Tomasz Borowski

M. Glanowski, S. Kachhap, T. Borowski, M. Szaleniec, Model Setup and Procedures for Prediction of Enzyme Reaction Kinetics with QM-Only and QM:MM Approaches, Methods Mol. Biol. 2385 (2022-01-01) 175-236.

M. Glanowski, P. Wójcik, M. Procner, T. Borowski, D. Lupa, P. Mielczarek, M. Oszajca, K. Świderek, V. Moliner, A.J. Bojarski, M. Szaleniec, Enzymatic Δ1‑Dehydrogenation of 3‑Ketosteroids - Reconciliation of Kinetic Isotope Effects with the Reaction Mechanism, ACS Catal. 11 (2021-01-01) 8211-8225.

R. Bonetta, G.J. Hunter, C.H. Trinh, T. Borowski, A.G. Fenech, M. Kulp, L.C. Tabares, S. Un, T. Hunter, Substitution of histidine 30 by asparagine in manganese superoxide dismutase alters biophysical properties and supports proliferation in a K562 leukemia cell line, Eur Biophys J 50 (2021-01-01) 571-585.

J. Andrys, J. Heider, T. Borowski, Comparison of different approaches to derive classical bonded force‑field parameters for a transition metal cofactor: a case study for non‑heme iron site of ectoine synthase, Theoretical Chemistry Accounts 140 (2021-01-01) 115.

B. Mrugała, A. Miłaczewska, P.J. Porebski, E. Niedzialkowska, M. Guzik, W. Minor, T. Borowski, A study on the structure, mechanism and biochemistry of kanamycin B dioxygenase (KanJ) ‐ an enzyme with a broad range of substrates, FEBS Journal 288 (2021-01-01) 1366-1386.

S. Pote, S. Kachhap, N. J. Mank, L. Daneshian, V. Klapper, S. Pye, A. K. Arnette, L. S. Shimizu, T. Borowski, M. Chruszcz, Comparative structural and mechanistic studies of 4-hydroxy-tetrahydrodipicolinate reductases from Mycobacterium tuberculosis and Vibrio vulnificus, BBA - General Subjects 1865 (2021-01-01) 129750.

A. Wójcik-Augustyn, A.J. Johansson, T. Borowski, Reaction mechanism catalyzed by the dissimilatory Adenosine 5’-Phosphosulfate Reductase. Adenosine 5`-monophosphate inhibitor and key role of Arginine 317 in switching the course of catalysis, Biochimica et Biophysica Acta – Bioenergetics 1862 (2021-01-01) 148333.

Z. Wojdyla, T. Borowski, Enzyme multifunctionality via control of substrate positioning within the catalytic cycle - a QM/MM study for clavaminic acid synthase, Chemistry – A European Journal 27 (2021-01-01) 2196-2211.

A. Kluza, Z. Wojdyla, B. Mrugała, K. Kurpiewska, P.J. Porebski, E. Niedzialkowska, W. Minor, M.S. Weiss, T. Borowski, Regioselectivity of hyoscyamine 6β-hydroxylase-catalysed hydroxylation as revealed by high-resolution structural information and QM/MM calculations, Dalton T. 49 (2020-01-01) 4454-4469.

S. Kachhap, Z. Wojdyla, P. Komorek, A. Kluza, K. Kurpiewska, B. Jachimska, T. Borowski, It takes two to tango - the case of thebaine 6-O-demethylase, International Journal of Biological Macromolecules 163 (2020-01-01) 718-729.

R. Aina, P. Dubiela, S. Geiselhart, M. Bublin, M. Bruschi, C. Radauer, C. Nagl, P. Humeniuk, R. Asero, C.G. Mortz, C. Hafner, K. Hoffmann-Sommergruber, T. Borowski, Distinct nsLTPs display different IgE-binding capacities which are affected by fatty acids binding, J. Allergy Clin. Immunol. 74 (2019-01-01) 827-831.

P. Dubiela, R. del Conte, F. Cantini, T. Borowski, R. Aina, C. Radauer, M. Bublin, K. Hoffmann-Sommergruber, S. Alessandri, Impact of lipid binding on the tertiary structure and allergenic potential of Jug r 3, the non-specific lipid transfer protein from walnut, Scientific Reports 9 (2019-01-01) 2007.

