Sponer lab

now out: doi.org/10.1016/j.ijbi… that parallel stranded d(GGGA)3GGG DNA G4 folds via multiple paths from a coil-like ensemble #moleculardynamics @sponer_lab

Our new article on UV-induced electron transfer through DNA, DNA self-repair and their dependence on the relative arrangement of nucleobases has just been published online in @ChemicalScience . A combination of #compchem and experiments. @PWr_Wroclaw 1/3 pubs.rsc.org/en/Content/Art…

Improving #RNA force field: we propose an LJ term correction for base-phosphate interactions, reducing intranucleotide clashes in anti-conformation, improving agreement with experimental data. Out in @JCIM_JCTC: doi.org/10.1021/acs.jc… @MichalOtyepka #moleculardynamics #compchem

Folding a G-quadruplex with all-atom #moleculardynamics. My last project for @sponer_lab is out, any feedback is appreciated. Many thanks to @bussilab and Vojtech for thorough training on enhanced-sampling MD 🧬💻

Proud to take part in this #RNA #FF project now presented at #CompChem @EuChemS by Dr. Mlynsky @sponer_lab @EXA4MIND @CatrinUP @IT4Innovations @UPOlomouc @vsbtuo

We also demonstrate that different unfolding intermediates can have very similar end-to-end distances, which complicates interpretations of spectroscopic data.

The unfolding mechanism depends on the force direction, GQ topology, and the pulling speed (the slower the speed, the more complex the unfolding pathways).

G-quadruplexes often need to be unwounded in cells. We characterize this process by steered #moleculardynamics simulations with force loads small enough to be reached by modern experimental pulling techniques. The work is now out in @JCIM_JCTC: doi.org/10.1021/acs.jc… @BFUavcr

computational work done by Petr Stadlbauer at @BFUavcr

In collaboration with @dmonchaud and Jun Zhou laboratories, we combined extensive theoretical and experimental approaches to reveal how DNA G-quadruplexes fine-tune their biocatalytic properties. #moleculardynamics

Atomistic mechanism of DNA Holliday Junction opening revealed by enhanced sampling #moleculardynamics using a modified force field. Great work by @Catcat_yq and Miroslav from @BFUavcr in cooperation with @bussilab and @petr_sulc. Now out in @JCIM_JCTC, enjoy reading!🧬💻

work by @hokru_science @Catcat_yq and Miroslav

In cooperation with Jens Wohnert’s team from @goetheuni of Frankfurt, our colleagues at @BFUavcr used #moleculardynamics and #QM to elucidate structural basis for function of pseudouridine - the most widespread chemical modification in eukaryotic transcriptome. Out in @RNAJournal

With @sponer_lab we (@CatrinUP) overviewed "Computer Aided Development of Nucleic Acid Applications in Nanotechnologies". Enjoy our Small contribution at doi.org/10.1002/smll.2…

our new work using #QM to evaluate AMBER force-field accuracy for anion-π interactions in RNA by @KlaudiMrazikova, @hokru_science and Vojtech is out:

Work by all-@BFUavcr team: Miroslav, @pokorna_pavlina, Vojtech, Petr and Jiri. Enjoy reading!

We study two RNA-protein complexes and show that RNA-protein binding is a multi-pathway process. A partially disordered pre-binding state is involved in one case. The work necessitated the development of a goal-specific force field modification to weaken RNA self-interactions.

What is the mechanism of #RNA-#protein binding? In our recent work, we visualize atomic pathways of single-stranded RNA binding to protein domains with unbiased MD simulations for the first time. Article available in @NAR_Open: doi.org/10.1093/nar/gk… #moleculardynamics,#compchem

@pokorna_pavlina, @Seb_Campagne

what can #moleculardynamics tell us about the structural dynamics of (dis)ordered #RNA-#protein complexes and where are the limits? Our new study revealing structural ensembles of the RNA-bound FUS protein is out at @JPhysChem: doi.org/10.1021/acs.jp…