Extended Data Fig. 10: NTD dimer conformational variability in MD simulations and experimental structures.
From: Architecture, dynamics and biogenesis of GluA3 AMPA glutamate receptors
a, The root-mean-square deviation (RMSD) in NTD dimer Cα atom positions are shown for the MD simulations of isolated NTD dimers (left) and of NTD-LBD tridomains (middle), along with NTD dimer displacement torsions for the NTD-LBD tridomain simulations (right) for wt (top) and R163I (bottom). The LBD limits the NTD mobility in the tridomain simulations with R163I exhibiting transient excursions to displaced states with torsions of around −20°, instead of stabilizing around −25° in the NTD only simulations (see Fig. 4b). b, Displacement torsion angle progression is shown for 3 MD simulations of a parallel NTD dimer (PDB: 3O21 chains C/D; left). Two of these runs (cyan and purple) show stabilization at −10 degrees, due to binding of a chloride ion (right). The other (red) transitions to displaced. c, The resolved experimental R163I structure has an NTD dimer in an intermediate conformation between the phosphate-bound and apo structures as illustrated in the displacement graph (left) and the structural overlay (middle zoomed view and right inset tridomain).
