Figure 1.
Homology model of GLUT4 and the simulation system.
(A) A cartoon representation of the GLUT4 homology model used for simulation studies with the two half helix bundle domains D1 and D2 colored in grey and green respectively. The N- and C-terminal end regions and the long cytoplasmic loop regions are colored in pink. Glucose and ATP binding sites also marked. (B) Snapshot of a representative simulation system. The protein is shown in cartoon representation. The P atoms of POPC lipid bilayer are shown in spheres and the rest of the bilayer as lines. The light blue color surface representation shows the water box.
Table 1.
Overview of the MD simulations performed.
Figure 2.
RMSD (Root Mean Square Deviation) and RMSF (Root Mean Square Fluctuation) profile.
(A) The Cα RMSD calculated for the 3 simulation systems. (B) RMSD analysis for the region excluding N-terminal, C-terminal ends and cytoplasmic loop between TM6 and TM7. (C) RMSF of each Cα atom as a function of time. The 12 transmembrane regions are also marked. In the figure apo, glucose and glucose-ATP bound forms are shown in black, red and green respectively.
Table 2.
RMSD of three simulations.
Figure 3.
Dominant motions in the three simulation systems using Principal Component Analysis (PCA).
(A) Porcupine plot of the first eigen vector from the apo (B) glucose bound (C) glucose-ATP bound simulations. For clarity, loop regions are not shown in the figure.
Figure 4.
(A) The glucose transport channel at the end of apo form simulation. Pore radius below 1.15 Å in red, between 1.15 Å and 2.30 Å in green and above 2.30 Å in blue color representation. Pore radius profile for the (B) apo, (C) glucose bound and (D) glucose-ATP bound forms at different intervals.
Table 3.
Inter-helical hydrogen bonds.
Figure 5.
Inter-helical hydrogen bonds formed during the three simulations.
The extracellular view of the stable inter-helical hydrogen bonds observed in the (A) apo (B) glucose-bound (C) glucose-ATP bound forms. The transporter is shown as cylindrical cartoon with domain D1 in grey and domain D2 in green. Hydrogen bond forming residues are represented with lines and hydrogen bonds are highlighted with dashed lines. The hydrogen bonds at the TM5-TM8 and TM2-TM11 interface (blue), the cytoplasmic half (magenta), and the extracellular half (red) are shown. (D) Residues at the TM1-TM5 interface and interactions at the TM1-TM5 interface. (E) Residues at the TM2-TM4 interface and interactions at the TM2-TM4 interface. The highly conserved residues across the GLUT family, G39 in TM1, G183 in TM5, G92 in TM2 and G146 in TM4 are underlined.
Figure 6.
(A)The sequence alignment of 14 members of GLUT family: the salt bridge forming residues are highlighted. The network of salt bridge which has a switching pattern is also highlighted. (B) The intra-domain salt bridge network E345-R350-E409 found with the presence of glucose. (C) The inter-domain salt bridge network E345-R169-E409 found with the presence of glucose-ATP.
Table 4.
Salt bridge details.
Figure 7.
Stable binding pose of ATP at the ATP binding site of GLUT4. The snapshot is taken from a representative of highly populated cluster of ATP bound complex obtained from the MD2 simulation trajectory.
Figure 8.
Proposed domain arrangements associated with the three simulations.
(A) apo (B) glucose bound (C) glucose-ATP bound forms. Residues involved in inter-domain interactions are marked, inter-domain salt bridge forming residues are shown in red. The arrow head shows the direction of domain movements observed from Principal Component Analysis (PCA).