# Networked Salt-Bridges Mediate Magnesium-Dependent Conformational Dynamics and Functional Regulation in Type IA Topoisomerases

## TL;DR

This study shows how magnesium ions control enzyme shape changes through salt-bridge networks, impacting DNA repair and enzyme activity.

## Contribution

Discovery of a magnesium-dependent salt-bridge network regulating conformational dynamics in Type IA topoisomerases.

## Key findings

- Mg2+ binding to a new site controls DNA gate opening and closing in TopIA.
- Salt-bridge networks modulate enzyme activity and protect against DNA damage when Mg2+ is low.
- The mechanism links environmental magnesium levels to enzyme function through structural changes.

## Abstract

Protein conformational dynamics are fundamental to enzyme function, yet the molecular mechanisms by which these dynamics are regulated remain poorly understood. Here, we reveal that a conserved network of salt-bridges, modulated by magnesium ions, serves as a key regulator of conformational transitions in Type IA topoisomerases (TopIA). Using a combination of molecular dynamics simulations, targeted protein mutagenesis, and functional assays, we demonstrate that Mg2+ binding to a previously unrecognized metal binding site orchestrates the opening and closing of the protein-mediated DNA gate—a critical step in TopIA’s catalytic cycle. Our results show that magnesium tunes the kinetics of the salt-bridge network’s configurational switching, directly impacting enzyme activity and providing a safeguard against DNA damage under Mg2+ depletion. This work provides a new chemical and structural framework for understanding divalent cation-dependent regulation of protein function via networked salt-bridges. Our findings open new avenues for the rational design of cation-sensitive proteins and inhibitors, and highlight an evolutionarily conserved strategy for coupling environmental sensing to molecular function.