Biology subjects

de Alba, E.

Publications and source records attributed to de Alba, E..

4 recordsLinked to original sources

bioRxiv2023

Natural and engineered isoforms of the inflammasome adaptor ASC form non-covalent, pH-responsive hydrogels

The protein ASC polymerizes into intricate filament networks to assemble the inflammasome, a filamentous multiprotein complex that triggers the inflammatory response. ASC carries two Death Domains integrally involved in protein self-association for filament assembly. We have leveraged this behavior to create non-covalent, pH-responsive hydrogels of full-length, folded ASC by carefully controlling the pH as a critical factor in the polymerization process. We show that natural variants of ASC (ASC isoforms) involved in inflammasome regulation also undergo hydrogelation. To further demonstrate this general capability, we engineered proteins inspired in the ASC structure that successfully form hydrogels. We analyzed the structural network of the natural and engineered protein hydrogels using transmission and scanning electron microscopy, and studied their viscoelastic behavior by shear rheology. Our results reveal one of the very few examples of hydrogels created by the self-assembly of globular proteins and domains in their native conformation and show that Death Domains can be used alone or as building blocks to engineer bioinspired hydrogels.

bioengineering↗

bioRxiv2022

Assembly mechanism of the AIM2 inflammasome sensorrevealed by single-molecule analysis

Pathogenic dsDNA prompts AIM2 (Absent In Melanoma 2) assembly leading to the formation of the inflammasome, a multimeric complex that triggers the inflammatory response. The recognition of foreign dsDNA involves AIM2 self-assembly concomitant with dsDNA binding. However, we lack mechanistic and kinetic information on the formation and propagation of the assembly, which can shed light on innate immunitys time response and specificity. Using correlative optical traps and fluorescence microscopy, we determine here the association and dissociation rates of the AIM2-DNA complex at the single-molecule level. We identify distinct mechanisms for oligomer growth via the binding of incoming AIM2 molecules to adjacent dsDNA or direct interaction with bound AIM2 assemblies, thus resembling primary and secondary nucleation processes. Through these mechanisms, AIM2 oligomers increase at least fourfold their size in seconds. Finally, our data indicate that single AIM2 molecules do not diffuse/scan along the DNA, suggesting that oligomerization depends on stochastic encounters with DNA and/or DNA-bound AIM2 molecules.

biophysics↗

bioRxiv2020

A twofold strategy for the protection of therapeutic peptides by attachment to the protease-resistant and fusogenic protein, saposin C

A great challenge of therapeutic peptides (biologics) is their short half-life. However, biologics can be protected by encapsulation in liposomes used as drug-delivery platforms. Liposomes are typically incorporated into cells by endocytic pathways, which eventually expose therapeutics to favorable proteolytic conditions. To enhance biologics protection, we report the design and characterization of a liposome-protein chimera combining the liposome fusogenic properties of peripheral-membrane protein saposin C, covalently linked to a proapoptotic peptide (the active domain of Bcl-2 protein PUMA). We show by NMR that the saposin C component of the chimera is capable of binding liposomes and that the peptide binds prosurvival Bcl-xL, thus following known PUMAs mechanism to induce cell death. These results indicate that the function of the individual components is preserved in the chimera. Our results point to a promising twofold strategy for drug delivery to; 1) avoid endocytosis by promoting liposome-membrane fusion, 2) provide additional protection by attachment to a stable, protease-resistant protein, which is a well-known method commonly used to prolong biologics half-life.

bioengineering↗

bioRxiv2019

Conformational Priming of RepA-WH1 for Functional Amyloid Conversion Detected by NMR Spectroscopy

How proteins with a stable globular fold acquire the amyloid state is still largely unknown. RepA is a versatile plasmidic DNA binding protein, functional either as a transcriptional repressor or as an initiator or inhibitor of DNA replication, the latter through the assembly of an amyloidogenic oligomer. Its N-terminal domain (WH1) is responsible for discrimination between these functional abilities by undergoing hitherto unknown structural changes. Furthermore, when expressed alone, RepA-WH1 behaves as a synthetic prion-like protein causing an amyloid proteinopathy in bacteria. RepA-WH1 is a stable dimer whose conformational dynamics had not been explored. Here we have studied it through NMR {1H}-15N relaxation and H/D exchange kinetics measurements. The N- and the C- terminal -helices, which lock the WH1 fold in each subunit of the dimer, as well as an internal amyloidogenic loop, show reduced stability and are partially unfolded in solution. S4-indigo, a small molecule ligand known to interfere with the amyloid assembly of RepA-WH1, binds to and tethers the N-terminal -helix and a {beta}-hairpin that is involved in dimerization, thus providing evidence for a priming role of fraying ends and dimerization switches in the amyloidogenesis of folded proteins.

biochemistry↗