Small publication about a large set of molecules
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: github.com
Students' success at research conference
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
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
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).
Two bachelor theses defended with honors
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
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.
Arian ranked 5th in a student research competition
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.
Michal received Humboldt Alumni Award 2021
Pleased to inform that this year Humboldt Alumni Award goes to Michal H. Kolář from UCT Prague. The Alexander von Humboldt Foundation is a German organization, which promotes international academic cooperation between excellent scientists and scholars. Each year, the Foundation awards up to 5 individuals from all over the world, who promote novel networking initiatives. Michal succeeded with a project with Czexpats in Science about sharing the academic experience of Czech researchers working abroad with those who reside in Czechia. The award will be officially announced during the virtual Annual Meeting in June.
The not so short story about writing a grant proposal
last update 2021-03-27
I have recently lost a collaborator with which we were preparing a grant proposal. He changed his mind and went with another more senior/competitive/secured partner. Because there was not a place for me in their proposal, I decided to apply on my own. Unfortunately, I must start from scratch because the previous topic does not make sense without the collaboration. So I take this opportunity to share my thoughts about the grant application, and write a cookbook which may be useful especially for those sailing in the deep waters of the Czech academic environment. The story might not be short (Latex users know).
The deadline is April 8. I'm starting now.
Three grants of the Internal Grant Agency approved
UCT Prague offers one-year funding through its Internal Grant Agency. We are pleased to announced that from our lab three grants, one research and two teaching, were approved. The research grant goes to Felipe, who will study peptide behavior in carbon nanotube. Michal is a PI and co-PI of two teaching grants, which aim at improving physical chemistry courses via an online search tool. Stay tuned for the updates.