Differences between the behavior of the trans-membrane part of the human sweet taste receptor in H2O vs D2O. (A) Structure of the TMD of the TAS1R2/TAS1R3 receptor with the probability density (volumetric map) of H2O (blue) or D2O (red) molecules within 10 Å from the protein evaluated using the VMD VolMap tool from the MD simulations at an isovalue of 0.5. The conserved water molecules in the x-ray templates are shown in cyan color. Water molecules predicted with the software OpenEye(51) are shown in licorice representation. (B) Time evolution of the radii of gyration in H2O (blue) and D2O (red) with mean values as dashed lines, showing that the protein is more compact in heavy water. (C) Representative snapshot of the trans-membrane part of the human sweet taste receptor color-coded that red/blue represents parts more/less rigid in D2O vs H2O. The embedding lipid membrane is represented in gray. (D) Difference in root mean square fluctuations in MD trajectories. Negative/positive values mean that structures are more/less rigid in D2O than in H2O. The red line represents the sum over all residues.

Contexts in source publication

Context 1

... of H2O molecules were compared among mGluR5 structures (PDB: 4OO9, 5CGC, and 5CGD), and two conserved positions were found. The H2O molecules in these two positions were merged with hTAS1R3 model and minimized ( Figure 6A). The water mapping protocol from OpenEye(51) enables mapping of water positions based on the energetics of water, and ~40 water molecules were predicted in the binding site using this protocol ( Figure 6A). ...

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... H2O molecules in these two positions were merged with hTAS1R3 model and minimized ( Figure 6A). The water mapping protocol from OpenEye(51) enables mapping of water positions based on the energetics of water, and ~40 water molecules were predicted in the binding site using this protocol ( Figure 6A). Water densities of H2O and D2O in the TMD of the TAS1R2/TAS1R3 receptor were calculated from MD simulations as described below. ...

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... densities of H2O and D2O in the TMD of the TAS1R2/TAS1R3 receptor were calculated from MD simulations as described below. Overall, all three methods suggest the possibility for at least some internal molecules (trapped in the TMD bundle) in addition to water that surrounds the extracellular and intracellular loops ( Figure 6A). Microsecond MD simulations of the TMD embedded in a phospatidylcholine (POPC) bilayer in either H2O or D2O were carried out (for details see SM). ...

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... have entered the TMD domain and have clustered at positions that overlap with the modeled water positions, see Figure 6A. These internal positions may have a differential effect between H2O and D2O, though differences between the averaged water densities are not very pronounced. ...

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... internal positions may have a differential effect between H2O and D2O, though differences between the averaged water densities are not very pronounced. Figure 6B shows the time evolution of the radius of gyration of the TMD domain, while Figures 6D presents the root mean square fluctuations (RMSF) of individual residues of the proteins superimposed on its structure and plotted in a graph together with the mean value of RMSF. A small but significant difference is apparent in the behavior of the protein in H2O vs D2O. ...

Context 6

... internal positions may have a differential effect between H2O and D2O, though differences between the averaged water densities are not very pronounced. Figure 6B shows the time evolution of the radius of gyration of the TMD domain, while Figures 6D presents the root mean square fluctuations (RMSF) of individual residues of the proteins superimposed on its structure and plotted in a graph together with the mean value of RMSF. A small but significant difference is apparent in the behavior of the protein in H2O vs D2O. ...

Context 7

... small but significant difference is apparent in the behavior of the protein in H2O vs D2O. Namely, structural fluctuations of most residues and of the protein as a whole are slightly attenuated in D2O, in which environment the protein is also somewhat more compact than in H2O ( Figure 6B). ...