Biology subjects

Stange, A. D.

Publications and source records attributed to Stange, A. D..

3 recordsLinked to original sources

bioRxiv2026

Structural characterisation of a spontaneous site 1 opening event in the insulin receptor

The insulin receptor samples multiple conformational states during ligand binding and activation, but the transient structural transitions connecting experimentally resolved receptor conformations remain poorly characterised. Here, we report a spontaneous opening event of insulin receptor site 1 observed during an unbiased molecular dynamics simulation initiated from the experimentally resolved singly insulin-bound IR1 receptor structure. The transition was characterised by separation of the L1 and FnIII-2 domains, rearrangement of site 1 contacts, and bending of the CT segment on the initially unoccupied receptor protomer. Structural comparison of the resulting conformation revealed similarity to the asymmetric IR2-A1 and IR2-A2 receptor states associated with hybrid insulin binding sites. Together, these findings suggest that conformations compatible with hybrid-site receptor states can emerge spontaneously from the intrinsic dynamics of the insulin receptor ectodomain, supporting a conformational selection model for receptor ligand engagement.

biochemistry↗

bioRxiv2026

Mechanistic Insights into Na+-dependent HCO3- Transport by NBCn2 (SLC4A10)

The 3D structure and mechanism of action are unknown for the integral plasma membrane transport protein Solute Carrier 4A10, which has been characterized functionally as an electroneutral Na+:HCO3- cotransporter. We used structure prediction and molecular dynamics simulations to study the binding of the transported ions to the Solute Carrier 4A10 protein and suggest a model of sequential binding of Na+ followed by HCO3- to the ion binding domain. The binding of HCO3- to the protein appears to depend absolutely on Na+ binding. Conversely, binding of HCO3- stabilizes the interaction between Na+ and its binding site. This allows the subsequent conformational changes of the Solute Carrier 4A10 protein and, thus, ion translocation. Measurements of intracellular pH and Na+ concentration revealed the dependence of Na+ on HCO3- transport. The study lays the necessary foundation for advanced analysis of ion translocation and the development of selective transport inhibitors of Solute Carrier 4A10 and other proteins of the protein family of HCO3- transporters.

biophysics↗

bioRxiv2026

Fluorinated RNA origami enables serum-stable nanodevices for sensing and targeting

Chemically modified RNAs with increased stability and reduced immunogenicity have transformed RNA therapeutics. Rational RNA design methods, including RNA origami, seek to further extend RNA medicine and biotechnology by encoding advanced functions such as signalling, targeting, and controlled release within the RNA polymer. However, current design methods lack the ability to integrate chemical modification or predict how it shapes the structure of large RNA assemblies inhibiting its use in RNA therapeutics. Here we demonstrate that 2-fluoro pyrimidine RNA (FY-RNA) origami structures can be co-transcriptionally folded to generate serum-stable nanodevices. Cryogenic electron microscopy reveals that FY-RNA can alter folding pathways and perturb tertiary motifs, while molecular dynamics simulations show how 2-fluoro modification affects hydrogen bonding, sugar pucker, and helix-helix interactions. Despite these structural perturbations, fluorogenic aptamers embedded within RNA origami retain partial activity and enable logic-based molecular sensing in human serum. Finally, we use an FY-RNA scaffold to determine the structure of an FY-RNA anti-Spike aptamer bound to the Spike protein at 3.4 [A] resolution, uncovering fluorine-specific structural motifs and protein interactions. Together, our results establish design principles for nuclease-resistant RNA architectures and position FY-RNA as a versatile polymer for constructing medical nanodevices and environmental sensors. More broadly, this work provides a framework for systematically exploring the folding landscape of chemically modified RNAs, expanding the chemical and functional diversity accessible to nucleic acid nanotechnology and RNA medicine.

biochemistry↗