COPASI's Use In Enzymology


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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 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

6 publications
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. Anal. Biochem. 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. Chem. Eur. J. 21:8826-31 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+. Biochim. Biophys Acta 1848:1514-23 Enzymology Link
Palaia T, Kumarb A, Bhattacharyaa PK (2015) Kinetic studies and model development for the formation of galacto-oligosaccharides from lactose using synthesized thermo-responsive bioconjugate. Enzyme Microbial Technol. 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 Chem. Biol. 11:398-400. Enzymology Link

5 publications
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. Biochem. Eng. J. 88:68-76 Biotechnology Enzymology Link
Spiaggi AJ (2014) Caracterización de los pasos involucrados en el transporte de K+ por la Na+/K+-ATPasa. PhD Thesis, Universidad de Buenos Aires, Argentina. Enzymology Link

4 publications
Kraut DA (2013) Slippery substrates impair ATP-dependent protease function by slowing unfolding. J. Biol. Chem. 288:34729-34735 Enzymology Link
Palai T, Bhattacharya PK (2013) Kinetics of lactose conversion to galacto-oligosaccharides by beta-galactosidase immobilized on PVDF membrane. J. Biosci. Bioeng. 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. J. Am. Chem. Soc 135:14985-14995 Chemistry Enzymology Link
Toney MD (2013) Common enzymological experiments allow free energy profile determination. Biochemistry 52:5952-5965 Enzymology Link

4 publications
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
Hill MP, Freer LH, Vang MC, Carroll EC, Larsen DS (2011) Multiphoton Manipulations of Enzymatic Photoactivity in Aspartate Aminotransferase. The Journal of Physical Chemistry B 115:4474–4483 Enzymology Link
Yang J (2011) Midazolam as a Probe Drug to Study Cytochrome P450 3A Allosterism. PhD Thesis, University of Washington, Seattle, USA. Enzymology Pharmacology Link

2 publications
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
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 H, 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

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