Varisco, M. | Search bioRxiv

bioRxiv2026

Atlantis: An integrative database for human proteome structural and functional sites

Understanding protein mechanisms in health and disease requires characterizing the functional roles of individual amino acid residues. To explore the role of residues and their mutations, we have developed Atlantis, a database that integrates structural and functional information at the human proteome residue level. A graph database enables complex queries and the retrieval of integrated information for multiple functional analysis of protein systems. A Model Context Protocol (MCP) connector allows the interrogation of the resource through Large Language Models (LLMs) or agentic frameworks for biomedical research. Atlantis annotates over 11M residues across 20k human proteins, identifying hundreds thousands intra- and inter-protein contacts in PDB as well as AlphaFoldDB structures. We also provide the possibility to analyze and integrate predicted 3D complexes inputted by the user, and we showcased these features on hundreds of AlphaFold-multimer complexes of GPCRs and LRRK2 interaction networks. The tool is freely accessible at https://atlantis.bioinfolab.sns.it/.

bioinformatics↗

bioRxiv2018

Nuclear Tau modulates VGluT1 expression: a new function for Tau

Summary\n\nTau displacement from microtubules is the first step in the onset of tauopathies, and is followed by toxic protein aggregation. However, other non-canonical functions of Tau might have a role in these pathologies. Here, we demonstrate that a small amount of Tau localizes in the nuclear compartment and accumulates in both the soluble and DNA-bound fractions. We show that nuclear Tau regulates the expression of VGluT1, a disease-relevant gene directly involved in glutamatergic synaptic transmission. Impeding Tau/tubulin interaction in the cytosol favours its nuclear translocation and increases VGluT1 expression. Remarkably, the P301L mutation impairs this mechanism leading to a loss of function. Altogether, our results provide the demonstration of a direct physiological role of Tau on gene expression. Alterations of this mechanism may be at the basis of the onset of neurodegeneration.

molecular biology↗