LSB @ CTU Prague

Publications

K. Adamkova et al. (2024). Structure-based explanation of substrate preference and RNA binding of Stenotrophomonas maltophilia nuclease SmNuc1 with a mobile active site motif. FEBS Journal, accepted.

K. Meskova, K. Martonova, P. Hrasnova, K. Sinska, M. Skrabanova, L. Fialova, S. Njemoga, O. Cehlar, O. Parmar, P. Kolenko, V. Pevala, R. Skrabana. (2023). Cost-Effective Protein Production in CHO Cells Following Polyethylenimine-Mediated Gene Delivery Showcased by the Production and Crystallization of Antibody Fabs. Antibodies, 12, e51.

M. Malý, P. Kolenko, J. Stránský, L. Švecová, J. Dušková, T. Kovaľ, T. Skálová, M. Trundová, K. Adámková, J. Černý, P. Božíková, J. Dohnálek. (2023). Tetracycline-modifying enzyme SmTetX from Stenotrophomonas maltophilia. Acta Cryst F79, 180-192.

P. Kolenko, P. Mikulecký, P.N. Pham, M. Malý, B. Schneider. (2023). Diffraction anisotropy and paired refinement: crystal structure of H33, a protein binder to interleukin 10. J. Appl. Cryst., 56, 1261-1266.

J. Svoboda, D. Berdár, P. Kolenko, J. Černý, Z. Nováková, J. Pavlíček, B. Schneider. (2023). Conformation-based refinement of 18-mer DNA structures. Acta Cryst. D79, 655-665.

J. Agirre, M. Atanasova, H. Bagdonas, C. B. Ballard, A. Baslé, J. Beilsten-Edmands, R. J. Borges, D. G. Brown, J. J. Burgos-Mármol, J. M. Berrisford, P. S. Bond, I. Caballero, L. Catapano, G. Chojnowski, A. G. Cook, K. D. Cowtan, T. I. Croll, J. É. Debreczeni, N. E. Devenish, E. J. Dodson, T. R. Drevon, P. Emsley, G. Evans, P. R. Evans, M. Fando, J. Foadi, L. Fuentes-Montero, E. F. Garman, M. Gerstel, R. J. Gildea, K. Hatti, M. L. Hekkelman, P. Heuser, S. W. Hoh, M. A. Hough, H. T. Jenkins, E. Jiménez, R. P. Joosten, R. M. Keegan, N. Keep, E. B. Krissinel, P. Kolenko, O. Kovalevskiy, V. S. Lamzin, D. M. Lawson, A. A. Lebedev, A. G. W. Leslie, B. Lohkamp, F. Long, M. Malý, A. J. McCoy, S. J. McNicholas, A. Medina, C. Millán, J. W. Murray, G. N. Murshudov, R. A. Nicholls, M. E. M. Noble, R. Oeffner, N. S. Pannu, J. M. Parkhurst, N. Pearce, J. Pereira, A. Perrakis, H. R. Powell, R. J. Read, D. J. Rigden, W. Rochira, M. Sammito, F. Sánchez Rodríguez, G. M. Sheldrick, K. L. Shelley, F. Simkovic, A. J. Simpkin, P. Skubak, E. Sobolev, R. A. Steiner, K. Stevenson, I. Tews, J. M. H. Thomas, A. Thorn, J. T. Valls, V. Uski, I. Usón, A. Vagin, S. Velankar, M. Vollmar, H. Walden, D. Waterman, K. S. Wilson, M. D. Winn, G. Winter, M. Wojdyr, K. Yamashita. (2023). The CCP4 suite: integrative software for macromolecular crystallography. Acta Cryst D79, 449-461.

K. Adámková, T. Koval, L.H. Oestergaard, J. Dušková, M. Malý, L. Švecová, T. Skálová, P. Kolenko, J. Dohnálek. (2022). Atomic resolution studies of S1 nuclease complexes revealing details of RNA interaction with enzyme despite the multiple lattice-translocation defect. Acta Cryst. D78, 1194-1209.

