Table 1.
Relative free−energy values (in kcal/mol) of the inactive, intermediate, and active states of the unliganded and liganded B2AR, together with the height of the barriers separating them.
Figure 1.
Free-energy of the unliganded receptor.
(A) Free-energy as a function of the position (s) along the activation pathway. Note that the curve has been shifted so that the lowest energy minima (indicated by stars) correspond to a reference free-energy value. (B) Free-energy as a function of ionic lock distance (dIL) and the toggle switch dihedral (χTS) molecular switches for the unliganded receptor; contour lines are reported every kBT.
Figure 2.
Simulation results for B2AR bound to the neutral antagonist alprenolol.
(A) Free-energy profile as a function of the position (s) along the activation pathway. Note that the curve has been shifted so that the minimum (indicated by a star) corresponds to a reference free-energy value. (B) Binding mode of alprenolol. Relevant residues interacting with the ligand (any atom within a 3 Å distance cutoff) are indicated in stick representations. Helices TM5, TM6 and TM7 are shown in orange, blue and light blue respectively. Helix TM3 is shown in purple transparent representation whereas TM4 has been removed for clarity. (C) Free-energy as a function of ionic lock distance (dIL) and the toggle switch dihedral (χTS) molecular switches.
Figure 3.
Simulation results for B2AR bound to the inverse agonists carazolol and ICI-118,551.
(A and D) Free-energy profiles as a function of the position (s) along the activation pathway for carazolol and ICI-118,551, respectively. Note that the curves have been shifted so that the minima (indicated by stars) correspond to reference free-energy values. (B and E) Binding modes of carazolol and ICI-118,551, respectively. Relevant residues interacting with the ligands (any atom within a 3 Å distance cutoff) are indicated in stick representations. Helices TM5, TM6 and TM7 are shown in orange, blue and light blue respectively. Helix TM3 is shown in purple transparent representation whereas TM4 has been removed for clarity. (C and F) Free-energies as a function of ionic lock distance (dIL) and the toggle switch dihedral (χTS) molecular switches for the carazolol- and ICI-118,551-bound B2AR, respectively.
Figure 4.
Simulation results for B2AR bound to the full agonist epinephrine, the very weak partial agonist catechol, and the weak partial agonist dopamine.
(A, D, and G) Free-energy profiles as a function of the position (s) along the activation pathway for epinephrine, catechol, and dopamine, respectively. Note that the curves have been shifted so that the minima (indicated by stars) correspond to reference free-energy values. (B, E, and H) Binding modes of epinephrine, catechol, and dopamine, respectively. Relevant residues interacting with the ligands (any atom within a 3 Å distance cutoff) are indicated in stick representations. Helices TM5, TM6 and TM7 are shown in orange, blue and light blue respectively. Helix TM3 is shown in purple transparent representation whereas TM4 has been removed for clarity. (C, F, and I) Free-energies as a function of ionic lock distance (dIL) and the toggle switch dihedral (χTS) molecular switches for the epinephrine-, catechol-, and dopamine-bound B2AR, respectively.
Figure 5.
Structural comparisons between ligand-specific B2AR conformations.
Specifically, these comparisons (viewed from the intracellular side) are between: (A) an inverse agonist (carazolol)-bound inactive state at s∼0.2 (blue color) and a partial agonist (dopamine)-stabilized intermediate conformation at s∼0.6 (orange color); (B) an inverse agonist (carazolol)-bound inactive state at s∼0.2 (blue color) and a full agonist (epinephrine)-stabilized active conformation at s∼0.9 (pink color); and (C) a partial agonist (dopamine)-bound intermediate conformation at s∼0.6 (orange color) and a full agonist (epinephrine)-stabilized active conformation at s∼0.9 (pink color). The position of the side chains of the residues involved in the ionic locks are indicated with sticks. For clarity, IL3 has been removed.