The MoD-QM/MM methodology for structural refinement of photosystem II and other biological macromolecules.
The MoD-QM/MM methodology for structural refinement of photosystem II and other biological macromolecules.
复制标题
DOI：
10.1007/s11120-009-9467-6
复制
发表时间：
2009-11
影响因子：
3.7
通讯作者：
Batista, Victor S.
中科院分区：
文献类型：
--
作者：
Sproviero, Eduardo M.;Newcomer, Michael B.;Gascon, Jose A.;Batista, Enrique R.;Brudvig, Gary W.;Batista, Victor S.
量子力学/分子力学（QM/MM）混合方法是目前用于研究大分子（例如蛋白质和核酸）的结构/功能关系和结构细化的最强大的计算工具。这些方法非常高效，因为它们采用量子化学技术，仅对在周围环境的影响下经历化学修饰、电荷转移等的系统的一小部分（QM 层）进行建模。系统的其余部分（MM 层）用分子力学力场进行描述，假设其对 QM 层的影响可以粗略地分解为静电相互作用和空间位阻。 QM/MM 方法的常见局限性包括未明确考虑极化效应时 MM 力场的不准确性，以及 QM 和 MM 层之间边界处静电相互作用的近似处理。本文回顾了计算协议开发的最新进展，这些协议允许对扩展系统中的静电相互作用进行严格建模，超越 QM/MM 混合方法的常见限制。我们专注于移动域 QM/MM (MoD-QM/MM) 方法，该方法将系统划分为许多分子域，并通过对组成分子片段的迭代自洽处理来获得整个系统的静电和结构特性。我们基于高分辨率光谱数据（扩展的 X 射线吸收精细结构光谱和交换耦合常数）说明了 MoD-QM/MM 方法应用于光系统 II 的描述以及与光谱约束 QM/MM 优化方法的应用相结合。
Quantum mechanics/molecular mechanics (QM/MM) hybrid methods are currently the most powerful computational tools for studies of structure/function relations and structural refinement of macrobiomolecules (e.g., proteins and nucleic acids). These methods are highly efficient since they implement quantum chemistry techniques for modeling only the small part of the system (QM layer) that undergoes chemical modifications, charge transfer, etc., under the influence of the surrounding environment. The rest of the system (MM layer) is described in terms of molecular mechanics force fields, assuming that its influence on the QM layer can be roughly decomposed in terms of electrostatic interactions and steric hindrance. Common limitations of QM/MM methods include inaccuracies in the MM force fields when polarization effects are not explicitly considered, and the approximate treatment of electrostatic interactions at the boundaries between QM and MM layers. This paper reviews recent advances in the development of computational protocols that allow for rigorous modeling of electrostatic interactions in extended systems beyond the common limitations of QM/MM hybrid methods. We focus on the Moving-Domain QM/MM (MoD-QM/MM) methodology that partitions the system into many molecular domains and obtains the electrostatic and structural properties of the whole system from an iterative self-consistent treatment of the constituent molecular fragments. We illustrate the MoD-QM/MM method as applied to the description of photosystem II as well as in conjunction with the application of spectroscopically constrained QM/MM optimization methods, based on high-resolution spectroscopic data (extended X-ray absorption fine structure spectra, and exchange coupling constants).
登录
查看更多内容
影响因子：
3.7
作者：
ASHLEY, CA;DONIACH, S
通讯作者：
DONIACH, S
影响因子：
2
作者：
GOLDFARB, D
通讯作者：
GOLDFARB, D
影响因子：
15
作者：
COOPER, SR;CALVIN, M
通讯作者：
CALVIN, M
影响因子：
2
作者：
BROYDEN, CG
通讯作者：
BROYDEN, CG
影响因子：
15
作者：
FLANK, AM;WEININGER, M;CRAMER, SP
通讯作者：
CRAMER, SP