Paper Citing NAMD - Abstract
Liu, Dongyan; Fan, Jianfen; Song, Xuezeng; Li, Rui; Li, Hui
MD simulations on the influences of an external force on the water transportation behavior through a cyclic peptide nanotube
COMPUTATIONAL MATERIALS SCIENCE, 78:47-54, OCT 2013
Steered molecular dynamics (SMD) simulations have been performed to study the gating mechanism of water permeation across a transmembrane peptide nanotube of 8 x cyclo-(W (L) under bar)(4)/POPE under an external force (0-2.0 nN) exerted on the C-5 atom of the P4 subunit. The results show that the diameter deformation quantity (delta(C3-C7)) of the P4 subunit increases with the augmentation of force. Because of the H-bonded interactions between the adjacent peptide subunits, the P3 and P5 subunits on both sides of the P4 subunit also have certain deformations. The structural deformation of the nanotube framework directly leads to a change in the water-chain structure, which causes the water molecular configuration in the zones between the P3 and P5 subunits to become different from that in the other regions of the nanotube. The free energies [G(N)] of different water molecular occupancies (N) under individual external forces indicate that the optimal number of water molecules changes from 22 to 18 when the external force increases to 2.0 nN. The H-bonded water-chain would be gradually destroyed with the increase of force. Due to the simultaneous formation of H-bonds between the two H atoms of a water molecule and the carbonyl oxygen atoms of the cyclic peptide nanotube (cyclic PNT) framework, the water molecular dipole orientations in the region between the P3 and P4 subunits tend to be more directed. The water flow in the nanotube decreases to zero under an external force of 2.0 nN, which indicates that the cyclic PNT was completely closed. These findings would likely cast light on the study of the response of water permeation through a nanotube to an external force. Crown Copyright (c) 2013 Published by Elsevier B.V. All rights reserved.
