Tomasz Borowski

Summary

Affiliation: Stockholm University
Country: Sweden

Publications

  1. ncbi request reprint Mechanism of dioxygen activation in 2-oxoglutarate-dependent enzymes: a hybrid DFT study
    Tomasz Borowski
    Department of Physics, Stockholm Center for Physics, Astronomy and Biotechnology, Stockholm University, 106 91 Stockholm, Sweden
    Chemistry 10:1031-41. 2004
  2. ncbi request reprint Ethylene biosynthesis by 1-aminocyclopropane-1-carboxylic acid oxidase: a DFT study
    Arianna Bassan
    Department of Physics, Stockholm Center for Physics, Astronomy and Biotechnology, Stockholm University, 10691 Stockholm, Sweden
    Chemistry 12:8835-46. 2006
  3. ncbi request reprint A hybrid density functional study of O-O bond cleavage and phenyl ring hydroxylation for a biomimetic non-heme iron complex
    Tomasz Borowski
    Department of Physics, Stockholm Center for Physics, Astronomy and Biotechnology, Stockholm University, S 106 91 Stockholm, Sweden
    Inorg Chem 43:3277-91. 2004
  4. ncbi request reprint 4-Hydroxyphenylpyruvate dioxygenase: a hybrid density functional study of the catalytic reaction mechanism
    Tomasz Borowski
    Department of Physics, Stockholm Center for Physics, Astronomy, and Biotechnology, Stockholm University, S 106 91, Stockholm, Sweden
    Biochemistry 43:12331-42. 2004
  5. ncbi request reprint Catalytic reaction mechanism of homogentisate dioxygenase: a hybrid DFT study
    Tomasz Borowski
    Department of Physics, Stockholm Center for Physics, Astronomy and Biotechnology, Stockholm University, S 106 91 Stockholm, Sweden
    J Am Chem Soc 127:17303-14. 2005
  6. ncbi request reprint Epimerization and desaturation by carbapenem synthase (CarC). A hybrid DFT study
    Tomasz Borowski
    Department of Physics, Stockholm Center for Physics, Astronomy and Biotechnology, Stockholm University, S 10691 Stockholm, Sweden
    J Comput Chem 27:740-8. 2006
  7. doi request reprint A comparison of the reaction mechanisms of iron- and manganese-containing 2,3-HPCD: an important spin transition for manganese
    Valentin Georgiev
    Department of Physics, Arrhenius Laboratories, Stockholm University, 106 91 Stockholm, Sweden
    J Biol Inorg Chem 13:929-40. 2008
  8. ncbi request reprint Theoretical study of the catalytic reaction mechanism of MndD
    Valentin Georgiev
    Department of Physics, Stockholm Center for Physics, Astronomy and Biotechnology, Stockholm University, 106 91, Stockholm, Sweden
    J Biol Inorg Chem 11:571-85. 2006
  9. doi request reprint DFT study on the catalytic reactivity of a functional model complex for intradiol-cleaving dioxygenases
    Valentin Georgiev
    Department of Physics, Arrhenius Laboratories, Stockholm University, S 106 91, Stockholm, Sweden
    J Phys Chem B 114:5878-85. 2010
  10. ncbi request reprint Theoretical studies of enzyme mechanisms involving high-valent iron intermediates
    Arianna Bassan
    Department of Physics, Stockholm University, AlbaNova University Center, Stockholm Center for Physics, Astronomy and Biotechnology, SE 106 91, Stockholm, Sweden
    J Inorg Biochem 100:727-43. 2006

