Dependences of water permeation through cyclic octa-peptide nanotubes on channel length and membrane thickness.

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 × (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 (~L(-2.0)). Energetic analysis showed that a series of water binding sites exist in these transmembrane PNTs, with the barriers of ~3k(B)T, which elucidates the tendency of p(f) well. Water diffusion permeability (p(d)) exhibits a relationship of ~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 × (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.

Molecular dynamics study of Na⁺ transportation in a cyclic peptide nanotube and its influences on water behaviors in the tube.

The dynamics of Na(+) transportation in a transmembrane cyclic peptide nanotube of 8 × (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 α-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 α-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.