COPASI

COPASI's Use In Enzymology

2025
Riepl D, Abou-Hamdan A, Gellner J, Biner O, Sjöstrand D, Högbom M, von Ballmoos C, Kaila VRI (2025) Molecular Principles of Proton-Coupled Quinone Reduction in the Membrane-Bound Superoxide Oxidase. Journal of the American Chemical Society 147:6866–6879 Enzymology Link

1 publication
2024
Erbez JP, Rangel GH, Davila M, Englade JA, Erbez AD, Rattanpal J, Li H, Chen Y, Toney MD (2024) Activation Heat Capacities in Pyridoxal Phosphate Enzymes. ACS Catalysis 14:11178–11195 Biochemistry Enzymology Link
Nashed A, Naidoo KJ (2024) Universal Glycosyltransferase Continuous Assay for Uniform Kinetics and Inhibition Database Development and Mechanistic Studies Illustrated on ST3GAL1, C1GALT1, and FUT1. ACS Omega 9:17518–17532 Enzymology Laboratory Method Link
Teshima M, Sutiono S, Döring M, Beer B, Boden M, Schenk G, Sieber V (2024) Development of a Highly Selective NAD+-Dependent Glyceraldehyde Dehydrogenase and its Application in Minimal Cell-Free Enzyme Cascades. ChemSusChem 17:e202301132 Metabolism Enzymology Link

3 publications
2023
Bloomer BJ, Natoli SN, Garcia-Borràs M, Pereira JH, Hu DB, Adams PD, Houk KN, Clark DS, Hartwig JF (2023) Mechanistic and structural characterization of an iridium-containing cytochrome reveals kinetically relevant cofactor dynamics. Nature Catalysis 6:39–51 Enzymology Link
Czarnievicz N, Rubanu MG, Iturralde M, Albarran-Velo J, Diamanti E, Gotor-Fernandez V, Skolimowski M, López-Gallego F (2023) A Multiplex Assay to Assess the Transaminase Activity toward Chemically Diverse Amine Donors. ChemBioChem 24:e202200614 Laboratory Method Enzymology Link
Katsyv A, Kumar A, Saura P, Pöverlein MC, Freibert SA, Stripp ST, Jain S, Gamiz-Hernandez AP, Kaila VRI, Müller V, Schuller JM (2023) Molecular Basis of the Electron Bifurcation Mechanism in the [FeFe]-Hydrogenase Complex HydABC. Journal of the American Chemical Society 145:5696–5709 Enzymology Biochemistry Link
Lauterbach S, Dienhart H, Range J, Malzacher S, Spöring J-D, Rother D, Pinto MF, Martins P, Lagerman CE, Bommarius AS, Høst AV, Woodley JM, Ngubane S, Kudanga T, Bergmann FT, Rohwer JM, Iglezakis D, Weidemann A, Wittig U, Kettner C, Swainston N, Schnell S, Pleiss J (2023) EnzymeML: seamless data flow and modeling of enzymatic data. Nature Methods 20:400–402 Computational Method Enzymology Link
Olsen LF (2023) Complex dynamics in an unexplored simple model of the peroxidase–oxidase reaction. Chaos 33:023102 Biochemistry Enzymology Link
Ouyang X, Liu G, Ji S, Luo S, Shi T, Xu P, Zhao Y-L, Tang H (2023) Dioxetane and lactone pathways in dioxygenolytic ring cleavage catalyzed by 2,5-dihydroxypyridine dioxygenase. Chem Catalysis 3:100480 Enzymology Link

