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Structure-Based Energetics of mRNA Decoding on the Ribosome
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
2014 (English)In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 53, no 10, 1714-1722 p.Article in journal (Refereed) Published
Abstract [en]

The origin of high fidelity in bacterial protein synthesis on the ribosome remains a fundamental unsolved problem despite available three-dimensional structures of different stages of the translation process. However, these structures open up the possibility of directly computing the energetics of tRNA selection that is required for an authentic understanding of fidelity in decoding. Here, we report extensive computer simulations that allow us to quantitatively calculate tRNA discrimination and uncover the energetics underlying accuracy in code translation. We show that the tRNA-mRNA interaction energetics varies drastically along the path from initial selection to peptide bond formation. While the selection process is obviously controlled by kinetics, the underlying thermodynamics explains the origin of the high degree of accuracy. The existence of both low- and high-selectivity states provides an efficient mechanism for initial selection and proofreading that does not require codon-dependent long-range structural signaling within the ribosome. It is instead the distinctly unequal population of the high-selectivity states for cognate and noncognate substrates that is the key discriminatory factor. The simulations reveal the essential roles played both by the 30S subunit conformational switch and by the common tRNA modification at position 37 in amplifying the accuracy.

Place, publisher, year, edition, pages
2014. Vol. 53, no 10, 1714-1722 p.
National Category
Natural Sciences
Identifiers
URN: urn:nbn:se:uu:diva-223891DOI: 10.1021/bi5000355ISI: 000333235600018OAI: oai:DiVA.org:uu-223891DiVA: diva2:715569
Available from: 2014-05-05 Created: 2014-04-28 Last updated: 2017-12-05Bibliographically approved

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Satpati, PriyadarshiSund, JohanÅqvist, Johan

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