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Garcia-Pardo, J.

Publications and source records attributed to Garcia-Pardo, J..

3 recordsLinked to original sources

EXPERIMENTAL KINETIC MECHANISM OF P53 CONDENSATION-AMYLOID AGGREGATION

The tumor suppressor p53 modulates the transcription of a variety of genes constituting a protective barrier against anomalous cellular proliferation. High frequency "hot-spot" mutations result in loss-of-function by the formation of amyloid-like aggregates that correlate with cancerous progression. We show that full-length p53 undergoes spontaneous homotypic condensation at sub-micromolar concentrations and in the absence of crowders, to yield dynamic coacervates that are stoichiometrically dissolved by DNA. These coacervates fuse and evolve into hydrogel-like clusters with strong thioflavin-T binding capacity, which further evolve into fibrillar species with a clearcut branching growth pattern. The amyloid-like coacervates can be rescued by the HPV master regulator E2 protein to yield large regular droplets. Furthermore, we kinetically dissected an overall condensation mechanism which consists of a nucleation-growth process by sequential addition of p53 tetramers, leading to discretely-sized and monodisperse early condensates followed by coalescence into bead-like coacervates that slowly evolve to the fibrillar species. Our results suggest strong similarities to condensation-to-amyloid transitions observed in neurological aggregopathies. Mechanistic insights uncover novel key early and intermediate stages of condensation that can be targeted for p53 rescuing drug discovery. SIGNIFICANT STATEMENTKnown as "the guardian of the genome", the tumor suppressor protein p53 becomes activated by injuries to the DNA genome, and determines whether the cell must undergo self-destruction to avoid cancerous proliferation. P53 is in fact inactivated by mutations in over 50% of all cancers, and restoring its function is recognized as a therapeutic cancer target. A recent biochemical revolution in cell physiology and pathology are liquid entities known as biomolecular condensates. We show that p53 form condensates en route to pathological forms in a surprisingly similar manner to neurological amyloid diseases such as Alzheime[r]s and Parkinso[n]s. We uncover the sequence of steps in the reaction, exposing flanks for a novel drug development platform based on the condensates paradigm.

biophysics↗

Cryo-EM Structure of a Mammalian-specific Alternative Amyloid Exon

hnRNPDL is a ribonucleoprotein (RNP) involved in transcription and RNA-processing, with missense mutations causing limb-girdle muscular dystrophy-3 (LGMDD3). Mammalian-specific alternative splicing (AS) renders three natural isoforms, hnRNPDL-2 being predominant in humans. We present the cryo-electron microscopy structure of full-length hnRNPDL-2 amyloid fibrils, which are stable, non-toxic, and bind nucleic acids, with the RNA binding domains building a solenoidal coat around them. The amyloid core consists of a single Gly/Tyr-rich and highly hydrophilic filament containing internal water channels. The architecture and activity of hnRNPDL-2 fibrils are reminiscent of functional amyloids, our results suggesting that LGMDD3 might be a loss-of-function disease associated with impaired fibrillation. Strikingly, the fibril core matches exon 6, absent in the soluble hnRNPDL-3 isoform. This provides structural evidence for AS controlling hnRNPDL assembly by precisely including/skipping an amyloid exon, a mechanism that holds the potential to generate functional diversity in RNPs.

biochemistry↗

A3D Database: Structure-based Protein Aggregation Predictions for the Human Proteome

MotivationProtein aggregation is associated with highly debilitating human disorders and constitutes a major bottleneck for producing therapeutic proteins. Our knowledge of the human protein structures repertoire has dramatically increased with the recent development of the AlphaFold (AF) deep-learning method. This structural information can be used to understand better protein aggregation properties and the rational design of protein solubility. This article uses the Aggrescan3D (A3D) tool to compute the structure-based aggregation predictions for the human proteome and make the predictions available in a database form. ResultsHere, we present the A3D Database, in which we analyze the AF-predicted human protein structures (for over 17 thousand non-membrane proteins) in terms of their aggregation properties using the A3D tool. Each entry of the A3D Database provides a detailed analysis of the structure-based aggregation propensity computed with A3D. The A3D Database implements simple but useful graphical tools for visualizing and interpreting protein structure datasets. We discuss case studies illustrating how the database could be used to analyze physiologically relevant proteins. Furthermore, the database enables testing the influence of user-selected mutations on protein solubility and stability, all integrated into a user-friendly interface. Availability and implementationA3D Database is freely available at: http://biocomp.chem.uw.edu.pl/A3D2/hproteome

bioinformatics↗