Biology subjects

Jungwirth, P.

Publications and source records attributed to Jungwirth, P..

7 recordsLinked to original sources

bioRxiv2026

Vesicle Internalization Proceeds via a Morphological Phase Transition

Vesicle internalization proceeds through a series of multivesicular topologies essential for endocytic transport and cellular compartmentalization. The energetic landscapes of related transitions, including vesicle budding and pearling, are known to be governed by the coupling of spontaneous curvature, leaflet area asymmetry, and reduced volume. However, the physical principles driving the structural transformation of hemifused intermediates remain unresolved. Using a continuum elastic model, we identify a morphological phase transition in hemifused invaginating vesicles, from an initial lens-like geometry to an elongated "kettle" geometry. This transition is discontinuous as long as the invaginating vesicles reduced volume is below a critical threshold, but continuous otherwise. The kettle-like morphology is metastable across a broad range of leaflet area asymmetries, potentially enabling a hysteretic externalization pathway. Increasing either the spontaneous curvature of the shared outer leaflet or the size of the invaginating vesicle, alone or in tandem with the host vesicle, turns the kettle morphology into the global free energy minimum. Notably, simply scaling up the size of both vesicles does not eliminate the free energy barrier. This quantitative characterization provides a structural reference for identifying internalization intermediates witnessed in experimental imaging, and maps the morphological evolution of the internalization pathway across its physical parameter space.

biophysics↗

bioRxiv2026

Direct Membrane Penetration of Oligoarginines by Fluorescence and Cryo-electron Microscopy Combined with Molecular Simulations

Arginine-rich peptides are short amino acid chains capable of spontaneously crossing cellular membranes, with great potential for drug or other cargo delivery. Yet, the mechanisms underlying their cellular penetration are not fully understood. Here, we investigate the modes of action of nonaarginine (R9) across membranes of increasing compositional and biological complexity. We combine computational, fluorescence microscopy, and cryo-EM approaches to both visualize the membrane structural changes arising from peptide-lipid interactions and provide a molecular rationale for the observed effects. In large unilamellar vesicles, R9 binds preferentially to anionic and PE-rich membranes, induces lipid reorganization, and drives pronounced remodelling, including budding, bifurcations, and time-dependent formation of multilamellar stacks. In cell-derived extracellular vesicles, R9-induced remodelling is largely confined to bilamellar bifurcations. In live cells, fluorescent R9 forms surface puncta that precede cytosolic entry. Correlative cryo-fluorescence and electron tomography reveals that these puncta correspond to strongly folded, multilamellar membrane structures. We propose that these seemingly contrasting observations can be reconciled within a single R9 mechanism of action, involving membrane folding and stacking, where the different observed morphologies arise from the size of the accessible membrane reservoir.

biophysics↗

bioRxiv2024

The Origins of Arginine "Magic": Guanidinium Like-Charge Ion Pairing and Oligoarginine Aggregation in Water by NMR, Cryoelectron Microscopy, and Molecular Dynamics Simulations

The phenomenon of like-charge pairing of hydrated ions is a physical manifestation of the unique solvation properties of certain ion pairs in water. Waters high dielectric constant and related ion screening capability significantly influence the interaction between like-charged ions, with the possibility to transform it - in some cases - from repulsion to attraction. Guanidinium cations (Gdm+) represent a quintessential example of such like-charge pairing due to their specific geometry and charge distribution. In this work, we present experimental quantification of Gdm+-Gdm+ contact ion pairing in water utilizing nuclear magnetic resonance (NMR) spectroscopy experiments complemented by molecular dynamics (MD) simulations and density functional theory (DFT) calculations. The observed interaction is very weak -- about -0.5 kJ{middle dot}mol-1 -- which aligns with theoretical estimation from MD simulations. We also contrast the behavior of Gdm+ with NH4+ cations, which do no exhibit contact ion pairing in water. DFT calculations predict that the NMR chemical shift of Gdm+ dimers is smaller than that of monomers, in agreement with NMR titration curves that display a non-linear Langmuir-like behavior. Additionally, we conducted cryo-electron microscopy experiments on oligoarginines R9, which (unlike nona-lysines K9) exhibit aggregation in water. This points again to like charge pairing of the guanidinium side chain groups, as corroborated also by molecular dynamics simulations of these peptides in water.

