Analysis of mechanism of branch migration by RuvB using molecular dynamics simulation

Ishida, Hisashi

Homologous recombination occurs in all organisms, allowing for genetic exchange, the reassortment of genes along chromosomes, and the repair of broken DNA strands. A four-stranded DNA structure called a Holliday junction (HJ) is a central intermediate state in homologous recombination, and one of the crucial steps in the process of recombination is branch migration of the HJ. In Escherichia coli, branch migration of the HJ is promoted by proteins RuvA and RuvB. To understand the relationship between the conformational changes in RuvB and the translocation of the HJ DNA, molecular dynamics (MD) simulations of the RuvA/RuvB/HJ DNA complex were carried out at a constant pressure of one bar and a temperature of 350 K. It was found that several low frequency modes showed the motions of the RuvB hexamer were coupled with the translational motion of DNA.