Single-channel water permeabilities of Escherichia coli aquaporins AqpZ and GlpF

Abstract

From equilibrium molecular dynamics simulations we have determined single-channel water permeabilities for Escherichia coli aquaporin Z (AqpZ) and aquaglyceroporin GlpF with the channels embedded in lipid bilayers. GlpF's osmotic water permeability constant pf exceeds by 2-3 times that of AqpZ and the diffusive permeability constant (pd) of GlpF is found to exceed that of AqpZ 2-9-fold. Achieving complete water selectivity in AqpZ consequently implies lower transport rates overall relative to the less selective, wider channel of GlpF. For AqpZ, the ratio pf/pd congruent with 12 is close to the average number of water molecules in the channel lumen, whereas for GlpF, pf/pd congruent with 4. This implies that single-file structure of the luminal water is more pronounced for AqpZ, the narrower channel of the two. Electrostatics profiles across the pore lumens reveal that AqpZ significantly reinforces water-channel interactions, and weaker water-water interactions in turn suppress water-water correlations relative to GlpF. Consequently, suppressed water-water correlations across the narrow selectivity filter become a key structural determinant for water permeation causing luminal water to permeate slower across AqpZ.

FIGURE 1

Simulation snapshot of AqpZ/POPE at t = 26.5 ns. Lipid molecules are displayed without hydrogen atoms. Selected water molecules permeating two of the four monomers are displayed in red and white.

FIGURE 2

Representative illustration of the collective coordinate n (Eqs. 5–6) as a function of simulation time for GlpF/POPC (a). Mean-square displacement of n, 〈n²〉 (Eq. 7) for GlpF/POPC (b) and for AqpZ/POPE (c).

FIGURE 3

Number of permeation events along +z and –z and their sum, i.e., N₊, N_–, and N_± displayed as a function of time for two representative systems, AqpZ/POPE (a) and GlpF/POPC (b). For GlpF/POPC (b), the vertical gray line delineates onset for elimination of headgroup charges; only the first 20 ns were included in the calculation of p_d (see text and Eq. 4). Panel c displays trajectories of selected permeation events for GlpF/POPC where the large number of permeation events (>150) allows for accurate estimation of the mean permeation (passage) time 〈τ〉 required to traverse the channel from one channel boundary to the other. The mean passage time through this constriction region is related to the number of unidirectional permeation events as 〈τ〉 = k₀⁻¹. The mean positions of the channel boundaries defining are delineated with dashed lines and taken as the average z-positions of R-206:H_η and G-65:O; z = −1.4 Å and z = 18.3 Å, respectively.

FIGURE 4

Dynamics of the SF in AqpZ(H-174:NH_δ). (a) Simulation snapshots of luminal water molecules, SF residues R-189, T-183, H-174, and of N-63 and N-186 of the NPA motifs. Some atoms have been omitted for clarity. The side chain of R-189 is seen to exist in three configurational states: “down”, “mid”, and “up”, according to the value of the dihedral angle . These states are depicted in left, central, and right panels, respectively. Instantaneous values of are given as insets. The side chain of H-174 is in a down configuration classified by means of (see also Fig. 5). (b) Dynamic behavior of of R-189 for the four monomers M1–M4 in the simulation of AqpZ(His-174:NH_δ).

FIGURE 5

Water disruption and configuration of the SF in AqpZ(His-174:NH_ε). (a) Simulation snapshots of the SF residues as in Fig. 4 a. The water file is hydrogen bonded across the SF region in the left panel whereas the hydrogen bonded network is disrupted in the right panel, despite an up configuration of the R-189 side chain (cf. Fig. 4 a). The side chain of H-174 is in an up configuration with (cf. Fig. 4 a). (b) Distributions of the dihedral angles of R-189 ( H-174 (), and F-43 () for all simulations of AqpZ. Distributions are annotated with u, m, d, c, and o for “up”, “mid”, “down”, “open”, and “closed”, respectively (see also Fig. 6).

FIGURE 6

Gating in the SF in AqpZ(His-174:NH ). (a) Simulation snapshots of the SF residues as in Fig. 4 a. The F-43 side chain is shown instead of T-183. Some atoms have been omitted for clarity. For a protonated state of H-174, the R-189 side chain seemingly exists in only two states, mid and up (cf. Fig. 4 a). The mid configuration is depicted here. Instantaneous values of are given as insets. The H-174 side chain is consistently the up configuration with The F-43 side chain, classified by means of exists in two states: parallel (“open”; left panel) and perpendicular (“closed”; right panel) to the channel axis. The latter blocks the periplasmic half-channel between the SF and the NPA region. (b) Dynamic behavior of of F-43 for the four monomers M1–M4 in AqpZ(His-174:NH_δ,ε). The open (parallel) orientation is seen to dominate (cf. Fig. 5 b). for R-189 is shown for reference.

FIGURE 7

Simulation snapshots of the water conducting part of AqpZ(His-174:NH_δ) (a) and GlpF (c) with the luminal water molecules lined up in the respective constriction regions as single files displayed along with channel radius profiles (b) computed using HOLE (55). The radius profiles are averages over 7000 configurations taken from the last part of the simulations and separated by 2 ps. Origin of the z axis was taken as the center between the asparagine N_δ atoms of the NPA motifs. Mean radii and root mean-square deviations from the mean computed within the constriction region (CR), 〈r〉_CR, are given for AqpZ and GlpF as insets in a and c, respectively. The bipolar configuration of the water molecules in a and c results from the electrostatic environment inside the channel and it ensures that protons cannot be conducted across aquaglyceroporins (,,,,–61).

FIGURE 8

Water-channel and water-water electrostatics profiles within the lumen of AqpZ(His-174:NH_δ) and GlpF (a) (for both embedded in POPE bilayers; results for the channels embedded in POPC bilayers are quantitatively similar and therefore not shown). The profiles were obtained from Eq. 9 by considering all water molecules residing within the lumen of the channel at time t and computing the sum of (untruncated) Coulombic interactions with the surrounding monomer (i.e., channel-luminal water interactions) as well as with other water molecules residing within the lumen of the channel (i.e., luminal water-luminal water interactions). The electrostatic energy (E(z)) was assigned to a position z along the channel axis by using the O atom position of that water whose electrostatic interaction was in question. Averaging was over 5000 configurations separated by 5 ps. Averaging over monomers provides the mean electrostatic energy E(z) with variance . Standard errors (SE) in E(z) are given as , with n_m = 4 being the number of monomers. Origin of z axis was taken as in Fig. 7 b. (b) Water-water correlation for AqpZ(His-174:NH_δ) and GlpF. Representative root mean-square deviations from the mean in the correlation profiles are shown for GlpF/POPC and AqpZ/POPC and obtained from the variances among 30, 500-ps-wide time windows. Origin of z axis was taken as in Fig. 7 b. Correlations were only computed within the constriction region according to Eq. 10.