D'Arrigo, G. | bioRxiv Science

bioRxiv2025

MICROGLIAL EXTRACELLULAR VESICLES MEDIATE C1Q DEPOSITION AT THE PRE-SYNAPSE AND PROMOTE SYNAPTIC PRUNING

C1q is released by microglia, localizes on weak synapses and acts as a tag for microglial synaptic pruning. However, how C1q tags synapses during the pruning period remains to be fully elucidated. Here, we report that C1q is delivered by microglia to pre-synaptic sites that externalize phosphatidylserine through extracellular vesicles. Using approaches to increase or reduce vesicles production in microglia, by C9orf72 knock out or pharmacological inhibition respectively, we provided mechanistic evidence linking extracellular vesicle release to pre-synaptic remodelling in neuron-microglia cultures. In C9orf72 knockout mice, we confirmed larger production of microglial extracellular vesicles, and showed augmented C1q presynaptic deposition associated with enhanced engulfment by microglia in the early postnatal hippocampus. Finally, we provide evidence that microglia physiologically release more vesicles during the period of postnatal circuit refinement. These findings implicate abnormal release of microglial extracellular vesicles in both neurodevelopmental and age-related disorders characterized by dysregulated microglia-mediated synaptic pruning.

neuroscience↗

bioRxiv2024

Computational screening of the effects of mutations on protein-protein off-rates and dissociation mechanisms by {tau}RAMD

The dissociation rate, or its reciprocal, the residence time ({tau}), is a crucial parameter for understanding the duration and biological impact of biomolecular interactions. Accurate prediction of {tau} is essential for understanding protein-protein interactions (PPIs) and identifying potential drug targets or modulators for tackling diseases. Conventional molecular dynamics simulation techniques are inherently constrained by their limited timescales, making it challenging to estimate residence times, which typically range from minutes to hours. Building upon its successful application in protein-small molecule systems, {tau}-Random Acceleration Molecular Dynamics ({tau}RAMD) is here investigated for estimating dissociation rates of protein-protein complexes. {tau}RAMD enables the observation of unbinding events on the nanosecond timescale, facilitating rapid and efficient computation of relative residence times. We tested this methodology for three protein-protein complexes and their extensive mutant datasets, achieving good agreement between computed and experimental data. By combining {tau}RAMD with MD-IFP (Interaction Fingerprint) analysis, dissociation mechanisms were characterized and their sensitivity to mutations investigated, enabling the identification of molecular hotspots for selective modulation of dissociation kinetics. In conclusion, our findings underscore the versatility of {tau}RAMD as a simple and computationally efficient approach for computing relative protein-protein dissociation rates and investigating dissociation mechanisms, thereby aiding the design of PPI modulators.

bioinformatics↗