Chemical friction along the minor groove of DNA facilitates enzymatic translocation of λ-exonuclease via electrostatic ratchet.

Abstract

DNA is a long polymeric substrate that provides specific binding sites for many proteins in cell nucleus. Both diffusion and directed translocation play an essential role for protein-DNA interactions in gene regulation processes but it is still not fully understood how specific proteins move and search their target sites in the myriad of DNA sequence repertoires. We use λ-exonuclease as a model of nucleic acid-molecular motors that processively translocates along the DNA. Here, we combined single molecule FRET and molecular dynamics (MD) simulation to examine how the dynamic interaction translates into overall enzymatic activity. Transient coupling between λ-exonuclease and its substrate DNA significantly alters its translocation by a factor of ∼30 due to chemical friction between a positive reside (ARG45) of the protein and electrostatic potential (EP) along the minor groove of DNA. Repulsive interaction gives rise to futile slippage events whereas attractive coupling between ARG45 and adenines at the minor grooves provides chemical ratcheting for unidirectional translocation, preventing diffusive backtracking by electrostatic friction. We propose an anti-friction-based ratchet for processive translocation. Our study provides new insights into not only interplay between dynamic chemophysical interaction and enzyme activity but also a role of the minor groove in regulating enzymatic activity based on DNA sequences.