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.

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.

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