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 at the University of South Bohemia (Institute of Physical Biology), Nove Hrady, Czech Republic. Supervisor Prof. R. Ettrich. Ph.D in biophysics, 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, researcher assistant, University of South Bohemia, Faculty of Sciences, Branisovska 31a, 370 05 Česke Budějovice
• 2007 - 2011, research assistant, Institute of Nanobiology and Structural Biology, Academy of Sciences of the Czech Republic, Zámek 136, 373 33 Nové Hrady
• 2011 - now, researcher, Institute of Microbiology, Academy of Sciences of the Czech Republic, Třebon

Teaching experiences

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

Selected publications

• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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
• 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
• 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
• 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
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.