title: Water permeation dynamics of AqpZ: a tale of two states.
abstract: Molecular dynamics simulations of aquaporin Z homotetramer which is a membrane protein facilitating rapid water movement through the plasma membrane of Escherichia coli were performed. Initial configurations were taken from the open and closed states of crystal structures separately. The resulting water osmotic permeability (pf) and diffusive permeability (pd) displayed distinct features. Consistent with previous studies, the side chain conformation of arginine189 was found to mediate the water permeability. A potential of mean force (PMF) as a function of the distance between NH1 of R189 and carbonyl oxygen of A117 was constructed based on the umbrella sampling technique. There are multiple local minima and transition states on the PMF. The assignment of the open or closed state was supported by the permeability pf, calculated within trajectories in umbrella sampling simulations. Our study disclosed a detailed mechanism of the gated water transport.
authors.affiliation: School of Civil and Environmental Engineering, Nanyang Technological University, Singapore.
authors.forename: Lin
authors.initials: L
authors.lastname: Xin
authors.forename: Haibin
authors.initials: H
authors.lastname: Su
authors.forename: Claus Helix
authors.initials: CH
authors.lastname: Nielsen
authors.forename: Chuyang
authors.initials: C
authors.lastname: Tang
authors.forename: Jaume
authors.initials: J
authors.lastname: Torres
authors.forename: Yuguang
authors.initials: Y
authors.lastname: Mu
mesh_terms: D000409:Alanine / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D019943:Amino Acid Substitution; D020346:Aquaporins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D001120:Arginine / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D001692:Biological Transport; D002462:Cell Membrane / Q000378:metabolism*; D002463:Cell Membrane Permeability; D004926:Escherichia coli / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D009154:Mutation; D009995:Osmosis; D009997:Osmotic Pressure; D011487:Protein Conformation; D012694:Serine / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D014867:Water / Q000737:chemistry / Q000378:metabolism*
chemical_list: D020346:Aquaporins; D029968:Escherichia coli Proteins; C106425:aqpZ protein, E coli; D014867:Water; D012694:Serine; D001120:Arginine; D000409:Alanine