可转移的极化高斯多极模型的静电参数。

Transferability of the Electrostatic Parameters of the Polarizable Gaussian Multipole Model.

机构信息

Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, University of California, Irvine, Irvine, California 92697, United States.

SBP Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States.

出版信息

J Chem Theory Comput. 2023 Feb 14;19(3):924-941. doi: 10.1021/acs.jctc.2c01048. Epub 2023 Jan 25.

Abstract

Accuracy and transferability are the two highly desirable properties of molecular mechanical force fields. Compared with the extensively used point-charge additive force fields that apply fixed atom-centered point partial charges to model electrostatic interactions, polarizable force fields are thought to have the advantage of modeling the atomic polarization effects. Previous works have demonstrated the accuracy of the recently developed polarizable Gaussian multipole (pGM) models. In this work, we assessed the transferability of the electrostatic parameters of the pGM models with (pGM-perm) and without (pGM-ind) atomic permanent dipoles in terms of reproducing the electrostatic potentials surrounding molecules/oligomers absent from electrostatic parameterizations. Encouragingly, both the pGM-perm and pGM-ind models show significantly improved transferability than the additive model in the tests (1) from water monomer to water oligomer clusters; (2) across different conformations of amino acid dipeptides and tetrapeptides; (3) from amino acid tetrapeptides to longer polypeptides; and (4) from nucleobase monomers to Watson-Crick base pair dimers and tetramers. Furthermore, we demonstrated that the double-conformation fittings using amino acid tetrapeptides in the αR and β conformations can result in good transferability not only across different tetrapeptide conformations but also from tetrapeptides to polypeptides with lengths ranging from 1 to 20 repetitive residues for both the pGM-ind and pGM-perm models. In addition, the observation that the pGM-ind model has significantly better accuracy and transferability than the point-charge additive model, even though they have an identical number of parameters, strongly suggest the importance of intramolecular polarization effects. In summary, this and previous works together show that the pGM models possess both accuracy and transferability, which are expected to serve as foundations for the development of next-generation polarizable force fields for modeling various polarization-sensitive biological systems and processes.

摘要

准确性和可转移性是分子力学力场的两个非常理想的特性。与广泛使用的点电荷加和力场不同,后者采用固定的原子中心点电荷来模拟静电相互作用,极化力场被认为具有模拟原子极化效应的优势。以前的工作已经证明了最近开发的极化高斯多极(pGM)模型的准确性。在这项工作中,我们评估了带有(pGM-perm)和不带有(pGM-ind)原子永久偶极子的 pGM 模型的静电参数的可转移性,以重现没有静电参数化的分子/低聚物周围的静电势。令人鼓舞的是,pGM-perm 和 pGM-ind 模型在测试中都表现出比加和模型显著提高的可转移性,这些测试包括:(1)从水分子单体到水分子寡聚体簇;(2)跨越不同构象的氨基酸二肽和四肽;(3)从氨基酸四肽到更长的多肽;(4)从碱基单体到 Watson-Crick 碱基对二聚体和四聚体。此外,我们还证明了使用αR 和β构象的氨基酸四肽进行双构象拟合不仅可以提高不同四肽构象之间的可转移性,而且对于 pGM-ind 和 pGM-perm 模型,从四肽到长度为 1 到 20 个重复残基的多肽都可以获得良好的可转移性。此外,观察到 pGM-ind 模型比点电荷加和模型具有更高的准确性和可转移性,即使它们具有相同数量的参数,这强烈表明分子内极化效应的重要性。总之,这项工作和以前的工作一起表明,pGM 模型具有准确性和可转移性,有望成为下一代极化力场的基础,用于模拟各种对极化敏感的生物系统和过程。

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