Distinct modes of folding assistance in cells by protein- and RNA-based chaperones
Year: 2026
Type: preprint
Abstract: How chaperones mediate protein folding in the crowded cell environment remains poorly understood. To gain insight, we developed CHAP-SEQ, a high-throughput approach for examining how chaperones affect protein folding in cells at amino acid resolution. Performing CHAP-SEQ using three protein-based chaperones and one RNA-based chaperone revealed distinct modes of folding assistance. The protein-based chaperones preferentially act in a partially redundant manner on hydrophobic core residues, whereas the RNA-based chaperone primarily targets structural or dynamic features of the client protein. Furthermore, while the chaperone RNA has little preference for client variants’ baseline stability, the protein-based chaperones preferentially assisted clients with greater intrinsic foldability. Together, these findings demonstrated that protein– and RNA-based chaperones promote protein folding through mechanistically distinct modes of action. Significance Statement Determining the structural basis of how individual chaperones act on client proteins remains challenging, particularly within living cells. This knowledge gap is especially pronounced for RNA-based chaperones, whose mechanisms of action remain largely unknown. Here we introduce CHAP-SEQ, a technique that maps chaperone effects across a client protein at the level of individual amino acid residues. CHAP-SEQ revealed distinct residue-level patterns of folding assistance by protein– and RNA-based chaperones, and provided insight into both how different chaperones act in a partially redundant, partially complementary manner to aid folding in cells.
Institutions: University of Denver, University of Colorado Boulder
Language: English
Topic: Heat shock proteins research
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W7154685343