The formation of amyloid aggregates upon protein misfolding is related to several devastating degenerative diseases. We developed PASTA to predict the propensities of protein sequences to aggregate into amyloids.
These propensities represent the presence of aggregation hot spots stabilizing pathological interactions, the establishing of cross-amyloid interactions between co-aggregating proteins and the stability of the amyloid cross-beta structure. We used aggregation, intrinsic disorder, hydrophobicity and secondary structure preferences to develop the SODA algorithm which estimates changes in solubility. Integrating these and other features can help explain the context-dependent behavior of proteins.
However, most tools focus on a single aspect, hampering a holistic understanding of protein structure. Our FELLS tool helps to visualize structural features from the protein sequence and estimated local propensities including amphipathicity. The calculations required for FELLS are extremely fast and suited for large-scale analysis while providing a detailed analysis of difficult cases.
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Alexander Miguel Monzon
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Damiano Piovesan
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Silvio C. E. Tosatto