Michal invited to SITOLA seminar
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.
New engineers of the group
Four students have recently successfully defended their theses. We are delighted to see the group fully engaged in mentoring and guiding students across all levels of higher education.
Before the summer holidays started, Martin Mašek completed his bachelor's studies in the Physical and Computational Chemistry program with a thesis focused on ancient ribosomes. Hugo McGrath excelled by defending his thesis, which delved into classification algorithms and their applications in biomolecular allostery studies as part of the Data Engineering program. Furthermore, Joe Cikhart accomplished his diploma thesis in the Physical Chemistry program, exploring peptides in non-aqueous solvents. Most recently, Aneta Leskourová defended her thesis centered around coarse-grained simulations of ribosomes. Congratulations to all to them on their achievements. We are proud of you!
A review about ribosome simulations
We are happy to announce that the review article we collaborated on with our colleagues and friends from Goettingen, Germany has recently been published in the Annual Reviews of Biophysics. This comprehensive piece summarizes the role of large-scale computer simulations in the study of the ribosome. We particularly focused on elucidating how molecular dynamics simulations can enhance experimental techniques, shedding light on the functional aspects of biomolecules.
Please read, enjoy and cite.
Reference: Bock LV, Gabrielli S, Kolar MH, Grubmüller H. Simulation of Complex Biomolecular Systems: The Ribosome Challenge. Annual Reviews (2023) 52, 15.1-15.30.
Jirka Kubíček's success
published 2023-07-10From 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!
Michal completed his habilitation
We are delighted to announce that Michal has completed his habilitation and soon will be awarded the docent degree. This is an equivalent of promoting Michal to the associated professor level. In the absence of tenure track system in Czech academia, habilitation represents a natural step on the academic carreer ladder. Below is the only photograph taken during the habilitation thesis defense. On the example of carrying coal to Newcastle (in Czech literaly "carying firewood to the forest") Michal explains his teaching contribution during the Běstvina summer schools. Photo courtesy of P. Slavíček.
A new text in Vesmír
Where did all Czech chemists disappeared? The questions is a title of a new article by Michal in the Czech popular science magazine Vesmír. The question is about the recent list of Highly Cited Researchers published annually by a British-American company Clarivate. The question is about an observation that contrary to past years, there are no chemist anymore in the list and also about how the situation is related to the newly adopted qualitative criteria filtering out the potential awardees. The text in Vesmír is inspired by the Retraction Watch report "Why misconduct could keep scientists from earning Highly Cited Researcher designations, and how our database plays a part." Recommended for non-Czech speakers.
full text: MH Kolář, Kam se poděli čeští chemici? (in Czech)
Two GAČR grants approved
We are excited to announce that our team at UCT Prague has been awarded two research grants from the Czech Science Foundation (aka GAČR) to further our study of ribosomes and protein synthesis. We are grateful for the support and look forward to the coming three years.
Attending IT4I User's Meeting
Recently, three members of our research group attended the annual User's meeting of the IT4Innovations, which was held in Ostrava at the largest supercomputing center of the Czech Republic. The conference provided a valuable opportunity for the team members to present their latest findings on the role of protein structure dynamics engage with leading experts in the field in Czechia.
During the conference, our researchers had the chance to attend a series of lectures and a poster session covering a wide range of topics across all fields of computational science. Hugo McGrath, an undergraduate student, substituted Michal, who stayed at home due to COVID, gave a talk about long-distace allostery within the bacterial ribosome recently published in the Biophysical Journal. Hugo also presented a poster on the same topic. A PhD candidate Felipe Nepomuceno presented a poster on the computational modelling of peptide dynamics in carbon nanotubes, and an undergraduate student Petr Linhart presented a poster about MD simulations of disordered fragments of ribosomal proteins. According to the guys, they best enjoyed the evening poster session with a strong networking environment (aka free beer).
Studying a long-range allostery through the ribosome
Hugo started studying a binding of peptide deformylase (PDF) onto the ribosome surface during his bachelor degree. The project turned promising, so we run all-atom MD simulations of the entire ribosome to better understand what effect the PDF has on the ribosome interior. Using a simple machine learning, we demonstrated that the PDF affects ribosome interior, namely the tip of the uL22 ribosomal protein.
Full paper: Biophysical Journal
Sample data and scripts: https://github.com/mhkoscience/mcgrath-pdfribo
The first engineer from our group
We are utterly happy that Tereza has defended his diploma thesis and became the first engineer, who finished with Michal.
Tereza started in the group after completing her bachelor in Forensic analysis. She quickly learned how to run GROMACS and performed extensive simulations of the ribosome exit tunnel. In her thesis, she tried to build Markov state models of the tunnel dynamics. We're still working on it, stay tuned.