Pulse labeling reveals the tail end of protein folding by proteome profiling

• Published in: Cell reports (Cambridge) Vol. 40; no. 3; p. 111096
• Main Authors: Zhu, Mang, Kuechler, Erich R., Wong, Ryan W.K., Calabrese, Gaetano, Sitarik, Ian M., Rana, Viraj, Stoynov, Nikolay, O’Brien, Edward P., Gsponer, Jörg, Mayor, Thibault
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 19-07-2022
• Subjects: heat stress; limited proteolysis; misfolding; Molecular Chaperones - metabolism; Peptides - metabolism; protein aggregation; Protein Binding; Protein Folding; protein mass spectrometry; Proteome - metabolism; proteomics; proteostasis; pulse SILAC; translation; heat stress; proteomics; protein mass spectrometry; protein aggregation; limited proteolysis; translation; pulse SILAC; CP: Molecular biology; protein folding; proteostasis; misfolding
• ISSN: 2211-1247; 2211-1247
• DOI: 10.1016/j.celrep.2022.111096

Accurate and efficient folding of nascent protein sequences into their native states requires support from the protein homeostasis network. Herein we probe which newly translated proteins are thermo-sensitive, making them susceptible to misfolding and aggregation under heat stress using pulse-SILAC mass spectrometry. We find a distinct group of proteins that is highly sensitive to this perturbation when newly synthesized but not once matured. These proteins are abundant and highly structured. Notably, they display a tendency to form β sheet secondary structures, have more complex folding topology, and are enriched for chaperone-binding motifs, suggesting a higher demand for chaperone-assisted folding. These polypeptides are also more often components of stable protein complexes in comparison with other proteins. Combining these findings suggests the existence of a specific subset of proteins in the cell that is particularly vulnerable to misfolding and aggregation following synthesis before reaching the native state.
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•A subset of newly synthesized proteins is more thermo-sensitive•Newly translated and thermo-sensitive proteins share distinct features•Thermo-sensitive proteins have more β sheet and complex folding topology•Many abundant proteins are sensitive to aggregation until reaching the native state
Zhu et al. reveal that a subset of proteins is more thermo-sensitive when newly synthesized but not once matured. These proteins have features associated with more complex folding topology in comparison with other proteins, suggesting they remain susceptible to misfolding and aggregation following synthesis before reaching their native states.