Paper Citing NAMD - Abstract
Dehez, Francois; Tarek, Mounir; Chipot, Christophe
Energetics of ion transport in a peptide nanotube
JOURNAL OF PHYSICAL CHEMISTRY B, 111:10633-10635, SEP 13 2007
Ion channels constitute an important family of integral membrane proteins responsible for the regulation of ion transport across the cell membrane. Yet, the underlying energetics of the permeation events and how the latter are modulated by the environment, specifically near the mouth of the pore, remain only partially characterized. Here, a synthetic membrane channel formed by cyclic peptides of alternated D- and L-hydrophobic (alpha-amino acids was considered. The free energy delineating the translocation of a sodium ion was measured along the conduction pathway by means of molecular dynamics simulations. The free-energy profiles that underly the permeation of the open-ended tubular structure are shown to not only depend on the characteristics of the latter but also inherently on the location of the mouth of the synthetic channel with respect to the membrane surface.
