Four members of our group just graduated
published 2024-06-30
We are pleased to announce that four members of our group have successfully completed their undergraduate studies and earned their degrees.
Aneta Hrádková studied peptide deformylases from various organisms, characterizing the dynamics of the deformylases using computer simulations. Aneta has enrolled in the Physical Chemistry program at UCT Prague, so she will continue working with us for a while longer. Petr Chalupský conducted simulations of a model peptide inside a carbon nanotube to better understand the factors driving peptide compaction. He is moving to Amsterdam, Netherlands, to join the Master's program in Computer Science. Arian Adam Ott focused on the interaction between a ribosomal protein and ribosomal RNA. He will continue his studies at UCT Prague, pursuing a Master's degree in Data Engineering in Chemistry. Finally, Petr Linhart earned his Master’s degree with a thesis on fragments of several ribosomal proteins. He has already signed a contract with Kearney, a global consulting firm.
We hope they have all gained valuable experience in handling molecular data from simulations, as well as working with data more broadly. We wish them the best of luck in their future careers. It has been a pleasure working with you all!
Petr Chalupský awarded by the Bakala Foundation
published 2024-06-18
We are pleased to announce that our group member, Petr Chalupský, has been awarded a scholarship by the Bakala Foundation. This scholarship will enable him to enroll in the computer science program at the University of Amsterdam. The Bakala Foundation has long supported students aiming for top universities worldwide. Petr succeeded in a competition against more than 160 students. Congratulations and best wishes to him in the Netherlands!
foto: Bakala Foundation
Conference on the academic culture
published 2024-06-16
On Wednesday, June 13, Czexpats in Science organized a conference titled "Through Academic Culture to Scientific Excellence." Over 80 researchers, research managers, and policymakers gathered to discuss the role of a positive working environment, trust, publication ethics, and interpersonal relationships in achieving groundbreaking discoveries. The keynote talks were delivered by Maria Leptin, President of the European Research Council; Kateřina Rohlenová, a cancer biologist from the Institute of Microbiology, CAS; and Matthew Rampley, an art historian from Masaryk University in Brno.
Michal H. Kolář gave the opening speech and moderated the afternoon panel discussion. This conference, the first of its kind in Czechia, concluded a three-year project awarded to Michal and Czexpats in Science by the Alexander von Humboldt Foundation.
foto: Jan Havlík
New group photos
published 2024-05-13
Our group has brand new photographs. In the photo below, we are sitting on a two-story park bench to the National Library of Technology. Another photo in front of the UCT Prague is in the Team page. Many thanks to Jonáš Priškin, who managed the photo shoot.
Three epochs of nascent protein translocation through the ribosome exit tunnel
published 2024-04-20
Proteins and peptides are fundamental to life. In all organisms, these molecules are synthesized by the ribosome — a large ribonucleoprotein complex — in a process known as translation. During this process, the nascent protein remains tethered to the ribosome for a significant duration. In our new study, we conceptualize this phase of the protein's life by dividing it into three distinct epochs. These epochs are characterized based on the position of the nascent polypeptide's N-terminus within the ribosome exit tunnel and its relationship to the catalytic center.
A preprint is now available an arXiv.
Two preprints now out
published 2024-02-05
What a start of this year. We have just posted two new preprints. The first one comes from our lab and features Felipe's non-equilibrium molecular dynamics simulations of peptides in carbon nanotubes. We describe the differences between pulling a peptide through confined spaces and pushing it in the same direction.
The other preprint is the outcome of our collaboration with K. Hlouchová group and includes simulations done by Martin during his bachelor thesis preparation. We show that short peptides derived from ribosomal proteins stabilize ancestral fragment of ribosomal RNA. Hence, the pepetides may have played a major role in the times of the Earth, when chemistry turned to biology.
arXiv: FC Nepomuceno, MH Kolář, Sensitivity of peptide conformational dynamics in carbon nanotubes to directional mechanical forces.
bioRxiv: S Codispoti, T Yamaguchi, M Makarov, VG Giacobelli, M Mašek, MH Kolář, AC Sanchez Rocha, K Fujishima, G Zanchetta, K Hlouchová, The interplay between peptides and RNA is critical for protoribosome compartmentalization and stability.
Happy reading!
Happy new year
published 2024-01-07
As we bid farewell to 2023, we reflect on what we did right in our research group and what can be done better. Michal completed his habilitation and secured tenure, four students successfully defended their theses, some of them flew out of the nest to the non-academic (aka real) world, we strengthened collaborations with our wonderful colleagues and friends, and left a comprehensive review on ribosome simulations within the scientific landscape. Looking ahead to 2024, we are excited about prospects of moving to new offices and welcoming three new students to the group. We wish you a happy new year with a linocut featuring the tRNA–mRNA interaction. We remain dedicated to exploring these molecular relationships.
7th Meeting of IT4Innovations
published 2023-11-06
We participated in the annual conference of the Czech supercomputing center in Ostrava. Michaela presented a poster on MD simulations of the ribosome catalytic center, while Petr Ch. showcased his first conference and poster presentation on metadynamics simulations of a short peptide in a carbon nanotube. Additionally, Michal delivered a talk on MD simulations of ancestral ribosomes, our contribution to a pleasing collaboration with Klára Hlouchová's lab at Charles University. A lot of discussions and new insights. The two days in Ostrava were well spent.
The slides of Michal's talk are available on GitHub.
RNA Club in Olšina
published 2023-10-30
We spent a couple of wonderful days at the Olšina resort, aka "Your entrance gate to Šumava mountains". The venue played host of this year's RNA Club organized by the folks from the University of South Bohemia. Michal gave a keynote talk on ribosome simulations (thanks for the invitation!), and Aneta, Joe, and Martin presented their work with posters. We enjoyed a relaxed atmosphere and discussions, and plenty of great food. The weather was totally Šumava-esque – rain and chill all the way. Good times!
The slides of Michal's talk are available on GitHub.
Michal invited to SITOLA seminar
published 2023-09-16
SITOLA is a laboratory located at the intersection of the Faculty of Informatics and the Institute of Computer Science at Masaryk University, Brno. Annualy, they have a get-together called SitSem (SITOLA seminar), which takes place at the University Center in Telč. In the historical city center protected as the UNESCO World Heritage Site, the lab folks meet and chat about all the stuff happening in their field. Every year, they invite some speakers who bring fresh ideas, not just from the lab's usual topics. This year, they had Michal, who talked about Exploring Biomolecular Dynamics Using Large-Scale Computer Simulations. It was awesome!
The slides of Michal's talk are available on GitHub.
