Solvent Channels and Electric Fields Guide Proton Delivery to the Active Site of Heme Peroxidases
Year: 2025
Type: article
Abstract: The active sites of heme enzymes have evolved to control the formation of highly reactive intermediates in oxidative catalysis. Proton delivery to the heme is essential, yet the mechanisms of proton delivery remain poorly understood. Here, we identify routes and drivers of proton delivery in a heme peroxidase (ascorbate peroxidase) using computational approaches that combine classical, quantum, and hybrid methods with enhanced sampling and local electric field (LEF) analyses. Our results show that networks of active‐site water molecules facilitate proton exchange with Arg38, which may act as a transient proton carrier at the γ‐heme edge where the substrate binds. The distal His42 residue aids proton transfer into the active site via solvent at the δ‐edge. Molecular dynamics simulations of three heme peroxidases identify hydrated channels leading to both γ‐ and δ‐edges, allowing solvent protons to reach the active site. Comparison with eight other heme peroxidases shows that these channels are conserved. LEF analyses reveal a continuous electrostatic funnel drawing protons toward the heme from the γ‐ and δ‐edges, a feature that is broadly conserved across other peroxidases. These results suggest that nature pre‐organizes electrostatic funnels and solvent channels to provide multiple well‐defined routes for proton delivery in peroxidase catalysis.
Language: English
Subfield: Inorganic Chemistry
Field: Chemistry
Domain: Physical Sciences
Open Access status: hybrid
Estimated APC paid: $5,510
Funders: Leverhulme Trust, Royal Society of Chemistry, University of Bristol, Ministerio de Ciencia, Tecnología e Innovación Productiva, UK Catalysis Hub, Engineering and Physical Sciences Research Council, Biotechnology and Biological Sciences Research Council, Agencia Estatal de Investigación, H2020 European Research Council
Awards: G109057329, G1311748377, G1840372032, G2262748287, G2817958078, G3480869486, G4132708698, G425668148, G4501296617, Predictive computational models for Enzyme Dynamics, Antimicrobial resistance, Catalysis and Thermoadaptation for Evolution and Design, G5345040221, Creating and comprehending the circuitry of life: precise biomolecular design of multi-centre redox enzymes for a synthetic metabolism, Defining the structure of ferryl heme, G7037072674, G7084143925, Biocatalysis & Biotransformation: A 5th Theme for the National Catalysis Hub, Multi-scale enzyme modelling for SynBio: optimizing biocatalysts for selective synthesis of bioactive compounds, G8372834321, G8423103424, G845458034
OpenAlex ID: W4414403592