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Elife. 2018 Nov 26;7. pii: e36326. doi: 10.7554/eLife.36326.

The shape of the bacterial ribosome exit tunnel affects cotranslational protein folding.

Author information

1
Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
2
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States.
3
Department of Structural Biology, Stanford University, Stanford, United States.
4
Science for Life Laboratory, Stockholm University, Solna, Sweden.
5
Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States.

Abstract

The E. coli ribosome exit tunnel can accommodate small folded proteins, while larger ones fold outside. It remains unclear, however, to what extent the geometry of the tunnel influences protein folding. Here, using E. coli ribosomes with deletions in loops in proteins uL23 and uL24 that protrude into the tunnel, we investigate how tunnel geometry determines where proteins of different sizes fold. We find that a 29-residue zinc-finger domain normally folding close to the uL23 loop folds deeper in the tunnel in uL23 Δloop ribosomes, while two ~ 100 residue proteins normally folding close to the uL24 loop near the tunnel exit port fold at deeper locations in uL24 Δloop ribosomes, in good agreement with results obtained by coarse-grained molecular dynamics simulations. This supports the idea that cotranslational folding commences once a protein domain reaches a location in the exit tunnel where there is sufficient space to house the folded structure.

KEYWORDS:

E. coli; arrest peptide; biochemistry; chemical biology; cotranslational; molecular biophysics; protein folding; ribosome; structural biology; uL23; uL24

PMID:
30475203
PMCID:
PMC6298777
DOI:
10.7554/eLife.36326
[Indexed for MEDLINE]
Free PMC Article

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