Structural Biology at the Czech Technical University in Prague

P. Kolenko

FJFI, České vysoké učení technické v Praze, Břehová 7, 115 19 Praha 1

kolenpe1@cvut.cz

Laboratory of Structural Biology at the Czech Technical University in Prague (LSB@CTU, https://kmlinux.fjfi.cvut.cz/~kolenpe1/) was founded in 2016. The initial goal of the laboratory was to provide the education support for students who were interested in structure biology at the Institute of Biotechnology AS CR, v.v.i. However, quite soon appeared a possibility to develop its own and partially independent research program.

LSB@CTU does not have the experimental background, and the experimental work totally depends on collaboration with laboratories of the Institute of Biotechnology in Vestec near Prague – Laboratory of Structure and Function of Biomolecules (head Jan Dohnálek) and Laboratory of Biomolecular Recognition (head Bohdan Schneider).

The background in physics and mathematics allows the members to focus on method development, mainly on development of crystallographic software. This work was pioneered by Jan Stránský, who developed several useful scripts focused mainly on experimental phasing or analysis of diffraction intensities.

The key outcome from the laboratory is program PAIREF [1,2] developed by Martin Malý. The program performs automatic paired refinement procedure. The program attracted an interest from the CCP4 developers. It has been included to the CCP4 software suite since 2022. The program was written in close collaboration with Kay Diederichs, who became a close partner of the laboratory.

Another program developed in the laboratory is SHELIXIR [3]. The program performs automatic screening for optimal parameters for experimental phasing procedures. Despite the availability of great structure prediction tools, the method itself belongs to a valuable repertoir of experimental approaches to reveal novel folds and crystal structures.

We are currently working on automatic corrections for multiple lattice-translocation defects. Jakub Hrubý is responsible for thorough testing. In near future, our focus will be diffraction anisotropy and potentially micro-ED. The members of LSB@CTU will benefit from close cooperation with the Institute of Biotechnology AS CR, v.v.i. and partner laboratories from abroad.

1. M. Malý, K. Diederichs, J. Dohnálek, P. Kolenko, IUCrJ, 7, (2020), pp. 681-692.

2. M. Malý, K. Diederichs, J. Dohnálek, P. Kolenko, Acta Cryst. F77, (2021), pp. 226-229.

3. P. Kolenko, J. Stránský, T. Kovaľ, M. Malý, J. Dohnálek, J. Appl. Cryst., 54, (2021), pp. 996-1005.

This publication was supported by the MEYS CR (projects CAAS – CZ.02.1.01/0.0/0.0/16_019/0000778).