L11 domain rearrangement upon binding to RNA and thiostrepton studied by NMR spectroscopy
Open Access
- 14 December 2006
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 35 (2), 441-454
- https://doi.org/10.1093/nar/gkl1066
Abstract
Ribosomal proteins are assumed to stabilize specific RNA structures and promote compact folding of the large rRNA. The conformational dynamics of the protein between the bound and unbound state play an important role in the binding process. We have studied those dynamical changes in detail for the highly conserved complex between the ribosomal protein L11 and the GTPase region of 23S rRNA. The RNA domain is compactly folded into a well defined tertiary structure, which is further stabilized by the association with the C-terminal domain of the L11 protein (L11 ctd ). In addition, the N-terminal domain of L11 (L11 ntd ) is implicated in the binding of the natural thiazole antibiotic thiostrepton, which disrupts the elongation factor function. We have studied the conformation of the ribosomal protein and its dynamics by NMR in the unbound state, the RNA bound state and in the ternary complex with the RNA and thiostrepton. Our data reveal a rearrangement of the L11 ntd , placing it closer to the RNA after binding of thiostrepton, which may prevent binding of elongation factors. We propose a model for the ternary L11–RNA–thiostrepton complex that is additionally based on interaction data and conformational information of the L11 protein. The model is consistent with earlier findings and provides an explanation for the role of L11 ntd in elongation factor binding.Keywords
This publication has 85 references indexed in Scilit:
- Crystal Structures of the Ribosome in Complex with Release Factors RF1 and RF2 Bound to a Cognate Stop CodonCell, 2005
- Localization of L11 protein on the ribosome and elucidation of its involvement in EF-G-dependent translocationJournal of Molecular Biology, 2001
- Stabilization of RNA tertiary structure by monovalent cationsJournal of Molecular Biology, 2000
- The Complete Atomic Structure of the Large Ribosomal Subunit at 2.4 Å ResolutionScience, 2000
- Prediction of Sterically Induced Alignment in a Dilute Liquid Crystalline Phase: Aid to Protein Structure Determination by NMRJournal of the American Chemical Society, 2000
- Measurement ofJand Dipolar Couplings from Simplified Two-Dimensional NMR SpectraJournal of Magnetic Resonance, 1998
- The antibiotic thiostrepton inhibits a functional transition within protein L11 at the ribosomal GTPase centreJournal of Molecular Biology, 1998
- The RNA binding domain of ribosomal protein L11: three-dimensional structure of the RNA-bound form of the protein and its interaction with 23 S rRNAJournal of Molecular Biology, 1997
- Affinities and selectivities of divalent cation binding sites within an RNA tertiary structureJournal of Molecular Biology, 1997
- NMRPipe: A multidimensional spectral processing system based on UNIX pipesJournal of Biomolecular NMR, 1995