6 publications
2022
de la Sovera V, Martínez S, Umpiérrez D, Vila MA, Gonzalez D, Seoane G, Veiga N, Carrera I (2022) Synthesis of Azido-Dienediols by Enzymatic Dioxygenation of Benzylazides: An Experimental and Theoretical Study. European Journal of Organic Chemistry 2022:e202101156 Chemistry Enzymology Link
Gallas JAC, Olsen LF (2022) Complexity in subnetworks of a peroxidase-oxidase reaction model. Chaos 32:063122 Biochemistry Enzymology Link
He Y, Li K, Wang J, Xu L, Yan J, Yang M, Yan Y (2022) A novel strategy for biodiesel production by combination of liquid lipase, deep eutectic solvent and ultrasonic-assistance in scaled-up reactor: Optimization and kinetics. Journal of Cleaner Production 372:133740 Enzymology Biotechnology Link
Knox HL, Sinner EK, Townsend CA, Boal AK, Booker SJ (2022) Structure of a B12-dependent radical SAM enzyme in carbapenem biosynthesis. Nature 602:343–348 Biochemistry Enzymology Link
Range J, Halupczok C, Lohmann J, Swainston N, Kettner C, Bergmann FT, Weidemann A, Wittig U, Schnell S, Pleiss J (2022) EnzymeML-a data exchange format for biocatalysis and enzymology. FEBS Journal 289:5864–5874 Enzymology Computational Method Link
Rietmeyer L (2022) Étude fonctionnelle et structurale des transférases de la famille Fem de Staphylococcus aureus. Ph.D. Thesis, Sorbonne Université, Paris, France Enzymology Link
Sinner EK, Townsend CA (2022) Purification and characterization of sequential cobalamin-dependent radical SAM methylases ThnK and TokK in carbapenem β-lactam antibiotic biosynthesis. Methods in Enzymology 669:29–44 Enzymology Link

7 publications
2021
Chen X, Ouyang X, Li J, Zhao Y-L (2021) Natural Syringyl Mediators Accelerate Laccase-Catalyzed β-O-4 Cleavage and Cα-Oxidation of a Guaiacyl Model Substrate via an Aggregation Mechanism. ACS Omega 6:22578–22588 Enzymology Link
Gallas JAC, Hauser MJB, Olsen LF (2021) Complexity of a peroxidase-oxidase reaction model. Physical Chemistry Chemical Physics 23:1943–1955 Enzymology Link
Huysmans GHM, Ciftci D, Wang X, Blanchard SC, Boudker O (2021) The high-energy transition state of the glutamate transporter homologue GltPh. EMBO Journal 40:e105415 Enzymology Link
Klimacek M, Zhong C, Nidetzky B (2021) Kinetic modeling of phosphorylase-catalyzed iterative β-1,4-glycosylation for degree of polymerization-controlled synthesis of soluble cello-oligosaccharides. Biotechnology for Biofuels and Bioproducts 14:134 Biotechnology Enzymology Link
Ribeiro de Barros H, García I, Kuttner C, Zeballos N, Camargo PHC, de Torresi SIC, López-Gallego F, Liz-Marzán LM (2021) Mechanistic Insights into the Light-Driven Catalysis of an Immobilized Lipase on Plasmonic Nanomaterials. ACS Catalysis 11:414–423 Enzymology Materials Science Link

5 publications
2020
Ferrall-Fairbanks MC, Kieslich CA, Platt MO (2020) Reassessing enzyme kinetics: Considering protease-as-substrate interactions in proteolytic networks. Proceedings of the National Academy of Sciences USA 117:3307–3318 Enzymology Link
Stines-Chaumeil C, Mavré F, Kauffmann B, Mano N, Limoges B (2020) Mechanism of Reconstitution/Activation of the Soluble PQQ-Dependent Glucose Dehydrogenase from Acinetobacter calcoaceticus: A Comprehensive Study. ACS Omega 5:2015–2026 Enzymology Link
Tian S, Jones SM, Solomon EI (2020) Role of a Tyrosine Radical in Human Ceruloplasmin Catalysis. ACS Central Science 6:1835–1843 Enzymology Link

