Transient knots in intrinsically disordered proteins and neurodegeneration

A tile model of circuit topology for self-entangled biopolymers

Building on the theory of circuit topology for intra-chain contacts in entangled proteins, we introduce tiles as a way to rigorously model local entanglements which are held in place by molecular forces. We develop operations that combine tiles so that entangled chains can be represented by algebraic expressions. Then we use our model to show that the only knot types that such entangled chains can have are [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text] and connected sums of these knots. This includes all proteins knots that have thus far been identified.

Protein Aggregation Landscape in Neurodegenerative Diseases: Clinical Relevance and Future Applications

Intrinsic disorder is a natural feature of polypeptide chains, resulting in the lack of a defined three-dimensional structure. Conformational changes in intrinsically disordered regions of a protein lead to unstable β-sheet enriched intermediates, which are stabilized by intermolecular interactions with other β-sheet enriched molecules, producing stable proteinaceous aggregates. Upon misfolding, several pathways may be undertaken depending on the composition of the amino acidic string and the surrounding environment, leading to different structures. Accumulating evidence is suggesting that the conformational state of a protein may initiate signalling pathways involved both in pathology and physiology. In this review, we will summarize the heterogeneity of structures that are produced from intrinsically disordered protein domains and highlight the routes that lead to the formation of physiological liquid droplets as well as pathogenic aggregates. The most common proteins found in aggregates in neurodegenerative diseases and their structural variability will be addressed. We will further evaluate the clinical relevance and future applications of the study of the structural heterogeneity of protein aggregates, which may aid the understanding of the phenotypic diversity observed in neurodegenerative disorders.