Universal protein misfolding intermediates can bypass the proteostasis network and remain soluble and less functional

Daniel A. Nissley, Yang Jiang, Fabio Trovato, Ian Sitarik, Karthik B. Narayan, Philip To, Yingzi Xia, Stephen D. Fried and Edward P. O’Brien ()
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Daniel A. Nissley: Pennsylvania State University
Yang Jiang: Pennsylvania State University
Fabio Trovato: Pennsylvania State University
Ian Sitarik: Pennsylvania State University
Karthik B. Narayan: Pennsylvania State University
Philip To: Johns Hopkins University
Yingzi Xia: Johns Hopkins University
Stephen D. Fried: Johns Hopkins University
Edward P. O’Brien: Pennsylvania State University

Nature Communications, 2022, vol. 13, issue 1, 1-16

Abstract: Abstract Some misfolded protein conformations can bypass proteostasis machinery and remain soluble in vivo. This is an unexpected observation, as cellular quality control mechanisms should remove misfolded proteins. Three questions, then, are: how do long-lived, soluble, misfolded proteins bypass proteostasis? How widespread are such misfolded states? And how long do they persist? We address these questions using coarse-grain molecular dynamics simulations of the synthesis, termination, and post-translational dynamics of a representative set of cytosolic E. coli proteins. We predict that half of proteins exhibit misfolded subpopulations that bypass molecular chaperones, avoid aggregation, and will not be rapidly degraded, with some misfolded states persisting for months or longer. The surface properties of these misfolded states are native-like, suggesting they will remain soluble, while self-entanglements make them long-lived kinetic traps. In terms of function, we predict that one-third of proteins can misfold into soluble less-functional states. For the heavily entangled protein glycerol-3-phosphate dehydrogenase, limited-proteolysis mass spectrometry experiments interrogating misfolded conformations of the protein are consistent with the structural changes predicted by our simulations. These results therefore provide an explanation for how proteins can misfold into soluble conformations with reduced functionality that can bypass proteostasis, and indicate, unexpectedly, this may be a wide-spread phenomenon.

Date: 2022
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DOI: 10.1038/s41467-022-30548-5

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