title: Molecular dynamics study of Na⁺ transportation in a cyclic peptide nanotube and its influences on water behaviors in the tube.
abstract: 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.
authors.affiliation: Faculty of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, 215123, People's Republic of China.
authors.forename: Xuezeng
authors.initials: X
authors.lastname: Song
authors.forename: Jianfen
authors.initials: J
authors.lastname: Fan
authors.forename: Dongyan
authors.initials: D
authors.lastname: Liu
authors.forename: Hui
authors.initials: H
authors.lastname: Li
authors.forename: Rui
authors.initials: R
authors.lastname: Li
mesh_terms: D002462:Cell Membrane / Q000737:chemistry; D002463:Cell Membrane Permeability; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D056004:Molecular Dynamics Simulation; D043942:Nanotubes / Q000737:chemistry*; D010456:Peptides, Cyclic / Q000737:chemistry*; D012964:Sodium / Q000737:chemistry*; D061210:Sodium Ionophores / Q000737:chemistry*; D013816:Thermodynamics; D014867:Water / Q000737:chemistry*
chemical_list: D010456:Peptides, Cyclic; D061210:Sodium Ionophores; D014867:Water; D012964:Sodium
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