Mazack Michael J M, Cembran Alessandro, Gao Jiali
Department of Chemistry, Digital Technology Center, and Supercomputing Institute University of Minnesota, Minneapolis, MN 55455.
J Chem Theory Comput. 2010 Nov 9;6(11):3601-3612. doi: 10.1021/ct100426m.
An analytical coarse-grained model (ACG) is introduced to represent individual macromolecules for simulation of dynamic processes in cells. In the ACG model, a macromolecular structure is treated as a fully coarse-grained entity with a uniform mass density without the explicit atomic details. The excluded volume and surface of the ACG macromolecular species are explicitly treated by a spherical harmonic representation in the present study (although ellipsoidal, solid, and radial augmented functions can be used), which can provide any desired accuracy and detail depending on the problem of interest. The present paper focuses on the description of the internal fluctuations of a single ACG macromolecule, modeled by the superposition of low frequency quasiharmonic modes from explicit molecular dynamics simulation. A procedure for estimating the amplitudes, time scales of the quasiharmonic motions and the corresponding phases is presented and used to synthesize the complex motion. The analytical description and numerical algorithm can provide an adequate representation of the internal protein fluctuations revealed from the corresponding atomistic simulations, although the internal motions of ACG macromolecules do not explore motions not exhibited in the dynamic simulations.
引入了一种分析型粗粒度模型（ACG）来表示单个大分子，以模拟细胞中的动态过程。在ACG模型中，大分子结构被视为一个完全粗粒度的实体，具有均匀的质量密度，没有明确的原子细节。在本研究中，通过球谐表示法明确处理了ACG大分子物种的排除体积和表面（尽管也可以使用椭球、固体和径向增强函数），这可以根据感兴趣的问题提供任何所需的精度和细节。本文重点描述了单个ACG大分子的内部波动，该波动由显式分子动力学模拟中的低频准谐波模式叠加建模。提出了一种估计准谐波运动的振幅、时间尺度和相应相位的方法，并用于合成复杂运动。尽管ACG大分子的内部运动没有探索动态模拟中未表现出的运动，但解析描述和数值算法可以充分表示从相应原子模拟中揭示的蛋白质内部波动。
