Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, Kazan, 420111, Russian Federation.
Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, Kazan, 420111, Russian Federation.
J Mol Graph Model. 2019 Mar;87:1-10. doi: 10.1016/j.jmgm.2018.11.003. Epub 2018 Nov 13.
Transmembrane pores play an important role in various cell processes. However, the detailed structures of these pores and their influence on the membrane properties remain undetermined. We performed microsecond coarse-grained molecular dynamics simulations to study the interaction of cationic β-structural peptides with multicomponent lipid bilayers consisting of two types of anionic (POPS, POPI) and two types of zwitterionic (POPE, POPC) lipids. The formation of semitoroidal pores was analyzed from a standpoint of self-organization of lipids and peptides. Our results showed that semitoroidal pores were mainly formed by POPI molecules with a strong negative charge. We found that peptide aggregation is a necessary step of pore formation; single peptide is unable to stabilize the semitoroidal pore. To characterize the influence of semitoroidal pores on membrane properties, we evaluated the bilayer thickness, the two-dimensional density maps of lipids, the deuterium order parameters, and the lateral diffusion coefficients of lipids. The pore formation induced perturbation of the phospholipid organization in membrane and facilitated the organization of zones with different electrostatic potential.
跨膜孔在各种细胞过程中起着重要作用。然而，这些孔的详细结构及其对膜性质的影响仍未确定。我们进行了微秒粗粒度分子动力学模拟，以研究阳离子β结构肽与由两种阴离子（POPS、POPI）和两种两性离子（POPE、POPC）脂质组成的多组分脂质双层的相互作用。从脂质和肽的自组织的角度分析了半环形孔的形成。我们的结果表明，半环形孔主要由带强负电荷的 POPI 分子形成。我们发现肽聚集是孔形成的必要步骤；单个肽无法稳定半环形孔。为了表征半环形孔对膜性质的影响，我们评估了双层厚度、脂质的二维密度图、氘序参数和脂质的横向扩散系数。孔形成诱导了磷脂在膜中的组织扰动，并促进了具有不同静电势的区域的组织。
