Examining weak protein-protein interactions in start codon recognition via NMR spectroscopy

FEBS J. 2014 Apr;281(8):1965-73. doi: 10.1111/febs.12667. Epub 2014 Jan 2.


Weak protein-protein interactions are critical in numerous biological processes. Unfortunately, they are difficult to characterize due to the high concentrations required for the production and detection of the complex population. The inherent sensitivity of NMR spectroscopy to the chemical environment makes it an excellent tool to tackle this problem. NMR permits the exploration of interactions over a range of affinities, yielding essential insights into dynamic biological processes. The conversion of messanger RNA to protein is one such process that requires the coordinated association of many low-affinity proteins. During start codon recognition, eukaryotic initiation factors assemble into high-order complexes that bind messanger RNA and bring it to the ribosome for decoding. Many of the structures of the eukaryotic initiation factors have been determined; however, little is known regarding the weak binary complexes formed and their structure-function mechanisms. Herein, we use start codon recognition as a model system to review the relevant NMR methods for the characterization of weak interactions and the development of small molecule inhibitors.

Keywords: chemical shift perturbation; cross saturation; fragment based screening; initiation factors; nuclear magnetic resonance; paramagnetic relaxation enhancement; residual dipolar couplings; small angle X-Ray scattering reconstitution assay; translation initiation; weak interactions.

Publication types

  • Research Support, N.I.H., Extramural
  • Review

MeSH terms

  • Codon, Initiator / chemistry
  • Codon, Initiator / metabolism*
  • Magnetic Resonance Spectroscopy / methods*
  • Protein Binding
  • Proteins / chemistry
  • Proteins / metabolism*


  • Codon, Initiator
  • Proteins