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| Item Type: | Article |
|---|---|
| Title: | How EF-Tu can contribute to efficient proofreading of aa-tRNA by the ribosome |
| Creators Name: | Noel, J.K. and Whitford, P.C. |
| 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. |
| Keywords: | Amino Acyl Transfer RNA, Guanosine Diphosphate, Kinetics, Molecular Dynamics Simulation, Molecular Models, Peptide Elongation Factor Tu, Protein Biosynthesis, Protein Conformation, Ribosomes, Static Electricity, Thermodynamics |
| Source: | Nature Communications |
| ISSN: | 2041-1723 |
| Publisher: | Nature Publishing Group |
| Volume: | 7 |
| Page Range: | 13314 |
| Date: | 31 October 2016 |
| Official Publication: | https://doi.org/10.1038/ncomms13314 |
| PubMed: | View item in PubMed |
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