Lago, A. V. | bioRxiv Science

bioRxiv2024

Ice Finder: Few-Shot Learning for Non-Vitrified Ice Segmentation

This study introduces Ice Finder, a novel tool for quantifying crystalline ice in tomography, filling a crucial gap in existing methodologies. We establish the first application of the meta-learning paradigm to tomography, demonstrating that various tomographic tasks across datasets can be unified under a single meta-learning framework. Our approach utilizes few-shot learning to enhance domain generalization and adaptability to domain shifts, facilitating rapid adaptation to new datasets with minimal examples. Ice Finders performance is evaluated on a comprehensive set of in situ datasets from EMPIAR, proving its ease of use and fast processing capabilities, with inference times in the milliseconds. This tool not only accelerates workflows but also enhances the precision of structural studies in structural biology.

bioinformatics↗

bioRxiv2024

Slippery sequences stall the 26S proteasome at multiple points along the translocation pathway

In eukaryotes, the ubiquitin-proteasome system is responsible for intracellular protein degradation. Proteins tagged with ubiquitin are recognized by ubiquitin receptors on the 19S regulatory particle (RP) of the 26S proteasome, unfolded, routed through the translocation channel of the RP, and are then degraded in the 20S core particle (CP). Aromatic paddles on the pore-1 loops of the RPs Rpt subunits grip the substrate and pull folded domains into the channel, thereby unfolding them. The sequence that the aromatic paddles grip while unfolding a substrate is therefore expected to influence the extent of unfolding, and low complexity sequences have been shown to interfere with grip. However, the detailed spatial requirements for grip while unfolding proteins, particularly from the N-terminus, remain unknown. We determined how the location of glycine-rich tracts relative to a folded domain impairs unfolding. We find that, in contrast to a previous report, inserting glycine-rich sequences closer to the folded domain reduced unfolding ability more than positioning them further away. Locations that have the biggest effect on unfolding map onto the regions where the aromatic paddles are predicted to interact with the substrate. Effects on unfolding from locations up to 67 amino acids away from the folded domain suggest that there are additional interactions between the substrate and the proteasome beyond the aromatic paddles that facilitate translocation of the substrate. In sum, this study deepens understanding of the mechanical interactions within the substrate channel by mapping the spacing of interactions between the substrate and the proteasome during unfolding. ImportanceThe proteasome processively unfolds and degrades target proteins in eukaryotes. However, some substrates are prematurely released, and the resulting partially degraded proteins can cause problems for cells and can be linked to neurodegenerative diseases. In this paper, we use a series of substrates that can stall the proteasome during degradation to probe the translocation pathway substrates must traverse during unfolding. We find that multiple points along the translocation pathway are impacted by these slippery substrates.

biochemistry↗