# Mechanistic models of asymmetric hand-over-hand translocation and nucleosome navigation by CMG helicase

## TL;DR

This study uses simulations to explain how the CMG helicase moves along DNA and navigates nucleosomes during eukaryotic replication.

## Contribution

The paper introduces a computational model showing how CMG helicase achieves directional translocation and interacts with nucleosomes.

## Key findings

- Asymmetric rotational transitions among ssDNA-binding states enable CMG directional translocation and DNA unwinding.
- Csm3/Tof1 suppresses backtracking by gripping the parental DNA, while RPA prevents lagging-strand clogging.
- The histone chaperone FACT lowers nucleosome traversal barriers and prevents histone transfer to the lagging strand.

## Abstract

Faithful replication of eukaryotic chromatin requires the CMG helicase to translocate directionally along single-stranded DNA (ssDNA) while unwinding double-stranded DNA (dsDNA) and navigating nucleosomes. However, the mechanism by which CMG achieves processive translocation and deals with nucleosomal barriers remains incompletely understood. Here, using coarse-grained molecular dynamics simulations with ATP-driven conformational switching, we show that asymmetric rotational transitions among four distinct ssDNA-binding states enable CMG to achieve directional translocation and DNA unwinding. We further demonstrate that the fork protection complex (Csm3/Tof1) and RPA enhance processivity through distinct mechanisms: Csm3/Tof1 grips the parental duplex to suppress backtracking, while RPA alleviates lagging-strand clogging. Upon nucleosome encounter, Csm3/Tof1 promoted partial unwrapping of the entry DNA, but further progression is energetically restricted near the nucleosomal dyad. The histone chaperone FACT lowers this barrier and simultaneously prevents inappropriate histone transfer to the lagging strand. Our results provide mechanistic insights into how the eukaryotic replisome coordinates helicase activity, nucleosome navigation, histone chaperone function, and histone recycling during eukaryotic DNA replication.

The replicative helicase CMG unidirectionally unwinds DNA during eukaryotic chromatin replication. Here, the authors computationally reproduce CMG translocation and show how it traverses a nucleosome with help of replication proteins.