Biology subjects

Grabmayr, H.

Publications and source records attributed to Grabmayr, H..

4 recordsLinked to original sources

bioRxiv2026

Combinatorial DNA-PAINT

State-of-the-art super-resolution microscopy enables nanometer-resolution imaging of proteins, but its multiplexing capacity has been fundamentally constrained. Here, we present Combi-PAINT, a combinatorial DNA barcoding strategy based on DNA-PAINT, that facilitates superlinear scaling of multiplexing with the number of imaging rounds. Instead of assigning one unique docking strand per target, Combi-PAINT encodes targets as combinations of orthogonal sequences, allowing nonlinear scaling of target number with imaging rounds. Using just six imaging rounds, we resolve 41 targets in a field-of-view of 100 x 100 m2 with [~]2.5 nm localization precision and [~]90% decoding accuracy in under 30 minutes, representing the fastest sub-10 nm super-resolution microscopy acquisition to date. We benchmark decoding fidelity and demonstrate robust in situ performance in mammalian cells, achieving 97% decoding accuracy. Combi-PAINT is compatible with existing DNA-PAINT workflows and speed-enhancing techniques, offering a scalable, accessible platform for high-content, single-molecule spatial proteomics.

biophysics↗

bioRxiv2025

STIM1 transmembrane helix dimerization captured by AI-guided transition path sampling

STIM1 is a Ca2+-sensing protein in the endoplasmic reticulum (ER) membrane. The depletion of ER Ca2+ stores induces a large conformational transition of the cytosolic STIM1 C-terminus, initiated by the dimerization of the transmembrane (TM) domain. We use the AI-guided transition path sampling algorithm aimmd to extensively sample the dimerization of STIM1-TM helices in an ER-mimicking lipid bilayer. In nearly 0.5 milliseconds of all-atom molecular dynamics simulations without bias potentials, we harvest over 170 transition paths, each about 1.2 {micro}s long on average. We find that STIM1 dimerizes into three distinct and coexisting configurations, which reconciles conflicting results from earlier crosslinking studies. The dominant X-shaped bound state centers around contacts supported by the SxxxG TM interfacial motif. Mutating residues in this contact interface allows us to tune the STIM1-dimerization propensity in fluorescence experiments. From the trained model of the committor probability of dimerization, we identify the transition state ensemble for TM-helix dimerization. At the transition state, interhelical contacts in the luminal halves of the two monomers dominate, which likely enables the luminal Ca2+-sensing domain in STIM1 to condition the dimerization of the TM helices. Our work demonstrates the unique power of AI-guided simulations to sample rare and slow molecular transitions, and to produce detailed atomistic insight into the mechanism of STIM1 TM-helix dimerization as a key step in ER Ca2+-sensing. SignificanceSTIM1 is a protein sensor that signals drops in the Ca2+ concentration inside the endoplasmic reticulum (ER) to the cytosol. As Ca2+ levels decrease, the STIM1 transmembrane (TM) helices dimerize. We sample this TM helix dimerization in AI-guided atomistic molecular simulations, revealing two distinct pathways of dimerization. We reconcile conflicting results of earlier crosslinking studies by showing that both reported dimer configurations coexist as the end points of distinct association pathways. The dominance of interhelical contacts on the luminal side at the transition state enables the luminal Ca2+-sensing domain to condition helix dimerization. AI-guided path sampling made it possible to sample rare helix dimerization events far outside the current reach of regular molecular simulations.

biophysics↗

bioRxiv2025

Angstrom-resolution imaging of cell-surface glycans

Glycobiology is rooted in the study of monosaccharides, [A]ngstrom-sized molecules that are the building blocks of intricate glycosylation patterns. Glycosylated biomolecules form the glycocalyx, a dense coat encasing every human cell with central relevance - among others - in immunology, oncology, and virology. In order to understand glycosylation function, visualizing its molecular structure is fundamental. However, the ability to visualize the molecular architecture of the glycocalyx has remained elusive. Techniques like mass spectrometry, electron microscopy, and fluorescence microscopy lack the necessary cellular context, specificity, and resolution. Here, we address these limitations by combining metabolic labeling with [A]ngstrom-resolution fluorescence microscopy, enabling the first-ever visualization of individual sugars within glycans on the cell surface. Our work provides unprecedented insights into the molecular architecture of the glycocalyx and constitutes the foundation for future explorations of its function in health and disease.

biophysics↗

bioRxiv2021

Dissecting gating mechanisms of Orai calcium channel paralogs using constitutively active Orai mutants that mimic STIM1-gated state

In humans, there are three paralogs of the Orai Ca2+ channel, which lie at the heart of the store-operated calcium entry (SOCE) machinery. While the STIM-mediated gating mechanism of Orai channels is still being actively investigated, several artificial and natural variants are known to cause constitutive activity of the human Orai1 channel. Surprisingly, little is known about the conservation of the gating mechanism among the different human Orai paralogs and orthologs in other species. In our work, we show that the mutation corresponding to the activating mutation H134A in transmembrane helix 2 (TM2) of human Orai1 also activates Orai2 and Orai3, likely via a similar mechanism. However, this cross-paralog conservation does not apply to the "ANSGA" nexus mutations in TM4 of human Orai1 which mimic the STIM1-activated state of the channel. Investigating the mechanistic background of these differences, we identified two positions, H171 and F246 in human Orai1, which directly control the channel activation triggered by the "ANSGA" mutations in Orai1. Our results shed new light on these important gating checkpoints and show that the gating mechanism of the Orai channels is affected by multiple factors that are not necessarily evolutionarily conserved, such as the TM4-TM3 coupling.

cell biology↗