具有明确长程色散处理的 Drude 极化脂质力场:饱和和单不饱和两性离子脂质的参数化和验证。
Drude Polarizable Lipid Force Field with Explicit Treatment of Long-Range Dispersion: Parametrization and Validation for Saturated and Monounsaturated Zwitterionic Lipids.
机构信息
Biophysics Graduate Program, University of Maryland, College Park, Maryland 20742, United States.
Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States.
出版信息
J Chem Theory Comput. 2023 May 9;19(9):2590-2605. doi: 10.1021/acs.jctc.3c00203. Epub 2023 Apr 18.
Accurate empirical force fields of lipid molecules are a critical component of molecular dynamics simulation studies aimed at investigating properties of monolayers, bilayers, micelles, vesicles, and liposomes, as well as heterogeneous systems, such as protein-membrane complexes, bacterial cell walls, and more. While the majority of lipid force field-based simulations have been performed using pairwise-additive nonpolarizable models, advances have been made in the development of the polarizable force field based on the classical Drude oscillator model. In the present study, we undertake further optimization of the Drude lipid force field, termed Drude2023, including improved treatment of the phosphate and glycerol linker region of PC and PE headgroups, additional optimization of the alkene group in monounsaturated lipids, and inclusion of long-range Lennard-Jones interactions using the particle-mesh Ewald method. Initial optimization targeted quantum mechanical (QM) data on small model compounds representative of the linker region. Subsequent optimization targeted QM data on larger model compounds, experimental data, and dihedral potentials of mean force from the CHARMM36 additive lipid force field using a parameter reweighting protocol. The use of both experimental and QM target data during the reweighting protocol is shown to produce physically reasonable parameters that reproduce a collection of experimental observables. Target data for optimization included surface area/lipid for DPPC, DSPC, DMPC, and DLPC bilayers and nuclear magnetic resonance (NMR) order parameters for DPPC bilayers. Validation data include prediction of membrane thickness, scattering form factors, electrostatic potential profiles, compressibility moduli, surface area per lipid, water permeability, NMR relaxation times, diffusion constants, and monolayer surface tensions for a variety of saturated and unsaturated lipid mono- and bilayers. Overall, the agreement with experimental data is quite good, though the results are less satisfactory for the NMR relaxation times for carbons near the ester groups. Notable improvements compared to the additive C36 force field were obtained for membrane dipole potentials, lipid diffusion coefficients, and water permeability with the exception of monounsaturated lipid bilayers. It is anticipated that the optimized polarizable Drude2023 force field will help generate more accurate molecular simulations of pure bilayers and heterogeneous systems containing membranes, advancing our understanding of the role of electronic polarization in these systems.
准确的脂质分子经验力场是旨在研究单层、双层、胶束、囊泡和脂质体以及蛋白质-膜复合物、细菌细胞壁等多相体系性质的分子动力学模拟研究的关键组成部分。虽然大多数基于脂质力场的模拟都是使用非极化的对力场进行的,但在基于经典 Drude 振子模型的极化力场的开发方面已经取得了进展。在本研究中,我们进一步优化了 Drude 脂质力场,称为 Drude2023,包括改进了 PC 和 PE 头部磷酸盐和甘油 linker 区域的处理,对单不饱和脂质的烯烃基团进行了额外的优化,以及使用粒子网格 Ewald 方法包含长程 Lennard-Jones 相互作用。最初的优化目标是针对代表 linker 区域的小分子模型化合物的量子力学 (QM) 数据。随后的优化目标是针对较大的模型化合物、实验数据和来自 CHARMM36 加性脂质力场的二面角势能平均力的 QM 数据,使用参数重新加权协议进行优化。在重新加权协议中使用实验和 QM 目标数据被证明可以产生物理合理的参数,这些参数可以再现一系列实验可观测值。用于优化的目标数据包括 DPPC、DSPC、DMPC 和 DLPC 双层的表面积/脂质以及 DPPC 双层的核磁共振 (NMR) 序参数。验证数据包括对各种饱和和不饱和脂质单层和双层的膜厚度、散射因子、静电势轮廓、压缩模量、每脂质的表面积、水渗透性、NMR 弛豫时间、扩散常数和单层表面张力的预测。总的来说,与实验数据的一致性非常好,尽管对于酯基团附近碳的 NMR 弛豫时间的结果不太令人满意。与加性 C36 力场相比,优化后的极化 Drude2023 力场在膜偶极势、脂质扩散系数和水渗透性方面取得了显著改进,除了单不饱和脂质双层。预计优化后的极化 Drude2023 力场将有助于生成更准确的纯双层和包含膜的多相体系的分子模拟,从而提高我们对这些体系中电子极化作用的理解。
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