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Bioexcel Webinar Special Edition: Summer School 2025Poster Prize Winners скачать в хорошем качестве

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Bioexcel Webinar Special Edition: Summer School 2025Poster Prize Winners
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Bioexcel Webinar Special Edition: Summer School 2025Poster Prize Winners

This special edition of the BioExcel webinar series features student speakers who were awarded poster prizes at the BioExcel Summer School 2025. Jan van Elteren: Investigating catalytic inhibition of full-length topoisomerase IIA through all-atom molecular simulations Type IIA topoisomerases (topo IIs) are complex molecular motors that alter the topological state of DNA. Their mechanism follows a complex catalytic cycle in which three gates open and close sequentially, enabling controlled passage of an intact DNA strand (T-segment) through a transiently cleaved one (G-segment). As they are crucial in maintaining genomic stability, they are broadly used as anticancer targets. Two mechanistically different classes of inhibitors are being investigated – topo II poisons and catalytic inhibitors. Topo II poisons trap the enzyme in a DNA-cleaved state, leading to cell death but also posing a risk of secondary cancers due to the accumulation of DNA double-strand breaks. To reduce the risk, catalytic inhibitors are being developed that inhibit the enzyme without causing DNA damage. Using all-atom molecular dynamics simulations, we investigated how two ATP-competitive catalytic inhibitors affect the overall dynamics of the full-length topo IIA. We compared the dynamics of catalytic inhibitor-bound complexes with native ATP-bound counterparts to identify key effects of ligand binding. Our simulations showed that catalytic inhibitors stabilize the closed conformation of the N-gate, clamping the T-segment and preventing its progression through the cleaved G-segment. Further differences were observed in interdomain tilting and twisting angles, average anti-correlations as well as hydrogen-bond patterns at the protein-DNA interface. These findings deepen the mechanistic understanding of the ATP-competitive catalytic inhibition of topo IIA and offer valuable guidelines for the rational design of next-generation catalytic inhibitors. Gesa Freimann: Molecular Dynamics Simulations of Af1503 – A Model Protein for Transmembrane Signaling Two-component signal transduction (TCST) receptors transmit information on small-molecule binding from extracellular sensory to intracellular effector domains along a transmembrane, four-helical coiled-coil backbone. Despite extensive research, the conformational changes underlying this process remain a matter of debate. Due to the difficulty of obtaining full-length experimental structures, previous studies have relied on receptor fragments or mutants, resulting in multiple, often conflicting, models of signal transduction—including vertical helix displacement (‘piston’), a scissor or see-saw motion of the transmembrane helices, and rotational motions in the plane of the membrane. In fact, no one has yet observed a complete receptor in action. Recently, Andrei Lupas and colleaques resolved the first full-length structure of a TCST receptor, Af1503 from Archaeoglobus fulgidus, identified palmitic acid as its ligand, and established it as a model protein for TCST research. This development, together with recent advances in computational power, now enables detailed investigations of transmembrane signal transduction using unbiased all-atom molecular dynamics (MD) simulations. Here, I present MD simulation results based on the experimentally determined Af1503 structure. Our analyses include simulations of the HAMP domain, the cytosolic coiled-coil region, and the complete receptor upon ligand binding. I discuss the structural dynamics revealed by these simulations and their implications for mechanistic models of TCST signaling. Zuzana Janáčková: Oligoarginine peptides bind preferentially to concave phospholipid membranes and induce membrane multilamellarity Oligoarginine peptides are potent cell-penetrating agents, yet the molecular mechanisms underlying their passive membrane translocation remain poorly understood. Using a combination of atomistic molecular dynamics simulations, enhanced sampling techniques, and cryo-electron microscopy, we investigate how membrane curvature and multilamellarity influence peptide–membrane interactions. Our simulations reveal that for R9 oligoarginine peptides the binding is significantly enhanced by negative membrane curvature. The increased affinity to concave surfaces likely arises from both geometric enclosure and a higher local density of accessible lipid headgroups. Furthermore, in the double-membrane systems, R9 peptides effectively bridge adjacent membranes and drive their spontaneous “zipping,” which is consistent with the multilamellarity observed in the cryo-EM experiments. These results provide direct atomistic evidence supporting experimental observations and highlight membrane curvature and multilamellarity as key contributors to the passive translocation mechanism of oligoarginine peptides.

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