We use all-atom molecular dynamics simulations on a massive scale to compute the standard binding free energy of the 13-residue antimicrobial peptide indolicidin to a lipid bilayer. The analysis of statistical convergence reveals systematic sampling errors that correlate with reorganization of the bilayer on the microsecond timescale and persist throughout a total of 1.4 ms of sampling. Consistent with experimental observations, indolicidin induces membrane thinning, although the simulations significantly overestimate the lipophilicity of the peptide.

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Identifying the mechanisms responsible for the interaction of peptides with cell membranes is critical to the design of new antimicrobial peptides and membrane transporters. We report here the results of a computational simulation of the interaction of the 13-residue peptide indolicidin with single-phase lipid bilayers of dioleoylphosphatidylcholine, distearoylphosphatidylcholine, dioleoylphosphatidylglycerol, and distearoylphosphatidylglycerol. Ensemble analysis of the membrane-bound peptide revealed that, in contrast to the extended, linear backbone structure reported for indolicidin in sodium dodecyl sulphate detergent micelles, the peptide adopts a boat-shaped conformation in both phosphatidylglycerol and phosphatidylcholine lipid bilayers, similar to that reported for dodecylphosphocholine micelles. In agreement with fluorescence and NMR experiments, simulations confirmed that the peptide localizes in the membrane interface, with the distance between phosphate headgroups of each leaflet being reduced in the presence of indolicidin. These data, along with a concomitant decrease in lipid order parameters for the upper-tail region, suggest that indolicidin binding results in membrane thinning, consistent with recent in situ atomic force microscopy studies.

Recent work has demonstrated that imaging platforms based on the integration of total internal reflection fluorescence microscopy (TIRFM)/spectroscopy with scanning probe microscopy are well-suited for investigations of biological phenomena, ranging from lipid bilayer dynamics and membrane protein assembly to cellular dynamics and structures. We have shown that this approach is particularly compelling for studies of protein-membrane interactions. While this functional imaging strategy has proved to be very useful for studies of cell dynamics, and most recently, in the study of single-molecule dynamics by TIRF-AFM-based force spectroscopy, a number of key challenges remain to be resolved.