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by Keyword: Protein aggregation


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Pallarès, Irantzu, de Groot, Natalia S., Iglesias, Valentín, Sant'Anna, Ricardo, Biosca, Arnau, Fernàndez-Busquets, Xavier, Ventura, Salvador, (2018). Discovering putative prion-like proteins in Plasmodium falciparum: A computational and experimental analysis Frontiers in Microbiology 9, Article 1737

Prions are a singular subset of proteins able to switch between a soluble conformation and a self-perpetuating amyloid state. Traditionally associated with neurodegenerative diseases, increasing evidence indicates that organisms exploit prion-like mechanisms for beneficial purposes. The ability to transit between conformations is encoded in the so-called prion domains, long disordered regions usually enriched in glutamine/asparagines residues. Interestingly, Plasmodium falciparum, the parasite that causes the most virulent form of malaria, is exceptionally rich in proteins bearing long Q/N-rich sequence stretches, accounting for roughly 30% of the proteome. This biased composition suggests that these protein regions might correspond to prion-like domains (PrLDs) and potentially form amyloid assemblies. To investigate this possibility, we performed a stringent computational survey for Q/N-rich PrLDs on P. falciparum. Our data indicate that ~10% of P. falciparum protein sequences have prionic signatures, and that this subproteome is enriched in regulatory proteins, such as transcription factors and RNA-binding proteins. Furthermore, we experimentally demonstrate for several of the identified PrLDs that, despite their disordered nature, they contain inner short sequences able to spontaneously self-assemble into amyloid-like structures. Although the ability of these sequences to nucleate the conformational conversion of the respective full-length proteins should still be demonstrated, our analysis suggests that, as previously described for other organisms, prion-like proteins might also play a functional role in P. falciparum.

Keywords: Plasmodium, Protein aggregation, Amyloid, Prion, Q-N-rich sequences, Protein Disorder


Villar-Pique, A., De Groot, N. S., Sabaté, R., Acebrón, S. P., Celaya, G., Fernàndez-Busquets, X., Muga, A., Ventura, S., (2012). The effect of amyloidogenic peptides on bacterial aging correlates with their intrinsic aggregation propensity Journal of Molecular Biology , 421, (2-3), 270-281

The formation of aggregates by misfolded proteins is thought to be inherently toxic, affecting cell fitness. This observation has led to the suggestion that selection against protein aggregation might be a major constraint on protein evolution. The precise fitness cost associated with protein aggregation has been traditionally difficult to evaluate. Moreover, it is not known if the detrimental effect of aggregates on cell physiology is generic or depends on the specific structural features of the protein deposit. In bacteria, the accumulation of intracellular protein aggregates reduces cell reproductive ability, promoting cellular aging. Here, we exploit the cell division defects promoted by the intracellular aggregation of Alzheimer's-disease-related amyloid β peptide in bacteria to demonstrate that the fitness cost associated with protein misfolding and aggregation is connected to the protein sequence, which controls both the in vivo aggregation rates and the conformational properties of the aggregates. We also show that the deleterious impact of protein aggregation on bacterial division can be buffered by molecular chaperones, likely broadening the sequential space on which natural selection can act. Overall, the results in the present work have potential implications for the evolution of proteins and provide a robust system to experimentally model and quantify the impact of protein aggregation on cell fitness.

Keywords: Amyloid fibrils, Chaperones, Escherichia coli, Inclusion bodies, Protein aggregation


Sabaté, R., Espargaró, A., de Groot, N. S., Valle-Delgado, J. J., Fernàndez-Busquets, X., Ventura, S., (2010). The role of protein sequence and amino acid composition in amyloid formation: Scrambling and backward reading of IAPP amyloid fibrils Journal of Molecular Biology , 404, (2), 337-352

The specific functional structure of natural proteins is determined by the way in which amino acids are sequentially connected in the polypeptide. The tight sequence/structure relationship governing protein folding does not seem to apply to amyloid fibril formation because many proteins without any sequence relationship have been shown to assemble into very similar β-sheet-enriched structures. Here, we have characterized the aggregation kinetics, seeding ability, morphology, conformation, stability, and toxicity of amyloid fibrils formed by a 20-residue domain of the islet amyloid polypeptide (IAPP), as well as of a backward and scrambled version of this peptide. The three IAPP peptides readily aggregate into ordered, β-sheet-enriched, amyloid-like fibrils. However, the mechanism of formation and the structural and functional properties of aggregates formed from these three peptides are different in such a way that they do not cross-seed each other despite sharing a common amino acid composition. The results confirm that, as for globular proteins, highly specific polypeptide sequential traits govern the assembly pathway, final fine structure, and cytotoxic properties of amyloid conformations.

Keywords: Amyloid formation, Islet amyloid polypeptide, Protein aggregation, Protein sequence, Retro proteins


Morell, M., Bravo, R., Espargaro, A., Sisquella, X., Aviles, F. X., Fernàndez-Busquets, X., Ventura, S., (2008). Inclusion bodies: Specificity in their aggregation process and amyloid-like structure Biochimica et Biophysica Acta - Molecular Cell Research , 1783, (10), 1815-1825

The accumulation of aggregated protein in the cell is associated with the pathology of many diseases and constitutes a major concern in protein production. Intracellular aggregates have been traditionally regarded as nonspecific associations of misfolded polypeptides. This view is challenged by studies demonstrating that, in vitro, aggregation often involves specific interactions. However, little is known about the specificity of in vivo protein deposition. Here, we investigate the degree of in vivo co-aggregation between two self-aggregating proteins, A beta A2 amyloid peptide and foot-and-mouth disease virus VP1 capsid protein, in prokaryotic cells. In addition, the ultrastructure of intracellular aggregates is explored to decipher whether amyloid fibrils and intracellular protein inclusions share structural properties. The data indicate that in vivo protein aggregation exhibits a remarkable specificity that depends on the establishment of selective interactions and results in the formation of oligomeric and fibrillar structures displaying amyloid-like properties. These features allow prokaryotic A beta A2 intracellular aggregates to act as effective seeds in the formation of A beta A2 amyloid fibrils. overall, our results suggest that conserved mechanisms underlie protein aggregation in different organisms. They also have important implications for biotechnological and biomedical applications of recombinant polypeptides.

Keywords: Protein aggregation, Inclusion bodies, Conformational diseases, Amyloid fibrils, Protein folding