掲載種別：研究論文（学術雑誌）   出版者・発行元：American Chemical Society (ACS)  

DOI： 10.1021/jacs.3c00389

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掲載種別：研究論文（学術雑誌）  

We conducted a series of coarse-grained molecular dynamics (CG-MD) simulations to investigate the complicated actions of melittin, which is an antimicrobial peptide (AMP) derived from honey bee venom, on a lipid membrane. To accurately simulate the AMP action, we developed and used a protein CG model as an extension of the pSPICA force field (FF), which was designed to reproduce several thermodynamic quantities and structural properties. At a low peptide-to-lipid (P/L) ratio (1/102), no defect was detected. At P/L = 1/51, toroidal pore formation was observed due to collective insertion of multiple melittin peptides from the N-termini. The pore formation was initiated by a local increase in membrane curvature in the vicinity of the peptide aggregate. At a higher P/L ratio (1/26), two more modes were detected, seemingly not controlled by the P/L ratio but by a local arrangement of melittin peptides: 1. Pore formation accompanied by lipid extraction by melittin peptides:a detergent-like mechanism. 2. A rapidly formed large pore in a significantly curved membrane: bursting. Thus, we observed three pore formation modes (toroidal pore formation, lipid extraction, and bursting) depending on the peptide concentration and local arrangement. These observations were consistent with experimental observations and hypothesized melittin modes. Through this study, we found that the local arrangements and population of melittin peptides and the area expansion rate by membrane deformation were key to the initiation of and competition among the multiple pore formation mechanisms.

DOI： 10.1016/j.bbamem.2022.183955

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掲載種別：研究論文（学術雑誌）   出版者・発行元：American Chemical Society (ACS)  

DOI： 10.1021/acs.jctc.1c01207

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掲載種別：研究論文（学術雑誌）  

We present a coarse-grained (CG) force field (FF), pSPICA, for lipid membranes that incorporates a CG polar water model, which guarantees a reasonable dielectric response for water. Using a relatively simple functional form for the interaction, the CG parameters were systematically optimized to reproduce surface/interfacial tension, density, solvation or transfer free energy, as well as distribution functions obtained from all-atom molecular dynamics trajectory generated with the CHARMM FF, following the scheme used in the SPICA FF. Lipid membranes simulated using the present CG FF demonstrate reasonable membrane area and thickness, elasticity, and line tension, which ensure that the simulated lipid membranes exhibit proper mesoscopic morphology. The major advantages of the pSPICA FF with a polar water model were its ability to simulate membrane electroporation and its superior performance in the morphological characterization of charged lipid aggregates. We also demonstrated that the pSPICA can better describe the membrane permeation of hydrophilic segments involving a water string formation.

DOI： 10.1021/acs.jctc.9b00946

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掲載種別：研究論文（学術雑誌）  

We combined two reverse mapping methods, a predetermined fragment database and fragment rotation, to generate atomistic configurations from coarse-grained structures. The combined method together with molecular dynamics simulations was applied to simulate perfluorosulfonic acid (PFSA) membranes with large length scales and to explore the origin of fracture under a uniaxial tensile loading. Through the analysis of voids in the deformed membrane, we found that void growth with tensile loading takes place at the boundary of the hydrophobic and hydrophilic regions, which may be the origin of the fracture in the PFSA membrane. This study demonstrates an efficient reverse mapping method, which is useful for simulating proton exchange membranes with realistic chain lengths.

DOI： 10.1016/j.polymer.2019.121766

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