Publications
Members of the COST Action COZYME publish in renowned academic journals. This page contains articles that result from the joint work of two or more Action members and their collaborators.
BOOK OF ABSTRACTS
Working group meeting
April 16th–17th, 2026
Belgrade, Serbia
Mobilizing the Biocatalysis Community for Reproducible and Reusable Data Collection
Marques S. M. Planas-Iglesias J., Velecký J., Musil M., Asano Y., Borowski T., Brissos V., Cespug M., Chorozian K., Dadashipour M., Erdem E., Ferrandi E. E., Grigorakis K., Kluza A., Lawniczek J., Makryniotis K., Monti D., Nestl B., Ngo A. C., Nikolaivits E., Patti S., Pentari C., Rodrigues C. F., Schopper T., Seweryn-Ożóg K., Szaleniec M., Taborda A., Tataruch M., Tischler D., Topakas E., Wang J., Wójcik P, Wojtkiewicz A. M., Woodley J. M., Zastawny O., Martins L. O., Fraaije M. W., Pleiss J., Schnell S., Damborsky J., Mazurenko S., Bedna D.
ACS Catalysis, 2026.
https://pubs.acs.org/doi/10.1021/acscatal.5c07904
Enzymes for synthesis and degradation of bio-based polyesters: automatic in silico screening and experimental validation
Todea, A., Fortuna, S., Vattovaz, D., di Stefano, D., Carosati, E., Vlad, M., Gardossi, L. ChemSusChem, 2026, 19, e202502311.
https://doi.org/10.1002/cssc.202502311Digital Object Identifier (DOI)
Reduced Processivity in a Chitobiohydrolase Enhances LPMO-Assisted Chitin Depolymerization
Votvik A. K., Forsberg Z., Gautieri A., Eijsink V. G. H., Sørlie M.
Biochemistry 2026, 65, 5, 591-602.
https://www.cell.com/iscience/fulltext/S2589-0042(25)02518-0
Accessible biocatalyst development by rapid in vitro semi-rational engineering (RISE) of enzymes
Telek A., Zsolt Gaják V., Dargó G., Mičan J., Bednář D.,
https://www.cell.com/iscience/fulltext/S2589-0042(25)02518-0
Regioselective Sesquiterpene Hydroxylation Directed by Tunnel Remodeling in Rieske Oxygenases
FireProtDB 2.0: large-scale manually curated database of the protein stability data
Artificial Metalloenzymes
Structure–Function Analysis of an Understudied Type of LPMO with Unique Redox Properties and Substrate Specificity
Development of a highly active engineered PETase enzyme for polyester degradation
Integrating Computational and Experimental Methods for the Rational Ecodesign and Synthesis of Functionalized Safe and Sustainable Biobased Oligoesters
Decoding Protein Stabilization: Impact on Aggregation, Solubility, and Unfolding Mechanisms
Biochemical and Computational Characterization of Haloalkane Dehalogenase Variants Designed by Generative AI: Accelerating the SN2 Step
Engineering Dehalogenase Enzymes Using Variational Autoencoder-Generated Latent Spaces and Microfluidics
Colloidal Protein–Silver Nanoparticle Metalloenzyme as Artificial Redox Biocatalyst
Developing and improving enzyme-driven technologies to synthesise emerging prebiotics
Network Dynamics as Fingerprints of Thermostability in an In Silico-Engineered DyP-Type Peroxidase
Best Practices for Machine Learning-Assisted Protein Engineering
Recombinant napin expression in Pichia pastoris: Structural and functional attributes in comparison with canola-derived napin
Allosteric regulation of L-lactate dehydrogenase: Beyond effector-mediated tetramerization
BOOK OF ABSTRACTS
Working group meeting
April 24th–25th, 2025
Athens, Greece
Structural and Mechanistic Characterization of the Flavin-Dependent Monooxygenase and Oxidase Involved in Sorbicillinoid Biosynthesis
Tjallinks, G., Angeleri, N., Nguyen, Q. T., Mannucci, B., Arentshorst, M., Visser, J., Ram, A. F. J., Fraaije, M. W., Mattevi, A., ACS Chemical biology, 2025, 20, 646–655.
Dehydrogenase versus oxidase function: the interplay between substrate binding and flavin microenvironment
Guerriere, T. B., Vancheri, A., Ricotti, I., Serapian, S. A., Eggerichs, D., Tischler, D., Colombo, G., Mascotti, M. L., Fraaije, M. W., Mattevi, A., ACS Catal. 2025, 15, 1046–1060.
