Molecular Mechanisms of DNA Damage and Repair
Student: Mgr. Ivo Durník
Supervisor: RNDr. Petr Kulhánek, Ph.D.
Group: Laboratory of Computational Chemistry
Reader: doc. RNDr. Karel Berka, Ph.D., doc. RNDr. Michal Čajan, Ph.D.
We are a small research group open to new directions in molecular modelling. Our interdisciplinary research, combining chemistry, physics, math, and information technology, is dedicated to advanced molecular modelling and property exploration of diverse chemical structures, spanning from supramolecular to biomolecular systems. We employ cutting-edge methodologies, encompassing quantum mechanical calculations, docking, molecular dynamics, free energy computations, chemoinformatics and bioinformatics analyses. Additionally, we contribute to the field through novel simulation protocols and methods, employing high-performance programming languages, primarily Fortran and C/C++.
Our current research focuses on three areas: the study of enzymatic reaction mechanisms, the description of the mechanical properties of biomolecules, and the calculation of binding affinities in supramolecular chemistry.
We are trying to describe the reaction mechanisms of glycosyltransferases. We mainly focus on bacterial glycosyltransferases with unknown or incomplete structural information. We use modern approaches to complement experimental knowledge. Comprehensive knowledge is crucial for pharmaceutical applications, e.g. inhibitors of glycosyltransferases from pathogenic bacteria are the subject of next-generation antibiotic development.
We also study the mechanical properties of biomolecules essential in key biomolecular processes. Specifically, we study how the properties of deoxyribonucleic acids (DNA) change in the presence of non-canonical base pairing. This knowledge is crucial for understanding repair mechanisms targeting DNA damage introduced during replication.
Finally, we investigate the binding free energies associated with the formation of supramolecular complexes. Our methodology provides enthalpy, entropy, and free energy calculations from a single simulation. Their knowledge is crucial for understanding the effect of enthalpy/entropy compensation (ECC). This effect greatly complicates the rational design of new drugs.
Our team members and students work primarily in a Linux environment and have experience in scripting languages such as bash, awk, Gnuplot and python. Team members have expertise in using advanced computational tools such as AMBER for biomolecular simulations, Orca and Gaussian for quantum chemical calculations, AutoDock, Amsterdam Modelling Suite and many others. In addition, they are well prepared to perform large-scale simulations in supercomputing centres such as MetaCentrum from the Czech national grid infrastructure.