Probing the dynamic stalk region of the ribosome using solution NMR

Sci Rep. 2019 Sep 19;9(1):13528. doi: 10.1038/s41598-019-49190-1.

Abstract

We describe an NMR approach based on the measurement of residual dipolar couplings (RDCs) to probe the structural and motional properties of the dynamic regions of the ribosome. Alignment of intact 70S ribosomes in filamentous bacteriophage enabled measurement of RDCs in the mobile C-terminal domain (CTD) of the stalk protein bL12. A structural refinement of this domain using the observed RDCs did not show large changes relative to the isolated protein in the absence of the ribosome, and we also found that alignment of the CTD was almost independent of the presence of the core ribosome particle, indicating that the inter-domain linker has significant flexibility. The nature of this linker was subsequently probed in more detail using a paramagnetic alignment strategy, which revealed partial propagation of alignment between neighbouring domains, providing direct experimental validation of a structural ensemble previously derived from SAXS and NMR relaxation measurements. Our results demonstrate the prospect of better characterising dynamical and functional regions of more challenging macromolecular machines and systems, for example ribosome-nascent chain complexes.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Escherichia coli Proteins / metabolism
  • Macromolecular Substances / metabolism
  • Magnetic Resonance Spectroscopy / methods
  • Nuclear Magnetic Resonance, Biomolecular / methods
  • Protein Conformation
  • Protein Structural Elements / physiology
  • Ribosome Subunits, Large, Bacterial / metabolism*
  • Ribosome Subunits, Large, Bacterial / ultrastructure*
  • Ribosomes / metabolism
  • Ribosomes / ultrastructure
  • Structure-Activity Relationship
  • X-Ray Diffraction / methods

Substances

  • Escherichia coli Proteins
  • Macromolecular Substances