Katarzyna Świderek
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Profesor Titular de Universidad / Associate professor
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About
Katarzyna Świderek is an Associate Professor at Universitat Jaume I in Spain. Her research areas include enzyme design, molecular simulations, and the applications of artificial intelligence in biochemical studies. Recent articles authored by Professor Świderek explore topics such as protein template diversity, the mechanisms of proteases, and strategies for addressing SARS-CoV-2 pandemic threats.
Recent Grants
Grant: Open
Deciphering the structural and kinetic principles of enzymes to design advanced protein-based catalysts for enhanced biocatalysis
Open Date: 2025-04-01
Close Date: 2027-03-01
Grant: Close
Computational design of new enzymes to degrade poly(ethylene terephthalate), PET
Open Date: 2025-01-01
Close Date: 2025-06-01
Grant: Open
Theoretical studies of reactivity in cellular processes
Open Date: 2022-01-01
Close Date: 2026-12-01
Grant: Close
Unravelling the Reaction and Inhibition Mechanism of Proteasome 20S and Rhomboid Protease by QM/MM Theoretical Methods: two Bio-Macromolecules Involved in Cancer Proliferation.
Open Date: 2020-06-01
Close Date: 2022-12-01
Grant: Close
Computational studies of mechanism and inhibition of enzymatic proteolysis as complementary approach to the world of modern drug discovery.
Open Date: 2020-06-01
Close Date: 2022-12-01
Articles (10)
Year:
2025
Year:
2025
Year:
2025
Secondary amines, due to their reactivity, can transform protein templates into catalytically active entities, accelerating the development of artificial enzymes. However, existing methods, predominantly reliant on modified ligands or N‐terminal prolines, impose significant limitations on template selection. In this study, genetic code expansion was used to break this boundary, enabling secondary amines to be incorporated into alternative proteins and positions of choice. Pyrrolysine analogues carrying different secondary amines could be incorporated into superfolder green fluorescent protein (sfGFP), multidrug‐binding LmrR and nucleotide‐binding dihydrofolate reductase (DHFR). Notably, the analogue containing a D‐proline moiety demonstrated both proteolytic stability and catalytic activity, conferring LmrR and DHFR with the desired transfer hydrogenation activity. While the LmrR variants were confined to the biomimetic 1‐benzyl‐1,4‐dihydronicotinamide (BNAH) as the hydride source, the optimal DHFR variant favorably used the pro‐ R hydride from NADPH for stereoselective reactions ( e.r . up to 92 : 8), highlighting that a switch of protein template could broaden the nucleophile option for catalysis. Owing to the cofactor compatibility, the DHFR‐based secondary amine catalysis could be integrated into an enzymatic recycling scheme. This established method shows substantial potential in enzyme design, applicable from studies on enzyme evolution to the development of new biocatalysts.
Year:
2024
Year:
2024
Year:
2024
Year:
2024
Year:
2024
Year:
2023
Year:
2023
Collaborators (5)
Louis Y. P. Luk
-
Miguel Alcalde
CSIC Research Professor
-
Haritz Sardon
-
Sergio Martí
Profesor Titular de Universidad
Universitat Jaume I
carlos simmerling
Professor
Stony Brook University
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