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Comparative Study
. 2004 Jan;86(1 Pt 1):50-7.
doi: 10.1016/S0006-3495(04)74082-5.

Theory and simulation of water permeation in aquaporin-1

Fangqiang Zhu  1 , Emad Tajkhorshid, Klaus Schulten
Affiliations
Comparative Study

Theory and simulation of water permeation in aquaporin-1

Fangqiang Zhu et al. Biophys J. 2004 Jan.

Abstract

We discuss the difference between osmotic permeability pf and diffusion permeability pd of single-file water channels and demonstrate that the pf/pd ratio corresponds to the number of effective steps a water molecule needs to take to permeate a channel. While pd can be directly obtained from equilibrium molecular dynamics simulations, pf can be best determined from simulations in which a chemical potential difference of water has been established on the two sides of the channel. In light of this, we suggest a method to induce in molecular dynamics simulations a hydrostatic pressure difference across the membrane, from which pf can be measured. Simulations using this method are performed on aquaporin-1 channels in a lipid bilayer, resulting in a calculated pf of 7.1 x 10(-14) cm(3)/s, which is in close agreement with observation. Using a previously determined pd value, we conclude that pf/pd for aquaporin-1 measures approximately 12. This number is explained in terms of channel architecture and conduction mechanism.

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Figures

FIGURE 1
FIGURE 1
Illustration of the method to produce a pressure difference in MD simulations. The two membranes shown in the figure are “images” of each other under periodic boundary conditions. A constant force f is exerted on water molecules in region III.
FIGURE 2
FIGURE 2
Side view of the unit cell including the AQP1 tetramer, POPE lipid molecules, and water molecules. The protein is shown in tube representation; lipids in line representation (hydrogen atoms not shown); phosphorus atoms of lipids are drawn as vdW spheres; water molecules are shown in line representation, with those in region III (see Fig. 1) colored blue.
FIGURE 3
FIGURE 3
Water density distribution along the z-direction in region III (within the dashed lines) and part of regions I and II. Data points marked by circles, diamonds, stars, and squares represent sim1, sim2, sim3, and sim4, respectively. The density is measured by averaging the number of water molecules within a 1-Å thick slab over the last 4 ns of each trajectory.
FIGURE 4
FIGURE 4
(a) An AQP1 monomer with channel water and nearby bulk water. Water molecules in the constriction (single-file) region, the vestibules of the channel, and in the bulk are rendered in vdW, CPK, and line representations, respectively. The two bars indicate the 15-Å long region in which water movement is analyzed as described in the text. (b) Trajectories (from sim1) of seven water molecules in the constriction region during 500 ps.
FIGURE 5
FIGURE 5
Trajectories of the collective coordinate X for water molecules in the defined region in an AQP1 monomer, determined as described in the text. The four curves were obtained from simulations sim1, sim2, sim3, and sim4, respectively.
FIGURE 6
FIGURE 6
The dependence of water flux on the applied pressure difference. Values of pressure differences and water fluxes are taken from Tables 1 and 3, respectively. A line with the best-fit slope for the four data points is also shown in the figure.
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