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Principles of stop-codon reading 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.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
2010 (English)In: Nature, ISSN 0028-0836, Vol. 465, no 7300, 947-U12 p.Article in journal (Refereed) Published
Abstract [en]

In termination of protein synthesis, the bacterial release factors RF1 and RF2 bind to the ribosome through specific recognition of messenger RNA stop codons and trigger hydrolysis of the bond between the nascent polypeptide and the transfer RNA at the peptidyl-tRNA site, thereby releasing the newly synthesized protein. The release factors are highly specific for a U in the first stop-codon position 1 and recognize different combinations of purines in the second and third positions, with RF1 reading UAA and UAG and RF2 reading UAA and UGA. With recently determined crystal structures of termination complexes(2-4), it has become possible to decipher the energetics of stop-codon reading by computational analysis and to clarify the origin of the high release-factor binding accuracy. Here we report molecular dynamics free-energy calculations on different cognate and non-cognate termination complexes. The simulations quantitatively explain the basic principles of decoding in all three codon positions and reveal the key elements responsible for specificity of the release factors. The overall reading mechanism involves hitherto unidentified interactions and recognition switches that cannot be described in terms of a tripeptide anticodon model. Further simulations of complexes with tRNA(Trp), the tRNA recognizing the triplet codon for Trp, explain the observation of a 'leaky' stop codon 5 and highlight the fundamentally different third position reading by RF2, which leads to a high stop-codon specificity with strong discrimination against the Trp codon. The simulations clearly illustrate the versatility of codon reading by protein, which goes far beyond tRNA mimicry.

Place, publisher, year, edition, pages
2010. Vol. 465, no 7300, 947-U12 p.
National Category
Biochemistry and Molecular Biology
URN: urn:nbn:se:uu:diva-135541DOI: 10.1038/nature09082ISI: 000278804500042OAI: oai:DiVA.org:uu-135541DiVA: diva2:377767
Available from: 2010-12-14 Created: 2010-12-07 Last updated: 2014-01-23Bibliographically approved
In thesis
1. From Structure to Function with Binding Free Energy Calculations for Codon Reading, Riboswitches and Lectins
Open this publication in new window or tab >>From Structure to Function with Binding Free Energy Calculations for Codon Reading, Riboswitches and Lectins
2013 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Molecular association is part of many important processes in living cells. Computational methods for calculating binding free energies allows for a quantitative examination of biomolecular structures and hypotheses drawn from biochemical experiments. Here, binding free energy calculations for tRNAs and release factors binding to mRNA codons on the ribosome, sugars binding to lectins and purine analogs binding to the purine riboswitch are presented.

The relative affinities between cognate and non-cognate tRNAs for different states involved in codon reading on the ribosome were determined. The calculations show that tRNA discrimination varies between different conformations of the 30S subunit, where the existence of both low and high selectivity states provides an efficient common mechanism for initial selection and proofreading. The simulations reveal a desolvation mechanism for the 30S conformational switch with which the accuracy of peptide bond formation can be amplified.

When an mRNA stop codon (UAA, UAG or UGA) is located in the ribosomal A-site release factors bind to the ribosome and the synthesized protein is released. RF1 is specific for UAA and UAG whereas RF2 is specific for UAA and UGA. The free energy calculations and an analysis of the performed simulations show the mechanisms for how RF1 and RF2 are able to read the stop codons with different specificities. Also mitochondrial release factors were investigated. Vertebrate mitochondria have four stop codons, UAA, UAG, AGA and AGG and two release factors mtRF1 and mtRF1a. The calculations show how the specificities of both mtRF1 and mtRF1a agree with RF1 and that none of them are likely to read the non-standard stop codons AGA and AGG.

The linear interaction energy method has also been examined for the RSL and PA-IIL lectins and for the purine riboswitch. The standard parameterization of the method works well for RSL, but fails for PA-IIL and the purine riboswitch due to compositions of the active sites in these systems. The development of new parameterizations to overcome these problems leads to a better understanding of both the method and the binding mechanisms in these systems.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2013. 58 p.
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1072
binding free energy, ribosome, codon reading, release factor, mitochondrial translation, purine riboswitch, lectin, molecular dynamics, free energy perturbation
National Category
Structural Biology
Research subject
Biology with specialization in Structural Biology
urn:nbn:se:uu:diva-207140 (URN)978-91-554-8750-8 (ISBN)
Public defence
2013-10-24, C8:301, BMC, Husargatan 3, Uppsala, 13:00 (English)
Available from: 2013-10-02 Created: 2013-09-09 Last updated: 2014-01-23

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