Bridging experiment and theory: a computational exploration of UMG-SP3 dynamics
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Luís M. C. Teixeira
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.
Funding source: Novo Nordisk Fonden
Award Identifier / Grant number: NNF22OC0072891
Funding source: Fundação para a Ciência e a Tecnologia
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.
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Research ethics: Not applicable.
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Informed consent: Not applicable.
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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.
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Use of Large Language Models, AI and Machine Learning Tools: None declared.
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Conflict of interest: The authors state no conflict of interest.
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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.
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Data availability: The cartesian coordinates of the modelled complex and equilibrated structures, along with the force field parameters, are provided in the Supporting Information.
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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).
© 2025 IUPAC & De Gruyter
Artikel in diesem Heft
- Frontmatter
- Review Articles
- Minimum energy path methods and reactivity for enzyme reaction mechanisms: a perspective
- The quantum revolution in enzymatic chemistry: combining quantum and classical mechanics to understand biochemical processes
- A quantum chemical perspective of photoactivated biological functions
- Does chemistry need more physics?
- Rotational dynamics of ATP synthase: mechanical constraints and energy dissipative channels
- Transforming dreams into reality: a fairy-tale wedding of chemistry with quantum mechanics
- The quantum chemistry revolution and the instrumental revolution as evidenced by the Nobel Prizes in chemistry
- Influence of symmetry on the second-order NLO properties: insights from the few state approximations
- The dichotomy between chemical concepts and numbers after almost 100 years of quantum chemistry: conceptual density functional theory as a case study
- How ‘de facto variational’ are fully iterative, approximate iterative, and quasiperturbative coupled cluster methods near equilibrium geometries?
- Electronic structure of methyl radical photodissociation
- Bridging experiment and theory: a computational exploration of UMG-SP3 dynamics
- Research Articles
- O–Li⋯O and C–Li⋯C lithium bonds in small closed shell and open shell systems as analogues of hydrogen bonds
- Metal–ligand bonding and noncovalent interactions of mutated myoglobin proteins: a quantum mechanical study
Artikel in diesem Heft
- Frontmatter
- Review Articles
- Minimum energy path methods and reactivity for enzyme reaction mechanisms: a perspective
- The quantum revolution in enzymatic chemistry: combining quantum and classical mechanics to understand biochemical processes
- A quantum chemical perspective of photoactivated biological functions
- Does chemistry need more physics?
- Rotational dynamics of ATP synthase: mechanical constraints and energy dissipative channels
- Transforming dreams into reality: a fairy-tale wedding of chemistry with quantum mechanics
- The quantum chemistry revolution and the instrumental revolution as evidenced by the Nobel Prizes in chemistry
- Influence of symmetry on the second-order NLO properties: insights from the few state approximations
- The dichotomy between chemical concepts and numbers after almost 100 years of quantum chemistry: conceptual density functional theory as a case study
- How ‘de facto variational’ are fully iterative, approximate iterative, and quasiperturbative coupled cluster methods near equilibrium geometries?
- Electronic structure of methyl radical photodissociation
- Bridging experiment and theory: a computational exploration of UMG-SP3 dynamics
- Research Articles
- O–Li⋯O and C–Li⋯C lithium bonds in small closed shell and open shell systems as analogues of hydrogen bonds
- Metal–ligand bonding and noncovalent interactions of mutated myoglobin proteins: a quantum mechanical study