A. Stańczak, A. Miłaczewska, T. Borowski, Reaction mechanism between Cu(II)-enolate complex and O2 as a test case for methodology used in DFT computational studies, Journal of Molecular Modeling 25 (2019-01-01) 122.

A. Wójcik-Augustyn, A.J. Johansson, T. Borowski, Mechanism of Sulfate Activation Catalyzed by ATP Sulfurylase - Magnesium Inhibits the Activity, Computational and Structural Biotechnology Journal Elsevier 17 (2019-01-01) 770-784.

A. Miłaczewska, T. Borowski, On the reaction mechanism of an endoperoxide ring formation by fumitremorgin B endoperoxidase. The right arrangement makes a difference, Dalton Transactions (2019-01-01) 16211-16221.

C.R. Schlachter, L. Daneshian, J. Amaya, V. Klapper, N. Wybouw, T. Borowski, T. Van Leeuwen, V. Grbic, M. Grbic, T.M. Makris, M. Chruszcz, Structural and functional characterization of an intradiol ring-cleavage dioxygenase from the polyphagous spider mite herbivore Tetranychus urticae Koch, Insect Biochemistry and Molecular Biology Elsevier 107 (2019-01-01) 19-30.

T. Borowski, M. Szaleniec, Challenges in Modelling Metalloenzymes, Transition Metals in Coordination Environments. Challenges and Advances in Computational Chemistry and Physics Springer Cham 29 (2019-01-01) 503-525.

A. Miłaczewska, E. Kot, J.A. Amaya, T.M. Makris, M. Zając, J. Korecki, A. Chumakov, B. Trzewik, S. Kędracka-Krok, W. Minor, M. Chruszcz, T. Borowski, On structure and reaction mechanism of human acireductone dioxygenase, CHEM-EUR J (2018-01-01) 5225-5237.

T. Hunter, R. Bonetta, A. Sacco, M. Vella, P-M. Sultana, C.H. Trinh, H.B.R. Fadia, T. Borowski. R. Garcia-Fandino, T. Stockner, G.J. Hunter, A Single Mutation is Sufficient to Modify the Metal Selectivity and Specificity of a Eukaryotic Manganese Superoxide Dismutase to Encompass Iron, Chem Eur J (2018-01-01) 5303-5308.

A. Kluza, E. Niedzialkowska, K. Kurpiewska, Z. Wojdyla, M. Quesne, E. Kot, P.J. Porebski, T. Borowski, Crystal structure of thebaine 6-O-demethylase from the morphine biosynthesis pathway, Journal of Structural Biology Elsevier (2018-01-01) 229-235.

Z. Wojdyla, T. Borowski, On how the binding cavity of AsqJ dioxygenase controls the desaturation reaction regioselectivity: a QM/MM study., J Biol Inorg Chem Springer 23 (2018-01-01) 795-808.

M. Szaleniec, A. Wojtkiewicz, R. Bernhardt, T. Borowski, M. Donova, Bacterial steroid hydroxylases: enzyme classes, their functions and comparison of their catalytic mechanisms, Appl. Microbiol. Biotechnol. Springer 10219 (2018-01-01) 8153-8171.

A. Timmins, M. Quesne, T. Borowski, S. de Visser, Group transfer to an aliphatic bond: A biomimetic study inspired by nonheme iron halogenases., ACS Catalysis ACS 8 (2018-01-01) 8685-8698.

P. Dubiela, R. Aina, D. Polak, S. Geiselhart, P. Humeniuk, B. Bohle, S. Alessandri, R. Del Conte, F. Cantini, T. Borowski, M. Bublin, K. Hoffmann-Sommergruber, Enhanced Pru p 3 IgE-binding activity by selective free fatty acid interaction, J Allergy Clin Immunol (2017-01-01) 1728-1731.

M.G. Quesne, T. Borowski, S.P. de Visser, Quantum Mechanics/Molecular Mechanics Modeling of Enzymatic Processes: Caveats and Breakthroughs, Chemistry - A European Journal Wiley-VCH Verlag GmbH & Co. 22 (2016-01-01) 2562 – 2581.

A. Wójcik, M. Radoń, T. Borowski, Mechanism of O2 Activation by alpha-Ketoglutarate Dependent Oxygenases Revisited. A Quantum Chemical Study, J Phys Chem A ACS 120 (2016-01-01) 1261-1274.

