Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Modulating co-translational protein folding by rational design and ribosome engineering.
Journal, issue, pages	Nat Commun, Vol. 13, Issue 1, Page 4243, Year 2022
Publish date	Jul 22, 2022
Authors	Minkoo Ahn / Tomasz Włodarski / Alkistis Mitropoulou / Sammy H S Chan / Haneesh Sidhu / Elena Plessa / Thomas A Becker / Nediljko Budisa / Christopher A Waudby / Roland Beckmann / Anaïs M E Cassaignau / Lisa D Cabrita / John Christodoulou /
PubMed Abstract	Co-translational folding is a fundamental process for the efficient biosynthesis of nascent polypeptides that emerge through the ribosome exit tunnel. To understand how this process is modulated by ...Co-translational folding is a fundamental process for the efficient biosynthesis of nascent polypeptides that emerge through the ribosome exit tunnel. To understand how this process is modulated by the shape and surface of the narrow tunnel, we have rationally engineered three exit tunnel protein loops (uL22, uL23 and uL24) of the 70S ribosome by CRISPR/Cas9 gene editing, and studied the co-translational folding of an immunoglobulin-like filamin domain (FLN5). Our thermodynamics measurements employing F/N/methyl-TROSY NMR spectroscopy together with cryo-EM and molecular dynamics simulations reveal how the variations in the lengths of the loops present across species exert their distinct effects on the free energy of FLN5 folding. A concerted interplay of the uL23 and uL24 loops is sufficient to alter co-translational folding energetics, which we highlight by the opposite folding outcomes resulting from their extensions. These subtle modulations occur through a combination of the steric effects relating to the shape of the tunnel, the dynamic interactions between the ribosome surface and the unfolded nascent chain, and its altered exit pathway within the vestibule. These results illustrate the role of the exit tunnel structure in co-translational folding, and provide principles for how to remodel it to elicit a desired folding outcome.
External links	Nat Commun / PubMed:35869078 / PubMed Central
Methods	EM (single particle)
Resolution	2.2 - 2.75 Å
Structure data	14454 7z20 EMDB-14454, PDB-7z20: 70S E. coli ribosome with an extended uL23 loop from Candidatus marinimicrobia and a stalled filamin domain 5 nascent chain Method: EM (single particle) / Resolution: 2.29 Å 14846 7zod EMDB-14846, PDB-7zod: 70S E. coli ribosome with an extended uL23 loop from Candidatus marinimicrobia Method: EM (single particle) / Resolution: 2.56 Å 14850 7zp8 EMDB-14850, PDB-7zp8: 70S E. coli ribosome with a stalled filamin domain 5 nascent chain Method: EM (single particle) / Resolution: 2.2 Å 14864 7zq5 EMDB-14864, PDB-7zq5: 70S E. coli ribosome with truncated uL23 and uL24 loops Method: EM (single particle) / Resolution: 2.7 Å 14865 7zq6 EMDB-14865, PDB-7zq6: 70S E. coli ribosome with truncated uL23 and uL24 loops and a stalled filamin domain 5 nascent chain Method: EM (single particle) / Resolution: 2.75 Å
Source	Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) escherichia coli (E. coli) dictyostelium discoideum (eukaryote)
Keywords	RIBOSOME / exit tunnel / structural modification / ribosomal protein / folded nascent chain