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Investigating Hydrophilic Pores in Model Lipid Bilayers using Molecular Simulations: Correlating Bilayer Properties with Pore Formation Thermodynamics

机译：使用分子模拟研究模型脂质双层中的亲水孔：将双层性能与孔形成热力学相关

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摘要

Cell-penetrating and antimicrobial peptides show remarkable ability to translocate across physiological membranes. Along with factors such as electric potential induced-perturbations of membrane structure and surface tension effects, experiments invoke pore-like membrane configurations during the solute transfer process into vesicles and cells. The initiation and formation of pores are associated with a non-trivial free energy cost, thus necessitating consideration of the factors associated with pore formation and attendant free energetics. Due to experimental and modeling challenges related to the long timescales of the translocation process, we use umbrella-sampling molecular dynamics simulations with a lipid-density based order parameter to investigate membrane pore-formation free energy employing Martini coarse-grained models. We investigate structure and thermodynamic features of the pore in 18 lipids spanning a range of head-groups, charge states, acyl chain lengths and saturation. We probe the dependence of pore-formation barriers on area per lipid, lipid bilayer thickness, membrane bending rigidities in three different lipid classes. The pore formation free energy in pure bilayers and peptide translocating scenarios are significantly coupled with bilayer thickness. Thicker bilayers require more reversible work to create pores. Pore formation free energy is higher in peptide-lipid systems relative to the peptide-free lipid systems due to penalties to maintain solvation of charged hydrophilic solutes within the membrane environment.
机译：细胞穿透肽和抗菌肽表现出显着的跨生理膜转运的能力。除了诸如电势引起的膜结构扰动和表面张力效应等因素外，实验还在溶质转移到囊泡和细胞的过程中调用了孔状膜结构。孔的引发和形成与不平凡的自由能成本相关，因此必须考虑与孔形成和伴随的自由能有关的因素。由于与迁移过程的长时程相关的实验和建模挑战，我们使用基于脂质密度的阶跃参数的伞式采样分子动力学模拟，以马蒂尼粗粒模型研究膜孔形成自由能。我们研究了18个脂质中的孔的结构和热力学特征，这些脂质跨越了一系列的头基，电荷状态，酰基链长度和饱和度。我们探讨了三种不同脂质类别中孔形成障碍对每个脂质面积，脂质双层厚度，膜弯曲刚度的依赖性。纯双层和肽易位情况下的孔形成自由能与双层厚度显着相关。较厚的双层需要更多可逆的工作才能产生毛孔。相对于不含肽的脂质系统，肽-脂质系统中的孔形成自由能更高，这是因为要在膜环境中保持带电亲水性溶质的溶剂化。

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