Studying a long-range allostery through the ribosome

published 2022-11-01

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

Preprint: biorxiv

Sample data and scripts:

Peptide deformylase on the ribosome

The first engineer from our group

published 2022-08-10

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.

Two bachelor theses defended with honors

published 2022-07-25

Two students from our group obtained their BSc. with honors. Warmest congratulations to Petr and Honza!

Petr is a Běstvina alumnus, who has finished the Chemistry program. During bachelor studies, he learned how to run MD simulations in GROMACS. He performed and analyzed simulations of the uL22 ribosomal protein. Honza has also finished the Chemistry program. For his thesis, he pythoned a Monte Carlo scheme to derive partial atomic charges. Both guys continue at UCT Prague for their Master degrees, enrolling the Data engineering study program.

Small publication about a large set of molecules

published 2022-02-13

A new publication has emerged from Aneta's bachelor thesis. The electrostatic potential around halogens is anisotropic, which possesses a challenge for molecular mechanical models with partial charges fitted by RESP or similar techniques. The anisotropy – known as a σ-hole – is modeled as a positive pseudo-atom. On a large set of molecules, we investigated how the pseudo-atom affects other partial charges in the molecule. We show that the effect is spatially localized to atoms within three covalent bonds from the halogen.

Full paper (most likely behind a paywall): J. Comput. Chem. (PDF).

Preprint: arXiv (PDF)

Sample data and scripts:

2300 sigma-holes modelled by off-center charges

Students' success at research conference

published 2021-12-02

Tereza Svatoňová and Petr Linhart have received 2nd place in their sections of the Students' research competition at UCT Prague. Congratulations!

Tereza is a MSc. student of Sensorics and cybernetics in chemistry. She studies ribosome tunnel and the ribosomal proteins that contribute to the tunnel walls. Petr is finishing his BSc. studies of Chemistry. He focuses on a fragment of a ribosomal protein uL22 to describe its folding-unfolding equilibrium.

Michal presented on the 5th Users' meeting of IT4Innovations

published 2021-11-09

At short notice, the conference was turned online due to COVID (sure you knew it). Michal introduced computer simulations of large biomolecular complexes and presented some results of Hugo and Michaela about peptide deformylase. Slides are available on here (mostly figures, though).

The first moments in the life of protein

published 2021-10-15

Proteins are synthesized on ribosomes in a process called translation. It takes seconds before the complete protein is released from the ribosome. Michal reviewed the events that happend during translation, co called co-transationally, for the Czech audience. It mostly rests on what he talked about on the Summer school for high-school teachers and students.

Full paper is available online: Chemické listy 2021 (PDF).

Ribosome, its tunnel, and peptide elongation overview.

Two bachelor theses defended with honors

published 2021-08-29

Two students from our group obtained their BSc. with honors. Warmest congratulations!

Hugo defended his thesis about MD simulations of the ribosome, where he focused on the interaction between ribosome surface and an enzyme important for protein biogenesis. Hugo plans to stay with the group pursuing his interest in simulations and advanced statistical analysis (aka machine learnine).

Iva defended her thesis about nascent protein unfolding within the ribosome tunnel. She used enhanced sampling techniques to quantify energetics of co-translational folding/unfolding. From September 2021, she's a student of Neurobiology at University of Copenhagen.

Protein birth on the Summer school for teachers

published 2021-08-26

Michal gave a talk on the 35th Summer school for high-school teachers and students. The event was organized by UCT Prague and the talks took place in the Balling hall of the National library of technology. The modern lecture hall is named after a Prague chemist, who, among other achievements, developed a scale for beer strength.

The talk was entitled "How proteins are born". Michal usually prefers slides with low information content. Anyways, for Czech audience they are available here. If you wish to put yourself in the protein mood, give yourself a bisceps massage or ruffle your hair. They are full of protein.

How proteins are born?

Arian ranked 5th in a student research competition

published 2021-06-25

Arian Adam Ott is a high-school student from a small town in West Bohemia. Last year, he started studying short peptides in the ribosome exit tunnel using atomistic simulations. Now he ranked 5th in Biology section in the National exhibition of student research projects, also known as SOČ. Congratulations! We are looking forward to your future studies at UCT Prague.

Arian rakend 5th in a student research competition.