Miroslav Krepl

Parallel DNA Holliday Junctions: Myth or Reality? An Atomistic Molecular Dynamics Study

This study uses molecular dynamics simulations to investigate whether parallel Holliday junctions exist in solution, finding they are thermodynamically metastable but rarely observed.

Enhanced RNA Formation Under Amine-Rich Local Atmospheres from 2',3'- Cyclic Nucleotides

This study shows that ammonium and alkylammonium counterions enhance RNA polymerization from 2,3-cyclic nucleotides under dry, geologically plausible conditions.

Destabilization of Structured RNAs by OPC and TIP4PD Water Models

This study compares OPC and TIP4PD water models in simulating structured RNAs, finding they destabilize RNA structures compared to three-point water models.

Sequence-Dependent Dynamics of U:U Mismatches in RNA Revealed by Molecular Dynamics Simulations

This study uses molecular dynamics simulations to show that U:U mismatches in RNA adopt multiple conformations influenced by neighboring base pairs and environmental factors.

The Kink-Turn Motif: A Powerful Test for Revealing Weaknesses in RNA Force Fields

This paper evaluates RNA force fields by testing their ability to simulate the kink-turn motif, finding that some perform better than others in capturing its structural features.

Can We Ever Develop an Ideal RNA Force Field? Lessons Learned from Simulations of UUCG RNA Tetraloop and Other Systems.

This study evaluates RNA force fields using MD simulations of UUCG tetraloops, finding that some recent variants better preserve native structures but still show discrepancies in folding free energy estimates.

How Binding Site Flexibility Promotes RNA Scanning in TbRGG2 RRM: A Molecular Dynamics Simulation Study

This study uses molecular dynamics simulations to show how TbRGG2 RRM binds uridine-rich RNAs through dynamic binding modes and auxiliary states, enabling efficient scanning while maintaining selectivity.

Transcriptome-scale analysis uncovers conserved residues in the hydrophobic core of the bacterial RNA chaperone Hfq required for small regulatory RNA stability

The paper identifies two conserved residues in Hfq critical for stabilizing small regulatory RNAs under nitrogen starvation.

The Drosophila RNA binding protein Hrp48 binds a specificRNA sequence of the msl-2 mRNA 3' UTR to regulatetranslation

This paper identifies the RNA binding specificity of Hrp48, showing it binds the msl-2 mRNA 3' UTR independently of Sxl and Unr downstream of their binding sites.

Comprehensive Assessment of Force-Field Performance in Molecular Dynamics Simulations of DNA/RNA Hybrid Duplexes

This study benchmarks force-field performance for DNA/RNA hybrid duplexes, finding no force field accurately reproduces all structural features and highlighting parameter conflicts.

Conformational Heterogeneity of RNA Stem-Loop Hairpins Bound to FUS RNA Recognition Motif with Disordered RGG Tail Revealed by Unbiased Molecular Dynamics Simulations.

The paper uses molecular dynamics simulations to study RNA-FUS interactions, revealing conformational heterogeneity and dynamic behavior that complement experimental data.

Spontaneous binding of single-stranded RNAs to RRM proteins visualised by unbiased atomistic simulations with rescaled RNA force field

This study uses atomistic simulations to observe spontaneous RNA binding to RRM domains of HuR and SRSF1 proteins, revealing dynamic binding pathways and the need for modified force fields.