Biomolecular simulations of membranes:: Physical properties from different force fields
Biomolecular simulations of membranes:: Physical properties from different force fields
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DOI：
10.1063/1.2897760
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发表时间：
2008-03-28
影响因子：
4.4
通讯作者：
Boeckmann, Rainer A.
中科院分区：
文献类型：
--
作者：
Siu, Shirley W. I.;Vacha, Robert;Boeckmann, Rainer A.
磷脂力场对于人工双层、膜的模拟以及膜蛋白的模拟都具有重要意义。在这里，我们比较了两个最适用于磷脂，全原子CHARMM 27和联合原子Berger力场，与一个新开发的全原子广义琥珀色力场（GAFF）二油酰磷脂酰胆碱分子的原子力场。只有后者显示实验观察到的两个酰基链之间的C2原子的顺序的差异。对于所有力场，脂羰基区域和本体水相之间的界面水动力学平稳地增加;然而，水的顺序和与它的跨双层的静电势表现出明显的力场之间的差异。Berger和GAFF都低估了脂质的自扩散。GAFF为生物膜的原子尺度模拟提供了一致的力场。(C)2008年美国物理学会。
Phospholipid force fields are of ample importance for the simulation of artificial bilayers, membranes, and also for the simulation of integral membrane proteins. Here, we compare the two most applied atomic force fields for phospholipids, the all-atom CHARMM27 and the united atom Berger force field, with a newly developed all-atom generalized AMBER force field (GAFF) for dioleoylphosphatidylcholine molecules. Only the latter displays the experimentally observed difference in the order of the C2 atom between the two acyl chains. The interfacial water dynamics is smoothly increased between the lipid carbonyl region and the bulk water phase for all force fields; however, the water order and with it the electrostatic potential across the bilayer showed distinct differences between the force fields. Both Berger and GAFF underestimate the lipid self-diffusion. GAFF offers a consistent force field for the atomic scale simulation of biomembranes. (C) 2008 American Institute of Physics.