Computational studies of M. smegmatis TOP1A open to closed transition

Type I topoisomerases relax DNA supercoils by cleaving a ssDNA backbone (G or gate strand) and passing an intact ssDNA (T or transfer strand). However, the catalytic cycle of type IA topoisomerases is not well characterized. Specifically, the gate opening, and strand-passage mechanisms are still not firmly established. MD simulations are a powerful tool in exploring the possible pathways of the topo gate opening mechanism. This work probes the molecular details of gate-opening process via the use of biased MD simulations using Metadynamics. In Metadynamics, sampling of a chosen degree of freedom known as the collective variable (CV) is enhanced via a history-dependent bias potential which is built during the simulation as a sum of repulsive Gaussians in the CV space. We used the method known as Well-Tempered Metadynamics (WT MetaD) where the deposited Gaussians are scaled down by a factor. We present our findings using Well-Tempered MetaD and different structures of the MSM Topo IA with and without ssDNA. Free Energy profiles combined with the structural conformation changes observed during the gate opening process provides further information to the elusive mechanism of topoisomerase gate-opening.