BP100, a short antimicrobial peptide, can form transmembrane pores

BP100 (H-KKLFKKILKYL-NH2) is a short-cationic antimicrobial peptide with high antimicrobial efficiency and low toxicity to mammalian cells. The proposed action mechanisms of antimicrobial peptides include the stave barrel pore, the toroidal pore, and the carpet-type membrane destruction. Previous results suggest that BP100 acts by different mechanisms at low and high peptide/lipid ratios (P/L). At low P/L, the peptide would be inserted into the membrane, causing local thinning and water penetration. At high P/L, BP100 would act through a carpet mechanism. However, the possibility of BP100 forming pores has yet to be considered. We conducted comprehensive research using molecular dynamics simulations to address this gap. All simulations used Gromacs 2022. Amber ff99sb-ildn-nmrforce field was used for BP100 and Slipids force field for the lipids. Using PackMol, twelve peptides were put together to form a cylinder-shaped structure. CHARMM-GUI was then used to put together the membrane pore in a bilayer with 128 1-palmitoyl-2-oleoyl-sn-glycero-3-[phospho-rac-(1-glycerol)] (POPG) molecules per leaflet. The system was relaxed for 100 ns with position restraints on the peptide backbone. The system was then simulated for 3 µs with no restraints. The membrane thickness was computed with SuAVE 2.0, the number of waters crossing the membrane was computed with LOOS, and the number of peptides inside the pore was calculated with a custom MDAnalysis script. The number of peptides inside the pore fluctuated around six and was highly dynamic, with peptides getting in and out of the pore. The number of waters crossing the membrane decreased within the first 500 ns from 20 waters/ns to around 2/ns. The pore remained stable for the 3 µs of simulation and displayed a highly dynamic structure. The computed pore structure is consistent with the disordered toroidal was proposed in previous works. Therefore, the disordered toroidal pore could be an additional mechanism of action for BP100.

This work was supported by: Conselho Nacional de Desenvolvimento Científico e Tecnológico, CNPq, 140663/2022-3; CNPq, 465259/2014-6, CNPq-304155/2021-7, Fundação de Amparo à Pesquisa do Estado de São Paulo, FAPESP, 2014/50983-3, the Coordination for the Improvement of Higher Education Personnel (CAPES) and the National Institute of Science and Technology Complex Fluids (INCT-FCx).