OPLS4的固态核磁共振验证:pc -脂质双分子层的结构及其脱水调节

IF 2.9 2区 化学 Q3 CHEMISTRY, PHYSICAL
Milla Kurki, Alexey M. Nesterenko, Nicolai E. Alsaker, Tiago M. Ferreira, Sami Kyllönen, Antti Poso, Piia Bartos and Markus S. Miettinen*, 
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引用次数: 0

摘要

原子分子动力学(MD)模拟是一种常用的研究生物膜结构和动力学的原子分辨率的工具。所得到的表示的有效性取决于MD模型(力场)的准确性和真实感。在这里,我们根据原子分辨率实验数据评估了Schrödinger, Inc.的专有OPLS4力场,并将其性能与CHARMM36进行了比较,CHARMM36是性能最好的公开力场之一。作为基准,我们使用高分辨率核磁共振(NMR)的C-H键序参数──通过MD模拟直接可靠地计算──在不同水合条件下测量磷脂酰胆碱(PC)脂质双层。比较了两个脱水数据集:来自文献的饱和(1,2-二肉豆醇酰基磷脂酰胆碱,DMPC)脂质双分子层和这里测量的不饱和(1-棕榈酰2-油基磷脂酰胆碱,POPC)脂质双分子层。我们的研究结果表明,OPLS4相当好地再现了pc -脂质双分子层的结构和脱水反应,甚至略优于CHARMM36。这两个模型的主要不准确性出现在(1)甘油主链和不饱和碳段的阶参数大小和(2)与实验相比,PC头基对脱水的结构响应在质量上存在差异。总之,这项工作强调了独立验证(专有)力场的重要性,并强调了OPLS4和CHARMM36在描述生物膜方面的惊人相似性和细微差异。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Solid-State NMR Validation of OPLS4: Structure of PC-Lipid Bilayers and Its Modulation by Dehydration

Atomistic molecular dynamics (MD) simulations are a much-used tool for investigating the structure and dynamics of biomembranes with atomic resolution. The validity of the representations obtained is determined by the accuracy and realism of the MD model (force field). Here, we evaluated the proprietary OPLS4 force field of Schrödinger, Inc. against atomic-resolution experimental data, and compared its performance to CHARMM36, one of the best-performing openly available force fields. As a benchmark, we used high-resolution nuclear magnetic resonance (NMR) order parameters for C–H bonds─directly and reliably calculable from MD simulations─measured in phosphatidylcholine (PC) lipid bilayers under varying hydration conditions. Comparisons were made with two dehydration data sets: for saturated (1,2-dimyristoylphosphatidylcholine, DMPC) lipid bilayers from the literature and for unsaturated (1-palmitoyl-2-oleoylphosphatidylcholine, POPC) lipid bilayers measured here. Our findings indicate that OPLS4 reproduces the structure and dehydration response of PC-lipid bilayers fairly well, even slightly outperforming CHARMM36. Both models’ main inaccuracies appear in (1) the order parameter magnitudes in the glycerol backbone and unsaturated carbon segments and (2) the qualitatively differing structural response of the PC headgroup to dehydration compared to experiments. In summary, this work underscores the importance of independent validation for (proprietary) force fields and highlights the striking similarities and nuanced differences between OPLS4 and CHARMM36 in describing biomembranes.

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来源期刊
CiteScore
5.80
自引率
9.10%
发文量
965
审稿时长
1.6 months
期刊介绍: An essential criterion for acceptance of research articles in the journal is that they provide new physical insight. Please refer to the New Physical Insights virtual issue on what constitutes new physical insight. Manuscripts that are essentially reporting data or applications of data are, in general, not suitable for publication in JPC B.
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