Kolář lab at UCT Prague

50th International Chemistry Olympiad

published 2018-07-31

This year, the International Chemistry Olympiad (IChO) has celebrated its 50th anniversary. The first IChO took place in Prague, Czechoslovakia in 1968, and, although it is usually not emphasized, it pop up during the period known as Prague spring. Slovak and Czech republics were also the organizing countries of this year issue. It was my pleasure to be a part of Scientific committee, and with Tom Kubař to prepare and evaluate one of the eight theoretical exam problems. It was all about DNA, and part of our motivation stemmed from the work of Prof. Jan Svoboda, a famous Czech virologist in the picture below. It is just coincidence that his surname means "freedom".

Introductory figure to the 1st theoretical problem of the 50th International Chemistry Olympiad

New Publication in Vesmír: Göttingen Cemetery

published 2018-07-20

Living in Göttingen for a couple of years, I had to visit the Town cemetery. The cemetery is famoust because of many prominent scientific figures including eight Nobel prize laureates and it is worth seeing. With Tom Kubař from Karlsruhe, we put together a text about the buried and their rich relationships when still alived. A sort of longer reading fits nicely to a summer double issue of the Vesmír journal. Just thinking, where to go next...

Göttingen cemetery. In Vesmír 2018/07.


published 2018-06-26

MPIbpc NEWS is a non-peer reviewed magazine, which highlights research of the MPI Biophysical Chemistry in Göttingen. Our contribution on ribosome simulations has recently been published and featured on the journal cover page.

MPIBPC News Cover Page

The figure shows dynamics of a macrolide antibiotic (in red) bound in the ribosome exit tunnel. In bacteria, the molecule interacts with certain nascent peptides and causes ribosome stalling. No surprise that bacteria don't like it.

New Publication in Vesmír: How Are Proteins Born?

published 2018-05-02

Birth - this is a fascinating topic in many areas of humanity. How it is with proteins, biomolecules that define the life as we know it? Protein are produced in ribosomes in a process called translation. According to an RNA blueprint, ribosomes catalyze peptide bond formation between amino acids and, what is more, they can regulate how proteins are produced.

How are protein born? In Vesmír 2018/05.

Last year, I joined a conference in Cambridge, UK about so called co-translational events. A large variety of things may happen to the nascent protein before it is released from translating ribosome. Many excellent talks in Cambridge motivated me to sum up the key ideas in a popular-science article. The article has just been published in a Czech magazine Vesmír (which has tradition since 1871!). The editorial board selected it for free-of-charge access, so you can enjoy it online without any paywall (in Czech only though).

Running Proteasome on Hazel Hen

published 2018-04-27

Hazel Hen, one of the largest supercomputers in Europe, has just "opened its processors" to our simulations. Our large-scale computational project has been awarded 40 million core-hours, which is a nice chunk of the supercomputing power. For comparison, it is equivalent to almost 70% of the power, which was provided for the whole Czech computational community by IT4I in its last call.

Human proteasome

So in the next 12 months, we will run all-atom molecular dynamics simulations of the human proteasome. It is a large biomolecular complex responsible for protein degradation. Interestingly, a few drugs and drug candidates act through affecting proteasome function. We will try to uncover, how these drug affect proteasome choreography.

Current Opinion Cover Page

published 2018-04-26

The Current Opinion in Structural Biology has featured our contribution on the journal cover page. Upon invitation, Helmut, Lars and me submitted a review to a special issue on Theory and simulation. Although the paper has been available since last year, the issue was released just last week. I have already posted a video about how the cover picture was done.

Current Opinion Cover Page

Making of Group Poster

published 2018-04-11

I've prepared a poster about our research group. This is how it has evolved.

The unstalled tnaC nascent peptide in the ribosome

Another nascent peptide in the ribosome tunnel. This is a so called tnaC peptide through which the ribosome senses a level of free tryptophane. The figure shows several tnaC conformations as obtained in several μs-long molecular dynamics simulations in the absence of free tryptophane.

published 2018-03-09

IT4I Project Approved

published 2018-01-30

The Czech supercomputing center IT4I in Ostrava is the largest facility of this kind in the Czech Republic. To date, its supercomputer Salomon is ranked around 90th place worldwide. I applied to the latest call with a simulation project which deals with a ribosome-regulatory peptide VemP. VemP regulates translation of two bacterial gene variants by modulating the catalytic center of the ribosome. The project received an allocation of about 420 thousand corehours. Compared to our previous LRZ computational project, it is a tiny amount, but I hope it will anyway help us clarify the role of environment on the VemP structure and dynamics. The figure show the VemP in the ribosome exit tunnel. We will simulate the VemP in neat water.

VemP peptide in the ribosome exit tunnel'

Publication Overview 2017

published 2018-01-19

The whole world of research seems to be obsessed by scientometry. Unfortunately, questions like "how many papers" or "what is the impact factor" replace questions, which may bring truly new advances and insights. The discussion with my colleagues are full of "papers" and "citations". Having a fresh experience from Germany, I feel the contrast even stronger here in Czechia. No wonder, the reason is clear: in the Czech Republic, the science funding depends strongly on the scientometric criteria of the applicant. Certain adaptation to this external pressure is inevitable for any scientist who really means it, now matter one agrees or disagrees with it. Here is my piece of the obsession. During 2017, I monitored my Google Scholar account using a simple python script. I provide a few observations, which attracted my attention.