However simplified, molecular dynamics (MD) provides an atom-level picture of the molecular mechanisms. I started using MD already for bachelor thesis, where I simulated the RNA helix and observed how the bounds break when one of the ends is pulled with a constant force. For my master's project, I joined a BioNano laboratory at the Center for New Technologies, University of Warsaw, under supervision of prof. Joanna Trylska . The project was financed from the grant called TEAM-project. The master's project was my first experience with the problem of antibiotics and the phenomenon of the antibiotic-resistance.

Designing a PNA molecule to halt bacterial translation

The project aimed at selecting a small (~10 bp) part of the bacterial 16S rRNA to be targeted with the molecule of artificial nucleic acid. I've annotated each base along the 16S rRNA molecule with information from multiple sources: mobility and accessibility from the molecular dynamics simulation, antibiotic binding sites, binding sites of other molecules, and so on. Later, after I graduated, the experimental partners confirmed that the anti-sense molecule targeting the site I've selected showed an inhibiting effect on the ribosome in the cell-free system.

The most difficult part of the project was conducting quite complex molecular dynamics of the small ribosomal subunit. I have developed a tool, MINT, that, given the .dcd file, provides a description of the behaviour of the RNA molecule during the molecular dynamics. A computational part of this project was largely conducted at the UCSD Mc Cammon group.

Górska A., Markowska-Zgrajek A., Równicki M., Trylska J. Scanning of 16S ribosomal RNA for peptide nucleic acid and targets
Górska A., Jasiński M., and Trylska J., MINT: Software to Identify Motifs and Short-Range Interactions in Trajectories of Nucleic Acids
MINT webserver to analyse and visualise an RNA molecule from a pdb file.
RiboScanner to browse and predict if the given sequence would bind to the bacterial rRNA.