Linker-mediated conformational coupling drives lesion recognition in MutY glycosylase

Maintaining genome stability requires accurate recognition of oxidative DNA damage. MutY glycosylase prevents mutagenic G:C→T:A transversions by excising adenine mispaired with 8-oxoguanine (8OG). While crystal structures have captured two endpoint states-the encounter complex (EC) and the lesion recognition complex (LRC)-the dynamic steps connecting these states have remained unresolved. Using large-scale enhanced-sampling molecular dynamics simulations, we mapped the free energy landscapes of lesion recognition and identified a dominant pathway in which adenine and 8OG undergo synchronized glycosidic rotations orchestrated by a flexible interdomain linker. This linker coordinates adenine flipping, dual base isomerization, and interdomain rearrangements into a unified, streamlined process that secures extrahelical adenine in a catalytically competent LRC state. These findings reveal a previously unrecognized mechanistic framework for MutY and related glycosylases with flexible linkers, highlighting how such linkers guide lesion interrogation and reinforce genome integrity.