Exploring catechol binding to laccase with insights into enzyme dynamics for biosensing applications

Abstract

There is growing interest in using enzymatic sensors and bioreactors for detecting and removing toxic compounds. Phenolic pollutants like catechol are a major concern, and laccase, a versatile oxidase, has been widely employed for catechol degradation due to its strong binding affinity. In this study, we reconstruct the binding mechanism of catechol to laccase from the white-rot fungus Trametes versicolor using molecular dynamics simulations, free-energy calculations, Markov state modeling (MSM), and transition path theory (TPT). Our approach identifies five distinct macrostates, offering atomic-level insights into the structural and energetic landscape of the laccase-catechol interaction. Critical transition states and intermediates were characterized, emphasizing the role of the active site loop (A161-F162-P163-L164) and a gate mechanism involving neighboring residues. TPT analysis further quantified transitions among macrostates, revealing two dominant pathways that guide catechol from the unbound state to the active site through sequential and cooperative conformational changes.