Dynamic allosteric networks drive adenosine A₁ receptor activation and G-protein coupling

Miguel A. Maria-Solano author has email address
Sun Choi author has email address

Global AI Drug Discovery Center, College of Pharmacy and Graduate School of Pharmaceutical Science, Ewha Womans University, 03760 Seoul, Republic of Korea

https://doi.org/10.63204/8637.1

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Figures and data

Free energy landscape (FEL) of A₁R activation in presence of adenosine (ADO).
(A) TM6 inward-to-outward conformational transition observed in the inactive (PDB 5N2S) and active (PDB 6D9H) X-Ray and Cryo-EM structures. (B) Features (TM6 torsion and TM3-TM6 center of mass distance of the intracellular ends) used to follow the TM6 inward-to-outward transition (receptor activation) in this work. The X-ray and Cryo-EM values are also shown. (C) Population analysis obtained from conventional molecular dynamics (cMD) simulations of A₁R activation starting from the inactive X-Ray and active Cryo-EM structures, the inactive X-ray and active Cryo-EM coordinates are projected as blue and magenta stars, respectively. (D) Reconstruction of the FEL associated with the A₁R activation obtained from metadynamics simulations. The most relevant conformational states are labeled from 1 to 5. Note that the lowest energy states (1,3 and 4) are labeled in gray while the other (2 and 5) in orange. The X-ray and Cryo-EM coordinates are also projected. (E) Representative structures of the inactive (1), Intermediate (2-3) and Pre-active (4-5) conformational states sampled along A₁R-ADO activation.

Protein energy networks (PEN) of A₁R-ADO along activation.
(A) PEN analysis of the A₁R conformational ensemble. The PEN identifies extra and intracellular communication centers together with the allosteric pathways that interconnect them. The PEN residues (nodes) are represented by colored spheres as a function of the receptor region (e.g. TM6 nodes in teal) while the allosteric pathways (edges) as yellow-orange sticks. The size of each edge and node correspond to their importance for the allosteric communication. The experimentally identified allosteric residues captured in the PEN nodes are labeled with a red asterisk. (B) Relevant interactions of the PEN in the upper region of the receptor. (C) PEN analysis of the A₁R ensemble split by conformational states (inactive, intermediate and pre-active). The allosteric communication is enhanced along the receptor activation. (D) Relevant interactions found in the PEN of the lower region of the receptor along the inactive, intermediate and pre-active conformational states.

Effect of G-proteins binding in the A₁R-ADO conformational ensemble.
(A) Population analysis of A₁R activation in the A₁R-ADO-G_i2 complex obtained from conventional molecular dynamics (cMD) simulations, the inactive and active X-ray and Cryo-EM coordinates are projected as blue and magenta stars, respectively. (B) Projection of the A₁R-ADO-G_i2 energy minima obtained from cMD over the FEL associated with the A₁R activation obtained from metadynamics simulations. The A₁R-ADO-G_i2 energy minima (depicted in red) is centered on the coordinates of the active Cryo-EM structure. (C) Overlay of the active Cryo-EM structure (PDB 6D9H) and a representative snapshot from the A₁R-ADO-G_i2 energy minima.

Effect of G-proteins binding in A₁R-ADO Protein Energy Networks (PEN).
The PEN residues (nodes) are represented by colored spheres as a function of the receptor region (e.g. TM6 nodes in teal) while the allosteric pathways (edges) as yellow-orange sticks. The size of each edge and node correspond to their importance for the allosteric communication. The experimentally identified allosteric residues captured in the PEN nodes are labeled with a red asterisk. Relevant interactions of the PEN in the upper and lower regions of the receptor are also shown.

Energy coupling between the transient pockets formed along activation.
(A) Iso-surface representation of the normalized frequency map (set at Φi =0.2 iso-value) obtained from MDPocked in the inactive (blue), intermediate (teal), pre-active (violet) and fully-active (red) ensembles. The transient pockets are labeled from A to N. The allosteric modulators that overlap with the pockets found are shown as dark gray sticks (PDB 7DL3, 5TZY and 5LWE) and spheres (PDB 4N6H). (B) Overlap of the transient pockets and the protein energy networks (PEN). The PEN residues (nodes) are represented by colored spheres as a function of the receptor region (e.g. TM6 nodes in teal) while the allosteric pathways (edges) as yellow-orange sticks.