Evidence of evolutionary selection for cotranslational folding

Proceedings of the National Academy of Sciences of the United States of America
William M Jacobs, Eugene I Shakhnovich

Abstract

Recent experiments and simulations have demonstrated that proteins can fold on the ribosome. However, the extent and generality of fitness effects resulting from cotranslational folding remain open questions. Here we report a genome-wide analysis that uncovers evidence of evolutionary selection for cotranslational folding. We describe a robust statistical approach to identify loci within genes that are both significantly enriched in slowly translated codons and evolutionarily conserved. Surprisingly, we find that domain boundaries can explain only a small fraction of these conserved loci. Instead, we propose that regions enriched in slowly translated codons are associated with cotranslational folding intermediates, which may be smaller than a single domain. We show that the intermediates predicted by a native-centric model of cotranslational folding account for the majority of these loci across more than 500 Escherichia coli proteins. By making a direct connection to protein folding, this analysis provides strong evidence that many synonymous substitutions have been selected to optimize translation rates at specific locations within genes. More generally, our results indicate that kinetics, and not just thermodynamics, can sign...Continue Reading

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Citations

Nov 13, 2019·The Journal of Biological Chemistry·Anne GershensonPatrick L Wintrode
Jan 9, 2020·Proceedings of the National Academy of Sciences of the United States of America·Amir BitranEugene Shakhnovich
Jun 21, 2019·PLoS Computational Biology·Ruth NussinovHyunbum Jang
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Nov 10, 2018·Proceedings of the National Academy of Sciences of the United States of America·Emily J GuinnSusan Marqusee
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Jul 1, 2020·Proceedings of the National Academy of Sciences of the United States of America·Hiroshi KadokuraKenji Inaba
Sep 19, 2018·Proceedings of the National Academy of Sciences of the United States of America·José Arcadio Farías-RicoGunnar von Heijne
Nov 11, 2018·Proceedings of the National Academy of Sciences of the United States of America·Pengfei TianRobert B Best
Dec 7, 2018·Annual Review of Biochemistry·Günter KramerBernd Bukau
Feb 6, 2020·Proceedings of the National Academy of Sciences of the United States of America·Ian M WalshPatricia L Clark
Dec 7, 2018·International Journal of Molecular Sciences·Jian TianNingfeng Wu
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Dec 17, 2021·Proceedings of the National Academy of Sciences of the United States of America·Ajeet K SharmaEdward P O'Brien
Aug 24, 2018··Scott EmrichAnabel Rodriguez

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Methods Mentioned

BETA
protein folding

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