Fig 1.
Homology-based models of human GLUT1 in (A) the outward-facing and (B) the inward-facing conformation.
The flexible cytoplasmic domains are omitted. The each 12 trans-membrane (TM) domain is labeled. TM1-6 form the N-domain (cyan) and TM7-12 form the C-domain (yellow).
Fig 2.
Comparison of interactions between TM domains and intracellular helices (ICH) domain of GLUT1.
(A) the opened inward-facing (X-ray structure). (B) the opened outward-facing conformation (the result of the CMD simulation). The N-terminal TM domain, C-terminal TM domain, and ICH domain are shown in cyan, orange, and green, respectively. The possible hydrogen bonds and the corresponding residues are described as dashed black lines and sticks, respectively.
Fig 3.
A substrate induced fit of the glucose-binding site from the fully opened outward- to the partially occluded outward-facing conformation.
The initial and final locations of each binding residue are shown in yellow and green, respectively. Putative hydrogen bonds, which were used for restraints in the SMD simulation, are shown as dash lines.
Fig 4.
A sequence of closing or opening of extracellular vestibule.
(A) The fully opened outward-facing conformation (the result of CMD and AMD simulations). (B) The partially occluded outward-facing conformation (the result of SMD and CMD for sugar binding). (C) The X-ray structure of GLUT1 in the opened inward-facing conformation. For clarity, the intracellular domains between TM6 and TM7, and the C-terminal loop domain are omitted. Bound glucose molecule is described by white (carbon) and red (oxygen) spheres. The N-domain and C-domain are shown in cyan and orange, respectively.
Fig 5.
Non-symmetrical rocker-switch movement between N- and C-domain in GLUT1 during the TMD simulations.
(A) Surface and cartoon presentation of the initial outward-facing conformation with color code based on the distance of each Cα atom that navigated during the TMD simulations. (B) Superimposed view of the initial partially occluded outward- (transparent gray) and the final fully opened inward-facing conformation without structural alignment. The N-domain and C-domain are shown in cyan and orange, respectively. For clarity, the intracellular domains and the C-terminal loop domain are omitted.
Fig 6.
Sugar translocation pathway in GLUT1.
Representative snapshots for the translocation of glucose and involved residues in TMD. Putative hydrogen bond interactions are in dash lines. The N-domain and C-domain are shown in cyan and orange, respectively.
Fig 7.
Water transport with substrate through GLUT1.
Representative snapshots of (A) the outward- and (B) the inward-facing conformation through the GLUT1 tunnel during TMD simulations. Water pathways are shown in ball and stick and gray surface map. Glucose molecule is colored in yellow. The water is always isolated either from the extracellular or the intracellular side at any given time so charged molecules could not pass through the transporter during the transport cycle.
Fig 8.
Sugar-releasing pathway in GLUT1.
Representative snapshots of the glucose movement from the inward binding site along the tunnel into intracellular side in SMD. Putative hydrogen interactions are in dash lines. The N-domain and C-domain are shown in cyan and orange, respectively. The last (D) describes the further glucose path through the tunnel toward the intracellular side.
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.