T. Kovalová, T. Koval, J. Stránský, P. Kolenko, J. Dušková, L. Švecová, P. Vodičková, V. Spiwok, E. Benešová, P. Lipovová, J. Dohnálek. (2022). The first structure-function study of GH151 alpha-L-fucosidase uncovers new oligomerization pattern, active site complementation, and selective substrate specificity. FEBS Journal, 289, 4998-5020.

J. Dohnálek, J. Dušková, G. Tishchenko, P. Kolenko, T. Skálová, P. Novák, K. Fejfarová, J. Šimůnek. (2021). Exochitinase Chit62J4 essential for chitin processing by human microbiome bacterium Clostridium paraputrificum J4. Molecules, 26, e5978.

M. Malý, K. Diederichs, J. Dohnálek, P. Kolenko. (2021). PAIREF: paired refinement also for Phenix users. Acta Cryst. F77, 226-229.

L. Švecová, L.H. Oestergaard, T. Skálová, K.M. Schnorr, T. Koval, P. Kolenko, J. Stránský, D. Sedlák, J. Dušková, M. Trundová, J. Hašek, J. Dohnálek. (2021). Crystallographic fragment screening-based study of a novel FAD-dependent oxidoreductase from Chaetomium thermophillum. Acta Cryst. D77, 755-775.

P. Kolenko, J. Stránský, T. Koval, M. Malý, J. Dohnálek. (2021). SHELIXIR: Automation of experimental phasing procedures using SHELX C/D/E. J. Appl. Cryst., 54, 996-1005.

P.N. Pham, M. Huličiak, L. Biedermannová, J. Černý, T. Charnavets, G. Fuertes, Š. Herynek, L. Kolářová, P. Kolenko, J. Pavlíček, J. Zahradník, P. Mikulecký, B. Schneider. (2021). Protein Binder (ProBi) as a New Classs of Structurally Robust Non-Antibody Protein Scaffold for Directed Evolution. Viruses, 13(2), 190.

A. Mazur, T. Prudnikova, P. Grinkevich, J.R. Mesters, D. Mrázová, R. Chaloupková, J. Damborský, M. Kutý, P. Kolenko, I. Kutá Smatanová. (2021). The tetrameric structure of a novel haloalkane dehalogenase DpaA from Paraglaciecola agarilytica NO2. Acta Cryst., D77, 347-356.

N. Taudte, M. Linnert, J.-U. Rahfeld, A. Piechotta, D. Ramsbeck, M. Buchholz, P. Kolenko, Ch. Parthier, J.A. Houston, F. Veillard, S. Eick, J. Potempa, S. Schilling, H.-U. Demuth, M.T. Stubbs. (2021). Mammalian-like type II glutaminyl cyclases in Porphyromonas gingivalis and other oral pathogenic bacteria as targets for treatment of periodontitis. J. Biol. Chem., 296, 100263. - minimal contribution.

P. Kolenko, J. Svoboda, J. Černý, T. Charnavets, B. Schneider. (2020). Structural variability of CG-rich DNA 18-mers accommodating double T-T mismatches. Acta Cryst. D76, 1233-1243.

M. Malý, K. Diederichs, J. Dohnálek, P. Kolenko. (2020). Paired refinement under the control of PAIREF. IUCrJ, 7, 681-692.

J. Ptacek, D. Zhang, L. Qiu, S. Kruspe, L. Motlová, P. Kolenko, Z. Nováková, S. Shubham, B. Havlínová, P. Baranova, S.-J. Chen, X. Zou, P. Giangrande, C. Barinka. (2020). Structural basis of prostate-specific membrane antigen recognition by the A9g RNA aptamer. Nuc. Acids Res.,19, 11130-11145. - LINK.