biophysics↗

bioRxiv2024

Effective Inclusion of Electronic Polarization Improves the Description of Electrostatic Interactions: The prosECCo75 Biomolecular Force Field

prosECCo75 is an optimized force field effectively incorporating electronic polarization via charge scaling. It aims to enhance the accuracy of nominally nonpolarizable molecular dynamics (MD) simulations for interactions in biologically relevant systems involving water, ions, proteins, lipids, and saccharides. Recognizing the inherent limitations of nonpolarizable force fields in precisely modeling electrostatic interactions essential for various biological processes, we mitigate these shortcomings by accounting for electronic polarizability in a physical rigorous mean-field way that does not add to computational costs. With this scaling of (both integer and partial) charges within the CHARMM36 framework, prosECCo75 addresses overbinding artifacts. This improves agreement with experimental ion binding data across a broad spectrum of systems -- lipid membranes, proteins (including peptides and amino acids), and saccharides -- without compromising their biomolecular structures. prosECCo75 thus emerges as a computationally efficient tool providing enhanced accuracy and broader applicability in simulating the complex interplay of interactions between ions and biomolecules, pivotal for improving our understanding of many biological processes.

biophysics↗

bioRxiv2023

Can calmodulin bind to lipids of the cytosolic leaflet of plasma membranes?

Calmodulin (CaM) is a ubiquitous calcium-sensitive messenger in eukaryotic cells. It was previously shown that CaM possesses an affinity for diverse lipid moieties, including those found on CaM-binding proteins. These facts together with our observation that CaM accumulates in membrane-rich protrusions of HeLa cells upon increased cytosolic calcium, motivated us to perform a systematic search for unmediated CaM interactions with model lipid membranes mimicking the cytosolic leaflet of plasma membranes. A range of experimental techniques and Molecular Dynamics simulations proves unambiguously that CaM interacts with lipid bilayers in the presence of calcium ions. Lipids phosphatidylserine (PS) and phosphatidylethanolamine (PE) hold the key to CaM-membrane interactions. Calcium induces an essential conformational rearrangement of CaM, but its binding to the headgroup of PS also neutralizes the membrane negative surface charge. More intriguingly, PE plays a dual role - it forms hydrogen bonds with CaM, but also destabilizes the lipid bilayer to increase exposure of hydrophobic acyl chains to the interacting proteins. Our findings suggest that upon increased intracellular calcium concentration, CaM and the cytosolic leaflet of cellular membranes can be functionally connected.

biophysics↗

bioRxiv2022

From the ear flap to the nerve: A complete computer model of the peripheral auditory system

Computer models of the individual components of the peripheral auditory system - the outer, middle, and inner ears and the auditory nerve - have been developed in the past, with varying level of detail, breadth, and faithfulness of the underlying parameters. Building on previous work, we advance the modeling of the ear by presenting a complete, physiologically justified, bottom-up computer model based on up-to-date experimental data that integrates all of these parts together seamlessly. The detailed bottom-up design of the present model allows for the investigation of partial hearing mechanisms and their defects, including genetic, molecular, and microscopic factors. Also, thanks to the completeness of the model, one can study microscopic effects in the context of their implications on hearing as a whole, enabling the correlation with neural recordings and non-invasive psychoacoustic methods. Such a model is instrumental for advancing quantitative understanding of the mechanism of hearing, for investigating various forms of deafness, as well as for devising next generation hearing aids and cochlear implants.

neuroscience↗

bioRxiv2020

Sweet taste of heavy water

Hydrogen to deuterium isotopic substitution has only a minor effect on physical and chemical properties of water and, as such, is not supposed to influence its neutral taste. Here we conclusively demonstrate that humans are, nevertheless, able to distinguish D2O from H2O by taste. Indeed, highly purified heavy water has a distinctly sweeter taste than same-purity normal water and adds to perceived sweetness of sweeteners. In contrast, mice do not prefer D2O over H2O, indicating that they are not likely to perceive heavy water as sweet. HEK 293T cells transfected with the TAS1R2/TAS1R3 heterodimer and chimeric G-proteins are activated by D2O but not by H2O. Lactisole, which is a known sweetness inhibitor acting via the TAS1R3 monomer of the TAS1R2/TAS1R3, suppresses the sweetness of D2O in human sensory tests, as well as the calcium release elicited by D2O in sweet taste receptor-expressing cells. The present multifaceted experimental study, complemented by homology modelling and molecular dynamics simulations, resolves a long-standing controversy about the taste of heavy water, shows that its sweet taste is mediated by the human TAS1R2/TAS1R3 taste receptor, and opens way to future studies of the detailed mechanism of action. One sentence summaryHeavy water elicits sweet taste for humans via the TAS1R2/TAS1R3 taste receptor.

biochemistry↗