Configurational entropies of lipids in pure and mixed bilayers from atomic-level and coarse-grained molecular dynamics simulations
Configurational entropies of lipids in pure and mixed bilayers from atomic-level and coarse-grained molecular dynamics simulations
复制标题
DOI：
10.1021/jp061627s
复制
发表时间：
2006-08-10
影响因子：
3.3
通讯作者：
van Gunsteren, Wilfred F.
中科院分区：
文献类型：
--
作者：
Baron, Riccardo;de Vries, Alex H.;van Gunsteren, Wilfred F.
使用准调和近似从分子动力学模拟中评估水合脂质双层中脂质尾部的单链和单片段构型熵。获得沿各个酰基尾部的熵分布，并将其与液相中相应烃链的熵分布进行比较。我们考虑纯二棕榈酰磷脂酰胆碱和混合二油酰磷脂酰胆碱/二油酰磷脂酰乙醇胺双层。这些系统以不同的空间分辨率级别进行建模：在原子级（AL）模型中，所有（重）原子都被明确模拟；在粗粒度 (CG) 模型中，使用代表共价键原子组的粒子（珠子），将大约四个非氢原子映射到一个相互作用位点。比较单链和单片段熵以及（单）酰基链运动之间的相关性。 AL 模型和 CG 模型的灵活性之间存在良好的对应关系。估计由于模型粗粒度时自由度数减少而导致的构型熵损失。 CG 模型显示链熵的收敛速度比更详细的 AL 模型快约 4 倍。发现 CG 模型对准调和熵估计的修正很小。对于 AL 模型，由模式非谐性引起的校正很小，但由成对（超线性）模式相关性引起的校正相当大。
Single-chain and single-fragment configurational entropies of lipid tails in hydrated lipid bilayers are evaluated from molecular dynamics simulations using the quasi-harmonic approximation. The entropy distribution along individual acyl tails is obtained and compared to that of corresponding hydrocarbon chains in the liquid phase. We consider pure dipalmitoylphosphatidylcholine and mixed dioleoylphosphatidylcholine/dioleoylphosphatidylethanolamine bilayers. The systems are modeled at different levels of spatial resolution: In an atomic-level (AL) model all (heavy) atoms are explicitly simulated; in a coarse-grained (CG) model particles (beads) representing groups of covalently bound atoms are used, which map approximately four non-hydrogen atoms to one interaction site. Single-chain and single-fragment entropies and correlations between the motions of ( single) acyl chains are compared. A good correspondence is found between the flexibility of the AL and CG models. The loss in configurational entropy due to the reduction in the number of degrees of freedom upon coarse-graining of the model is estimated. The CG model shows about 4 times faster convergence of the chain entropies than the more detailed AL model. Corrections to the quasi-harmonic entropy estimates were found to be small for the CG model. For the AL model, the correction due to mode anharmonicities is small, but the correction due to pairwise (supralinear) mode correlations is sizable.