Charge equilibration force fields for lipid environments: applications to fully hydrated DPPC bilayers and DMPC-embedded gramicidin A.
Charge equilibration force fields for lipid environments: applications to fully hydrated DPPC bilayers and DMPC-embedded gramicidin A.
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DOI：
10.1021/jp901088g
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发表时间：
2009-07-09
期刊：
影响因子：
--
通讯作者：
Patel S
中科院分区：
文献类型：
--
作者：
Davis JE;Patel S
用于脂质和溶剂环境的可极化力场用于完全水合的二棕榈酰磷脂酰胆碱（DPPC）双层和短杆菌肽A（GA）二聚体嵌入在二肉豆蔻酰磷脂酰胆碱（DMPC）双层的分子动力学模拟。使用CHARMM电荷平衡（CHEQ）可极化力场对脂质进行建模，并使用TIP 4P-FQ力场代表溶剂。对于DPPC双层系统，将结果与使用不可极化的CHARMM 27 r（C27 r）力场和TIP 3 P水模拟的相同系统进行比较。计算出的原子和电子密度分布，头基取向测量的磷-氮矢量取向，氘顺序参数被发现是与以前的模拟和实验一致。CHEQ模型表现出更大的水渗透到双层内部，证明了从水密度分布计算的平均力的潜力。这是水分子偶极从本体中的2.55 D变化到内部中的1.88 D的结果。我们讨论了这一发现的背景下，以前的研究（模拟和实验），已经调查了DPPC双层的水渗透的程度。我们还讨论了包括明确的极化对水的偶极矩变化作为从双层的距离的函数的影响。由于CHEQ模型允许电荷波动，因此我们显示了模拟过程中原子电荷的分布。我们计算了界面偶极电位，CHEQ模型预测为0.95 V，而C27 r模型预测为0.86 V。我们还讨论了介电常数的配置文件和两种模式之间产生的差异。我们获得的CHEQ模型（TIP 4P-FQ水）和C27 r（TIP 3 P）的体积值分别为72.77和91.22，并且在膜内部的值接近于1。最后，我们提出的模拟结果的GA嵌入在DMPC双层使用CHEQ模型和讨论的结构特性。
Polarizable force fields for lipid and solvent environments are used for molecular dynamics simulations of a fully hydrated dipalmitoylphosphatidylcholine (DPPC) bilayer and gramicidin A (gA) dimer embedded in a dimyristoylphosphatidylcholine (DMPC) bilayer. The lipid bilayer is modelled using the CHARMM charge equilibration (CHEQ) polarizable force field for lipids and the TIP4P-FQ force field to represent solvent. For the DPPC bilayer system, results are compared to the same system simulated using the nonpolarizable CHARMM27r (C27r) force field and TIP3P water. Calculated atomic and electron density profiles, headgroup orientations as measured by the phosphorus-nitrogen vector orientation, and deuterium order parameters are found to be consistent with previous simulations and with experiment. The CHEQ model exhibits greater water penetration into the bilayer interior, as demonstrated by the potential of mean force calculated from the water density profile. This is a result of the variation of the water molecular dipole from 2.55 D in the bulk to 1.88 D in the interior. We discuss this finding in the context of previous studies (both simulation and experiment) that have investigated the extent of penetration of water into DPPC bilayers. We also discuss the effects of including explicit polarization on the water dipole moment variation as a function of distance from the bilayer. We show distributions of atomic charges over the course of the simulation, since the CHEQ model allows the charges to fluctuate. We have calculated the interfacial dipole potential, which the CHEQ model predicts to be 0.95 V compared to 0.86 V as predicted by the C27r model. We also discuss dielectric permittivity profiles and the differences arising between the two models. We obtain bulk values of 72.77 for the CHEQ model (TIP4P-FQ water) and 91.22 for C27r (TIP3P), and values approaching unity in the membrane interior. Finally, we present results of simulations of gA embedded in a DMPC bilayer using the CHEQ model and discuss structural properties.
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影响因子：
3.3
作者：
Davis, Joseph E.;Warren, G. Lee;Patel, Sandeep
通讯作者：
Patel, Sandeep
影响因子：
5.5
作者：
Ensing, Bernd;Nielsen, Steven O.;Parrinello, Michele
通讯作者：
Parrinello, Michele
影响因子：
4.4
作者：
Chelli, R;Procacci, P
通讯作者：
Procacci, P
影响因子：
3
作者：
BROOKS, BR;BRUCCOLERI, RE;KARPLUS, M
通讯作者：
KARPLUS, M
影响因子：
--
作者：
Aliste MP;Tieleman DP
通讯作者：
Tieleman DP