经验分子力学力场如何很好地模拟胆固醇凝结效应?

IF 3.1 2区 化学 Q3 CHEMISTRY, PHYSICAL Journal of Chemical Physics Pub Date : 2025-01-28 DOI:10.1063/5.0238409
J Sawdon, T J Piggot, J W Essex
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引用次数: 0

摘要

膜的性质部分由脂质组成决定,而胆固醇在决定这些性质方面起着很大的作用。细胞膜显示出多种胆固醇组成,其影响包括细胞生物力学、脂筏形成、膜融合、信号通路、代谢、药物治疗效果和疾病发病的改变。此外,胆固醇在非细胞膜中起重要作用,其在皮肤脂质基质中的浓度与几种皮肤病有关。在磷脂膜中,胆固醇增加了邻近脂质的尾部排序,减少了膜的侧向面积,增加了膜的厚度。这种侧面区域的减少,被称为胆固醇凝结效应,是由于胆固醇-脂质混合物偏离了理想的混合。捕获胆固醇凝聚效应对于分子动力学模拟至关重要,因为它直接影响预测膜特性的准确性,这对于理解膜功能至关重要。我们对几种常用力场中的胆固醇模型进行了比较分析:CHARMM36、Slipids、Lipid17、GROMOS 53A6L、GROMOS- ckp、MARTINI 2、MARTINI 3和ELBA。对不同胆固醇浓度的1,2-二myristoyl- n-glycero-3-phosphocholine (DMPC)和1,2-dioleoyl- n-glycero-3-phosphocholine (DOPC)膜进行了模拟,计算了胆固醇的部分分子面积和其他凝聚参数,并与实验数据进行了对比验证。虽然所有测试的力场都预测了胆固醇- dopc膜中理想混合的小负偏差,但只有全原子力场捕获了DMPC膜中预期的较大偏差。联合原子模型和粗粒度模型低估了这种效应,将较少的相邻脂质压缩到较小的量级,导致与理想混合的偏差太小。这些结果表明,全原子力场,特别是CHARMM36或sliids,应该用于精确模拟含胆固醇膜。
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How well do empirical molecular mechanics force fields model the cholesterol condensing effect?

Membrane properties are determined in part by lipid composition, and cholesterol plays a large role in determining these properties. Cellular membranes show a diverse range of cholesterol compositions, the effects of which include alterations to cellular biomechanics, lipid raft formation, membrane fusion, signaling pathways, metabolism, pharmaceutical therapeutic efficacy, and disease onset. In addition, cholesterol plays an important role in non-cellular membranes, with its concentration in the skin lipid matrix being implicated in several skin diseases. In phospholipid membranes, cholesterol increases the tail ordering of neighboring lipids, decreasing the membrane lateral area and increasing the thickness. This reduction in the lateral area, known as the cholesterol condensing effect, results from cholesterol-lipid mixtures deviating from ideal mixing. Capturing the cholesterol condensing effect is crucial for molecular dynamics simulations as it directly affects the accuracy of predicted membrane properties, which are essential for understanding membrane function. We present a comparative analysis of cholesterol models across several popular force fields: CHARMM36, Slipids, Lipid17, GROMOS 53A6L, GROMOS-CKP, MARTINI 2, MARTINI 3, and ELBA. The simulations of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) membranes with varying cholesterol concentrations were conducted to calculate the partial-molecular areas of cholesterol and other condensing parameters, which are compared to the experimental data for validation. While all tested force fields predict small negative deviations from ideal mixing in cholesterol-DOPC membranes, only all-atom force fields capture the larger deviations expected in DMPC membranes. United-atom and coarse-grained models under-predict this effect, condensing fewer neighboring lipids by smaller magnitudes, resulting in too small deviations from ideal mixing. These results suggest that all-atom force fields, particularly CHARMM36 or Slipids, should be used for accurate simulations of cholesterol-containing membranes.

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来源期刊
Journal of Chemical Physics
Journal of Chemical Physics 物理-物理:原子、分子和化学物理
CiteScore
7.40
自引率
15.90%
发文量
1615
审稿时长
2 months
期刊介绍: The Journal of Chemical Physics publishes quantitative and rigorous science of long-lasting value in methods and applications of chemical physics. The Journal also publishes brief Communications of significant new findings, Perspectives on the latest advances in the field, and Special Topic issues. The Journal focuses on innovative research in experimental and theoretical areas of chemical physics, including spectroscopy, dynamics, kinetics, statistical mechanics, and quantum mechanics. In addition, topical areas such as polymers, soft matter, materials, surfaces/interfaces, and systems of biological relevance are of increasing importance. Topical coverage includes: Theoretical Methods and Algorithms Advanced Experimental Techniques Atoms, Molecules, and Clusters Liquids, Glasses, and Crystals Surfaces, Interfaces, and Materials Polymers and Soft Matter Biological Molecules and Networks.
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