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Aquaporin water channels, present in cell membranes, function as passive conduits for osmotically or hydrostatically-driven water transport.Mechanism and dynamics of water transport through channel proteins aquapofin-1 (AQP1), aquaporin0 (AQP0) and artificial nanochannels based on molecular dynamics simulations are presented.Free energy profiles and correlation coefficients of the water molecules within the proteins show that the tyrosine residue TYR23 of AQP0, pointing to the pore, disrupts the single-file transport of water molecules, which in turn causes the water transport rate one order of magnitude lower than that ofAQP1.Through detailed analysis of the van der Waals and electrostatic interactions between the protein and the water molecules within the pore, we find that the constriction region consisting of conservative aromatic/Arg (ar/R) residues, where presents the minimal protein-water, water-water interaction energies in both channels, is essential to the transport of water molecules.Meanwhile, the conservative Asn-Pro-Ala (NPA) region, where electrostatic interaction is dominant, presents energy barriers in both channels and impacts on the proton exclusion of aquaporins basically.