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/10.7554/eLife.90773.1

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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 used to follow the TM6 inward-to-outward transition (receptor activation) in this work. The TM6 torsion corresponds to the dihedral angle formed by the alpha carbon atoms of L236^6.37, W247^6.48, T277^7.42 and T270^7.35. For the TM3-TM6 intracellular ends distance, we computed the center of mass (COM) distances between the backbone atoms of TM3(Y226^6.27, G227^6.28, K228^6.29, L230^6.30 and E230^6.31) and TM6(R105^3.50, Y106^3.51, L107^3.52, R108^3.53 and V109^3.54). 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 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.

Protein energy networks (PEN) of A₁R-ADO in the inactive, intermediate and pre-active states.
(A) 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. The allosteric communication is enhanced along the receptor activation. (B) Relevant interactions found in the PEN of the lower region of the receptor that are altered along activation.

Effect of G-proteins binding in the A₁R-ADO conformational ensemble.
(A) Population analysis of A₁R activation in the ADO-A₁R-G_i2 complex obtained from conventional molecular dynamics (cMD) simulations. The TM6 torsion corresponds to the dihedral angle formed by the alpha carbon atoms of L236^6.37, W247^6.48, T277^7.42 and T270^7.35. For the TM3-TM6 intracellular ends distance, we computed the center of mass (COM) distances between the backbone atoms of TM3(Y226^6.27, G227^6.28, K228^6.29, L230^6.30 and E230^6.31) and TM6(R105^3.50, Y106^3.51, L107^3.52, R108^3.53 and V109^3.54). The inactive and active X-ray and Cryo-EM coordinates are projected as blue and magenta stars, respectively. (B) Projection of the ADO-A₁R-G_i2 energy minima obtained from cMD over the FEL associated with the A₁R activation obtained from metadynamics simulations. The ADO-A₁R-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 ADO-A₁R-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.

Energy coupling between PB and PD along activation.
Zoom view of the transient pockets and protein energy networks of the upper region of the receptor. Adenosine (ADO) in pocket B and the MIPS521 positive allosteric modulator (PAM) in pocket D, both aligned from PDB 7LD3, are depicted in gray and orange sticks, respectively. The PEN residues (nodes) are represented by light gray spheres. The experimentally identified allosteric residues located in pocked D that affects the PAM are colored as a function of the receptor region (TM6 nodes in teal and TM7 nodes in purple) and highlighted with a red asterisk. The allosteric pathways (edges) are depicted as yellow-orange sticks.

Effect of ADO and MIPS51 PAM binding in the A₁R-G_i2 Protein Energy Networks (PEN).
Adenosine (ADO) in pocket B and the MIPS521 positive allosteric modulator (PAM) in pocket D, both aligned from PDB 7LD3, are depicted in gray and orange sticks, respectively. Note that ADO and PAM sticks are displayed with transparency in the systems in which they are absent. 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 experimentally identified allosteric residues captured in the PEN nodes are labeled with a red asterisk.

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