Transforming Computational Power into Environmental Solutions: HPC-driven Research on Urethanase-mediated Plastic Degradation
Year: 2025
Type: conference-paper
Abstract: The extensive accumulation of persistent synthetic polymers has made plastics a rapidly expanding global concern. In this context, enzymatic degradation offers a viable and environmentally friendly alternative to the conventional plastic recycling methods. Here, we discuss how multi-microsecond Molecular Dynamics (MD) simulations and hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) methods have allowed us to shed light on the conformational dynamics and catalytic mechanisms underlying the activity of the polyurethane-degrading enzymes UMG-SP2 and UMG-SP3. Our findings emphasize the role of these computational approaches for the identification of the rate-limiting step, stationary states’ geometries, and residue-specific electrostatic effects, enabling subsequent mutagenesis studies to enhance the efficiency of these urethanases. The access to EuroHPC’s computing resources was essential to this research, as it allowed the extensive sampling of enzyme:substrate dynamics over large simulation timescales and the QM/MM-level resolution of the free-energy profile associated with the cleavage of the substrate’s urethane bond. This work demonstrates the relevant role of HPC-driven research in advancing mechanistic insights and highlights how the synergy between large-scale computational resources and enzymatic knowledge can enhance our understanding of plastic biodegradation.
Source: Procedia Computer Science
Authors: Pedro Paiva, Luís M.C. Teixeira, Pedro Ferreira, Daniel E. Otzen, Pedro A. Fernandes, Maria J. Ramos
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: diamond
Awards: G1240268737, G138060719, G1509028180, G1522114529, G1977608718, G2012127377, G2339299466, G2346795057, Laboratório Associado para a Química Verde - Tecnologias e Processos Limpos, Laboratório Associado para a Química Verde - Tecnologias e Processos Limpos, G2715139764, G2756637201, G2814222956, Estabelecimento computacional de mecanismos catalíticos enzimáticos com vista à biodegradação de plásticos e ao desenvolvimento de antídotos contra o envenenamento por serpentes baseados em inibidores enzimáticos., G332082475, G4046065984, G4073156454, G567200461, G5832795443, G5875825224, G5975318064, G6113984419, G6119126181, G6463117426, G6625491009, G6997658380, G824076568, G8334882390, Laboratório Associado para a Química Verde - Tecnologias e Processos Limpos, G8963217260
OpenAlex ID: W4414478437