Biochemical and structural insights into pinoresinol hydroxylase from Pseudomonas sp.
Guerriere, T. B., Fraaije, M. W., Mattevi, A., Archives of biochemistry and biophysics, 2025, 764, 110247.
Broadening the Catalytic Scope of the Peroxygenase Activity of a Bacterial Tyrosine Hydroxylase
Carraretto, D., Alonso-Cotchico, L., Martin, C., Trajković, M., L. van Beek, H., Mattevi, A., Fraaije, M.W., Lucas, M.F., Lončar. N., ChemCatChem, 2025, 17, e202401819.
Design of a gold nanoparticles site
in an engineered lipase: an artificial metalloenzyme with enantioselective
reductase-like activity.
Garcia-Sanz C., de las Rivas B; Palomo J. M. Nanoscale 2024, 16 (14), 6999-7010.
https://pubs.rsc.org/en/content/articlelanding/2024/nr/d4nr00573b
Artificial manganese metalloenzymes with
laccase-like activity: design, synthesis, and characterization.
Garcia-Sanz C., Andreu A., Pawlyta M., Vukoičić A., Milivojević A., de las Rivas
B., Bezbradica D., Palomo J. M. ACS Applied Bio Materials 2024, 7, 4760-4771. https://pubs.acs.org/doi/10.1021/acsabm.4c00571
Zinc Nanobiohybrids for the Photocatalytic Conversion of CO2 to Bicarbonate
Garcia-Sanz C., Palomo J.M. Zinc Nanobiohybrids for the Photocatalytic
Conversion of CO2 to Bicarbonate. ACS Sustain. Chem. Eng. 2024, 12 (36), 13678-13686.
Efficient biotransformation of biobased raw materials into novel polyesters/polyesteramides; comparative investigation of enzymatic synthesis of block and random copolymers and terpolymers
Benea, I.C., Dăescu, D., Todea, A., Nagy, L., Keki, S., Păușescu, I., Pellis, A., Peter, F., International Journal of Biological Macromolecules, 2024, 282, 137046.
Reactive natural deep eutectic solvents increase selectivity and efficiency of lipase catalyzed esterification of carbohydrate polyols
Buzatu, A.R, Soler, M.A., Fortuna, S., Ozkilinc, O., Dreavă, D.M., Bîtcan, I., Badea, V., Giannozzi, P., Fogolari, F., Gardossi, L., Peter, F., Todea, A., Boeriu, C.G., Catalysis Today, 2024, 426, 14373.
Enzymatic Synthesis and Structural Modeling of Bio-Based Oligoesters as an Approach for the Fast Screening of Marine Biodegradation and Ecotoxicity.
Todea, A., Bîtcan, I., Giannetto, M., Rădoi, I.I., Bruschi, R., Renzi, M., Anselmi, S., Provenza, F., Bentivoglio, T., Asaro, F., Carosati, A. Gardossi, L., Int. J. Mol. Sci. 2024, 25, 5433.
Lipase-catalysed esterification in a reactive natural deep eutectic solvent leads to lauroylcholine chloride rather than glucose ester
Buzatu, A.R., Soler, M.A., Ozge Ozkilinc, O, Fortuna, S., Dreavă, D.M., Bîtcan, I. Giannozzi, P., Fogolari, F., Gardossi, L., Peter, F., Todea, A., Gabriela Boeriu, C., React. Chem. Eng. 2024, 9, 2623.
https://pubs.rsc.org/en/content/articlelanding/2024/re/d4re00209a
New model compounds for the efficient colorimetric screening of medium chain length polyhydroxyalkanoate (mcl-PHA) depolymerases reveal mechanism of activity
Nenadović, M., Maršavelski, A., Škaro Bogojević, S., Maslak, V., Nikodinovć-Runić, J., Milovanović. J., International Journal of Biological Macromolecules, 2024, 283, 137672.
The STRENDA Biocatalysis Guidelines for cataloguing metadata
Malzacher, S., Meißner, D., Range, J., Findrik Blažević, Z., Rosenthal, K., Woodley, J.M., Wohlgemuth, R., Wied, P., Nidetzky, B., Giessmann, R.T., Prakinee, K., Chaiyen, P., Bommarius, A.S., Rohwer, J.M., de Souza, R.O.M.A., Halling, P.J., Pleiss, J., Kettner, C., Rother, D., Nature Catalysis, 2024, 7, 1245-1249.
CANDy: Automated analysis of domain architectures in carbohydrate-active enzymes
Windels, A., Franceus, J., Pleiss, J., Desmet, T., PLOS ONE, 2024, 19, 1–16.
