Journal
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Volume 99, Issue 10, Pages 6731-6736Publisher
NATL ACAD SCIENCES
DOI: 10.1073/pnas.102649299
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- NCRR NIH HHS [5 P41RR05969, P41 RR005969] Funding Source: Medline
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Aquaglyceroporin GIpF selectively conducts water and linear polyalcohols, such as glycerol, across the inner membrane of Escherichia coli. We report steered molecular dynamics simulations of glycerol conduction through GIpF, in which external forces accelerate the transchannel conduction in a manner that preserves the intrinsic conduction mechanism. The simulations reveal channel-glycerol hydrogen bonding interactions and the stereoselectivity of the channel. Employing Jarzynski's identity between free energy and irreversible work, we reconstruct the potential of mean force along the conduction pathway through a time series analysis of molecular dynamics trajectories. This potential locates binding sites and barriers inside the channel; it also reveals a low energy periplasmic vestibule suited for efficient uptake of glycerol from the environment.
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