一些处理蛋白质静电极化的实用方法。

Some practical approaches to treating electrostatic polarization of proteins.

机构信息

State Key Laboratory of Precision Spectroscopy, Institute of Theoretical and Computational Science, East China Normal University , Shanghai 200062, China.

出版信息

Acc Chem Res. 2014 Sep 16;47(9):2795-803. doi: 10.1021/ar500094n. Epub 2014 Jun 2.

Abstract

Conspectus Electrostatic interaction plays a significant role in determining many properties of biomolecules, which exist and function in aqueous solution, a highly polar environment. For example, proteins are composed of amino acids with charged, polar, and nonpolar side chains and their specific electrostatic properties are fundamental to the structure and function of proteins. An important issue that arises in computational study of biomolecular interaction and dynamics based on classical force field is lack of polarization. Polarization is a phenomenon in which the charge distribution of an isolated molecule will be distorted when interacting with another molecule or presented in an external electric field. The distortion of charge distribution is intended to lower the overall energy of the molecular system, which is counter balanced by the increased internal energy of individual molecules due to the distorted charge distributions. The amount of the charge redistribution, which characterizes the polarizability of a molecule, is determined by the level of the charge distortion. Polarization is inherently quantum mechanical, and therefore classical force fields with fixed atomic charges are incapable of capturing this important effect. As a result, simulation studies based on popular force fields, AMBER, CHARMM, etc., lack the polarization effect, which is a widely known deficiency in most computational studies of biomolecules today. Many efforts have been devoted to remedy this deficiency, such as adding additional movable charge on the atom, allowing atomic charges to fluctuate, or including induced multipoles. Although various successes have been achieved and progress at various levels has been reported over the past decades, the issue of lacking polarization in force field based simulations is far from over. For example, some of these methods do not always give converged results, and other methods require huge computational cost. This Account reviews recent work on developing polarized and polarizable force fields based on fragment quantum mechanical calculations for proteins. The methods described here are based on quantum mechanical calculations of proteins in solution, but with a different level of rigor and different computational efficiency for the molecular dynamics applications. In the general approach, a fragment quantum mechanical calculation for protein with implicit solvation is carried out to derive a polarized protein-specific charge (PPC) for any given protein structure. The PPC correctly reflects the polarization state of the protein in a given conformation, and it can also be dynamically changed as the protein changes conformation in dynamics simulations. Another approach that is computationally more efficient is the effective polarizable bond method in which only polar bonds or groups can be polarized and their polarizabilities are predetermined from quantum mechanical calculations of these groups in external electric fields. Both methods can be employed for applications in various situations by taking advantage of their unique features.

摘要

静电相互作用在决定生物分子的许多性质方面起着重要作用,这些性质存在于并在高度极性的水溶液环境中发挥作用。例如,蛋白质由带电荷、极性和非极性侧链的氨基酸组成,其特定的静电性质是蛋白质结构和功能的基础。在基于经典力场的生物分子相互作用和动力学的计算研究中,一个重要的问题是缺乏极化。极化是一种现象,即当一个孤立的分子与另一个分子相互作用或置于外部电场中时,其电荷分布会发生扭曲。电荷分布的扭曲旨在降低分子系统的总能量,而由于电荷分布的扭曲,单个分子的内部能量会增加,从而达到平衡。分子极化率的特征是电荷再分配的数量,由电荷扭曲的程度决定。极化是本质上的量子力学现象,因此带有固定原子电荷的经典力场无法捕捉到这一重要效应。因此,基于流行力场(如 AMBER、CHARMM 等)的模拟研究缺乏极化效应,这是当今大多数生物分子计算研究中广泛存在的一个缺陷。为了弥补这一缺陷,人们做出了许多努力,例如在原子上添加额外的可移动电荷、允许原子电荷波动或包含诱导偶极子。尽管在过去几十年中取得了各种成功,并在各个层面取得了进展,但基于力场的模拟中缺乏极化的问题远未得到解决。例如,其中一些方法并不总是给出收敛的结果,而其他方法则需要巨大的计算成本。本综述回顾了近年来基于片段量子力学计算开发蛋白质极化和极化力场的研究工作。这里描述的方法基于溶液中蛋白质的量子力学计算,但对于分子动力学应用,其严谨性和计算效率不同。在一般方法中,对具有隐式溶剂化的蛋白质进行片段量子力学计算,以得出给定蛋白质结构的极化蛋白特异性电荷(PPC)。PPC 正确反映了给定构象中蛋白质的极化状态,并且它也可以随着蛋白质在动力学模拟中构象的变化而动态变化。另一种计算效率更高的方法是有效极化键方法,其中只有极性键或基团可以被极化,并且它们的极化率可以从这些基团在外部电场中的量子力学计算中预先确定。这两种方法都可以利用其独特的功能,应用于各种情况。

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