Orientationally Averaged Version of the Rotne-Prager-Yamakawa Tensor Provides a Fast but Still Accurate Treatment of Hydrodynamic Interactions in Brownian Dynamics Simulations of Biological Macromolecules.
Orientationally Averaged Version of the Rotne-Prager-Yamakawa Tensor Provides a Fast but Still Accurate Treatment of Hydrodynamic Interactions in Brownian Dynamics Simulations of Biological Macromolecules.
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DOI：
10.1021/acs.jctc.3c00476
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发表时间：
2023-08-08
影响因子：
5.5
通讯作者：
Elcock, Adrian H. H.
中科院分区：
文献类型：
--
作者：
Tworek, John W. W.;Elcock, Adrian H. H.
布朗动力学（BD）模拟技术被广泛用于模拟由生物大分子组成的复杂系统的扩散和构象动力学。为了正确地描述大分子的扩散性质的BD模拟，它是必要的，包括流体动力学相互作用（HI）。例如，当在Rotne-Prager-Yamakawa（RPY）理论水平上建模时，孤立大分子的平移和旋转扩散系数可以准确地再现;然而，当忽略HI时，扩散系数可以被低估一个数量级或更多。在BD模拟中包含HI的主要缺点是它们的计算费用，并且先前的几项研究试图通过开发用于计算相关随机位移的快速近似来加速它们的建模。在这里，我们探索使用另一种方法来加速HI的计算，即，通过用取向平均（OA）版本替换完整的RPY张量，该版本保留了HI的距离依赖性，但将它们的取向依赖性平均化。我们在这里寻求确定这样的近似是否可以证明在典型的蛋白质和RNA的建模应用。我们表明，使用的OA-RPY张量允许平移扩散的大分子被建模的旋转扩散被低估了25%的成本，具有非常高的精度。我们表明，这一发现是独立的模拟的大分子的类型和模型中采用的结构分辨率的水平。然而，我们还表明，这些结果是严重依赖于包含一个非零项，描述了扩散张量的发散：当这个术语是省略模拟使用的OA-RPY模型，未折叠的大分子进行快速崩溃。我们的研究结果表明，取向平均RPY张量可能是一个有用的，快速的，近似的方式，包括在BD模拟的中间尺度系统的HI。
The Brownian dynamics (BD) simulation technique is widely used to model the diffusive and conformational dynamics of complex systems comprising biological macromolecules. For the diffusive properties of macromolecules to be described correctly by BD simulations, it is necessary to include hydrodynamic interactions (HIs). When modeled at the Rotne–Prager–Yamakawa (RPY) level of theory, for example, the translational and rotational diffusion coefficients of isolated macromolecules can be accurately reproduced; when HIs are neglected, however, diffusion coefficients can be underestimated by an order of magnitude or more. The principal drawback to the inclusion of HIs in BD simulations is their computational expense, and several previous studies have sought to accelerate their modeling by developing fast approximations for the calculation of the correlated random displacements. Here, we explore the use of an alternative way to accelerate the calculation of HIs, i.e., by replacing the full RPY tensor with an orientationally averaged (OA) version which retains the distance dependence of the HIs but averages out their orientational dependence. We seek here to determine whether such an approximation can be justified in application to the modeling of typical proteins and RNAs. We show that the use of an OA-RPY tensor allows translational diffusion of macromolecules to be modeled with very high accuracy at the cost of rotational diffusion being underestimated by ∼25%. We show that this finding is independent of the type of macromolecule simulated and the level of structural resolution employed in the models. We also show, however, that these results are critically dependent on the inclusion of a non-zero term that describes the divergence of the diffusion tensor: when this term is omitted from simulations that use the OA-RPY model, unfolded macromolecules undergo rapid collapse. Our results indicate that the orientationally averaged RPY tensor is likely to be a useful, fast, approximate way of including HIs in BD simulations of intermediate-scale systems.
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