T. Skalova, A. Lengalova, J. Dohnálek, K. Harlos, P. Mihalcin, P. Kolenko, M. Stránava, J. Bláha, T. Shimizu, M. Martínková. (2020). Disruption of the dimerization interface of the sensing domain in the dimeric heme-based oxygen sensor AfGcHK abolishes bacterial signal transduction. J. Biol. Chem., 295(6), 1587-1597.

T. Koval, L. Švecová, L.H. Østergaard, T. Skálová, J. Dušková, J. Hašek, P. Kolenko, K. Fejfarová, J. Stránský, M. Trundová, J. Dohnálek. (2019). Trp-His covalent adduct in bilirubin oxidase is crucial for effective bilirubin binding but has a minor role in electron transfer. Scientific Reports, 9, 13700.

P. Kolenko. (2019). Skript "baSHELiXir" usnadňuje řešení makromolekulárních struktur pomocí programu SHELX C/D/E. Chemické listy, 113, 610-614.

J. Zahradník, L. Kolářová, Y. Peleg, P. Kolenko, S. Svídenská, T. Charnavets, T. Unger, J.L. Sussman, B. Schneider. (2019). Flexible regions govern promiscuous binding of IL-24 to receptors IL-20R1 and IL-22R1. FEBS Journal, 286, 3858-3873.

J. Zahradník, L. Kolářová, H. Pařízková, P. Kolenko, B. Schneider. (2018). Interferons type II and their receptors R1 and R2 in fish species: Evolution, structure, and function. Fish and Shellfish Immunology, 79, 140-152.

J. Zahradník, P. Kolenko, A. Palyzová, J. Černý, L. Kolářová, E. Kyslíková, H. Marešová, M. Grulich, J. Nunvář, M. Šulc, P. Kyslík, B. Schneider. (2018). The crystal structure of XdpB, the bacterial Old Yellow Enzyme, in an FMN-free form. PLoS ONE, 13(4), e0195299.

M. Trundová, T. Koval, R.J. Owens, K. Fejfarová, J. Dušková, P. Kolenko, J. Dohnálek. (2018). Highly stable single-strand-specific 3'-nuclease/nucleotidase from Legionella pneumophila. Int. J. Biol. Macromol., 114, 776-787.

M. Stráňava, P Man, T. Skálová, P. Kolenko, J. Bláha, V. Fojtíková, V. Martínek, J. Dohnálek, A. Lengalová, M. Rosulek, T. Shimizu, M. Martínková. (2017). Coordination and redox state-dependent structural changes of the heme-based oxygen sensor AfGcHK associated with intraprotein signal transduction. J. Biol. Chem., 292, 20921-20935.

T. Koval, L.H. Oestergaard, J. Lehmbeck, A. Noergaard, P. Lipovová, J. Dušková, T. Skálová, M. Trundová, P. Kolenko, K. Fejfarová, J. Stránský, L. Švecová, J. Hašek, J. Dohnálek. (2016). Structural and Catalytic Properties of S1 Nuclease from Aspergillus oryzae Responsible for Substrate Recognition, Cleavage, Non-Specificity , and Inhibition. PLoS ONE, 11 (12), e0168832.

P. Mikulecký, J. Zahradník, P. Kolenko, J. Cerný, T. Charnavets, L. Kolářová, I. Nečasová, P.N. Pham and B. Schneider. (2016). Crystal structure of human interferon-gamma receptor 2 reveals the structural basis for receptor specificity. Acta Cryst. D72, 1017-1025.

J. Stránský, T. Koval, T. Podzimek, A. Týcová, P. Lipovová, J. Matoušek, P. Kolenko, K. Fejfarová, J. Dušková, T. Skálová, J. Hašek, J. Dohnálek. (2015). The structure of a mutant of tomato multifunctional nuclease TBN1 with phosphate ion bound in the active centre explains the stabilization of the conserved crystal-packing motif of molecular superhelices. Acta Cryst., F71, 1408-1415.