The shape of the bacterial ribosome exit tunnel affects cotranslational protein folding
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 int...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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eLife Sciences Publications Ltd
2018-11-01
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| Series: | eLife |
| Subjects: | |
| Online Access: | https://elifesciences.org/articles/36326 |
| _version_ | 1797997577860284416 |
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| author | Renuka Kudva Pengfei Tian Fátima Pardo-Avila Marta Carroni Robert B Best Harris D Bernstein Gunnar von Heijne |
| author_facet | Renuka Kudva Pengfei Tian Fátima Pardo-Avila Marta Carroni Robert B Best Harris D Bernstein Gunnar von Heijne |
| author_sort | Renuka Kudva |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-11T10:34:52Z |
| format | Article |
| id | doaj.art-b8a00e7659374bc399c67af75ad5de29 |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-04-11T10:34:52Z |
| publishDate | 2018-11-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-b8a00e7659374bc399c67af75ad5de292022-12-22T04:29:20ZengeLife Sciences Publications LtdeLife2050-084X2018-11-01710.7554/eLife.36326The shape of the bacterial ribosome exit tunnel affects cotranslational protein foldingRenuka Kudva0https://orcid.org/0000-0003-0426-3716Pengfei Tian1Fátima Pardo-Avila2Marta Carroni3https://orcid.org/0000-0002-7697-6427Robert B Best4https://orcid.org/0000-0002-7893-3543Harris D Bernstein5https://orcid.org/0000-0002-4941-3741Gunnar von Heijne6https://orcid.org/0000-0002-4490-8569Department of Biochemistry and Biophysics, Stockholm University, Stockholm, SwedenLaboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United StatesDepartment of Structural Biology, Stanford University, Stanford, United StatesDepartment of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden; Science for Life Laboratory, Stockholm University, Solna, SwedenLaboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United StatesGenetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United StatesDepartment of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden; Science for Life Laboratory, Stockholm University, Solna, SwedenThe 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.https://elifesciences.org/articles/36326protein foldingribosomecotranslationalarrest peptideuL23uL24 |
| spellingShingle | Renuka Kudva Pengfei Tian Fátima Pardo-Avila Marta Carroni Robert B Best Harris D Bernstein Gunnar von Heijne The shape of the bacterial ribosome exit tunnel affects cotranslational protein folding eLife protein folding ribosome cotranslational arrest peptide uL23 uL24 |
| title | The shape of the bacterial ribosome exit tunnel affects cotranslational protein folding |
| title_full | The shape of the bacterial ribosome exit tunnel affects cotranslational protein folding |
| title_fullStr | The shape of the bacterial ribosome exit tunnel affects cotranslational protein folding |
| title_full_unstemmed | The shape of the bacterial ribosome exit tunnel affects cotranslational protein folding |
| title_short | The shape of the bacterial ribosome exit tunnel affects cotranslational protein folding |
| title_sort | shape of the bacterial ribosome exit tunnel affects cotranslational protein folding |
| topic | protein folding ribosome cotranslational arrest peptide uL23 uL24 |
| url | https://elifesciences.org/articles/36326 |
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