Exploring the Binding Mechanism and Dynamics of EndoMS/NucS to Mismatched dsDNA.

Yanjun Zhang,Shengyou Huang

doi:10.3390/ijms20205142

Abstract

The well-known mismatch repair (MMR) machinery, MutS/MutL, is absent in numerous Archaea and some Bacteria. Recent studies have shown that EndoMS/NucS has the ability to cleave double-stranded DNA (dsDNA) containing a mismatched base pair, which suggests a novel mismatch repair process. However, the recognition mechanism and the binding process of EndoMS/NucS in the MMR pathway remain unclear. In this study, we investigate the binding dynamics of EndoMS/NucS to mismatched dsDNA and its energy as a function of the angle between the two C-terminal domains of EndoMS/NucS, through molecular docking and extensive molecular dynamics (MD) simulations. It is found that there exists a half-open transition state corresponding to an energy barrier (at an activation angle of approximately 80) between the open state and the closed state, according to the energy curve. When the angle is larger than the activation angle, the C-terminal domains can move freely and tend to change to the open state (local energy minimum). Otherwise, the C-terminal domains will interact with the mismatched dsDNA directly and converge to the closed state at the global energy minimum. As such, this two-state system enables the exposed N-terminal domains of EndoMS/NucS to recognize mismatched dsDNA during the open state and then stabilize the binding of the C-terminal domains of EndoMS/NucS to the mismatched dsDNA during the closed state. We also investigate how the EndoMS/NucS recognizes and binds to mismatched dsDNA, as well as the effects of K ions. The results provide insights into the recognition and binding mechanisms of EndoMS/NucS to mismatched dsDNA in the MMR pathway.

Highlights

IntroductionThe fidelity of DNA replication is crucial for accurate transfer of generic information between generations
For all living organisms, the fidelity of DNA replication is crucial for accurate transfer of generic information between generations
The C-terminal domains will interact with the mismatched double-stranded DNA (dsDNA) directly and converge to the closed state at the global energy minimum

Summary

Introduction

The fidelity of DNA replication is crucial for accurate transfer of generic information between generations. No gene has been identified as encoding the MutS/MutL homolog and the genes encoding MutS/MutL homologs are dispensable in archaeal species, the rates and spectra of spontaneous mutations in these organisms are comparable to the prokaryotes which have the MutS/MutL mismatch repair system [19,20,21]. A recent study has identified a novel endonuclease, named EndoMS (endonuclease mismatch-specific), in the hyperthermophilic Archaea: Pyrococcus furiosus and Thermococcus kodakarensis, which recognizes mismatched bases in the DNA strand and cleaves both strands to produce 5 -protruding ends and suggests a novel MMR pathway in archaeal species that operates without the MutS/MutL homology [14,15,22,23,24,25]

Methods

Results

Conclusion