Curriculum vitae

Ing. Natalia Kulik, Ph.D.

ORCID: 0000-0003-2005-8165

Affiliation

Centre Algatech, Institute of Microbiology, Academy of Sciences of the Czech Republic, Novohradská 237 - Opatovický mlýn, 379 01 Třebon, Czech Republic

Appointment

Postdoctoral Fellow

Education

• 2000 - 2005, Belarussian National Technical University (Faculty of Natural Resources and Ecology), Minsk, Belarus, degree - Ing.
• 2006 - 2011, Doctoral study in Biophysics at the University of South Bohemia (Institute of Physical Biology), Nové Hrady, Czech Republic. Supervisor Prof. R. Ettrich, thesis “Modeling substrate-enzyme interactions in fungal hydrolases", Ph.D. degree
• 2013, Gaussian workshop
• 2021, CHARMM-GUI CECAM School
• 2024, Python programming in biology and chemistry

Employment

• 2007 - 2011, research assistant, University of South Bohemia, Faculty of Sciences, Branišovská 31a, 370 05 České Budějovice, CZ
• 2007 - 2011, research assistant, Institute of Nanobiology and Structural Biology, Academy of Sciences of the Czech Republic, Zámek 136, 373 33 Nové Hrady, CZ
• 2011 - 2016, postdoctoral fellow, Institute of Nanobiology and Structural Biology, Academy of Sciences of the Czech Republic, Zámek 136, 373 33 Nové Hrady, CZ
• 2016 - 2022, postdoctoral fellow, Institute of Microbiology, Academy of Sciences of the Czech Republic, Zámek 136, 373 33 Nové Hrady, CZ
• 2023 - nyní, postdoctoral fellow, Centre Algatech, Institute of Microbiology, Academy of Sciences of the Czech Republic, Novohradská 237 - Opatovický mlýn, 379 01 Třeboň, CZ

Teaching experience

Leading a foreign student’s work on scientific projects during International Summer Schools organized by the University of South Bohemia and Academy of Sciences of the Czech Republic in Nové Hrady. Assistance during a course of Bioinformatics, organized by the University of South Bohemia.

Research interest

Experience in computational structural biology including the following areas:

• homology modeling of soluble proteins, membrane proteins (TRK channels and photosystem II);
• phylogentic analysis;
• prediction and analysis of mutations for enzyme engineering;
• virtual screening of inhibitors and ligand docking;
• analysis of molecular properties and interactions by MD simulation (GROMACS, Yasara);
• participate as review editor in “Biological Modeling and Simulation” journal

