Paper Citing NAMD - Abstract
Liu, Jian; Fan, Jianfen; Tang, Min; Zhou, Weiqun
Molecular Dynamics Simulation for the Structure of the Water Chain in a Transmembrane Peptide Nanotube
JOURNAL OF PHYSICAL CHEMISTRY A, 114:2376-2383, FEB 18 2010
The structure of the water chain in the 8 x cyclo-(W (L) under bar)(4) peptide nanotube embedded in the POPE lipid bilayer is studied by molecular dynamics simulations. The distribution profiles of water molecules along the nanotube axis proposes a wavelike pattern of the water chain in the nanotube, arraying in the form of a 1-2-1-2 file, in contrast to the single file in other nanochannels studied widely. Cylindrical distribution functions of water at different zones and potential of mean force of a water molecule along the axis suggest that the primary reason for forming the water-chain pattern is steric constraints. A novel hydrogen bond network in the nanotube is present such that each water in the alpha-plane zones forms two hydrogen bonds (as a donor) with the two water molecules in the adjacent midplane zone, and each water molecule in the midplane zones forms one hydrogen bond with the water molecule in the adjacent a-plane zone and a poor hydrogen bond with the carbonyl groups in the nanotube. Strong orientations of the water dipoles near the two opening ends pointing to the opposite directions are found, and the potential energy of a water O or H atom along the axis is explored to explain the water dipole orientations' reversing in the nanotube. Defects of the hydrogen bond network exist in the central gaps of the cyclic peptide nanotube.
