Investigating protein aggregation in protein-carbohydrate interfaces using sequence and structural features

The interaction between carbohydrates and proteins plays a crucial role in various cellular processes, including adhesion, immune responses, metabolism, and cell signaling. Experimental studies have demonstrated the carbohydrate-binding capacity of aggregating peptides, raising the question of whether aggregation-prone regions (APRs) in proteins exhibit a similar capability. In this study, we conducted a systematic analysis of APRs in a curated set of protein-carbohydrate complexes, examining their correspondence to carbohydrate-binding residues at both protein sequence and structural levels. We found that carbohydrate-binding proteins are enriched with APRs, with 40% of carbohydrate-binding residues being aggregation-prone. This indicates that APRs are tolerated at carbohydrate-binding sites, contrary to the prevalent association of solvent-exposed APRs with proteostasis disruption. Furthermore, even non-overlapping APRs are observed in spatial proximity to carbohydrate-binding sites, participating in inter-residue contacts that may contribute to functional interactions. Notably, we have observed these functional APRs (fAPRs), denoting parts of APRs that bind carbohydrate, are enriched with aromatic residues that promote carbohydrate-binding. We observed that aggregation propensity and carbohydrate-binding affinity are not correlated at fAPRs, indicating that aggregation and carbohydrate-binding can be independently modulated. Interestingly, 85% of human fAPRs harbor at least one mutation predicted to be 'likely pathogenic', highlighting their relevance in enhancing interpretability in predicting mutation effects. This study reveals fAPRs, where aggregation and carbohydrate-binding intersect, as key sites of functional importance, frequently harboring disease-associated mutations.