prof. Ing. Petr Kolenko Ph.D.

Substrate preference, RNA binding and active site versatility of Stenotrophomonas maltophilia nuclease SmNuc1, explained by a structural study

Year of publication
2025
Publication
The FEBS Journal. 2025, 292(1), 129-152. ISSN 1742-4658.
Authors
Adámková, K. Trundová, M. Kovaľ, T. Husťáková, B. Kolenko, P. Dušková, J. Skálová, T. Dohnálek, J.
Link
https://doi.org/10.1111/febs.17265

Diffraction anisotropy and paired refinement: crystal structure of H33, a protein binder to interleukin 10

Year of publication
2023
Publication
Journal of Applied Crystallography. 2023, 56(4), 1261-1266. ISSN 1600-5767.
Authors
Kolenko, P. Mikulecký, P. Pham, P.N. Malý, M.
Link
https://doi.org/10.1107/S160057672300479X

Cost-Effective Protein Production in CHO Cells Following Polyethylenimine-Mediated Gene Delivery Showcased by the Production and Crystallization of Antibody Fabs

Year of publication
2023
Publication
Antibodies. 2023, 12 1-13. ISSN 2073-4468.
Authors
Meskova, K. Martonova, K. Hrasnova, P. Sinska, K. Skrabanova, M. Fialova, L. Njemoga, S. Cehlar, O. Parmar, O. Kolenko, P. Pevala, V. Skrabana, R.
Link
https://doi.org/10.3390/antib12030051

The CCP4 suite: integrative software for macromolecular crystallography

Year of publication
2023
Publication
Acta Crystallographica Section D: Structural Biology. 2023, 79(6), 449-461. ISSN 2059-7983.
Authors
Agirre, J. Atanasova, M. Bagdonas, H. Ballard, Charles B. Kolenko, P. Malý, M.
Link
https://doi.org/10.1107/S2059798323003595

Conformation-based refinement of 18-mer DNA structures

Year of publication
2023
Publication
Acta Crystallographica Section D: Structural Biology. 2023, 79(7), 655-665. ISSN 2059-7983.
Authors
Svoboda, J. Berdar, D. Kolenko, P. Cerny, J.
Link
https://doi.org/10.1107/S2059798323004679

Tetracycline-modifying enzyme SmTetX from Stenotrophomonas maltophilia

Year of publication
2023
Publication
Acta Crystallographica Section F STRUCTURAL BIOLOGY COMMUNICATIONS. 2023, 79(7), 180-192. ISSN 2053-230X.
Authors
Malý, M. Kolenko, P. Stránský, J. Švecová, L. Dušková, J. Kovaľ, T. Skálová, T. Trundová, M. Adámková, K. Černý, J. Božíková, P. Dohnálek, J.
Link
https://doi.org/10.1107/S2053230X23005381

Atomic resolution studies of S1 nuclease complexes reveal details of RNA interaction with the enzyme despite multiple lattice-translocation defects

Year of publication
2022
Publication
Acta Crystallographica Section D: Structural Biology. 2022, 78(10), 1194-1209. ISSN 2059-7983.
Authors
Adamkova, K. Koval, T. Ostergaard, Lars H. Duskova, J. Malý, M. Kolenko, P.
Link
https://doi.org/10.1107/S2059798322008397

Crystallographic fragment screening-based study of a novel FAD-dependent oxidoreductase from Chaetomium thermophillum

Year of publication
2021
Publication
Acta Crystallographica Section D: Structural Biology. 2021, 77(6), 755-775. ISSN 2059-7983.
Authors
Švecová, L. Oestergaard, L.H. Skálová, T. Schnorr, K.M. Kovaľ, T. Kolenko, P. Stránský, J. Sedlák, D. Dušková, J. Trundová, M. Hašek, J. Dohnálek, J.
Link
https://doi.org/10.1107/S2059798321003533

Crystallographic fragment screening-based study of a novel FAD-dependent oxidoreductase from Chaetomium thermophilum. Corrigendum

Year of publication
2021
Publication
Acta Crystallographica Section D: Structural Biology. 2021, 77 980-981. ISSN 2059-7983.
Authors
Švecová, L. Oestergaard, L.H. Skálová, T. Schnorr, K.M. Kovaľ, T. Kolenko, P. Stránský, J. Sedlák, D. Dušková, J. Trundová, M. Hašek, J. Dohnálek, J.
Link
https://doi.org/10.1107/S205979832100610

PAIREF: paired refinement also for Phenix users

Year of publication
2021
Publication
Acta Crystallographica Section F STRUCTURAL BIOLOGY COMMUNICATIONS. 2021, 77(7), 226-229. ISSN 2053-230X.
Authors
Malý, M. Diederichs, K. Dohnálek, J. Kolenko, P.
Link
https://doi.org/10.1107/S2053230X21006129

The tetrameric structure of the novel haloalkane dehalogenase DpaA from Paraglaciecola agarilytica NO2

Year of publication
2021
Publication
Acta Crystallographica Section D: Structural Biology. 2021, 77(3), 347-356. ISSN 2059-7983.
Authors
Mazur, A. Prudnikova, T. Grinkevich, P. Mesters, J.S. Mrazova, D. Chaloupkova, R. Damborsky, J. Kuty, M. Kolenko, P. Smatanova, I.K.
Link
https://doi.org/10.1107/S2059798321000486

