Branching Suppresses Self-Aggregation while Preserving Membrane Association in SET-M33: An Atomistic Molecular Dynamics Study

Abstract

Branched antimicrobial peptides offer a promising strategy for improving the stability and activity of membrane-active peptides, but how branching alters self-association and membrane binding remains unclear. We used all-atom molecular dynamics simulations to compare tetra-branched SET-M33 with its linear branch sequence Q33 (KKIRVRLSA) in water and at an anionic bacterial-membrane model, to do this, systems containing equivalent numbers of Q33 sequence units were simulated. Q33 formed dimers and higher-order oligomers, particularly at the membrane interface and under hydration-tuned enhanced sampling. In contrast, SET-M33 remained more dispersed, as the branched scaffold and its high cationic charge limited peptide-peptide association while allowing multivalent membrane binding. Both architectures associated rapidly with the bilayer but remained predominantly surface-bound, without persistent pore formation or complete insertion. Q33 showed stronger membrane-induced helical stabilization, whereas SET-M33 retained a more heterogeneous conformational ensemble. Overall, branching primarily altered lateral peptide organization while preserving close membrane association, suppressing uncontrolled self-aggregation and providing an atomistic rationale for the distinct behavior of SET-M33 relative to Q33.