Dynamic Differences in Clinically relevant Pen β-Lactamases from Burkholderia spp.

Antimicrobial resistance (AMR) is a global threat, with Burkholderia species contributing significantly to difficult-to-treat infections. Ambler Class A Pen β-lactamases are produced by all Burkholderia spp., and their mutation or overproduction leads to the resistance of β-lactam antibiotics. In this study we investigate the dynamic differences between four clinically relevant Pen β-lactamases (PenA, PenI, PenL and PenP) using machine learning driven enhanced sampling molecular dynamics simulations and the BindSiteS-CNN deep learning model. Although sharing the same structural fold, these enzymes exhibit distinct dynamic features due low sequence identity, resulting in different substrate profiles and catalytic turnover. The BindSiteS-CNN deep learning model further reveals local active site dynamics, offering insights into the Pen β-lactamase evolutionary adaptation. The findings reported here identify critical mutations and proposes new hotspots affecting Pen β-lactamase flexibility and function, which can be used to fight emerging resistance in these enzymes.