大型蛋白质晶体模拟中的原子级精度。
Atomic-level accuracy in simulations of large protein crystals.
作者信息
York D M, Wlodawer A, Pedersen L G, Darden T A
机构信息
Department of Chemistry, Duke University, Durham, NC 27706.
出版信息
Proc Natl Acad Sci U S A. 1994 Aug 30;91(18):8715-8. doi: 10.1073/pnas.91.18.8715.
Abstract
Proper treatment of long-range Coulombic forces presents a major obstacle to providing realistic molecular dynamics simulations of macromolecules. Traditional approximations made to lessen computational cost ultimately lead to unrealistic behavior. The particle mesh Ewald method accommodates long-range Coulombic forces accurately and efficiently by use of fast Fourier transform techniques. We report a 1-ns simulation of bovine pancreatic trypsin inhibitor in a crystal unit cell using the particle mesh Ewald methodology. We find an rms backbone deviation from the x-ray structure (0.33 A) that is lower than that observed between bovine pancreatic trypsin inhibitor in different crystal forms and much lower than those of previous simulations. These results bridge the gap between structures obtained from molecular simulation and those from experiment.
摘要
正确处理长程库仑力是对大分子进行逼真分子动力学模拟的一个主要障碍。为降低计算成本而采用的传统近似方法最终会导致不切实际的行为。粒子网格埃瓦尔德方法通过使用快速傅里叶变换技术，能够准确而高效地处理长程库仑力。我们报告了使用粒子网格埃瓦尔德方法对牛胰蛋白酶抑制剂在晶体晶胞中的1纳秒模拟。我们发现，与X射线结构相比，主链均方根偏差为0.33 Å，低于在不同晶体形式的牛胰蛋白酶抑制剂之间观察到的偏差，并且远低于先前模拟的结果。这些结果弥合了分子模拟得到的结构与实验得到的结构之间的差距。
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