Paper Citing NAMD - Abstract
Zhang, Y. B.; Chen, L. Y.
In silico study of Aquaporin V: Effects and affinity of the central pore-occluding lipid
BIOPHYSICAL CHEMISTRY, 171:24-30, JAN 2013
Because of its roles in human physiology, Aquaporin V (AQP5), a major intrinsic protein, has been a subject of many in vitro studies. In particular, a 2008 experiment produced its crystal structure at 2.0 angstrom resolution, which is in a tetrameric conformation consisting of four protomers. Each protomer forms an amphipathic pore that is fit for water permeation. The tetramer has a pore along its quasi-symmetry axis formed by quadruplets of hydrophobic residues (every protomer contributes equally to the quadruplets). A lipid, phosphatidylserine (PS6), is bound to AQP5 in the central pore, totally occluding it. A 2009 experiment showed that AQP5 facilitates not only permeation of water but also permeation of hydrophobic gas molecules across the cell membrane. In this article, we present an in silico study of AQP5 to elucidate the effects of PS6's binding to and dissociating from AQP5's central pore. Computing the lipid's chemical-potential along its dissociation path, we find that PS6 inhibits the function of the central pore with an IC50 in the micromolar range. Examining the central pore and the interstices between two adjacent protomers, we propose that nonpolar gas molecules (O-2) permeate through AQP5's hydrophobic central pore when un-occluded. (C) 2012 Elsevier B.V. All rights reserved.
