Park Soohyung, Rice Amy, Im Wonpil, Pastor Richard W
Departments of Biological Sciences and Chemistry, Lehigh University, Bethlehem, Pennsylvania, USA.
Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA.
J Comput Chem. 2024 Apr 5;45(9):512-522. doi: 10.1002/jcc.27261. Epub 2023 Nov 22.
Peptides and proteins play crucial roles in membrane remodeling by inducing spontaneous curvature. However, extracting spontaneous curvatures from simulations of asymmetric bilayers is challenging because differential stress (i.e., the difference of the leaflet surface tensions) arising from leaflet area strains can vary substantially among initial conditions. This study investigates peptide-induced spontaneous curvature in asymmetric bilayers consisting of a single lipid type and a peptide confined to one leaflet; is calculated from the Helfrich equation using the first moment of the lateral pressure tensor and an alternative expression using the differential stress. It is shown that differential stress introduced during initial system generation is effectively relaxed by equilibrating using P2 periodic boundary conditions, which allows lipids to switch leaflets across cell boundaries and equalize their chemical potentials across leaflets. This procedure leads to robust estimates of for the systems simulated, and is recommended when equality of chemical potentials between the leaflets is a primary consideration.
肽和蛋白质通过诱导自发曲率在膜重塑中发挥关键作用。然而，从不对称双层膜的模拟中提取自发曲率具有挑战性，因为由小叶面积应变引起的微分应力（即小叶表面张力的差异）在初始条件之间可能有很大变化。本研究调查了由单一脂质类型和局限于一个小叶的肽组成的不对称双层膜中肽诱导的自发曲率；使用横向压力张量的一阶矩根据赫尔弗里希方程计算，并使用微分应力的另一种表达式计算。结果表明，在初始系统生成过程中引入的微分应力通过使用P2周期性边界条件进行平衡而有效松弛，这使得脂质能够跨细胞边界切换小叶并使它们在小叶之间的化学势相等。该过程导致对所模拟系统的自发曲率进行稳健估计，并且当小叶之间化学势相等是主要考虑因素时推荐使用。