Z. Wojdyła, T. Borowski, DFT study of the mechanism of manganese quercetin 2,3-dioxygenase: quest for origins of enzyme unique nitroxygenase activity and regioselectivity, J. Biol. Inorg. Chem. Springer 21 (2016-01-01) 475-489.

S. Saraf, A. Miłaczewska, T. Borowski, C. James, D. Tierney, M. Popova, A. Arif, L. Berreau, Anion Effects in Oxidative Aliphatic Carbon-carbon Bond Cleavage Reactions of Cu(II) Chlorodiketonate Complexes, Inorg. Chem. ACS 55 (2016-01-01) 6916-6928.

B. Trzewik, K. Chruszcz-Lipska, A. Miłaczewska, J. Opalińska-Piskorz, R. Karcz, R. Gryboś, M. Oszajca, K. Luberda-Durnaś, W. Łasocha, A. N. Fitch, B. Sulikowski, T. Borowski, Synthesis and crystal structure of dimeric 1-hydroxyhexane-2,3-dione and spectral characteristics of a model acireductone, New J Chem 40 (2016-01-01) 9291-9303.

K. Hupert-Kocurek, D. Wojcieszyńska, U. Guzik, T. Borowski, A single amino acid substitution within catalitically nonactive N-terminal domain of catechol 2,3-dioxygenase (C23O) increasees enzyme activity towards 4-chlorocatechol", J. Mol. Cat. B. Enz. 122 (2015-01-01) 64-71.

T. Borowski, M. Quesne, M. Szaleniec, QM and QM/MM methods compared: case studies on reaction mechanisms of metalloenzymes, Advances in Protein Chemistry and Structural Biology Academic PressBurlington 100 (2015-01-01) 187-224.

L.R. Offermann, M. Bublin, M.L. Perdue, S. Pfeifer, P. Dubiela, T. Borowski, M. Chruszcz, K. Hoffmann-Sommergruber, Struture and functional characterization of the hazelnut allergen Cor a 8, J. Agric. Food Chem. ACS 63 (2015-01-01) 9150-9158.

M.R.A. Blomberg, T. Borowski, F. Himo, R.-Z. Liao, P.E.M. Siegbahn, Quantum Chemical Studies of Mechanisms for Metalloenzymes, Chem. Rev. 114 (2014-01-01) 3601-3658.

T. Borowski, E. Brocławik, Bioinorganic Reaction Mechanisms – Quantum Chemistry Approach, Springer-VerlagBerlin Heidelberg (2014-01-01) 783–808.

M. Szaleniec, A. Dudzik, B. Kozik, T. Borowski, J. Heider, M. Witko,, Mechanistic basis for the Enantioselectivity of the Anaerobic Hydroxylation of Alkylaromatic compounds by Ethylbenzene Dehydrogenase, J. Inorg. Biochem. 139 (2014-01-01) 9–20.

C.J. Allpress, A. Miłaczewska, T. Borowski, J.R. Bennett, D.L. Tierney, A.M. Arif, L.M. Berreau, Halide-promoted dioxygenolysis of a carbon-carbon bond by a copper(II) diketonate complex., J. Am. Chem. Soc. 136 (2014-01-01) 7821-7824.

A. Wójcik, E. Brocławik, P.E.M. Siegbahn, M. Lundberg, G. Moran, T. Borowski, The role of substrate positioning in the catalytic reaction of 4-hydroxyphenylpyruvate dioxygenase – a QM/MM study, J. Am. Chem. Soc. ACS 136 (2014-01-01) 14472-14485.

M. Lundberg, T. Borowski, Oxoferryl species in mononuclear non-heme iron enzymes: Biosynthesis, properties and reactivity from a theoretical perspective., Coordination Chemistry Reviews 257 (2013-01-01) 277-289.

A. Miłaczewska, E. Brocławik, T. Borowski, On the catalytic mechanism of (S)-2-hydroxypropylphosphonic acid epoxidase (HppE). A Hybrid DFT Study., Chemistry - A European Journal 19 (2013-01-01) 771-781.

A. Dudzik, B. Kozik, M. Tataruch, A. Wójcik, D. Knack, T. Borowski, J. Heider, M. Witko, M. Szaleniec, The reaction mechanism of chiral hydroxylation of p-OH and p-NH2 substituted compounds by ethylbenzene dehydrogenase, Can. J. Chem. 91 (2013-01-01) 775-786.

