TCB Publications - Abstract

Fangqiang Zhu, Emad Tajkhorshid, and Klaus Schulten. Theory and simulation of water permeation in aquaporin-1. Biophysical Journal, 86:50-57, 2004. (PMC: 1303818)

ZHU2004 The paper starts with a detailed discussion of the difference between osmotic permeability $p_f$ and diffusion permeability $p_d$ of single- file water channels, demonstrating that the $p_f/p_d$ ratio corresponds to the number of effective steps a water molecule needs to take to permeate the channel. While $p_d$ can be directly obtained from equilibrium molecular dynamics simulations, $p_f$ must be 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 here a method to induce in molecular dynamics simulations a hydrostatic pressure difference across the membrane, from which $p_f$ can be measured. Simulations using this method are performed on aquaporin-1 channels in a lipid bilayer, resulting in a calculated $p_f$ of 7.1$\times$10$^{-14}$cm$^3$/s, which is in close agreement with observation. Using a previously determined $p_d$ value, we conclude that $p_f/p_d$ for aquaporin-1 measures about 12. This number is explained in terms of channel architecture and conduction mechanism.

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