3 publications
2019
Adelson CN, Johnston EM, Hilmer KM, Watts H, Dey SG, Brown DE, Broderick JB, Shepard EM, Dooley DM, Solomon EI (2019) Characterization of the Preprocessed Copper Site Equilibrium in Amine Oxidase and Assignment of the Reactive Copper Site in Topaquinone Biogenesis. Journal of the American Chemical Society 141:8877–8890 Enzymology Biochemistry Link
Faraj SE, Centeno M, Rossi RC, Montes MR (2019) A kinetic comparison between E2P and the E2P-like state induced by a beryllium fluoride complex in the Na,K-ATPase. Interactions with Rb. Biochimica Et Biophysica Acta. Biomembranes 1861:355–365 Enzymology Link
Meyer-Almes F-J (2019) Determination of the binding mechanism of histone deacetylase inhibitors. Chemical Biology & Drug Design 93:1214–1250 Enzymology Link
Muth M, Jänsch N, Kopranovic A, Krämer A, Wössner N, Jung M, Kirschhöfer F, Brenner-Weiß G, Meyer-Almes F-J (2019) Covalent inhibition of histone deacetylase 8 by 3,4-dihydro-2H-pyrimido[1,2-c][1,3]benzothiazin-6-imine. Biochimica et Biophysica Acta 1863:577–585 Enzymology Biochemistry Link
Saffioti NA, de Sautu M, Ferreira-Gomes MS, Rossi RC, Berlin J, Rossi JPFC, Mangialavori IC (2019) E2P-like states of plasma membrane Ca2+‑ATPase characterization of vanadate and fluoride-stabilized phosphoenzyme analogues. Biochimica et Biophysica Acta 1861:366–379 Enzymology Link
Schilling IE, Hess R, Bolotin J, Lal R, Hofstetter TB, Kohler H-PE (2019) Kinetic Isotope Effects of the Enzymatic Transformation of γ-Hexachlorocyclohexane by the Lindane Dehydrochlorinase Variants LinA1 and LinA2. Environmental Science & Technology 53:2353–2363 Enzymology Environmental Sciences Link
Schweipert M, Jänsch N, Sugiarto WO, Meyer-Almes F-J (2019) Kinetically selective and potent inhibitors of HDAC8. Biological Chemistry 400:733–743 Enzymology Link
Sinner EK, Lichstrahl MS, Li R, Marous DR, Townsend CA (2019) Methylations in complex carbapenem biosynthesis are catalyzed by a single cobalamin-dependent radical S-adenosylmethionine enzyme. Chemical Communications 55:14934–14937 Enzymology Link
Toney MD (2019) Carbon Acidity in Enzyme Active Sites. Frontiers in Bioengineering and Biotechnology 7:25 Enzymology Link

9 publications
2018
Nguyen VD, Styevkó G, Ta LP, Tran ATM, Bujna E, Orbán P, Dam MS, Nguyen QD (2018) Immobilization and some properties of commercial enzyme preparation for production of lactulose-based oligosaccharides. Food and Bioproducts Processing 107:97–103 Biotechnology Enzymology Link
Oh S, Boudker O (2018) Kinetic mechanism of coupled binding in sodium-aspartate symporter GltPh. eLife 7:e37291 Enzymology Link
Vögeli B (2018) Control of reactive intermediates in enzymes and enzyme complexes. Ph.D. Thesis, Philipps-Universität Marburg, Germany. Enzymology Link
Vranish JN, Ancona MG, Oh E, Susumu K, Lasarte Aragonés G, Breger JC, Walper SA, Medintz IL (2018) Enhancing Coupled Enzymatic Activity by Colocalization on Nanoparticle Surfaces: Kinetic Evidence for Directed Channeling of Intermediates. ACS Nano 12:7911–7926 Biotechnology Enzymology Link

