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Cited by 57RNA and protein synthesis mechanismsEvolution and Genetic DynamicsProtein Structure and Dynamics

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The Ribosome as an Optimal Decoder: A Lesson in Molecular Recognition

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Savir, Yonatan, Tlusty, Tsvi·2013·Cell
DOI 10.1016/j.cell.2013.03.032
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Abstract

The ribosome is a complex molecular machine that, in order to synthesize proteins, has to decode mRNAs by pairing their codons with matching tRNAs. Decoding is a major determinant of fitness and requires accurate and fast selection of correct tRNAs among many similar competitors. However, it is unclear whether the modern ribosome, and in particular its large conformational changes during decoding, are the outcome of adaptation to its task as a decoder or the result of other constraints. Here, we derive the energy landscape that provides optimal discrimination between competing substrates and thereby optimal tRNA decoding. We show that the measured landscape of the prokaryotic ribosome is sculpted in this way. This model suggests that conformational changes of the ribosome and tRNA during decoding are means to obtain an optimal decoder. Our analysis puts forward a generic mechanism that may be utilized broadly by molecular recognition systems.

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Metadata

Authors
Savir, Y., & Tlusty, T.
Affiliations
  • Harvard University (US)
  • Institute for Advanced Study (US)
Corresponding author
Tlusty, Tsvi
ORCID
Venue
Cell
Publisher
Elsevier BV
Published
2013-04
Volume
153
Issue
2
Pages
471-479
ISSN
0092-8674 (ISSN-L)
DOI
10.1016/j.cell.2013.03.032
OpenAlex
W2018622616
Cited by
57
References
2
Citations by year
2025: 4 · 2024: 3 · 2023: 3 · 2022: 4 · 2021: 5 · 2020: 5 · 2019: 9 · 2018: 4 · 2017: 5 · 2016: 7 · 2015: 4 · 2014: 3 · 2013: 1
FWCI
1.88
Type
journal article
Language
en
Open access
Licence
Locations
  • Cell (publishedVersion)
  • PubMed (publishedVersion)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Keywords
ribosome, tRNA decoding, codon-anticodon pairing, energy landscape, molecular recognition, conformational change, prokaryotic ribosomes, protein synthesis
MeSH terms
Energy Metabolism, Prokaryotic Cells, Ribosomes, RNA, Transfer, Thermodynamics, Protein Biosynthesis

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