Publications

1. Křístková, B, Martínková, L*, Rucká, L, Kotik, M, Kulik, N, Rädisch, R, Winkler, M, Pátek, M: Immobilization of aldoxime dehydratases on metal affinity resins and use of the immobilized catalysts for the synthesis of nitriles important in fragrance industry. Journal of Biotechnology 384, 12-19, 2024. https://doi.org/10.1016/j.jbiotec.2024.02.005
2. Kulik N., Minofar B., Jugl A., Pekař M. Computational Study of Complex Formation between Hyaluronan Polymers and Polyarginine Peptides at Various Ratios. Langmuir (2023) 39(40),14212-14222.
3. Kulik N., Kutý M., Řeha D. The study of conformational changes in photosystem II during a charge separation. J. Mol. Model. (2020) 26(4), 75.
4. Nekvasilová P., Kulik N., Kotik M., Petrásková L., Slámová K., Křen V., Bojarová P.: Mutation hotspot for changing the substrate specificity of β-N-Acetylhexosaminidase: a library of GlcNAcases. Int. J. Mol.Sci. (2022) 23(20), 12456.
5. Weber P., Mészáros Z., Jagečić D., Hribljan V., Mitrečić D., Bojarová P., Slámová K., Vrba J., Kulik N., Křen V., Stütz A. E.: Diaminocyclopentane-derived O-GlcNAcase inhibitors for combating tau hyperphosphorylation in Alzheimer’s disease. Chem. Commun. (2022) 58(63), 8838–8841.
6. Mészáros Z., Petrásková L., Kulik N., Pelantová H., Bojarová P., Křen V., Slámová K.: Hypertransglycosylating variants of the GH20 β-N-Acetylhexosaminidase for the synthesis of chitooligomers Adv. Synth. Catal. (2022) 364, 2009.
7. Pingitore V., Martinez-Bailen M., Carmona A.T., Meszaros Z., Kulik N., Slamova K., Kren V., Bojarova P., Robina I., Moreno-Vargas A.J.: Discovery of human hexosaminidase inhibitors by in situ screening of a library of mono- and divalent pyrrolidine iminosugars. Bioorg. Chem. (2022) 120, 105650.
8. Fadaei F., Seifert M., Raymond J. R., Řeha D., Kulik N., Minofar B., Heitz M. P.: Interactions between a dsDNA oligonucleotide and imidazolium chloride ionic liquids: effect of alkyl chain length, Part I. Molecules  (2021) 27(1), 116. IF (2021) = 4.927
9. Hovorková M., Kulik N., Konvalinková D., Petrásková L., Křen V., Bojarová P.: Mutagenesis of catalytic nucleophile of β-galactosidase retains residual hydrolytic activity and affords a transgalactosidase. ChemCatChem, (2021) 13(21), 4532-4542. IF (2021) = 5.497
10. Shamayeva K., Spurna K., Kulik N., Kale D., Munko O., Spurny P., Zayats V., Ludwig J.: MPM motifs of the yeast SKT protein Trk1 can assemble to form a functional K+-translocation system. BBA-Biomembranes (2021) 1863(2), 183513. IF (2021) = 4.019
11. Martínková L., Příhodová R., Kulik N., Pelantová H., Křístková B., Petrásková L., Biedermann D.: Biocatalyzed reactions towards functional food components 4-Alkylcatechols and their analogues. Catalysts (2020) 10(9), 1077. IF (2020) = 4.146
12. Rucká L., Kulik N., Novotný P., Sedova A., Petrásková L., Příhodová R., Křístková B., Halada P., Pátek M., Martínková L.: Plant nitrilase homologues in fungi: phylogenetic and functional analysis with focus on nitrilases in Trametes versicolor and Agaricus bisporus. Molecules (2020) 25(17), 3861.
13. Nekvasilová P., Kulik N., Rychlá N., Pelantová H., Petrásková L., Bosáková Z., Cvačka J., Slámová K., Křen V., Bojarová P.: How site-directed mutagenesis boosted selectivity of a promiscuous enzyme. Adv. Synth. Catal. (2020) 362, 4138.
14. Garcia-Oliva C., Hoyos P., Petrásková L., Kulik N., Pelantová H., Cabanillas A.H., Rumbero Á., Křen V., Hernáiz M.J., Bojarová P.: Acceptor specificity of β-N-Acetylhexosaminidase from Talaromyces flavus: a rational explanation. Int. J. Mol. Sci. (2019) 20(24), 6181.
15. Rucká L., Chmátal M., Kulik N., Petrásková L., Pelantová H., Novotný P., Příhodová R., Pátek M., Martínková L.: Genetic and functional diversity of nitrilases in agaricomycotina.  Int. J. Mol. Sci. (2019). 20(23), 5990.
16. Bojarová P., Kulik N., Hovorková M., Slámová K., Pelantová H., Křen V.: The β-N-Acetylhexosaminidase in the synthesis of bioactive glycans: protein and reaction engineering. Molecules (2019) 24(3), 599.
17. Bojarová P., Kulik N., Slámová K., Hubálek M., Kotik M., Cvačka J., Pelantová H., Křen V.: Selective β-N-acetylhexosaminidase from Aspergillus versicolor-a tool for producing bioactive carbohydrates. Appl. Microbiol. Biot. (2019) 103(4), 1737–1753.
18. D'Oronzo E., Secundo F., Minofar B., Kulik N., Pometun A.A., Tishkov V.I.: Activation/inactivation role of ionic liquids on formate dehydrogenase from Pseudomonas sp. 101 and its mutated thermostable form. ChemCatChem (2018) 10, 3247.
19. Borthakur P., Boruah P.K., Das M.R., Kulik N., Minofar B.: Adsorption of 17α-ethynyl estradiol and β-estradiol on graphene oxide surface: An experimental and computational study. J. Mol. Liq. (2018) 269, 160-168.