Facilitated water permeation through narrow biological channels is fundamental for all forms of life. This process involves dehydration of bulk water entering the single-file region and hydrogen bond formation with channel lining amino acid residues. Despite its significance in health and disease as well as for biotechnological applications the energetics of water permeation are still elusive. Whereas the enthalpic contribution to Gibbs free energy is readily accessible via temperature dependent water permeability measurements, estimation of the entropic contribution requires information on the temperature dependence of the rate of water permeation. By means of accurate activation energy measurements of water permeation through AQP1 and by determining the accurate single channel permeability we were, for the first time, able to estimate the entropic barrier of water permeation through a narrow biological channel. This is a first step in understanding the energetic contributions in various biological and artificial channels exhibiting vastly different pore geometries.

GROMACS, 2020, 2021

Files and structures for performing and analysing molecular dynamics simulations of water permeation through AQP1 and AQPZ embedded in a model of E. Coli PLE. If you use E. Coli PLE please also cite doi:10.1186/s12915-020-00936-8. You can find additional files and scripts for E Coli PLE on my github https://github.com/KristynaPluhackova/MD_models_Ecoli-PLE