Molecular Dynamics Simulations of the Human Glucose Transporter GLUT1
Fig 9
The movement of D-glucose toward the intracellular side by Steered Molecular Dynamics (SMD) simulations.
(A) Representative snapshots of D-glucose movement along the tunnel. D-glucose molecules from different snapshots are shown as white and red large spheres. Contact 15 residues in GLUT1 that contributes to D-glucose binding free energy are shown. Side bar represents pulling distance of D-glucose along the z-axis from the sugar-release pocket corresponding to the PMF profile in (B). (B) Potential of Mean Force (PMF) profile as a function of the movement of sugar along the z-axis toward the intracellular side. Jarzynski estimator (black), liner extrapolation (red), and cumulative integral (CI) extrapolation (green) are shown for PMF average and standard deviation. The PMF profile computed using 10 SMD simulations from a conformational ensemble. (C) the putative transient binding site that may cause a shoulder or a local minimum at pulling distance of ~7Å on the PMF profile.