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Bridging experiment and theory: a computational exploration of UMG-SP3 dynamics

  • Luís M. C. Teixeira , Pedro Paiva , Pedro Ferreira , Laura Rotilio , Jens P. Morth , Daniel E. Otzen , Pedro A. Fernandes und Maria J. Ramos ORCID logo EMAIL logo
Veröffentlicht/Copyright: 27. August 2025

Abstract

Understanding how dynamical behaviour and structural features influence protein function and stability is crucial. While extensive experimental data exist, studying real-time protein dynamics and enzyme catalysis remains challenging. Computational advances have been instrumental in overcoming experimental limitations, enabling molecular-level insights into biological macromolecules. The integration of experimental and computational approaches has proven to be very valuable in protein studies. Here, we demonstrate this synergy by investigating the conformational stability of the urethanase UMG-SP3, which exhibited a lower optimum temperature than expected and rapid loss of activity. Molecular dynamics simulations of the UMG-SP3-substrate complex at various temperatures revealed structural rearrangements outside the optimum temperature range (25–35 °C), leading to loss of the native protein fold and impaired substrate binding. Even at the optimum temperature for activity, the enzyme struggled to maintain a catalytically favourable orientation, aligning with experimental findings. Unfolding profiles were determined through differential scanning fluorimetry. Notably, the computational results provided a rationaly for the structural instability observed experimentally, emphasizing the strength of computational methods in elucidating protein behaviour at the atomic level. This study highlights the importance of combining experimental and computational approaches to deepen our understanding of protein stability and function.


Corresponding author: Maria J. Ramos, LAQV/REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal; and EnZync Center for Enzymatic Deconstruction of Thermoset Plastics, Aarhus , Denmark, e-mail:
Article note: A collection of invited papers to celebrate the UN’s proclamation of 2025 as the International Year of Quantum Science and Technology.

Funding source: Novo Nordisk Fonden

Award Identifier / Grant number: NNF22OC0072891

Award Identifier / Grant number: UID/50006

Acknowledgments

LMCT, PP, PF, PAF and MJR would like to thank the European High-Performance Computing Joint Undertaking (EuroHPC JU) that granted the access to MeluXina, the petascale Euro-HPC supercomputer located in Bissen, Luxembourg, under proposal EHPC-REG2023R03-163. PF thanks FCT for funding (Ref. CEECINST/00136/2021/CP2820/CT0002 DOI 10.54499/CEECINST/00136/2021/CP2820/CT0002. LMCT would also like to thank FCT/MECI for funding his PhD project through the grant 2024.05090.BD.

  1. Research ethics: Not applicable.

  2. Informed consent: Not applicable.

  3. Author contributions: Conceptualization: LMCT, PP, PF, LR, JPM, DEO, PAF, and MJR; Methodology: LMCT, PP, PF, LR, PAF, and MJR; Formal Analysis: LMCT and PP; Investigation: LMCT, PP, and LR; Writing – Original Draft: LMCT; Writing – Review & Editing: LMCT, PP, PF, LR, JPM, DEO, PAF, and MJR; Project Administration: JPM, DEO, PAF, and MJR; Funding Acquisition: PAF and MJR.

  4. Use of Large Language Models, AI and Machine Learning Tools: None declared.

  5. Conflict of interest: The authors state no conflict of interest.

  6. Research funding: The authors would like to thank the EnZync consortium, and the financial support received by the Novo Nordisk Fonden, under project NNF22OC0072891 (Challenge Programme 2022 - Recycling or a Sustainable Society). This work received financial support from the PT national funds (FCT/MECI, Fundação para a Ciência e Tecnologia and Ministério da Educação, Ciência e Inovação) through the project UID/50006 -Laboratório Associado para a Química Verde - Tecnologias e Processos Limpos.

  7. Data availability: The cartesian coordinates of the modelled complex and equilibrated structures, along with the force field parameters, are provided in the Supporting Information.

  8. Software availability: The initial PDB structure (9FW1) is available for download at https://www.rcsb.org/structure/9FW1. System preparation, minimization, and molecular dynamics simulations were performed using the AMBER 18 package, which can be purchased at https://ambermd.org/. The pKa prediction was carried out using the ProteinPrepare web server (https://open.playmolecule.org/tools/proteinprepare) and PROPKA 3.0, which is available for download at https://propka.readthedocs.io/en/latest. Visualization of the system was done using VMD, which can be downloaded from https://www.ks.uiuc.edu/Research/vmd/. Parameterization of DUE-MDA was performed using Gaussian 09 D01, which can be purchased at https://gaussian.com/. The enzyme-substrate complex was modelled using PyMOL, available at https://www.pymol.org/.

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Supplementary Material

This article contains supplementary material (https://doi.org/10.1515/pac-2025-0489).


Received: 2025-04-22
Accepted: 2025-08-08
Published Online: 2025-08-27
Published in Print: 2025-10-27

© 2025 IUPAC & De Gruyter

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