Sodt Alexander J, Beaven Andrew H, Andersen Olaf S, Im Wonpil, Pastor Richard W
Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland.
Department of Chemistry, The University of Kansas, Lawrence, Kansas.
Biophys J. 2017 Mar 28;112(6):1198-1213. doi: 10.1016/j.bpj.2017.01.035.
To change conformation, a protein must deform the surrounding bilayer. In this work, a three-dimensional continuum elastic model for gramicidin A in a lipid bilayer is shown to describe the sensitivity to thickness, curvature stress, and the mechanical properties of the lipid bilayer. A method is demonstrated to extract the gramicidin-lipid boundary condition from all-atom simulations that can be used in the three-dimensional continuum model. The boundary condition affects the deformation dramatically, potentially much more than typical variations in the material stiffness do as lipid composition is changed. Moreover, it directly controls the sensitivity to curvature stress. The curvature stress and hydrophobic surfaces of the all-atom and continuum models are found to be in excellent agreement. The continuum model is applied to estimate the enrichment of hydrophobically matched lipids near the channel in a mixture, and the results agree with single-channel experiments and extended molecular dynamics simulations from the companion article by Beaven et al. in this issue of Biophysical Journal.
为了改变构象，蛋白质必须使周围的双层膜变形。在这项工作中，脂质双层中短杆菌肽A的三维连续弹性模型被证明可以描述对脂质双层厚度、曲率应力和力学性质的敏感性。展示了一种从全原子模拟中提取可用于三维连续模型的短杆菌肽 - 脂质边界条件的方法。该边界条件对变形有显著影响，可能比随着脂质组成变化时材料刚度的典型变化影响更大。此外，它直接控制对曲率应力的敏感性。发现全原子模型和连续模型的曲率应力及疏水表面非常吻合。连续模型被用于估计混合物中通道附近疏水匹配脂质的富集情况，结果与单通道实验以及本期《生物物理杂志》中Beaven等人的配套文章中的扩展分子动力学模拟结果一致。
