Using Lambda Dynamics to Study Protonation States of GLIC

Ligand-gated ion channels have become a fascinating field of research. Their involvement in neural signalling has been the cause of a large number of studies into the behaviour of mammalian channels and their bacterial counterparts. Members of the family include the ubiquitous glycinereceptors (GlyR) and γ-aminobutyric acid receptors (GABA), among others. The pentameric ligand gated ion channel from Gloeobacter violaceus (GLIC) is one of the more thoroughly studied members of the family. A prokaryotic channel, it has the same pentameric base structure as the rest of the family, and is activated at lower pH. The channel has been one of the first ones being successfully crystallized, with more structural information available from a number of cryo-electronmicroscopy studies under different conditions, to understand the complex gating mechanism. Understanding the pH gating of the channel has been a challenging topic. Simulation studies using fixed protonation states have in the past used slightly different sets of protonated and de-protonated residues. One promising approach remains the use of constant pH Molecular Dynamics (cpHMD) simulations. The issue with many of the currently used methods is that they rely on Monte-Carlo steps to change explicit protonation states, leading to inherent hysteresis when trying to model solvated systems. We here present preliminary work using a lambda dynamics based cpHMD simulation approach. This method differs from the Monte-Carlo based methods by treating protonation as additional system variables that are integrate with the rest of the simulated system. Through this, the method avoids hysteresis from abruptly changing protonation states, while still keeping the ability to adopt to the surroundings. We use this method to study the titration of residues involved in gating GLIC, to understand how the shifting protonation states at different external pH values affect the structure of the channel.