Model for RuvAB-mediated branch migration of Holliday junctions.

During RuvAB-mediated Holliday-junction migration two opposite arms of double-stranded DNA (dsDNA) are driven to translocate unidirectional by two respective ring-like hexameric RuvB proteins. However, how the RuvB protein, powered by ATP hydrolysis, drives unidirectional translocation of dsDNA is not clear. Here a model is presented for this mechanochemical-coupling mechanism. In the model, the unidirectional translocation is resulted from both the ATP hydrolysis-induced rotation (power stroke) of the RuvB subunits and the passage of the strong DNA binding from the previous to next RuvB subunits during the sequential ATPase activities around the ring. Using the model, the relationship between the power-stroke size, the step size of DNA translocation and the ratio of the rotational rate of DNA over that of RuvB relative to RuvA is predicted.