Figure 1.
Structure of human AQP5 and the simulated tetrameric systems.
(A) Tertiary structure of the crystallographic HsAQP5 (PDB databank code 3D9S) [22]. Secondary structure consists of six plus two halves of transmembrane helices connected by loops (all colored differently). Crystallographic water oxygens are shown as red balls, while important residues in the ar/R constricted selectivity filter (SF) and NPA motif regions – highlighted in darker ellipses – are shown in licorice representation, with carbons in cyan, oxygens in red, and nitrogens in blue. Panels (B) and (C) show a top view of the fully equilibrated tetramers with and without the central POPS lipid, respectively. Each channel of the tetramer is shown in a different color. Lipids are shown in line representation, with phosphorus atoms as tan balls. The central lipid is shown in ball representation with atoms colored the same as in (A). Water molecules and hydrogen atoms were removed for clarity. All renderings were done in VMD [69].
Figure 2.
Order parameters characterizing the states of the selectivity filter (SF) and of the cytoplasmic end (CE).
(A) Evolution of D1 order parameter (distance between -nitrogen (NE2) of His173 ring and backbone oxygen (O) of Ser183) show transitions between wide and narrow states in the selectivity filter, which are mainly caused by the His173’s ring reorientation (see inset). (B) D2 order parameter (distance between the
-carbon (CB) of His67 and CD carbon of Ile165) shows that CE region can be characterized by open (green channel) and closed (the other channels) states. Transitions to intermediate states of D2 (6.5 Å to 7.5 Å) are correlated with His67’s sidechain orientation (see inset).
Figure 3.
Structural view of the states of the SF and CE regions.
Side view sections of (A) structure having SF and CE regions in the wide and open states (i.e., water-conducting), and of (B) structure with SF and CE regions in the narrow and closed states. Cyan wireframe surfaces show spaces occupied by water, with explicit molecular models (oxygen in red and hydrogen in white) near and inside the channel. For clarity protein is shown in yellow cartoon representation. In orange and magenta are shown the loops that go through major changes on the extracellular side and CE region, respectively (see details in the text). Residues used in order parameter definitions in the SF (His173, Ser183) and CE (His67, Ile165) regions are shown in licorice representation. Zoom on the SF region of wide (C) and narrow (E) states, and on the CE region of the open (D) and closed (F) states. Representations are kept the same as in (A) and (B). For clarity, waters were removed and protein color is the same as in previous plots. All renderings were done in VMD [69].
Table 1.
Single channel osmotic and diffusive permeabilities and
in units of
calculated over representative sections of simulations with or without central lipid that represent best the state of the SF and CE regions.
Figure 4.
HsAQP5 water permeation and population.
(A) Cumulative number of water molecule permeations as a function of time through each channel (averaged over positive and negative permeations). The regions highlighted with thick lines represent the time periods of interest, specified by the two-letter code. The first letter indicates the status of the SF (W - wide, N - narrow), while the second that of the CE region (O - open, C - closed). These portions were fit by linear functions to extract the permeation rates, shown in the legend. (B) – (E) As in panel (A), we highlighted the regions of interest and used them to extract the average number of waters in a channel in that specific state . These averages are listed in Table 1 of the main text.
Figure 5.
Comparison emphasizing the state of the cytoplasmic side gate (): closed (dotted line), intermediate (dashed lines) and open (solid). In the SF region (
) for radii greater than 1.1 Å the pore is in the wide state. Below, the pore corresponds to the narrow state.