T. Borowski, A. Wójcik, A. Miłaczewska, V. Georgiev, M.R.A. Blomberg, P.E.M. Siegbahn, The alkenyl migration mechanism catalyzed by extradiol dioxygenases: a hybrid DFT study., Journal of Biological Inorganic Chemistry 17 (2012-01-01) 881-890.

A. Wójcik, E. Brocławik, P.E.M. Siegbahn, T. Borowski, Mechanism of benzylic hydroxylation by 4-Hydroxymandelate synthase. A computational study., Biochemistry 51 (2012-01-01) 9570-9580.

M. Szaleniec, A. Salwiński, T. Borowski, J. Heider, M. Witko, Quantum chemical modeling studies of ethylbenzene dehydrogenase activity, Int. J. Quant. Chem. 112 (2012-01-01) 1990–1999.

P.E.M. Siegbahn, T. Borowski, Comparison of QM-only and QM/MM models for the mechanism of tyrosinase, Faraday Discuss. 148 (2011-01-01) 109-117.

L.M. Berreau, T. Borowski, K. Grubel, C. Allpress, J.P. Wikstrom, M.E. Germain, E.V. Rybak-Akimova, D.L. Tierney, Mechanistic Studies of the O2-dependent Aliphatic Carbon-carbon bond Cleavage Reaction of a Nickel Enolate Complex, Inorg. Chem. 50 (2011-01-01) 1047-1057.

A. Wójcik, T. Borowski, E. Brocławik, The mechanism of the reaction of intradiol dioxygenase with hydroperoxy probe. A DFT study, Cat. Today (2011-01-01) 207-216.

T. Borowski, P.E.M. Siegbahn, Density Functional Theory Studies on Non-Heme Iron Enzymes, Iron-Containing Enzymes RCS PublishingCambridge (2011-01-01) 88-118.

V. Georgiev, H. Noack, T. Borowski, M.R.A. Blomberg, P.E.M. Siegbahn, DFT Study on the Catalytic Reactivity of a Functional Model Complex for Intradiol-Cleaving Dioxygenases, J. Phys. Chem. B 114 (2010-01-01) 5878-5885.

T. Borowski, H. Noack, M. Radoń, K. Zych, P.E.M. Siegbahn, Mechanism of Selective Halogenation by SyrB2 - a Computational Study, J. Am. Chem. Soc. 132 (2010-01-01) 12887-12898.

T. Borowski, V. Georgiev, P.E.M. Siegbahn, On the observation of a gem diol intermediate after O-O bond cleavage by extradiol dioxygenases. A Hybrid DFT Study, J. Mol. Model. 16 (2010-01-01) 1673-1677.

M. Szaleniec, T. Borowski, K. Schühle, M. Witko, J. Heider, Ab inito modeling of ethylbenzene dehydrogenase reaction mechanism, J. Am. Chem. Soc. 132 (2010-01-01) 6014-6024.

V. Georgiev, T. Borowski, M.R.A. Blomberg, P.E.M. Siegbahn, A Comparison of the Reaction Mechanisms of Iron and Manganese-Containing 2,3-HPCD: an Important Spin Transition for Manganese, J. Biol. Inorg. Chem. 13 (2008-01-01) 929-940.

T. Borowski, M.R.A. Blomberg, P.E.M. Siegbahn, Reaction Mechanism of Apocarotenoid Oxygenase (ACO). A DFT Study, Chem. Eur. J. 14 (2008-01-01) 2264-2276.

T. Borowski, S. de Marothy, E. Brocławik, C.J. Schofield, P.E.M. Siegbahn, Mechanism for Cyclization Reaction by Clavaminic Acid Synthase. Insights from Modeling Studies, Biochemistry 46 (2007-01-01) 3682-3691.

S. S. Ng, K. L. Kavanagh, M. A. McDonough, D. Butler, E. S. Pilka, B. M. Lienard, J. E. Bray, P. Savitsky, O. Gileadi, F. von Delft, N. R. Rose, J. Offer, J. C. Scheinost, T. Borowski, M. Sundstrom, C. J. Schofield, U. Oppermann, Crystal Structures of Histone Demethylase JMJD2A Reveal Basis for Substrate Specificity, Nature 448 (2007-01-01) 87-91.

A. Bassan, M.R.A. Blomberg, T. Borowski, P.E.M. Siegbahn, Theoretical Studies of Enzyme Mechanisms Involving High-Valent Iron Intermediates, J. Inorg. Bioch. 100 (2006-01-01) 727-743.

