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

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.

Control of Genome Stability by EndoMS/NucS-Mediated Non-Canonical Mismatch Repair

“…The structure of the archaeal T. kodakarensis NucS-dsDNA complex reflected how NucS binds to its substrate [29,31]. The mismatched bases are flipped out from the dsDNA and arranged into a DNA binding site (recognition site) belonging to both N-terminal domains of the dimer, with a cluster of residues involved in the recognition and contact with the mismatched bases in the DNA.…”

Archaeal DNA Repair Mechanisms

“…Apo-and mismatched DNA:NucS/EndoMS complex structures suggest the enzyme forms a functional dimer and uses a "base-flipping" mechanism used by many DNA glycosylases (re Base Excision Repair) for recognition of mismatched bases [82][83][84]. Strikingly, offset cuts are made on opposite strands in vitro by NucS/EndoMS after mismatch recognition, resulting in a substrate akin to a DSB with two 4 nt 5 overhangs [70,85]. If this activity is maintained in vivo, the potentially cytotoxic consequences of DSBs (re DSBR in Archaea) must then be dealt with-a seemingly disadvantageous way of dealing with a simple mismatched base.…”