4 publications
2017
Amdahl MB, Sparacino-Watkins CE, Corti P, Gladwin MT, Tejero J (2017) Efficient Reduction of Vertebrate Cytoglobins by the Cytochrome b 5/Cytochrome b 5 Reductase/NADH System. Biochemistry 56:3993–4004 Biochemistry Enzymology Link
Hay S (2017) Extracting Kinetic Isotope Effects From a Global Analysis of Reaction Progress Curves. Methods in Enzymology 596:85–111 Enzymology Link
Karasik A, Ledwitch KV, Arányi T, Váradi A, Roberts AG, Szeri F (2017) Boosted coupling of ATP hydrolysis to substrate transport upon cooperative estradiol-17-β-D-glucuronide binding in a Drosophila ATP binding cassette type-C transporter. FASEB Journal 32:fj–201700606R Enzymology Link
Meyners C, Meyer-Almes F-J (2017) Impact of binding mechanism on selective inhibition of histone deacetylase isoforms. Chemical Biology & Drug Design 90:1215–1225 Enzymology Pharmacology Link
Milivojević A, Ćorović M, Carević M, Banjanac K, Vujisić L, Veličković D, Bezbradica D (2017) Highly efficient enzymatic acetylation of flavonoids: Development of solvent-free process and kinetic evaluation. Biochemical Engineering Journal 128:106–115 Biotechnology Enzymology Link
Schmölzer K, Eibinger M, Nidetzky B (2017) Active-Site His85 of Pasteurella dagmatis Sialyltransferase Facilitates Productive Sialyl Transfer and So Prevents Futile Hydrolysis of CMP-Neu5Ac. ChemBioChem 18:1544–1550 Enzymology Link
Trieu MM, Devine EL, Lamarche LB, Ammerman AE, Greco JA, Birge RR, Theobald DL, Oprian DD (2017) Expression, purification, and spectral tuning of RhoGC, a retinylidene/guanylyl cyclase fusion protein and optogenetics tool from the aquatic fungus Blastocladiella emersonii. Journal of Biological Chemistry 292:10379–10389 Enzymology Laboratory Method Link
Vranish JN, Ancona MG, Oh E, Susumu K, Medintz IL (2017) Enhancing coupled enzymatic activity by conjugating one enzyme to a nanoparticle. Nanoscale 9:5172–5187 Enzymology Biotechnology Link
Zhang Y, Kouril T, Snoep JL, Siebers B, Barberis M, Westerhoff HV (2017) The peculiar glycolytic pathway in hyperthermophylic archaea: understanding its whims by experimentation in silico. International Journal of Molecular Sciences 18:876 Metabolism Microbiology Enzymology Link

9 publications
2016
Espejo Mojica ÁJ (2016) Producción, purificación y caracterización de tres hexosaminidasas lisosomales recombinantes en pichia pastoris. Ph.D. Thesis, Pontificia Universidad Javeriana, Bogotá, Colombia Enzymology Metabolism Link
Firdaus MY, Brask J, Nielsen PM, Guo Z, Fedosov SN (2016) Kinetic model of biodiesel production catalyzed by free liquid lipase from Thermomyces lanuginosus. Journal of Molecular Catalysis B: Enzymatic 133:55–64 Biotechnology Enzymology Link
Jung J, Czabany T, Wilding B, Klempier N, Nidetzky B (2016) Kinetic analysis and probing with substrate analogues of the reaction pathway of the nitrile reductase QueF from Escherichia coli. Journal of Biological Chemistry 291:25411–25426 Enzymology Link
Levin MD, Kaphan DM, Hong CM, Bergman RG, Raymond KN, Toste FD (2016) Scope and Mechanism of Cooperativity at the Intersection of Organometallic and Supramolecular Catalysis. Journal of the American Chemical Society 138:9682–9693 Enzymology Chemistry Link
Rentergent J, Driscoll MD, Hay S (2016) Time course analysis of enzyme-catalyzed DNA polymerization. Biochemistry 55:5622–5634 Biochemistry Enzymology Macromolecular Biochemistry Link
Seo D, Soeta T, Sakurai H, Sétif P, Sakurai T (2016) Pre-steady-state kinetic studies of redox reactions catalysed by Bacillus subtilis ferredoxin-NADP+ oxidoreductase with NADP+/NADPH and ferredoxin. Biochimica et Biophysica Acta 1857:678–687 Microbiology Enzymology Link
Stanger FV, Burmann BM, Harms A, Aragão H, Mazur A, Sharpe T, Dehio C, Hiller S, Schirmer T (2016) Intrinsic regulation of FIC-domain AMP-transferases by oligomerization and automodification. Proceedings of the National Academy of Sciences USA 113:E529–E537 Enzymology Link
Vranish JN, Das D, Barondeau DP (2016) Real-Time Kinetic Probes Support Monothiol Glutaredoxins As Intermediate Carriers in Fe–S Cluster Biosynthetic Pathways. ACS Chemical Biology 11:3114–3121 Enzymology Biochemistry Link

