Fig. 2.

Comparison of calcium ion binding sites determined by MD simulations and cryo-EM. Two representative snapshots (Left and Right panels) from a continuous MD simulation of GluA2(Q), as previously reported (29), illustrate two distinct Ca²⁺ binding modes (gray spheres) during ion permeation. These snapshots are overlaid onto the Ca²⁺ binding sites (orange mesh) identified in a high-resolution cryo-EM structure of AMPAR (PDB ID: 8FQ1) (25). AMPAR subunits are shown as ribbons, with selected residues displayed in licorice representation. Ion binding sites identified in our MD simulations, along with the experimentally resolved site-G (25), are labeled on the two-dimensional plot of Ca²⁺ occupancy (Middle panel, modified from ref. 29), calculated for simulations where a large number of ion permeation events were observed. In unedited receptors, Ca²⁺ also exhibits strong occupancy at a site just above the Q/R site (not labeled here). Ion occupancy is color-coded based on the free energy difference relative to the bulk solution outside the channel.