New preprint about coarse-grained ribosome

published 2025-04-12

Our group focuses on computer simulations of ribosomes and other biomolecular complexes. We specialize in atomistic molecular dynamics simulations, where the motion of each individual atom is tracked over time. These simulation systems typically comprise around 2 million atoms, making them computationally demanding. In some cases, atomic-level resolution is unnecessary, and simpler models can be used. In such approaches, groups of atoms representing biomolecular building blocks, such as sugar moieties or nucleobases, are combined into a single coarse-grained unit called bead.

We have recently posted a preprint on simulating the bacterial ribosome using the general coarse-grained model MARTINI. Our work details the simulation protocol and highlights both the strengths and limitations of the model.

Michal has joined Czech Science Foundation

published 2025-04-03

Michal has taken on a new role at the Czech Science Foundation. Until now, he had only been a grant applicant, but starting this year, he will also be involved in evaluating grant proposals. As a member of Evaluation Panel 205 – Biophysics, Macromolecular Physics, and Quantum Optics – he will be responsible for assessing applications for scientific research funding.

The Czech Science Foundation (GACR) is an independent public organisation supporting basic research throughout all scientific fields from public funds. GACR is the only institution in the Czech Republic, which provides public funding exclusively for basic research projects.

Rudolf succeeded with his poster in Hünfeld

published 2025-03-20

Rudolf Kvasňovský, a third-year student of the bachelor's program Chemistry, won second place in the competition for the best poster at the Hünfeld 2025: Workshop on Computer Simulation and Theory of Macromolecules conference. Congratulations!

R. Kvasňovský focuses on simulations of the mitochondrial ribosome. Unlike universal ribosomes, which are found in the cytosol or on the endoplasmic reticulum of eukaryotic cells, the mitochondrial ribosome is highly specialized. In human cells, it synthesizes only 13 proteins, whereas universal ribosomes synthesize several tens of thousands of proteins. R. Kvasňovský's poster, titled Simulation Model of the Mitochondrial Ribosome, represents nearly a year of work.

Michal has joined the Editorial board of Communications Biology

published 2024-12-15

Michal will strengthen the Biophysics and Structural Biology section of the editorial board. Although he works at the Department of physical chemistry, UCT Prague, his research focuses on biomolecules and their conformational dynamics. His team investigates the conditions under which proteins are formed in cells.

Communications Biology is an Open Access journal that publishes fundamental research findings across all subfields of biology, with a strong emphasis on rigorous and rapid peer review, including options such as double-blind or open review. The editorial processing of each manuscript is handled by a global team of in-house editors and editorial board members.

Project of ribosome abiogenesis funded

published 2024-12-07

We are delighted to announce that our research proposal entitled The Role of Peptides in the Emergence of Primordial Ribosomes, submitted to the Czech Science Foundation, has been approved for funding. Over the next three years, we will be uncovering the molecular secrets of life’s beginnings, focusing on how ribosomes – the molecular machines central to protein synthesis – may have emerged from the primordial soup.

The project will build upon our wonderful collaborative with Klára Hlouchová's research group at Charles University in Prague.

Student conference at UCT Prague

published 2024-12-02

Four members of our team participated in the student conference organized by UCT Prague. The conference offered a fresh perspective on the scientific projects investigated by research teams accross the university.

At the Department of Physical Chemistry:

• Aneta achieved 2nd place with her talk on the dynamics of peptide deformylases.
• Martin earned 3rd place with his presentation on coarse-grained simulations of ancestral RNAs.
• Rudolf presented his simulation model of the mitochondrial ribosome.
• Tom introduced his project on bacterial release factors.

Standing out in front of a committee takes courage – congratulations to all participants for their efforts!

New publication about ribosome exit tunnel

published 2024-11-06

The protein synthesis on ribosomes is the main scientific topic of our group. We run molecular dynamics simulations to understand the details of ribosome action. One of our favourite ribosome parts is the exit tunnel, through which all nascent polypeptides leave the catalytic center. In the recent publication, entitled "Three stages of nascent protein translocation through the ribosome exit tunnel" Michal and three PhD students review this rather overlooked aspect of the protein elongation process.

Full text: WIREs RNA, 2024, 15:e1873.
Preprint: arXiv

Michal joined the Reclaiming Europe inaugural conference

published 2024-10-10

The war in Ukraine underscores the urgent need for a reimagined Europe that embraces a more inclusive and forward-thinking cultural identity particularly by addressing the neglect of diverse perspectives from regions often mislabeled as "Eastern Europe." Academia should be a key driver of this transformation due to its openness, critical inquiry, and potential to inspire innovative solutions.

Berlin-Brandenburg Academy of Sciences and Humanities (BBAW) has initiated a platform called "Young Network TransEurope" (YNT) and invited yound scholars, especially from underrepresented regions, to take action. The manifesto Reclaiming Europe is the cornerstone of teh platform.

Michal was invited to the inaugural conference held in Gdansk, Poland in October 13–15, 2024, to help shaping the newly created body from outside, as a YNT non-member. In round-table discussions and short speeches, he presented his ideas about the role of the academic environment on the international collaboration.

Protoribosome coacervation study published

published 2024-10-05

After nearly two years of simulations and experiments, our collaborative efforts have been published in Nucleic Acids Research. The team, led by Dr. Klára Hlouchová from Charles University in Prague, investigated the effects of peptides on the coacervation of protoribosomal RNA (prRNA). Our key finding is that peptides stabilize prRNA and help protect it from degradation by UV light and RNases. This has significant implications for understanding abiogenesis and the biophysical optimization of the protein synthesis apparatus.

Our work on this topic is far from over. We are continuing our research on ancestral RNAs to uncover the mechanisms that led to the emergence of the modern ribosome.

Full text: Nucleic Acids Research, 2024, gkae823.
Preprint: bioRxiv
Press release: Faculty of Science, Charles University in Prague