Molecular dynamics simulations of histidine-containing cod antimicrobial peptide paralogs in self-assembled bilayers

摘要: Gaduscidin-1 and -2 (GAD-1 GAD-2) are antimicrobial peptides (AMPs) that contain several histidine residues thus expected to exhibit pH-dependent activity. In order help elucidate their mechanism of membrane disruption, we have performed molecular dynamics simulations with the in both histidine-charged histidine-neutral forms, along 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid molecules. The employed GROMACS software an OPLS-AA force field. Initially, peptide lipids were placed randomly simulation box then allowed self-assemble. results demonstrated a marked preference for regions sequential pairs associate closely bilayer pores. This is observed even when histidines uncharged form. It appears relative compactness rigidity require more aqueous disordered environment pores satisfy hydrophilic interactions. final structures exhibited wide variety topologies, most helical positioning parallel surface less ordered interacting pore. Thus, give atomistic insight into those models AMP promote importance structural heterogeneity imperfect amphipathicity activity selectivity.