Preprint about constriction in the ribosomal exit tunnel

published 2026-03-20

A new preprint is out on bioRxiv. The study combines analysis of 222 experimental structures of the E. coli ribosome with all-atom molecular dynamics simulations on the LUMI supercomputer to show that the narrowest point of the ribosomal exit tunnel is far more dynamic than commonly assumed. This so-called the constriction site, formed by proteins uL4 and uL22, can transiently close below the diameter of a water molecule, yet also open wide enough to accommodate a narrow α-helix.

The conserved residue Arg92 of uL22 emerges as a molecular gatekeeper, being both the most flexible residue at the constriction and the one most frequently defining its width. The simulations further show that even a short nascent peptide shifts the constriction toward wider conformations, indicating the tunnel actively adapts to its contents. These findings carry implications for nascent protein translocation, macrolide antibiotic action, and the translational ramp.

We acknowledge the Czech Science Foundation grant 23-05557S of Michal.

H McGrath, M Černeková, M Kolář: "Early nascent polypeptide dynamics are coupled to the flexibility of the ribosomal tunnel constriction" DOI: 10.64898/2026.03.10.710814v1

Kamil has joined the team

published 2026-01-12

We are happy to welcome Dr. Kamil Wojtkowiak, a postdoctoral researcher from the University of Wrocław, Poland, who has joined our lab for a short internship. Kamil's background is in quantum chemistry of noncovalent interactions. Supported by a grant from the National Science Center Poland, he will focus on all-atom molecular dynamics simulations of prebiotic RNAs.

Welcome aboard, Kamil!

Michal's talk at RNA Club

published 2025-11-04

Michal gave a contributed talk at RNA Club 2025 held at IMG CAS in Prague (Czechia). The talk, titled Primordial interactions between RNA and short peptides explored how short peptides stabilize ancestral ribosomal RNA and promote protoribosome aggregation. The simulations were largely carried out by Simone, a PhD student from the University of Milan (Italy), who visited our lab during the summer. The project is a collaboration with the Hlouchová and Zanchetta labs.

Slides from the talk are available on GitHub.

New publication about peptide translocation

published 2025-09-03

We have been studying protein synthesis on ribosomes for many years. One of the open questions concerns the translocation of the nascent protein through the ribosome during synthesis. It is still unclear what forces drive the peptide from the catalytic center, buried deep within the ribosome, toward the ribosome surface.

To address this, we performed a series of non-equilibrium molecular dynamics simulations on a simplified system. Specifically, we examined how a peptide moves through a carbon nanotube under an applied mechanical force. We were particularly interested in the difference between pulling the peptide and pushing it in the same direction. Does it matter where the force probe is attached? And would that choice affect the conformational ensemble of the peptide?

Highlights

• It's fairly easy to move a peptide through a narrow channel when an external force is applied.
• Pulling the peptide makes its movement smoother than pushing, though in both cases the peptide's own flexibility adds complexity.
• Where the force is applied matters less than the peptide's sequence or how quickly the force is applied.

full text: Physical chemistry chemical physics
preprint: https://arxiv.org/abs/2401.02352
funding: Czech Science Foundation 23-05557S

Bachelor theses defended

published 2025-08-30

Two new chemistry graduates have successfully defended their bachelor's theses and received their degrees. Rudolf Kvasňovský and Tomáš Kuzma both gained valuable experience in setting up, running, and analyzing MD simulations in GROAMCS. Congratulations! We wish you many more successful simulations ahead.

Project retreat in Jáchymov

published 2025-07-25

Our grant from the Czech Science Foundation has been active since January. In collaboration with the Hlouchová group, we are investigating evolutionary early protein–RNA interactions. It felt like the right time to bring the two research groups together to share experimental and simulation results. We met in Jáchymov, a UNESCO World Heritage site with a long mining history. It was from here that Marie Sklodowska-Curie obtained uranium ore, leading to the discovery of the radioactive elements radium and polonium.

The two days were intense, featuring more than ten presentations, a long hike through the steep surrounding landscape, and, for most of the time, heavy rain.

Current opinion on RNA–protein interactions

published 2025-06-20

With Klára Hlouchová from Charles University in Prague, we have recently finished a review paper about the evolution of protein–RNA interactions. In fact, we have focused on the events that happened before the biological (Darwinian) evolution started to contribute.

Highlights

• The history of protein–RNA interactions reflects both prebiotic biophysical optimization and Darwinian evolution.
• The structure of extant ribosomes provides insights into the evolutionary history of protein–RNA interactions.
• Early peptide–RNA complexes could involve non-canonical amino acid residues.
• Divalent metal ions and basic amino acids played a crucial role in the emergence of protocellular assemblies.

full text: Current opinion in structural biology
preprint: https://arxiv.org/abs/2505.02037

Welcome new interns

published 2025-06-14

We are excited to welcome two new students who have joined our group for their internships.

Simone Codispoti, from the University of Milan, Italy, will be learning how to simulate protein–RNA mixtures using computational methods. As an experimental biophysicist, he will explore the molecular features of liquid–liquid phase separation in samples he previously studied during his Master's and PhD work.

We also warmly welcome Tatiana Šimeková, a talented high school student from Slovakia, who will focus on investigating unusual nascent peptides in the ribosome exit tunnel.

We’re thrilled to host you here in Prague and look forward to a productive and inspiring collaboration!

Two new engineers have graduated

published 2025-06-10

We are proud to announce that two members of our group have successfully graduated and obtained their engineering degrees from UCT Prague.

Martin Mašek completed his studies in Physical Chemistry and defended his thesis on molecular dynamics simulations of the protoribosome. He is now heading to Berlin, Germany, to begin a PhD program in computational chemistry.

Jakub Žváček graduated from the Data Engineering program, defending his thesis on the structure and dynamics of tRNA analogues. He has already joined a consulting and technology company as a data analyst.

We thank both of them for their contributions over the years and wish them all the best in their future careers.