@article{8454fc6b8c00477fb853c0d70fea13eb,
title = "Diffusion of glycerol through Escherichia coli aquaglyceroporin GlpF",
abstract = "The glycerol uptake facilitator, GlpF, a major intrinsic protein found in Escherichia coli, selectively conducts 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 timescale spanning 0.12 ms. To overcome the free energy barriers of the conduction pathway, an adaptive biasing force 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. These free energy calculations reveal that glycerol tumbles and isomerizes on a timescale comparable to that spanned by its adaptive-biasing-force-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.",
author = "J{\'e}r{\^o}me H{\'e}nin and Emad Tajkhorshid and Klaus Schulten and Christophe Chipot",
note = "Glycerol conduction in GlpF has been investigated from the perspective of unprecedented equilibrium free energy calculations executed over a timescale spanning 0.12 μ s. Compared to shorter, irreversible pulling experiments, the length of these simulations and their reversible character allow the permeant to reorient and isomerize freely as it diffuses slowly through the conduction pathway. The simulations further illuminate that orientational and conformational relaxation of glycerol and its ABF-assisted transport along the tripathic channels span comparable timescales. The structure of the free energy profile characterizing GlpF permeation by glycerol is qualitatively simple and features a single free energy barrier located at the SF. The height of the free energy barrier separating the periplasmic vestibule from the NPA motif, initially modulated by the original orientation of glycerol in the channel, converges after appropriate sampling toward the experimentally determined activation energy (17) . In this respect, these free energy calculations constitute an important, albeit still incomplete step toward the full understanding of glycerol diffusion in GlpF. Of particular interest are the symptomatic quasi-nonequilibrium effects that modulate the height of the free energy barrier in the SF region and can be ascribed to both the choice of the reaction coordinate and the convergence of the adaptive bias. These results imply that conduction in aquaglyceroporins does not exhibit complete timescale separation, but rather depends on fluctuations that are slow compared with the motion along the conduction pathway. Gating of membrane channels generally obeys such a reaction mechanism. Advancing our understanding of assisted transport phenomena across membranes necessarily requires better characterization of the slow fluctuations that are coupled to self-diffusion in aquaporins and other channels. Application of diffusional kinetic theory based on the measured free energy profile and position-dependent diffusion coefficient yields a predicted rate constant that appears to be overestimated compared to the available experimental value. Although the latter relies upon arguable assumptions and only provides a rough idea of the associated kinetics, this apparent discrepancy calls for additional investigations. Extending this approach to other transport phenomena, well-characterized experimentally, is envisioned to help assess whether mean-field models (that is, diffusion in a one-dimensional potential of mean force) describe in a reliable and effective way the statistical distribution of the permeation events that underlie the observable, macroscopic transport rate. The authors are grateful to Mario Borgnia, Christophe Dellago, Andrew Pohorille, Eric Vanden-Eijnden, and Yi Wang for helpful and enlightening discussions. E.T. and K.S. acknowledge support from the National Institutes of Health (grants No. P41RR05969 and R01-GM67887).",
year = "2008",
month = jan,
day = "2",
doi = "10.1529/biophysj.107.115105",
language = "English (US)",
volume = "94",
pages = "832--839",
journal = "Biophysical journal",
issn = "0006-3495",
publisher = "Elsevier Inc.",
number = "3",
}