Paper Citing NAMD - Abstract
Comer, Jeffrey; Dehez, Francois; Cai, Wensheng; Chipot, Christophe
Water Conduction through a Peptide Nanotube
JOURNAL OF PHYSICAL CHEMISTRY C, 117:26797-26803, DEC 19 2013
When inserted into lipid bilayers, synthetic channels formed by cyclic peptides of alternated D- and L-alpha-amino acids have been shown to modulate the permeability of the cell wall, thereby endowing them with potential bactericidal capability. Details of the underlying energetics of the permeation events remain, however, only fragmentary. Water conduction in a peptide nanotube formed by eight cyclo-(LW)(4) subunits embedded in a fully hydrated palmitoyloleylphosphatidylcholine bilayer has been investigated using molecular-dynamics simulations with a time-dependent bias. The topology of the reconstructed free-energy landscape delineating the transport of water mirrors the arrangement of the cyclic peptides in the open-ended tubular structure. Within the nanotube, the small, periodic free-energy barriers, on the order of k(B)T, arising between adjacent peptide subunits, are suggestive of unhampered translocation. It still remains that translational diffusion of water in the hollow cylindrical cavity is necessarily affected by its interaction with the accessible polar moieties of the constituent D- and L-alpha-amino acids. By combining diffusivity measurements with the free-energy landscape, we put forth a reaction-rate theory to describe the conduction kinetics of water inside the peptide nanotube.
