Shen Hujun, Li Yan, Ren Pengyu, Zhang Dinglin, Li Guohui
Laboratory of Molecular Modeling and Design, State key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Rd. Dalian 116023, PR China.
Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA.
J Chem Theory Comput. 2014 Feb 10;10(2):731-750. doi: 10.1021/ct400974z.
Gay-Berne anisotropic potential has been widely used to evaluate the non-bonded 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 non-bonded interactions (particularly electrostatic component) between hetero-/homo-dimers (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.
盖伊 - 伯恩各向异性势已被广泛用于评估被描述为椭圆刚体的粗粒度粒子之间的非键相互作用。在本文中,我们基于各向异性盖伊 - 伯恩势和点电多极(EMP)势,提出了一种针对二十种氨基酸和蛋白质的粗粒度模型。我们证明,这种各向异性粗粒度模型,即GBEMP模型,能够重现从实验蛋白质结构(邓布拉克文库)以及原子力场模拟(使用AMOEBA、AMBER和CHARMM力场)中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至200倍。更重要的是,与其他粗粒度方法不同,我们的框架基于基本的分子间力,对静电和排斥 - 色散力进行了明确处理。因此,该粗粒度蛋白质模型能够准确描述异质/同质二聚体(如肽 - 肽、肽 - 水)之间的非键相互作用(特别是静电成分)。此外,在肽偶极矩的计算中,GBEMP模型与AMOEBA模型之间的出色相关性反映了该模型令人鼓舞的性能。简而言之,这里给出的GBEMP模型具有通用性和可转移性,适用于模拟复杂的生物分子系统。