Supporting MD trajectories for the paper "In Situ Captured Antibacterial Action of Membrane-Incising Peptide Lamellae"

Source data and molecular dynamic trajectories for the article "In Situ Captured Antibacterial Action of Membrane-Incising Peptide Lamellae" New compounds with unique mechanisms of action are needed to combat the growing issue of antimicrobial resistance. Supramolecular assemblies, which combine the complex membrane attacking mechanisms of natural host defense peptides with the improved biostability of non-natural compounds offer a promising alternative to current small molecule antibiotics. However, for such membrane-targeting compounds the direct visual insight on the toxic agents in bacteria is still lacking. To this end, we employed a design strategy focusing on an inducible assembly mechanism and utilized electron microscopy (EM) to follow the formation of supramolecular peptide structures triggered by bacterial cell surface lipopolysaccharides (LPS). Inspired by the alternating chirality backbone pattern of some effective peptide antimicrobials, we designed lysine-rich heterochiral β3-peptides, termed lamellin-2K and lamellin-3K, with optimal residual spacing for enhanced coordination on the phosphate groups of LPS. Combined molecular dynamics simulations (MD), EM and bacterial assays confirmed that the phosphate-induced conformational change of these lamellins led to the formation of thin, striped lamellar layers, where each stripe represents double arrays of H-bonded peptide molecules that are interconnected by phosphate ions. EM micrographs of Gram-negative bacteria show that the lamellae incised the cell envelope, while leakage and antibacterial activity assays prove that growth inhibition starts already at submicromolar concentrations. Detailed image analysis demonstrated that the lamellae penetrating deep into the bacterial cell have a rather uniform size distribution and, surprisingly, only a few of these supramolecules are sufficient to cause major cell wall damage making them efficient in destroying target cells. Our findings also provide a missing mechanistic link for membrane-targeting agents, connecting how the antibiotic mechanism is built up from individual molecules through on-site formation of the active supramolecules that lead to bactericidal activity. Molecular dynamics trajectories from the production runs of single beta-peptide strands in water + 150 mM NaCl + 50:1 MePO4^(2-):peptide. Altogether 8 runs were performed, each one starting from a different helical conformation (H10, H12 and H14, both positive and negative winding) of the peptide. In the first half (500 ns) of the simulation, the intra-chain hydrogen bonds responsible for the actual helix were kept together by distance restraints. In the second half (again 500 ns), these restraints were instantaneously lifted and the system was left to evolve from the same state. In all cases the helical structure unwound in a very short time (under 100 ns), and did not refold in any helix.本数据集为论文《原位捕获膜切割肽片层的抗菌作用》("In Situ Captured Antibacterial Action of Membrane-Incising Peptide Lamellae")配套的源数据与分子动力学轨迹。 针对日益严峻的抗菌耐药性问题，亟需开发作用机制独特的新型化合物。超分子组装体将天然宿主防御肽复杂的膜攻击机制与非天然化合物优异的生物稳定性相结合，为当前的小分子抗生素提供了极具前景的替代方案。然而，对于这类靶向膜结构的化合物，学界仍缺乏对其细菌内毒性作用因子的直接可视化观测证据。为此，本研究采用聚焦于诱导组装机制的设计策略，并借助电子显微镜（electron microscopy, EM）追踪由细菌细胞表面脂多糖（lipopolysaccharides, LPS）触发的肽超分子结构形成过程。受部分高效肽类抗菌剂交替手性骨架模式的启发，我们设计了富含赖氨酸的异手性β3-肽（β3-peptide），将其命名为lamellin-2K与lamellin-3K，其残基间距经过优化，可增强与LPS磷酸基团的配位作用。结合分子动力学模拟（molecular dynamics simulations, MD）、电子显微镜成像与细菌实验证实：这些lamellin的构象经磷酸根诱导发生改变后，会形成薄片状条纹层结构，每条条纹代表由磷酸离子相互连接的氢键结合肽分子双阵列。革兰氏阴性菌的电子显微镜显微图像显示，该肽片层可切割细菌细胞包膜；渗漏实验与抗菌活性实验则证明，在亚微摩尔浓度下即可启动生长抑制作用。详细的图像分析表明，深入细菌细胞内部的肽片层具有较为均一的尺寸分布，且令人意外的是，仅需少量这类超分子组装体即可造成严重的细胞壁损伤，使其能高效破坏靶标细胞。本研究结果还为靶向膜结构的抗菌剂填补了一项机制空白，阐明了抗菌作用如何由单个分子通过活性超分子组装体的原位形成逐步构建，最终发挥杀菌活性。 本数据集包含单条β3-肽链在水+150 mM氯化钠+50:1 甲基磷酸根（MePO₄²⁻）与肽的摩尔比体系下的生产模拟分子动力学轨迹。共计开展8组模拟，每组均从该肽的不同螺旋构象（H10、H12、H14，涵盖正向与反向缠绕形式）起始。模拟的前半阶段（500 ns），通过距离约束维持形成螺旋结构所需的链内氢键；后半阶段（同样为500 ns），立即解除上述约束，使体系从同一初始状态自行演化。所有模拟中，螺旋结构均在极短时间内（100 ns以内）解旋，且未重新折叠为任何螺旋构象。