Sponer lab

Jiri Sponer research group at @BFUavcr. computational studies of nucleic acids, force-field development, origin of life, #RNA,#DNA,#moleculardynamics,#compchem

[Pavlína Pokorná @pokorna_pavlina]

now out: https://t.co/O1YmDT3pzr that parallel stranded d(GGGA)3GGG DNA G4 folds via multiple paths from a coil-like ensemble #moleculardynamics @sponer_lab

[Rafał Szabla @rafal_szabla]

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

https://t.co/I2Yhqmvm9O

[Sponer lab @sponer_lab]

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: https://t.co/I4gICpXPUK @MichalOtyepka #moleculardynamics #compchem

[Pavlína Pokorná @pokorna_pavlina]

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 🧬💻

[michal otyepka @MichalOtyepka]

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

[Sponer lab @sponer_lab]

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

[Sponer lab @sponer_lab]

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: https://t.co/w3ypijc0kN @BFUavcr

[Sponer lab @sponer_lab]

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

[Sponer lab @sponer_lab]

computational work done by Petr Stadlbauer at @BFUavcr

[Sponer lab @sponer_lab]

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

[Sponer lab @sponer_lab]

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!🧬💻

[Zhengyue Zhang @zhengyue_zhang]

Very glad to have the work about Holliday Junction opening-closing dynamics published! The system-specific force field modification and CV-guided enhanced sampling facilitate the mechanism understanding of this HJ dynamics:) @sponer_lab
https://t.co/qhQ79uDNDb

[Sponer lab @sponer_lab]

work by @hokru_science @Catcat_yq and Miroslav

[Sponer lab @sponer_lab]

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

[RNA @RNAJournal]

Pseudouridine modifications of RNA can destabilize or stabilize RNA structures. NMR spectroscopy and MD simulations show that this depends on the exact structural context. #pseudouridine #RNA #NMR https://t.co/B7K8VDj9ZE

[michal otyepka @MichalOtyepka]

With @sponer_lab we (@CatrinUP) overviewed "Computer Aided Development of Nucleic Acid Applications in Nanotechnologies". Enjoy our Small contribution at https://t.co/zD3bWlSloC

[Sponer lab @sponer_lab]

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:

[Klaudia Mrazikova @KlaudiMrazikova]

Polarization matters! Look at AMBER force-field performance for anion-π (phosphate...π and thiophosphate...π) interactions in RNA :) @JCIM_JCTC @sponer_lab #compchem https://t.co/TaRNFBgwEE

[Sponer lab @sponer_lab]

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

[Sponer lab @sponer_lab]

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: https://t.co/TJI7qUccuZ
#moleculardynamics,#compchem

[Sponer lab @sponer_lab]

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.

[Sponer lab @sponer_lab]

@pokorna_pavlina, @Seb_Campagne

[Sponer lab @sponer_lab]

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: https://t.co/UxfQO9lT6I