Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, 06269.
J Comput Chem. 2017 Jun 15;38(16):1462-1471. doi: 10.1002/jcc.24694. Epub 2017 Jan 19.
The PACE force field presents an attractive model for conducting molecular dynamics simulations of membrane-protein systems. PACE is a hybrid model, in which lipids and solvents are coarse-grained consistent with the MARTINI mapping, while proteins are described by a united atom model. However, given PACE is linked to MARTINI, which is widely used to study membranes, the behavior of proteins interacting with membranes has only been limitedly examined in PACE. In this study, PACE is used to examine the behavior of several peptides in membrane environments, namely WALP peptides, melittin and influenza hemagglutinin fusion peptide (HAfp). Overall, we find PACE provides an improvement over MARTINI for modeling helical peptides, based on the membrane insertion energetics for WALP16 and more realistic melittin pore dynamics. Our studies on HAfp, which forms a helical hairpin structure, do not show the hairpin structure to be stable, which may point toward a deficiency in the model. © 2017 Wiley Periodicals, Inc.
PACE 力场为膜蛋白体系的分子动力学模拟提供了一个有吸引力的模型。PACE 是一种混合模型，其中脂质和溶剂与 MARTINI 映射一致地进行粗粒化，而蛋白质则用统一原子模型来描述。然而，鉴于 PACE 与 MARTINI 相关联，而 MARTINI 被广泛用于研究膜，因此 PACE 中仅有限地研究了与膜相互作用的蛋白质的行为。在这项研究中，PACE 用于研究几种肽在膜环境中的行为，即 WALP 肽、蜂毒素和流感血凝素融合肽（HAfp）。总的来说，我们发现 PACE 为建模螺旋肽提供了比 MARTINI 更好的改进，这基于 WALP16 的膜插入能和更现实的蜂毒素孔动力学。我们对形成螺旋发夹结构的 HAfp 的研究表明，该发夹结构不稳定，这可能表明该模型存在缺陷。 © 2017 威利父子公司