Collaborators

Detail Information

Publications17

  1. ncbi request reprint Mechanism of dioxygen activation in 2-oxoglutarate-dependent enzymes: a hybrid DFT study
    Tomasz Borowski
    Department of Physics, Stockholm Center for Physics, Astronomy and Biotechnology, Stockholm University, 106 91 Stockholm, Sweden
    Chemistry 10:1031-41. 2004
    ..The relative stability of different forms of the active iron-oxo species is assessed, and the quintet five-coordinate complex is found to be most stable...
  2. ncbi request reprint Ethylene biosynthesis by 1-aminocyclopropane-1-carboxylic acid oxidase: a DFT study
    Arianna Bassan
    Department of Physics, Stockholm Center for Physics, Astronomy and Biotechnology, Stockholm University, 10691 Stockholm, Sweden
    Chemistry 12:8835-46. 2006
    ..The reaction is assisted by bicarbonate located in the second coordination sphere of the metal...
  3. ncbi request reprint A hybrid density functional study of O-O bond cleavage and phenyl ring hydroxylation for a biomimetic non-heme iron complex
    Tomasz Borowski
    Department of Physics, Stockholm Center for Physics, Astronomy and Biotechnology, Stockholm University, S 106 91 Stockholm, Sweden
    Inorg Chem 43:3277-91. 2004
    ..The calculated activation barrier (enthalpy and entropy) and the overall reaction energy profile agree well with experimental data. A comparison to the enzymatic process, which is suggested to occur on the quintet surface, has been made...
  4. ncbi request reprint 4-Hydroxyphenylpyruvate dioxygenase: a hybrid density functional study of the catalytic reaction mechanism
    Tomasz Borowski
    Department of Physics, Stockholm Center for Physics, Astronomy, and Biotechnology, Stockholm University, S 106 91, Stockholm, Sweden
    Biochemistry 43:12331-42. 2004
    ..In addition, the benzylic hydroxylation reaction, catalyzed by 4-hydroxymandelate synthase, was also studied. The results are in good agreement with the experimental findings...
  5. ncbi request reprint Catalytic reaction mechanism of homogentisate dioxygenase: a hybrid DFT study
    Tomasz Borowski
    Department of Physics, Stockholm Center for Physics, Astronomy and Biotechnology, Stockholm University, S 106 91 Stockholm, Sweden
    J Am Chem Soc 127:17303-14. 2005
    ..Interestingly, the results indicate that the type of ring scission, intra or extra with respect to the substituents coordinating to iron, is controlled by the barrier heights for the decay of the arene oxide radical intermediate...
  6. ncbi request reprint Epimerization and desaturation by carbapenem synthase (CarC). A hybrid DFT study
    Tomasz Borowski
    Department of Physics, Stockholm Center for Physics, Astronomy and Biotechnology, Stockholm University, S 10691 Stockholm, Sweden
    J Comput Chem 27:740-8. 2006
    ..The calculated energetics and barrier heights support this hypothesis, and are consistent with the known experimental data concerning CarC and other 2-oxoglutarate dependent dioxygenases...
  7. doi request reprint A comparison of the reaction mechanisms of iron- and manganese-containing 2,3-HPCD: an important spin transition for manganese
    Valentin Georgiev
    Department of Physics, Arrhenius Laboratories, Stockholm University, 106 91 Stockholm, Sweden
    J Biol Inorg Chem 13:929-40. 2008
    ..Thus the two 83% identical enzymes, using different metal ions as co-factors, were found to have similar activation energies (in agreement with experiment), but different rate-limiting steps...
  8. ncbi request reprint Theoretical study of the catalytic reaction mechanism of MndD
    Valentin Georgiev
    Department of Physics, Stockholm Center for Physics, Astronomy and Biotechnology, Stockholm University, 106 91, Stockholm, Sweden
    J Biol Inorg Chem 11:571-85. 2006
    ..The selectivity between the extra- and intra-cleavage pathways was found to be determined by the barriers for the decay of the radical state...
  9. doi request reprint DFT study on the catalytic reactivity of a functional model complex for intradiol-cleaving dioxygenases
    Valentin Georgiev
    Department of Physics, Arrhenius Laboratories, Stockholm University, S 106 91, Stockholm, Sweden
    J Phys Chem B 114:5878-85. 2010
    ..In contrast to the subsequent barrier-free intradiol C-C bond cleavage, the extradiol pathway proceeds via the formation of an epoxide, which requires an additional activation barrier...
  10. ncbi request reprint Theoretical studies of enzyme mechanisms involving high-valent iron intermediates
    Arianna Bassan
    Department of Physics, Stockholm University, AlbaNova University Center, Stockholm Center for Physics, Astronomy and Biotechnology, SE 106 91, Stockholm, Sweden
    J Inorg Biochem 100:727-43. 2006
    ..Similarities between the three classes of enzymes dominate, but significant differences also exist...
  11. ncbi request reprint Modeling enzymatic reactions involving transition metals
    Per E M Siegbahn
    Department of Physics, Stockholm University, SE 106 91 Stockholm, Sweden
    Acc Chem Res 39:729-38. 2006
    ..In this Account, methods and models will be described and examples of recent applications given. The examples are chosen to illustrate trends and to show cases where theory has predicted new mechanisms not suggested previously...
  12. ncbi request reprint Comparison of QM-only and QM/MM models for the mechanism of tyrosinase
    Per E M Siegbahn
    Department of Physics, AlbaNova, Department of Biochemistry and Biophysics, Arrhenius Laboratory, Stockholm University, S 106 91 Stockholm, Sweden
    Faraday Discuss 148:109-17; discussion 207-28. 2011
    ..In the present study, this discrepancy between the previous studies is investigated by new QM-only and QM/MM calculations...
  13. doi request reprint Reaction mechanism of apocarotenoid oxygenase (ACO): a DFT study
    Tomasz Borowski
    Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences ul Niezapominajek 8, 30 239 Cracow, Poland
    Chemistry 14:2264-76. 2008
    ..The calculated activation barriers favor the dioxetane mechanism, yet the mechanism involving the epoxide intermediate cannot be ruled out...
  14. ncbi request reprint Mechanism for catechol ring cleavage by non-heme iron intradiol dioxygenases: a hybrid DFT study
    Tomasz Borowski
    Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, ul Niezapominajek 8, 30 239 Cracow, Poland
    J Am Chem Soc 128:12941-53. 2006
    ..Another interesting result is that under some conditions, a homolytic O-O bond cleavage might compete with the Criegee rearrangement. The role of the second-shell residues and the substituent effects are also discussed...
  15. ncbi request reprint Crystal structures of histone demethylase JMJD2A reveal basis for substrate specificity
    Stanley S Ng
    Structural Genomics Consortium, Botnar Research Center, University of Oxford, Oxford OX3 7LD, UK
    Nature 448:87-91. 2007
    ....
  16. ncbi request reprint Mechanism for cyclization reaction by clavaminic acid synthase. Insights from modeling studies
    Tomasz Borowski
    Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, ul Niezapominajek 8, 30 239, Cracow, Poland
    Biochemistry 46:3682-91. 2007
    ..Precedent for the new proposed mechanism comes from the reported synthesis of oxapenams via 1,3-dipolar cycloaddition reactions of aldehydes and ketones...
  17. ncbi request reprint Force-field parametrization and molecular dynamics simulations of Congo red
    Marcin Krol
    Department of Bioinformatics and Telemedicine, Collegium Medicum, Jagiellonian University, Kopernika 17, 31 501 Krakow, Poland
    J Comput Aided Mol Des 18:41-53. 2004
    ..Comparison of results obtained from micelles molecular dynamics simulations with experimental data shows that the thermal dependence of micelle creation is well reproduced...