A molecule-centered method for accelerating the calculation of hydrodynamic interactions in Brownian dynamics simulations containing many flexible biomolecules.
A molecule-centered method for accelerating the calculation of hydrodynamic interactions in Brownian dynamics simulations containing many flexible biomolecules.
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DOI：
10.1021/ct400240w
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发表时间：
2013-07-09
影响因子：
5.5
通讯作者：
Elcock, Adrian H.
中科院分区：
文献类型：
--
作者：
Elcock, Adrian H.
如果生物大分子要表现出正确的平移和旋转扩散，则在隐式处理溶剂的生物大分子模拟中，包含流体动力学相互作用 (HI) 至关重要。目前的工作描述了一种简单方法的开发和测试，旨在允许在包含大量柔性大分子的系统的粗粒度布朗动力学模拟中更快速地计算 HI。该方法结合了分子内 HI 的完整处理和分子间 HI 的近似处理（假设分子实际上是球形的）；所有 HI 都是在 Rotne-Prager-Yamakawa 理论水平上计算的。当与 Fixman 的切比雪夫多项式方法相结合来计算相关随机位移时，所提出的方法提供了一种编程简单但速度足够快的方法，使得在大规模模拟中包含 HI 在计算上是可行的。对丙酮酸脱氢酶 (PDH) E2 复合物的非常粗粒度模型和 ParM 寡聚物（大小范围从 1 到 20 个单体）进行的测试计算表明，该方法令人惊讶地很好地再现了更完整的 HI 模拟中看到的平移扩散行为；该方法在捕获旋转扩散方面表现较差，但其差异随着模拟组件尺寸的增加而减小。对两个四聚体蛋白质模型的残基水平模型的模拟表明，当模拟中使用结构更详细的模型时，该方法也能很好地发挥作用。最后，对包含多达 1024 个粗粒度 PDH 分子的系统进行的测试模拟表明，所提出的方法很快变得比传统的 BD 方法更有效，在传统的 BD 方法中，相关随机位移是通过完整扩散张量的 Cholesky 分解获得的。
Inclusion of hydrodynamic interactions (HIs) is essential in simulations of biological macromolecules that treat the solvent implicitly if the macromolecules are to exhibit correct translational and rotational diffusion. The present work describes the development and testing of a simple approach aimed at allowing more rapid computation of HIs in coarse-grained Brownian dynamics simulations of systems that contain large numbers of flexible macromolecules. The method combines a complete treatment of intramolecular HIs with an approximate treatment of the intermolecular HIs which assumes that the molecules are effectively spherical; all of the HIs are calculated at the Rotne-Prager-Yamakawa level of theory. When combined with Fixman’s Chebyshev polynomial method for calculating correlated random displacements, the proposed method provides an approach that is simple to program but sufficiently fast that it makes it computationally viable to include HIs in large-scale simulations. Test calculations performed on very coarse-grained models of the pyruvate dehydrogenase (PDH) E2 complex and on oligomers of ParM (ranging in size from 1 to 20 monomers) indicate that the method reproduces the translational diffusion behavior seen in more complete HI simulations surprisingly well; the method performs less well at capturing rotational diffusion but its discrepancies diminish with increasing size of the simulated assembly. Simulations of residue-level models of two tetrameric protein models demonstrate that the method also works well when more structurally detailed models are used in the simulations. Finally, test simulations of systems containing up to 1024 coarse-grained PDH molecules indicate that the proposed method rapidly becomes more efficient than the conventional BD approach in which correlated random displacements are obtained via a Cholesky decomposition of the complete diffusion tensor.
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影响因子：
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