Jiri Sponer research group at @BFUavcr. computational studies of nucleic acids, force-field development, origin of life, #RNA,#DNA,#moleculardynamics,#compchem
Brno, Czech Republic
Joined March 2022
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Sponer lab retweeted
now out: doi.org/10.1016/j.ijbiomac.2… that parallel stranded d(GGGA)3GGG DNA G4 folds via multiple paths from a coil-like ensemble #moleculardynamics @sponer_lab
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 🧬💻
Sponer lab retweeted
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/Arti…
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.jctc.3c0… @MichalOtyepka #moleculardynamics #compchem
Sponer lab retweeted
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 🧬💻
Parallel G-quadruplex folds via multiple paths involving G-tract stacking and structuring from coil ensemble biorxiv.org/cgi/content/shor… #bioRxiv
Sponer lab retweeted
Proud to take part in this #RNA #FF project now presented at #CompChem @EuChemS by Dr. Mlynsky
@sponer_lab @EXA4MIND @CatrinUP @IT4Innovations @UPOlomouc @vsbtuo
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.jcim.3c0… @BFUavcr
The unfolding mechanism depends on the force direction, GQ topology, and the pulling speed (the slower the speed, the more complex the unfolding pathways).
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
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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!🧬💻
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
pubs.acs.org/doi/full/10.102…
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
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 bit.ly/3F1iB9r
ALT Pseudouridine modifications of RNA can destabilize or stabilize RNA structures. NMR spectroscopy and MD simulations show that this depends on the exact structural context
Sponer lab retweeted
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.2022044…
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:
Polarization matters! Look at AMBER force-field performance for anion-π (phosphate...π and thiophosphate...π) interactions in RNA :) @JCIM_JCTC @sponer_lab #compchem pubs.acs.org/doi/full/10.102…
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/gkac1106
#moleculardynamics,#compchem
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.
Work by all-@BFUavcr team: Miroslav, @pokorna_pavlina, Vojtech, Petr and Jiri. Enjoy reading!
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.jpcb.2c0…