A. Bassan, T. Borowski, M. Lundberg, P.E.M. Siegbahn, Theoretical Modeling of Redox Processes in Enzymes and Biomimetic Systems, Concepts and Model Systems in Bioinorganic Chemistry Wiley-VChWeinheim Germany (2006-01-01) .

T. Borowski, A. Bassan, P. E. M. Siegbahn, DFT Study of the Uncatalyzed Dioxygenation of Acireductone, J. Mol. Struct. Theochem. 772 (2006-01-01) 89-92.

T. Borowski, E. Brocławik, C. J. Schofield, P. E. M. Siegbahn, Epimerization and Desaturation by Carbapenem Synthase (CarC). A Hybrid DFT Study, J. Comput. Chem. 27 (2006-01-01) 740-748.

A. Bassan, T. Borowski, C. J. Schofield, P. E. M. Siegbahn, Ethylene Biosynthesis by 1-Aminocyclopropane-1-Carboxylic Acid Oxidase: A DFT Study, Chem. - Eur. J. 12 (2006-01-01) 8835-8846.

T. Borowski, P. E. M. Siegbahn, Mechanism for Catechol Ring-Cleavage by Non-Heme Iron Intradiol Dioxygenases. A Hybrid DFT Study, J. Am. Chem. Soc. 128 (2006-01-01) 12941-12953.

V. Georgiev, T. Borowski, P. E. M. Siegbahn, Theoretical Study of the Catalytic Reaction Mechanism of MndD, J. Biol. Inorg. Chem. 11 (2006-01-01) 571-585.

T. Borowski, V. Georgiev, P.E.M. Siegbahn, Catalytic Reaction Mechanism of Homogentisate Dioxygenase. A Hybrid DFT Study, J. Am. Chem. Soc. 127 (2005-01-01) 17303-17314.

T. Borowski, A. Bassan, N.G.J. Richards, P.E.M. Siegbahn, Catalytic Reaction Mechanism of Oxalate Oxidase (Germin). A Hybrid DFT Study, J. Chem. Theory Comput 1 (2005-01-01) 686-693.

A. Bassan, T. Borowski, P.E.M. Siegbahn, Quantum Chemical Studies of Dioxygen Activation by Mononuclear Non-Heme Iron Enzymes with the 2-His-1-carboxylate Facial Triad, Dalton T. 20 (2004-01-01) 3153-3162.

A. Bassan, M.R.A. Blomberg, T. Borowski, P.E.M. Siegbahn, Oxygen Activation by Rieske Non-Heme Iron Oxygenases, a Theoretical Insight, J. Phys. Chem. B 108 (2004-01-01) 13031-13041.

T. Borowski, A. Bassan, P.E.M. Siegbahn, 4-Hydroxyphenylpyruvate Dioxygenase: A Hybrid Density Functional Study of the Catalytic Reaction Mechanism, Biochemistry 43 (2004-01-01) 12331-12342.

T. Borowski, A. Bassan, P.E.M. Siegbahn, A Hybrid Density Functional Study of O-O Bond Cleavage and Phenyl Ring Hydroxylation for a Biomimetic Non-Heme Iron Complex, Inorg. Chem. 43 (2004-01-01) 3277-3291.

T. Borowski, A. Bassan, P.E.M. Siegbahn, Mechanism of Dioxygen Activation in 2-Oxoglutarate-Dependent Enzymes: A Hybrid DFT Study, Chem. Eur. J. 10 (2004-01-01) 1031-1041.

M. Król, T. Borowski, I. Roterman, B. Piekarska, B. Stopa, J. Rybarska, L. Konieczny, Force-field Parametrization and Molecular Dynamics Simulations of Congo Red, J. Comput. Aid. Mol. Des. 18 (2004-01-01) 41-53.

T. Borowski, W. Szczepanik, M. Chruszcz, E. Brocławik, First Principle Calculations for the Active Centres in Vanadium-Containing Chloroperoxidase and its Functional Models: Geometrical and Spectral Properties, Int. J. Quantum Chem. 99 (2004-01-01) 864-875.

T. Borowski, E. Brocławik, Catalytic Reaction Mechanism of Lipoxygenase. A Density Functional Theory Study, J. Phys. Chem. B 107 (2003-01-01) 4639-4646.