8 publications
2015
Czabany T, Schmölzer K, Luley-Goedl C, Ribitsch D, Nidetzky B (2015) All-in-one assay for beta-D-galactoside sialyltransferases: quantification of productive turnover, error hydrolysis and site selectivity. Analytical Biochemistry 483:47-53 Laboratory Method Enzymology Link
Jones AR, Rentergent J, Scrutton NS, Hay S (2015) Probing reversible chemistry in coenzyme B12-dependent ethanolamine amonnia lyase with kinetic isotope effects. Chemistry – A European Journal 21:8826-31 Enzymology Link
Lai M, Brun D, Edelstein SJ, Le Novère N (2015) Modulation of calmodulin lobes by different targets: an allosteric model with hemiconcerted conformational transitions. PLOS Computational Biology 11:e1004063 Biochemistry Enzymology Link
Maggi M, Chiarelli LR, Valentini G, Scotti C (2015) Engineering of Helicobacter pylori L-asparaginase: characterization of two functionally distinct groups of mutants. PLOS One 10:e0117025 Microbiology Biotechnology Enzymology Link
Montes MR, Ferreira-Gomes MS, Centeno M, Rossi RC (2015) The E2P-like state induced by magnesium fluoride complexes in the Na, K-ATPase. Kinetics of formation and interaction with Rb+. Biochimica et Biophysica Acta 1848:1514-23 Enzymology Link
Palai T, Kumar A, Bhattacharya PK (2015) Kinetic studies and model development for the formation of galacto-oligosaccharides from lactose using synthesized thermo-responsive bioconjugate. Enzyme and Microbial Technology 70:42-49 Biotechnology Enzymology Link
Rosenthal RG, Vögeli B, Quade N, Capitani G, Kiefer P, Vorholt JA, Ebert MO, Erb TJ (2015) The use of ene adducts to study and engineer enoyl-thioester reductases. Nature Chemical Biology 11:398-400. Enzymology Link

7 publications
2014
Guillaud F, Dröse S, Kowald A, Brandt U, Klipp E (2014) Superoxide production by cytochrome bc 1 complex: A mathematical model. Biochimica et Biophysica Acta 1837:1643–1652 Enzymology Link
Khandekar DC, Palai T, Agarwal A, Bhattacharya PK (2014) Kinetics of sucrose conversion to fructo-oligosaccharides using enzyme (invertase) under free condition. Bioprocess and Biosystems Engineering 37:2529–2537 Enzymology Biotechnology Link
Palai T, Singh AK, Bhattacharya PK (2014) Enzyme, beta-galactosidase immobilized on membrane surface for galacto-oligosaccharides formation from lactose: kinetic study with feed flow under recirculation loop. Biochemical Engineering Journal 88:68-76 Biotechnology Enzymology Link
Spiaggi AJ (2014) Caracterización de los pasos involucrados en el transporte de K+ por la Na+/K+-ATPasa. Ph.D. Thesis, Universidad de Buenos Aires, Argentina. Enzymology Link

4 publications
2013
Fedosov SN, Brask J, Pedersen AK, Nordblad M, Woodley JM, Xu X (2013) Kinetic model of biodiesel production using immobilized lipase Candida antarctica lipase B. Journal of Molecular Catalysis B: Enzymatic 85–86:156–168 Biotechnology Enzymology Link
Kraut DA (2013) Slippery substrates impair ATP-dependent protease function by slowing unfolding. Journal of Biological Chemistry 288:34729-34735 Enzymology Link
Palai T, Bhattacharya PK (2013) Kinetics of lactose conversion to galacto-oligosaccharides by beta-galactosidase immobilized on PVDF membrane. Journal of Bioscience and Bioengineering 115:668-673 Enzymology Link
Scheller S, Goenrich M, Thauer RK, Jaun B (2013) Methyl-coenzyme M reductase from methanogenic archaea: isotope effects on label exchange and ethane formation with the homologous substrate ethyl-coenzyme M. Journal of the American Chemical Society 135:14985-14995 Chemistry Enzymology Link
Toney MD (2013) Common enzymological experiments allow free energy profile determination. Biochemistry 52:5952-5965 Enzymology Link

