Table 1.
Prediction of vulnerability of T164I variation by computational programs and calculation of total structural deviation.
Table 2.
Calculation of binding site properties of wild and T164I variant β2AR.
Fig 1.
The overlapping cartoon depicts binding cavities of wild (green solid) and T164I (red mesh) β2AR.
Volume of the cavity in wild β2AR is 404.48 Å3, upon substitution the cavity expands to 520.70 Å3. Poses of salbutamol (Sea green in wild, and pink in T164I variant) are shown in the binding cavity.
Fig 2.
Structural perturbation incurred in β2AR upon T164I variation analyzed by simulations.
(A) RMSD calculated for 10 ns of simulation trajectory for wild and T64I β2AR. β2AR is rendered with high conformational flexibility upon T164I substitution as observed from gradual rise in RMSD after 2.7 ns for T64I β2AR. (B) RMSF calculated for residues in wild and T164I variant. Purple bars indicate active site residues; arrow pointing the peak represents the site of variation. (C) Compactness of wild and T164I β2AR assessed by calculating radius of gyration. Trajectory lines for wild and T164I β2AR are represented in red and black color respectively.
Table 3.
Energy descriptors determining the binding efficiency of salbutamol in wild and T164I variant.
Table 4.
Interaction profile of salbutamol in wild and T164I variant of β2AR.
Fig 3.
Molecular interaction diagrams of salbutamol deduced from molecular docking.
(A) Salbutamol in Wild and (B) Salbutamol in T164I β2AR. Residues in green participate in van der Waals interaction, residues in pink form electrostatic interactions with the salbutamol. Hydrogen bonds are shown as blue (acceptor) and pink (donor) arrows. Pi-pi interactions are shown with orange solid line.
Fig 4.
Interactions of Salbutamol docked in the agonist binding site.
H bond and pi-pi networks of salbutamol in (A) wild and (B) T164I β2AR. Black discontinuous lines are H bonds, blue line represent pi-pi interactions.
Table 5.
Energy analysis of ligand-receptor complex over simulation trajectory.
Fig 5.
“Ligand fit in protein” RMSD for salbutamol in wild (red) and T164I β2AR (black) projected at a simulation trajectory of 10 ns.
Fig 6.
Trajectory analysis of salbutamol in complex with wild and T164I β2AR.
(A) RMSD of salbutamol with respect to the reference conformation in wild and T164I β2AR. (B) ‘Fit on protein' line shows atomic fluctuations (RMSF) with respect to the receptor. Corresponding atoms of salbutamol is shown as 2D structure in the top panel. (C) Solvent accessible surface area of salbutamol in course of simulation. Trajectory lines for wild and T164I β2AR are represented in red and black color respectively.
Fig 7.
Contact fractions of ligand-receptor interactions in course of simulation.
Simulation interaction diagram showing contact fractions of residues interacting with salbutamol in (A) wild and (B) T164I variant of β2AR.
Fig 8.
Timeline representation of ligand—Receptor interactions.
Residues interacting (all the interactions including H-bonds, Hydrophobic, Ionic, Water bridges) with salbutamol in (A) wild and (B) T164I variant of β2AR.
Fig 9.
Number of H bonds contacts established by salbutamol with wild (red) and T164I β2AR (black) in each frame of simulation.
Reduced H bond contacts for T164I variant can be observed.
Fig 10.
Total contacts (H-bonds, Hydrophobic, Ionic, Water bridges) of salbutamol with wild (red) and T164I (black) β2AR recorded at each frame of simulation.
Declined contacts of salbutamol in T164I variant are apparent.