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Proc Natl Acad Sci U S A. 2018 Nov 27;115(48):E11284-E11293. doi: 10.1073/pnas.1810523115. Epub 2018 Nov 9.

Folding pathway of an Ig domain is conserved on and off the ribosome.

Author information

1
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892.
2
Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom.
3
Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden.
4
Gene Center, Department of Biochemistry, Ludwig Maximilian University of Munich, 81377 Munich, Germany.
5
Center for Integrated Protein Science Munich, Ludwig Maximilian University of Munich, 81377 Munich, Germany.
6
Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden; gunnar@dbb.su.se jc162@cam.ac.uk robert.best2@nih.gov.
7
Science for Life Laboratory, Stockholm University, SE-171 21 Solna, Sweden.
8
Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom; gunnar@dbb.su.se jc162@cam.ac.uk robert.best2@nih.gov.
9
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892; gunnar@dbb.su.se jc162@cam.ac.uk robert.best2@nih.gov.

Abstract

Proteins that fold cotranslationally may do so in a restricted configurational space, due to the volume occupied by the ribosome. How does this environment, coupled with the close proximity of the ribosome, affect the folding pathway of a protein? Previous studies have shown that the cotranslational folding process for many proteins, including small, single domains, is directly affected by the ribosome. Here, we investigate the cotranslational folding of an all-β Ig domain, titin I27. Using an arrest peptide-based assay and structural studies by cryo-EM, we show that I27 folds in the mouth of the ribosome exit tunnel. Simulations that use a kinetic model for the force dependence of escape from arrest accurately predict the fraction of folded protein as a function of length. We used these simulations to probe the folding pathway on and off the ribosome. Our simulations-which also reproduce experiments on mutant forms of I27-show that I27 folds, while still sequestered in the mouth of the ribosome exit tunnel, by essentially the same pathway as free I27, with only subtle shifts of critical contacts from the C to the N terminus.

KEYWORDS:

arrest peptide; fraction folded; kinetic model; mechanical force; molecular simulation

PMID:
30413621
PMCID:
PMC6275497
DOI:
10.1073/pnas.1810523115
[Indexed for MEDLINE]
Free PMC Article

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