Protein representations: Encoding biological information for machine learning in biocatalysis
Harding-Larsen D., Funk J., Madsen N.G., Gharabli H., Acevedo-Rocha C.G., Mazurenko S., Welner D.H., Biotechnology Advances, 2024, 77, 108459.
Unlocking Catalytic Diversity of a Formate Dehydrogenase: Formamide Activity for NADPH Regeneration and Amine Supply for Asymmetric Reductive Amination
Maier A., Knaus T., Mutti F.G., Tischler D., ACS Catal. 2024, 14, 2207−2215.
Structure, mechanism, and evolution of the last step in vitamin C biosynthesis
Biosynthetic Strategies of Berberine Bridge Enzyme-like Flavoprotein Oxidases toward Structural Diversification in Natural Product Biosynthesis
Evolution, structure, and drug-metabolizing activity of mammalian prenylcysteine oxidases
Distal mutations enhance efficiency of free and immobilized NOV1 dioxygenase for vanillin synthesis
De Simone M., Alonso-Cotchico L., Lucas M. L., Brissos V., Martins L. O., Journal of Biotechnology, 2024, 391, 92–98.
Biomimetic CO2 Capture Unlocked through Enzyme Mining: Discovery of a Highly Thermo- and Alkali-Stable Carbonic Anhydrase
BOOK OF ABSTRACTS
COZYME meeting at University of Zagreb Faculty of Science //
Enzymatic detection of histamine: Applications, challenges, and improvement potential through biocatalyst engineering
Rodríguez-Núñez, K., Serey, M., Pastén, M-J., Bernal, C., Ensari, Y., Davari, M. D., Martinez, R., Food Control, 2024, 162, 110436.
https://doi.org/10.1016/j.
Fluent Integration of Laboratory Data into Biocatalytic Process Simulation Using EnzymeML, DWSIM, and Ontologies
Behr, A. S., Surkamp, J., Abbaspour, E., Häußler, M., Lütz, S., Pleiss, J., Kockmann, N., Rosenthal, K., Processes, 2024, 12, 597.
Discovery and biochemical characterization of thermostable glycerol oxidases
Santema, L.L., Rotilio, L., Xiang, R., Tjallinks, G., Guallar, V., Mattevi, A., Fraaije, M.W., Appl. Microbiol. Biotechnol., 2024, 108, 61.
Exploring new galaxies: Perspectives on the discovery of novel PET-degrading enzymes
Mican, J., Jaradat, D. M. M., Liu, W., Weber, G., Mazurenko, S., Bornscheuer, U. T., Damborsky, J., Wei, R., Bednar. D., Applied Catalysis B: Environmental , 2024, 342,
Tailoring FPOX enzymes for enhanced stability and expanded substrate recognition
Estiri, H., Bhattacharya, S., Buitrago, J.A.R.. Castagna, R., Legzdina, L., Casucci, G., Ricci, A., Parisini, E., Gautieri, A., Scientific Reports, 2023, 13, 18610.
Modulating Substrate Specificity of Rhizobium sp. Histamine Dehydrogenase through Protein Engineering for Food Quality Applications
Rodríguez-Núñez, K., Cortés-Monroy, A., Serey, M., Ensari, Y., Davari, M.D., Bernal, C., Martinez, R., Molecules, 2023,
Brave new surfactant world revisited by thermoalkalophilic lipases: computational insights into the role of SDS as a substrate analog
Shehata, M., Unlu, A., Iglesias-Fernandez, J., Osuna, S., Sezerman, O. U., Timucin, E., PhysChemChemPhys, 2023, 25, 2234-2247.
EnzymeML: seamless data flow and modeling of enzymatic data
Lauterbach, S., Dienhart, H., Range, J., Malzacher, S., Spöring, J.-D., Rother, D., Pinto, M.F., Martins, P., Lagerman, C.E., Bommarius, A.S., Høst, A.V., Woodley, J.M., Ngubane, S., Kudanga, T., Bergmann, F.T., Rohwer, J.M., Iglezakis, D., Weidemann, A., Wittig, U., Kettner, C., Swainston, N., Schnell, S., Pleiss, J., Nature Methods, 2023, 20, 400-402.
Curse and Blessing of Non-Proteinogenic Parts in Computational Enzyme Engineering
Machine Learning-Guided Protein Engineering
Kouba P., Kohout P., Haddadi F., Bushuiev A., Samusevich R., Sedlar J., Damborsky J., Pluskal T., Sivic J., Mazurenko S., ACS Catalysis, 2023, 13, 13863-13895.
