Residue-Specialized Membrane Poration Kinetics of Melittin and Its Variants: Insight from Mechanistic Landscapes

Pore-forming peptides have promising potentials for biomedical uses due to their ability to permeabilize cell membranes. However, to molecularly engineer them for practical applications is still blocked by the poor understanding of the specific roles of individual residues in peptides' activity. Herein, using an advanced computational approach that combines Coarse-Grained molecular dynamics and well-tempered metadynamics, the membrane activities of melittin, a representative pore-forming peptide, and its gain-of-function variants, are characterized from the kinetics and thermodynamics perspectives. Unbiased simulations elucidate the molecular details of peptide-induced membrane poration; during which, some vital intermediate states, including the aggregation and U-shape configuration formation of peptides in the membrane, are observed and further applied as collective variables to construct the multi-dimensional free energy landscapes of the peptide membrane interactions. Such a combination of kinetic and thermodynamic descriptions of the interaction process provides crucial information of residue-specialized contribution in chain conformation and consequently membrane perforation ability of the peptide. It is found that residues at the kink part (e.g. Thr) determine the chain flexibility and U-shape bending of the peptide, while residues near the C-terminus (e.g. Arg and Lys) are responsible for recruiting neighboring peptides for inter-molecular cooperation; the probable reaction pathway and the poration efficiency are consequently regulated. These results are helpful for a comprehensive understanding of the complicated molecular mechanism of pore-forming peptides and pave the way to rationally design and/or engineer the peptides for practical applications.