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The Unavoidable Threat of Aggregation: Implications for Folding and Function of a β-Rich Protein

Protein aggregation has been implicated in several catastrophic diseases (neurodegeneration, diabetes, ALS) and its complexity has also become a major obstacle in large-scale production of protein-based therapeutics. Despite the generic behavior of proteins to aggregate, only a few globular proteins have known aggregation mechanisms. At present, there have been no clear connections between a protein folding, function and aggregation. We have tackled the challenge of understanding the links between a protein's natural tendency to fold and function with its propensity to misfold and aggregate. Using a predominantly beta-sheet protein whose in vitro folding has been explored in detail: cellular retinoic acid-binding protein I (CRABP 1), as a model, we investigated sequence determinants for folding and aggregation. In addition, we characterized the aggregation-prone intermediate under native conditions. Our studies revealed similar contiguous aggregation cores in in vitro and in vivo aggregates of CRABP 1 validating the importance of sequence information under extremely different conditions. Hydrophobic stretches that comprise the interface in aggregates include residues surrounding the ligand binding portal and residues at the C-terminal strands of CRABP 1. Folding studies reveal that docking of the N and C terminals happen in the early stages of barrel closure of CRABP 1 emphasizing the role of folding in preventing exposure of risky aggregation-prone sequences. We further examined the intermediate that initiates aggregation under native conditions. We found that inherent structural fluctuations in the native protein, relevant to ligand binding of CRABP 1, expose aggregation-prone sequences. Binding of the ligand, retinoic acid decreases the aggregation of CRABP 1 illustrating the contribution functional interactions in avoiding aggregation. Our study implies that because of the evolutionary requirement for proteins to fold and function, aggregation becomes an unavoidable risk.
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