Dynamics of monomeric and hexameric helicases

Abstract

Helicases are a ubiquitous class of enzymes that use the energy of ATP hydrolysis to unwind nucleic acid (NA) duplex. According to the structures, helicases can be classified as the non-ring-shaped (or monomeric) and ring-shaped (or hexameric). To understand the NA unwinding mechanism, here we study theoretically the unwinding dynamics of both the monomeric and hexameric helicases based on our proposed model. Various available single-molecule experimental data on unwinding speed of both the monomeric and hexameric helicases versus the external force applied to the ends of the NA duplex to unzip the duplex or versus the stability of the NA duplex are consistently and quantitatively explained. We provide quantitative explanations of the experimental data showing that while the unwinding speeds of some monomeric helicases are insensitively dependent on the external force they are sensitively dependent on the stability of the NA duplex. The experimental data showing that wild-type Rep translocates along ssDNA with a lower speed than RepΔ2B (removal of the 2B subdomain of Rep) and that RepΔ2B monomer can unwind DNA whereas the wild-type monomer is unable to unwind DNA are also quantitatively explained. Our studies indicate that although the monomeric and hexameric helicases show very different features on the dependence of NA unwinding speed upon the external force, they use much similar active mechanisms to unwind NA duplex.