gay–Berne and point electric multipole (EMP) potentials. We demonstrate that the anisotropic coarse-grained model, namely GBEMP model, is able to reproduce many key features observed from experimental protein structures (Dunbrack Library), as well as from atomistic force field simulations (using AMOEBA, AMBER, and CHARMM force fields), while saving the computational cost by a factor of about 10–200 depending on specific cases and atomistic models. More importantly, unlike other coarse-grained approaches, our framework is based on the fundamental intermolecular forces with explicit treatment of electrostatic and repulsion-dispersion forces. As a result, the coarse-grained protein model presented an accurate description of nonbonded interactions (particularly electrostatic component) between hetero/homodimers (such as peptide–peptide, peptide–water). In addition, the encouraging performance of the model was reflected by the excellent correlation between GBEMP and AMOEBA models in the calculations of the dipole moment of peptides. In brief, the GBEMP model given here is general and transferable, suitable for simulating complex biomolecular systems.
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