Paper Citing NAMD - Abstract
Liu, Jian; Fan, Jianfen; Cen, Min; Song, Xuezeng; Liu, Dongyan; Zhou, Weiqun; Liu, Zhao; Yan, Jianfeng
Dependences of Water Permeation through Cyclic Octa-peptide Nanotubes on Channel Length and Membrane Thickness
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 52:2132-2138, AUG 2012
Effects of the channel length and membrane thickness on the water permeation through the transmembrane cyclic octa-peptide nanotubes (octa-PNTs) have been studied by molecular dynamics (MD) simulations. The water osmotic permeability (p(f)) through the PNTs of k x (WL)(4)/POPE (1-palmitoyl-2-oleoyl-glycerophosphoethanolamine; k = 6, 7, 8, 9, and 10) was found to decay with the channel length (L) along the axis (similar to L-2.0). Energetic analysis showed that a series of water binding sites exist in these transmembrane PNTs, with the barriers of similar to 3k(B)T, which elucidates the tendency of p(f) well. Water diffusion permeability (p(d)) exhibits a relationship of similar to L-1.8, which results from the novel 1-2-1-2 structure of water chain in such Confined nanolumens: In the range of simulation accuracy, the ratio (p(f)/p(d)) of the water osmotic and diffusion permeability is approximately a constant. MD simulations of water permeation through the transmembrane PNTs of 8 x (WL)(4)/octane with the different octane membrane thickness revealed that the water osmotic and diffusion permeability (p(f) and p(d)) are both independent of the octane membrane thickness, confirmed by the weak and nearly same interactions between the channel water and octane membranes with the different thickness. The results may be helpful for revealing the permeation mechanisms of biological water channels and designing artificial nanochannels.
