Jonathan Lasham

This study uses molecular dynamics simulations to investigate conformational changes in the ND2 subunit of complex I, revealing a previously unobserved structural transition linked to proton pumping.

The paper develops a workflow to predict sidechain conformations of acidic amino acids in cryo-EM maps, validated through Q-score and molecular dynamics simulations.

This study shows that using pre-determined protonation states in MD simulations improves structural accuracy for membrane proteins, highlighting the importance of protonation state calculations before simulations.