Figures and data
AVP SuMD and mwSuMD binding simulations to V2R (100 ps time windows).
For each set of settings (a-d) the RMSD of AVP Cα atoms to the cryo-EM structure 7DW9 is reported during the time course of each SuMD (a) or mwSuMD (b-d) replica alongside the RMSD values distribution and the snapshot corresponding to the lowest RMSD values (AVP from the cryo-EM structure 7DW9 is in a cyan stick representation, while AVP from simulations is in a tan stick representation). A complete description of the simulation settings is reported in Table S1 and the Methods section. The dashed red line indicates the AVP RMSD during a classic (unsupervised) equilibrium MD simulation of the X-ray AVP:V2R complex (Figure S2).
G protein binding simulations to β2AR and A1R.
a) RMSD of Gsα to the experimental complex (PDB 3NS6) during three mwSuMD replicas; b) RMSD of Gsβ to the experimental complex (PDB 3NS6) during three mwSuMD replicas; c) superposition of the experimental Gs:β2 AR complex (transparent ribbon) and the MD frame with the lowest Gsα RMSD (3.94 Å); d) RMSD of Giα (residues 243-355) to the A1R experimental complex (PDB 6D9H) during a mwSuMD simulation (red, magnified in the box) and a 1000-ns long classic MD simulation (black); e) two-view superposition of the experimental Gi:A1 R complex (transparent ribbon) and the MD frame with the lowest Giα RMSD (4.82 Å).
mwSuMD simulation of PF06882961 binding to GLP-1R and receptor activation.
Each panel reports the root mean square deviation (RMSD) to a GLP-1R structural element or the position of the ligand in the active state (top panel), over the time course (all but ECL3 converging to the active state). ECD: extracellular domain; TM: transmembrane helix; ECL: extracellular loop. The mwSuMD simulation was performed with four different settings over 1 microsecond in total. The red dashed lines show the initial RMSD value for reference.
GLP-1R activation and Gs binding.
a) Rotation of TM6 during GLP-1R activation simulated by mwSuMD. The angle was measured as the dihedral formed by the backbone alpha carbon atoms T353, I357, T362, and I366. The angle values of the inactive and active cryo-EM structures are reported as references; b) RMSD of Gsα to the experimental GLP-1R:Gs complex (PDB 7LCJ) during three mwSuMD replicas; c) PF06882961 MM-GBSA binding energy during Gs binding; d) GDP MM-GBSA binding energy during Gs binding; e-f) sequence of simulated events during the mwSuMD Gs:GLP-1R simulations.
A2AR:D2R heterodimerization and formation of the ternary complex with C26.
a) Distance between the centroids of A2AR and D2R during the hybrid mwSuMD/metadynamics/aMD/ simulation; b) distance between the centroids of A2AR and D2R during the successive cMD simulation; c) MM-PBSA binding energy between A2AR and D2R during the hybrid metadynamics/aMD/mwSuMD simulation; d) MM-PBSA binding energy between A2AR and D2R during the successive cMD simulation; e) MM-PBSA binding energy between A2AR and D2R during the mwSuMD binding of C26. f) A2AR:D2R heterodimer (white ribbon) after 1.5 μs of cMD; POPC residues (green stick) were involved in polar and hydrophobic interactions; g) extracellular view of the A2AR:D2R:C26 ternary complex (D2R TM2 and TM3 removed for clarity).
