How EF-Tu can contribute to efficient proofreading of aa-tRNA by the ribosome

Nat Commun. 2016 Oct 31:7:13314. doi: 10.1038/ncomms13314.

Abstract

It has long been recognized that the thermodynamics of mRNA-tRNA base pairing is insufficient to explain the high fidelity and efficiency of aminoacyl-tRNA (aa-tRNA) selection by the ribosome. To rationalize this apparent inconsistency, Hopfield proposed that the ribosome may improve accuracy by utilizing a multi-step kinetic proofreading mechanism. While biochemical, structural and single-molecule studies have provided a detailed characterization of aa-tRNA selection, there is a limited understanding of how the physical-chemical properties of the ribosome enable proofreading. To this end, we probe the role of EF-Tu during aa-tRNA accommodation (the proofreading step) through the use of energy landscape principles, molecular dynamics simulations and kinetic models. We find that the steric composition of EF-Tu can reduce the free-energy barrier associated with the first step of accommodation: elbow accommodation. We interpret this effect within an extended kinetic model of accommodation and show how EF-Tu can contribute to efficient and accurate proofreading.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Guanosine Diphosphate / chemistry
  • Kinetics
  • Models, Molecular
  • Molecular Dynamics Simulation
  • Peptide Elongation Factor Tu / metabolism*
  • Protein Biosynthesis
  • Protein Conformation
  • RNA, Transfer, Amino Acyl / metabolism*
  • Ribosomes / metabolism*
  • Static Electricity
  • Thermodynamics

Substances

  • RNA, Transfer, Amino Acyl
  • Guanosine Diphosphate
  • Peptide Elongation Factor Tu