5 publications
2012
Davies O, Mendes P, Smallbone K, Malys N (2012) Characterisation of multiple substrate-specific (d)ITP/(d)XTPase and modelling of deaminated purine nucleotide metabolism. BMB reports 45:259-264 Enzymology Metabolism Link
Gatti DL (2012) Biapenem Inactivation by B2 Metallo β-Lactamases: Energy Landscape of the Post-Hydrolysis Reactions. PLOS One 7:e30079 Enzymology Link
Gebhard LG, Kaufman SB, Gamarnik AV (2012) Novel ATP-Independent RNA Annealing Activity of the Dengue Virus NS3 Helicase. PLOS One 7:e36244 Enzymology Link
Guo C, Gow C-H, Li Y, Gardner A, Khan S, Zhang J (2012) Regulated Clearance of Histone Deacetylase 3 Protects Independent Formation of Nuclear Receptor Corepressor Complexes. Journal of Biological Chemistry 287:12111-12120 Enzymology Link
Hultqvist G, Punekar AS, Morrone A, Chi CN, Engström Å, Selmer M, Gianni S, Jemth P (2012) Tolerance of Protein Folding to a Circular Permutation in a PDZ Domain. PLOS One 7:e50055 Enzymology Link
Stefan MI, Marshall DP, Le Novère N (2012) Structural Analysis and Stochastic Modelling Suggest a Mechanism for Calmodulin Trapping by CaMKII. PLOS One 7:e29406 Enzymology Link

6 publications
2011
Fabrini R, Bocedi A, Dawood KF, Turella P, Stella L, Parker MW, Pedersen JZ, Federici G, Antonini G, Ricci G (2011) The extended catalysis of glutathione transferase. FEBS Letters 585:341–345 Enzymology Link
Hill MP, Freer LH, Vang MC, Carroll EC, Larsen DS (2011) Multiphoton Manipulations of Enzymatic Photoactivity in Aspartate Aminotransferase. Journal of Physical Chemistry B 115:4474–4483 Enzymology Link
Tsaloglou M-N, Attard GS, Dymond MK (2011) The effect of lipids on the enzymatic activity of 6-phosphofructo-1-kinase from B. stearothermophilus. Chemistry and Physics of Lipids 164:713–721 Enzymology Metabolism Microbiology Link
Yang J (2011) Midazolam as a Probe Drug to Study Cytochrome P450 3A Allosterism. Ph.D. Thesis, University of Washington, Seattle, USA. Enzymology Pharmacology Link

4 publications
2010
Hill MP, Carroll EC, Vang MC, Addington TA, Toney MD, Larsen DS (2010) Light-Enhanced Catalysis by Pyridoxal Phosphate-Dependent Aspartate Aminotransferase. Journal of the American Chemical Society 132:16953–16961 Enzymology Link
Pezzola S, Antonini G, Geroni C, Beria I, Colombo M, Broggini M, Mongelli N, Leboffe L, MacArthur R, Mozzi AF, Federici G, Caccuri AM (2010) Role of Glutathione Transferases in the Mechanism of Brostallicin Activation. Biochemistry 49:226–235 Enzymology Link
Zhang R, Monsma F (2010) Binding kinetics and mechanism of action: toward the discovery and development of better and best in class drugs. Expert Opinion on Drug Discovery 5:1023–1029 Enzymology Pharmacology Link

3 publications
2009
Kona F, Tao P, Martin P, Xu X, Gatti DL (2009) Electronic Structure of the Metal Center in the Cd 2+ , Zn 2+ , and Cu 2+ Substituted Forms of KDO8P Synthase: Implications for Catalysis. Biochemistry 48:3610–3630 Enzymology Biochemistry Link
Mendes P, Messiha HL, Malys N, Hoops S (2009) Enzyme Kinetics and Computational Modeling for Systems Biology. Methods in Enzymology 467:583–599 Enzymology Computational Method Link
Ricagno S, Caccia S, Sorrentino G, Antonini G, Bolognesi M (2009) Human Neuroserpin: Structure and Time-Dependent Inhibition. Journal of Molecular Biology 388:109–121 Enzymology Macromolecular Biochemistry Link

3 publications
2008

0 publication
2007

0 publication
2006

0 publication
2005

0 publication