Free Energy Analysis\nof Peptide-Induced Pore Formation\nin Lipid Membranes by Bridging Atomistic and Coarse-Grained Simulations

Antimicrobial peptides (AMPs) are attractive materials\nfor combating\nthe antimicrobial resistance crisis because they can kill target microbes\nby directly disrupting cell membranes. Although thousands of AMPs\nhave been discovered, their molecular mechanisms of action are still\npoorly understood. One broad mechanism for membrane disruption is\nthe formation of membrane-spanning hydrophilic pores which can be\nstabilized by AMPs. In this study, we use molecular dynamics simulations\nto investigate the thermodynamics of pore formation in model single-component\nlipid membranes in the presence of one of three AMPs: aurein 1.2,\nmelittin and magainin 2. To overcome the general challenge of modeling\nlong time scale membrane-related behaviors, including AMP binding,\nclustering, and pore formation, we develop a generalizable methodology\nfor sampling AMP-induced pore formation. This approach involves the\nlong equilibration of peptides around a pore created with a nucleation\ncollective variable by performing coarse-grained simulations, then\nbackmapping equilibrated AMP-membrane configurations to all-atom resolution.\nWe then perform all-atom simulations to resolve free energy profiles\nfor pore formation while accurately modeling the interplay of lipid–peptide–solvent\ninteractions that dictate pore formation free energies. Using this\napproach, we quantify free energy barriers for pore formation without\ndirect biases on peptides or whole lipids, allowing us to investigate\nmechanisms of pore formation for these 3 AMPs that are a consequence\nof unbiased peptide diffusion and clustering. Further analysis of\nsimulation trajectories then relates variations in pore lining by\nAMPs, AMP-induced lipid disruptions, and salt bridges between AMPs\nto the observed pore formation free energies and corresponding mechanisms.\nThis methodology and mechanistic analysis have the potential to generalize\nbeyond the AMPs in this study to improve our understanding of pore\nformation by AMPs and related antimicrobial materials.