TCB Publications - Abstract

Jerome Henin, Emad Tajkhorshid, Klaus Schulten, and Christophe Chipot. Diffusion of glycerol through Escherichia coli aquaglyceroporin GlpF. Biophysical Journal, 94:832-839, 2008. (PMC: 2186255)

HENI2008 The glycerol uptake facilitator, GlpF, a major intrinsic protein found in Escherichia coli, conducts selectively water and glycerol across the inner membrane. The free energy landscape characterizing the assisted transport of glycerol by this homotetrameric aquaglyceroporin has been explored by means of equilibrium molecular dynamics over a time scale spanning 0.12$\mu$s. In order to overcome the free energy barriers of the conduction pathway, an adaptive biasing force (ABF) is applied to the glycerol molecule confined in each of the four channels. The results illuminate the critical role played by intramolecular relaxation on the diffusion properties of the permeant. The present free energy calculations reveal that glycerol tumbles and isomerizes on a time scale comparable to that spanned by its ABF-assisted conduction in GlpF. As a result, reorientation and conformational equilibrium of glycerol in GlpF constitute a bottleneck in the molecular simulations of the permeation event. A profile characterizing the position-dependent diffusion of the permeant has been determined, allowing reaction rate theory to be applied for investigating conduction kinetics based on the measured free energy landscape.

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