Extended Data Figure 7: MD simulations of the apo GCGR.
From: Structure of the full-length glucagon class B G-protein-coupled receptor
a, Main chain r.m.s.d. values of the ECD versus simulation time in the three 1-μs molecular dynamics simulations. The values were calculated from snapshots at 100-ps intervals. All the structures were superimposed to the crystal structure of full-length GCGR using the main chain atoms of residues S150–L160 (helix I), I176–V193 (helix II), A227–G246 (helix III), G271–P275 (helix IV), V311–I321 (helix V), T351–L358 (helix VI) and Q392–Y400 (helix VII). b–d, Comparison between the results of simulations and the full-length GCGR crystal structure. The full-length GCGR crystal structure is shown as grey cartoon. The results of the three simulations are shown in cartoon representation, and coloured in yellow, cyan and orange, respectively. The ECDs of the receptors are also shown in surface representation. The N-terminal portion of stalk (residues G125–Q131) and the ECL1 region (residues T200–D218), which are analysed in panel e, are coloured green and magenta, respectively. The red arrows indicate the movements of the ECDs and ECL1 (d) in the simulations. e, Secondary structure as a function of time for the stalk (residues G125–Q131) and ECL1 (residues T200–D218) regions in the crystal structure and simulations.
