Simulation data I (molecular dynamics) for 'Trans–Cis Proline Switches in a Pentameric Ligand-Gated Ion Channel - How They Are Affected by and How They Affect the Biomolecular Environment'

Pentameric ligand-gated ion channels (pLGICs) are important neuroreceptors, embedded in neuronal membranes, that mediate fast synaptic transmission. The molecular details of their working mechanisms have still to be fully unravelled due to their complexity and limited structural information available. Here we focus on a potential molecular switch in a prototypical pLGIC, the serotonin-activated 5-HT3 receptor, consisting of the trans–cis isomerization of a proline at the interface between the extracellular and transmembrane domain. We investigate this switch within the receptor with molecular dynamics (data reported here) and metadynamics simulations. The molecular dynamics simulations regard four different models, named 5Trans (with Pro281 in the trans conformation for all the five subunits), 3Cis (with Pro281 in the cis conformation in subunits 1, 3 and 4), 5Cis (with the five Pro281 in cis), and 5Trans5Cis (with the five Pro281 in trans and the five Pro274 in cis).