SHELIXIR: Automation of experimental phasing procedures using SHELX C/D/E

Year of publication
2021
Publication
Journal of Applied Crystallography. 2021, 54(3), 996-1005. ISSN 1600-5767.
Authors
Kolenko, P. Stránský, J. Kovaľ, T. Malý, M. Dohnálek, J.
Link
https://doi.org/10.1107/S1600576721002454

Mammalian-like type II glutaminyl cyclases in Porphyromonas gingivalis and other oral pathogenic bacteria as targets for treatment of periodontitis

Year of publication
2021
Publication
Journal of Biological Chemistry. 2021, 296 ISSN 1083-351X.
Authors
Taudte, N. Linnert, M. Rahfeld, J. Piechotta, A. Kolenko, P.
Link
https://doi.org/10.1016/j.jbc.2021.100263

Structural variability of CG-rich DNA 18-mers accommodating double T-T mismatches

Year of publication
2020
Publication
Acta Crystallographica Section D: Structural Biology. 2020, D76(12), 1233-1243. ISSN 2059-7983.
Authors
Kolenko, P. Svoboda, J. Černý, J. Charnavets, T. Schneider, B.
Link
https://doi.org/10.1107/S2059798320014151

Structural basis of prostate-specific membrane antigen recognition by the A9g RNA aptamer

Year of publication
2020
Publication
Nucleic Acids Research. 2020, 19(48), 11130-11145. ISSN 0305-1048.
Authors
Ptacek, J. Zhang, D. Qiu, L. Kruspe, S. Motlova, L. Kolenko, P. Novakova, Z. Shubham, S. Havlinova, B. Baranova, P. Chen, S.-J. Zou, X. Giangrande, P. Barinka, C.
Link
https://doi.org/10.1093/nar/gkaa494

Disruption of the dimerization interface of the sensing domain in the dimeric heme-based oxygen sensor AfGcHK abolishes bacterial signal transduction

Year of publication
2020
Publication
Journal of Biological Chemistry. 2020, 295(6), 1587-1597. ISSN 1083-351X.
Authors
Skalova, T. Lengalova, Al. Dohnalek, J. Harlos, K. Mihalcin, P. Kolenko, P. Stranava, M. Blaha, J. Shimizu, T. Martínková, M.
Link
https://doi.org/10.1074/jbc.RA119.011574

Flexible regions govern promiscuous binding of IL-24 to receptors IL-20R1 and IL-22R1

Year of publication
2019
Publication
The FEBS Journal. 2019, 286(19), 3858-3873. ISSN 1742-464X.
Authors
Zahradník, J. Kolářová, L. Peleg, Y. Kolenko, P. Svidenská, S. Charnavets, T. Unger, T. Sussman, J.L. Schneider, B.
Link
https://doi.org/10.1111/febs.14945

baSHELiXir: A Bash Script for Automated Experimental Phasing Using Shelx C/D/E

Year of publication
2019
Publication
Chemické listy. 2019, 113(10), 610-614. ISSN 0009-2770.
Authors
Kolenko, P.

Trp–His covalent adduct in bilirubin oxidase is crucial for effective bilirubin binding but has a minor role in electron transfer

Year of publication
2019
Publication
Scientific Reports. 2019, 2019(9), 13700(1)-13700(13). ISSN 2045-2322.
Authors
Kovaľ, T. Švecová, L. Oestergaard, L.H. Skalova, T. Dušková, J. Hašek, J. Kolenko, P. Fejfarová, K. Stránský, J. Trundová, M. Dohnálek, J.
Link
https://doi.org/10.1038/s41598-019-50105-3

The crystal structure of XdpB, the bacterial old yellow enzyme, in an FMN-free form

Year of publication
2018
Publication
PLoS ONE. 2018, 13(4), 1-18. ISSN 1932-6203.
Authors
Zahradník, J. Kolenko, P. Palyzová, A. Černý, J. Kolářová, L. Kyslíková, E. Marešová, H. Grulich, M. Nunvar, J. Šulc, M. Kyslík, P. Schneider, B.

Coordination and redox state-dependent structural changes of the heme-based oxygen sensor AfGcHK associated with intraprotein signal transduction

Year of publication
2017
Publication
Journal of Biological Chemistry. 2017, 292(51), 20921-20935. ISSN 1083-351X.
Authors
Stranava, M. Man, P. Skálová, T. Kolenko, P. Blaha, J. Fojtikova, V. Martínek, V. Dohnálek, J. Lengalova, A. Rosůlek, M. Shimizu, T. Martínková, M.
Link
https://doi.org/10.1074/jbc.M117.817023

Phosphate binding in the active centre of tomato multifunctional nuclease TBN1 and analysis of superhelix formation by the enzyme

Year of publication
2015
Publication
Acta Crystallographica Section F STRUCTURAL BIOLOGY COMMUNICATIONS. 2015, 71(11), 1408-1415. ISSN 2053-230X.
Authors
Stránský, J. Koval', T. Podzimek, T. Tycova, A. Kolenko, P.
Link
https://doi.org/10.1107/S2053230X15018324

L-Fucose in crystal structures of IgG-Fc: Reinterpretation of experimental data

Year of publication
2008
Publication
Collection of Czechoslovak Chemical Communications. 2008, 73(5), 608-615. ISSN 0010-0765.
Authors
Kolenko, P. Skálová, T. Dohnálek, J. Hašek, J.
Link
https://doi.org/10.1135/cccc20080608