Observation of Mechanical and Kinetic Distinctions between Individual Isoleucine and Arginine Residues in a Peptide Dissociating from a Model Lipid Bilayer

Abstract

Peptide–lipid membrane interactions underlie many essential biological processes, yet the molecular determinants of peptide partitioning and dissociation from lipid bilayers remain incompletely understood. Here, we combine coarse-grained molecular dynamics (CG MD) simulations and atomic force microscopy (AFM)-based force spectroscopy to study the structural dynamics, energetics, and kinetics of penta-X5 peptides (WLLLX, with X = R or I) interacting with POPC bilayers. To elucidate how the position and identity of a single guest residue X modulates peptide–membrane interactions, we present these results in the context of the canonical Wimley–White penta-X (WLXLL) motif. Our findings from CG simulations are consistent with penta-X5 peptides adopting snorkeling conformations beneath the bilayer surface and with a dissociation scenario in which the final two or three residues detach almost simultaneously under the applied pulling force. Ensemble analyses of the reconstructed potential of mean force profiles lead to multiple energetic dissociation pathways. In combination with kinetic modeling of AFM rupture force distributions, the data reveal that both the mechanics (dissociation force) and kinetics (off rate) of peptide detachment are sensitive to the identity and sequence position of individual residues. These results highlight the power of integrating CG MD and single-molecule force spectroscopy to unravel residue-specific, sequence-dependent factors underlying peptide–lipid interactions.