Pore formation by membrane-active peptides, naturally encountered in innate immunity and infection, could have important medical and technological applications. Recently, the well-studied lytic peptide melittin has formed the basis for the development of combinatorial libraries from which potent pore-forming peptides have been derived, optimized to work under different conditions. We investigate three such peptides, macrolittin70, which is most active at neutral pH; pHD15, which is active only at low pH; and MelP5_Δ6, which was rationally designed to be active at low pH but formed only small pores. There are three, six, and six acidic residues in macrolittin70, pHD15, and MelP5_Δ6, respectively. We perform multi-microsecond simulations in 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) of hexamers of these peptides starting from transmembrane orientations at neutral pH (all residues at standard protonation), low pH (acidic residues and His protonated), and highly acidic environments in which C-termini are also protonated. Previous simulations of the parent peptides melittin and MelP5 in 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) are repeated in POPC. We find that the most potent pore-forming peptides exhibit strong interpeptide interactions, including salt bridges, H-bonds, and polar interactions. Protonation of the C-terminus promotes helicity and pore size. The proximity of the peptides allows fewer lipid headgroups to line the pores than in previous simulations, making the pores intermediate between barrel stave and toroidal. Based on these structures and geometrical arguments, we attempt to rationalize the factors that under different conditions can increase or decrease pore stability and propose mutations that could be tested experimentally.

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什么是好的成孔剂：合成蜂毒肽衍生物的研究

在先天免疫和感染中自然遇到的膜活性肽的孔形成可能具有重要的医学和技术应用。最近，经过充分研究的裂解肽蜂毒肽已成为开发组合文库的基础，从中衍生出有效的成孔肽，并优化在不同条件下工作。我们研究了三种这样的肽，macrolittin70，它在中性 pH 值下最活跃；pHD15，仅在低pH值下才有效；和 MelP5_Δ6，它被合理设计为在低 pH 值下具有活性，但仅形成小孔。在macrolittin70、pHD15和MelP5_Δ6中分别有3个、6个和6个酸性残基。我们在这些肽的六聚体的 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) 中进行多微秒模拟，从中性 pH（标准质子化的所有残基）、低 pH（酸性残基）的跨膜方向开始和 His 质子化），以及 C 端也被质子化的高酸性环境。先前在 1,2-二肉豆蔻酰-sn-甘油-3-磷酸胆碱 (DMPC) 中对母肽蜂毒肽和 MelP5 的模拟在 POPC 中重复。我们发现最有效的成孔肽表现出很强的肽间相互作用，包括盐桥、H 键和极性相互作用。C-末端的质子化促进了螺旋度和孔径。与之前的模拟相比，肽的接近允许更少的脂质头基排列在毛孔中，使孔介于桶壁和环形之间。基于这些结构和几何参数，我们试图合理化在不同条件下可以增加或减少孔稳定性的因素，并提出可以通过实验测试的突变。