Jirka Kubíček's success

published 2023-07-10

From June 16th to 18th, 2023, the 45th National Exhibition of Student Professional Activities (aka SOČ) took place in Plzeň. Jiří Kubíček, a student from Gymnázium Nad Kavalírkou in Prague, working in our group, placed 4th in the Chemistry section with a project titled "Investigation of the Helicity of C-Terminal Fragments of Peptide Deformylases." Congratulations!

Jiří is a third-year gymnasium student who enjoys swimming with fins. Besides sports, he cultivates an interest in chemistry and natural sciences. He met the head of the laboratory, doc. Kolář, during the Summer School for Young Chemists and Biologists at Běstvina and shortly after that, he started studying the details of bacterial proteosynthesis.

Protein synthesis occurs in a similar manner in all organisms, but there are certain differences. One of them is the presence of a peptide deformylase (PDF) in bacteria, which is absent in higher organisms. PDF's role is to chemically modify the beginning of each protein produced by bacteria, and thus, it represents one of the targets for antibiotic therapy. PDF binds to the ribosome, the cellular protein factory, through its C-terminal part. It turns out that different bacteria have PDFs with different C-terminal segments. Some are capable of forming an α-helix, thus binding to the ribosome, while it is not known how others, which probably do not form α-helices, bind to the ribosome. Jiří Kubíček's research focused on the C-terminal segment.

He performed molecular dynamics computer simulations to elucidate the propensity of various PDFs to form α-helices, so-called helicity. Out of the five studied C-terminal segments, only one exhibited high helicity. The other segments behaved comparably in terms of helicity and formed almost no α-helices. Knowledge gained during the study sheds light on the binding of non-helical PDF C-termini on the ribosome. This may, in the long term, help discover new strategies to fight bacterial infections.

SOČ is a multidisciplinary competition held since 1979 for high school students interested in science. During the school, district, regional, and national rounds of the competition, participants have to defend their scientific projects before expert committees, which they usually develop in collaboration with universities or scientific institutions. Thus, participants have the opportunity to experience real research, including literature review, obtaining results, and their critical evaluation, while still in high school. The best participants then represent the Czech Republic in international competitions of a similar format.