Biology subjects

Lemmens, T.

Publications and source records attributed to Lemmens, T..

3 recordsLinked to original sources

bioRxiv2026

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

Holliday junctions (HJs) are key intermediates of homologous recombination and fundamental building blocks in DNA nanotechnology. Although the canonical antiparallel stacked-X conformation has been extensively characterized by X-ray crystallography, whether parallel HJ conformations exist in aqueous solution remains unresolved. Here, we address this question using extensive atomistic molecular dynamics (MD) simulations and replica-exchange umbrella sampling (REUS) free-energy calculations. Starting from canonical antiparallel HJs, standard MD simulations occasionally revealed spontaneous transitions to parallel conformations on the microsecond timescale without disrupting the DNA duplexes or passing through an open junction intermediate. REUS free-energy profiles confirmed the antiparallel state as the global minimum but also identified the parallel conformation as a well-defined local minimum, indicating it is thermodynamically metastable despite an estimated solution population below 1%. The combination of low equilibrium occupancy, microsecond interconversion dynamics, and the surprisingly close structural similarity between antiparallel and parallel junctions provides a plausible explanation for the lack of direct experimental detection. We further found that the free-energy landscape is only weakly affected by branching-point sequence and salt concentration. These results reconcile the apparent absence of experimental evidence for parallel HJs with their structural feasibility in solution and offer a fresh perspective on the historical debate. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=61 SRC="FIGDIR/small/737670v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@1616b7forg.highwire.dtl.DTLVardef@d868c9org.highwire.dtl.DTLVardef@1c795cborg.highwire.dtl.DTLVardef@3b52b9_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2025

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

The kink-turn is a recurrent RNA structural motif that induces a sharp bend (kink) in the A-form RNA helix. It is defined by key structural features, including consecutive sheared AG base pairs, an A-minor interaction, and multiple base-sugar interactions. Accurate representation of these densely packed non-canonical motifs in molecular dynamics simulations poses a significant challenge for contemporary force fields (FFs). Here, we present extended simulations of ribosomal kink-turn 7 (Kt-7) using a broad spectrum of pair-additive and polarizable RNA FFs. None of the tested FFs manage to flawlessly describe all the specific structural features of the Kt-7, which are described in detail in this work. Still, several FFs provide rather acceptable results and should not cause problems in simulations of larger RNAs containing a kink-turn. On aggregate, the widely used OL3 (ff99bsc0{chi}OL3) and polarizable AMOEBA FFs achieve the best performance. On the other hand, some more recently parametrized FF variants struggle to describe the Kt-7s tertiary A-minor interaction - an ubiquitous tertiary contact in RNA. This raises some concerns about the broader applicability of these FFs and suggests that they may be overfitted to small RNA model systems, such as RNA tetranucleotides. The difficulties manifest as either reversible local disruptions of the A-minor interaction and other tertiary contacts or, in some cases, irreversible unkinking of the entire motif. Based on our findings, we strongly suggest including the kink-turn motif in training and benchmarking datasets as the quintessential regression test to enhance the robustness and accuracy of RNA FF parametrization efforts.

biophysics↗

bioRxiv2024

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

RNA Recognition Motifs (RRMs) are a key class of proteins that primarily bind single-stranded RNAs. In this study, we use unbiased molecular dynamics simulations to obtain insights into the intricate binding dynamics between uridine-rich RNAs and TbRGG2 RRM. Complementing structural experiments that unveil a primary binding mode with a single uridine bound, our simulations uncover two supplementary binding modes where adjacent nucleotides encroach upon the binding pocket. This leads to a unique molecular mechanism through which TbRGG2 RRM is capable of rapidly transitioning the U-rich sequence. In contrast, presence of non-native cytidines induces stalling and destabilization of the complex. By leveraging extensive equilibrium dynamics and large variety of binding states, TbRGG2 RRM effectively expedites diffusion along the RNA substrate while ensuring robust selectivity for U-rich sequences despite featuring a solitary binding pocket. Using recently developed Stafix potential, we substantiate our description of the complex dynamics by simulating fully spontaneous association process of U-rich sequences to the TbRGG2 RRM. Our study highlights critical role of dynamics and auxiliary binding states in interface dynamics employed by RNA-binding proteins, which is not readily apparent in traditional structural studies, but could represent a general type of binding strategy employed by many RNA-binding proteins.

biophysics↗