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Cotranslational Protein Folding inside the Ribosome Exit Tunnel.

ABSTRACT: At what point during translation do proteins fold? It is well established that proteins can fold cotranslationally outside the ribosome exit tunnel, whereas studies of folding inside the exit tunnel have so far detected only the formation of helical secondary structure and collapsed or partially structured folding intermediates. Here, using a combination of cotranslational nascent chain force measurements, inter-subunit fluorescence resonance energy transfer studies on single translating ribosomes, molecular dynamics simulations, and cryoelectron microscopy, we show that a small zinc-finger domain protein can fold deep inside the vestibule of the ribosome exit tunnel. Thus, for small protein domains, the ribosome itself can provide the kind of sheltered folding environment that chaperones provide for larger proteins.

SUBMITTER: Nilsson OB

PROVIDER: S-EPMC4571824 | biostudies-literature | 2015 Sep

REPOSITORIES: biostudies-literature

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Cotranslational Protein Folding inside the Ribosome Exit Tunnel.

Nilsson Ola B OB Hedman Rickard R Marino Jacopo J Wickles Stephan S Bischoff Lukas L Johansson Magnus M Müller-Lucks Annika A Trovato Fabio F Puglisi Joseph D JD O'Brien Edward P EP Beckmann Roland R von Heijne Gunnar G

Cell reports 20150828 10

At what point during translation do proteins fold? It is well established that proteins can fold cotranslationally outside the ribosome exit tunnel, whereas studies of folding inside the exit tunnel have so far detected only the formation of helical secondary structure and collapsed or partially structured folding intermediates. Here, using a combination of cotranslational nascent chain force measurements, inter-subunit fluorescence resonance energy transfer studies on single translating ribosom ...[more]

PMID: 26321634

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A functional connection between translation elongation and protein folding at the ribosome exit tunnel in Saccharomyces cerevisiae

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2020-11-25 | GSE151632 | GEO

Disome-seq reveals widespread ribosome collisions that promote cotranslational protein folding.

Project description:BackgroundThe folding of proteins is challenging in the highly crowded and sticky environment of a cell. Regulation of translation elongation may play a crucial role in ensuring the correct folding of proteins. Much of our knowledge regarding translation elongation comes from the sequencing of mRNA fragments protected by single ribosomes by ribo-seq. However, larger protected mRNA fragments have been observed, suggesting the existence of an alternative and previously hidden layer of regulation.ResultsIn this study, we performed disome-seq to sequence mRNA fragments protected by two stacked ribosomes, a product of translational pauses during which the 5'-elongating ribosome collides with the 3'-paused one. We detected widespread ribosome collisions that are related to slow ribosome release when stop codons are at the A-site, slow peptide bond formation from proline, glycine, asparagine, and cysteine when they are at the P-site, and slow leaving of polylysine from the exit tunnel of ribosomes. The structure of disomes obtained by cryo-electron microscopy suggests a different conformation from the substrate of the ribosome-associated protein quality control pathway. Collisions occurred more frequently in the gap regions between α-helices, where a translational pause can prevent the folding interference from the downstream peptides. Paused or collided ribosomes are associated with specific chaperones, which can aid in the cotranslational folding of the nascent peptides.ConclusionsTherefore, cells use regulated ribosome collisions to ensure protein homeostasis.

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Folding of VemP into translation-arresting secondary structure is driven by the ribosome exit tunnel.

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