Molecular Dynamics Simulations of Macromolecular Crystals.,Wiley Interdisciplinary Reviews: Computational Molecular Science

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Molecular Dynamics Simulations of Macromolecular Crystals.
Wiley Interdisciplinary Reviews: Computational Molecular Science ( IF 16.8 ) Pub Date : 2018-11-16 , DOI: 10.1002/wcms.1402
David S Cerutti ₁ , David A Case ₁

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The structures of biological macromolecules would not be known to their present extent without X‐ray crystallography. Most simulations of globular proteins in solution begin by surrounding the crystal structure of the monomer in a bath of water molecules, but the standard simulation employing periodic boundary conditions is already close to a crystal lattice environment. With simple protocols, the same software and molecular models can perform simulations of the crystal lattice, including all asymmetric units and solvent to fill the box. Throughout the history of molecular dynamics, studies of crystal lattices have served to investigate the quality of the underlying force fields, correlate the simulated ensembles to experimental structure factors, and extrapolate the behavior in lattices to behavior in solution. Powerful new computers are enabling molecular simulations with greater realism and statistical convergence. Meanwhile, the advent of exciting new methods in crystallography, including femtosecond free‐electron lasers and image reconstruction for time‐resolved crystallography on slurries of small crystals, is expanding the range of structures accessible to X‐ray diffraction. We review past fusions of simulations and crystallography, then look ahead to the ways that simulations of crystal structures will enhance structural biology in the future.

中文翻译：

大分子晶体的分子动力学模拟。

没有X射线晶体学，就目前的程度而言，生物大分子的结构是未知的。溶液中大多数球状蛋白质的模拟都是从围绕水分子浴中单体的晶体结构开始的，但是采用周期性边界条件的标准模拟已经接近晶格环境。通过简单的协议，相同的软件和分子模型可以执行晶格的模拟，包括所有不对称单元和填充盒的溶剂。在整个分子动力学的历史中，对晶格的研究一直在研究基础力场的质量，将模拟的集成体与实验结构因子相关联，并将晶格中的行为推断为溶液中的行为。功能强大的新型计算机使分子模拟具有更大的真实性和统计收敛性。同时，晶体学中激动人心的新方法的出现，包括飞秒自由电子激光器和小晶体浆料上时间分辨晶体学的图像重建，扩大了X射线衍射可及的结构范围。我们回顾了过去模拟和晶体学的融合，然后展望了晶体结构的模拟将在未来增强结构生物学的方式。正在扩大X射线衍射可接近的结构范围。我们回顾了过去模拟和晶体学的融合，然后展望了晶体结构的模拟将在未来增强结构生物学的方式。正在扩大X射线衍射可接近的结构范围。我们回顾了过去模拟和晶体学的融合，然后展望了晶体结构的模拟将在未来增强结构生物学的方式。

更新日期：2018-11-16

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