Paper Citing NAMD - Abstract
Song, Xuezeng; Fan, Jianfen; Liu, Dongyan; Li, Hui; Li, Rui
Molecular dynamics study of Na+ transportation in a cyclic peptide nanotube and its influences on water behaviors in the tube
JOURNAL OF MOLECULAR MODELING, 19:4271-4282, OCT 2013
The dynamics of Na+ transportation in a transmembrane cyclic peptide nanotube of 8 x (WL)(4)/POPE has been simulated. The curve of PMF (potential of mean force) for Na+ moving through the tube, based on ABF (adaptive biasing force) method, indicates that Na+ possesses lower free energy in an alpha-plane region than in a mid-plane one. It was found that Na+ would desorb one or two water molecules in the first solvation shell when entering the tube and later maintain in a solvation state. The average numbers of water molecules around Na+ are 4.50, 4.09 in the first solvation shell, and 3.10, 4.08 in the second one for Na+ locating in an alpha-plane zone and a mid-plane region, respectively. However, water molecules far away from Na+ location still nearly arrange in a form of 1-2-1-2 file. The dipole orientations of water molecules in the regions of gaps 1 and 7 display "D-defects", resulted from the simultaneous electrostatic potentials generated by Na+ and the bare carbonyls at the tube mouths. Such "D-defects" accommodate the energetically favorable water orientations thereby.
