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Synonymous codon usage influences the local protein structure observed

Translation of mRNA into protein is a unidirectional information flow process. Analysing the input (mRNA) and output (protein) of translation, we find that local protein structure information is encoded in the mRNA nucleotide sequence. The Coding Sequence and Structure (CSandS) database developed in...

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Autores principales: Saunders, Rhodri, Deane, Charlotte M.
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2965230/
https://www.ncbi.nlm.nih.gov/pubmed/20530529
http://dx.doi.org/10.1093/nar/gkq495
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author Saunders, Rhodri
Deane, Charlotte M.
author_facet Saunders, Rhodri
Deane, Charlotte M.
author_sort Saunders, Rhodri
collection PubMed
description Translation of mRNA into protein is a unidirectional information flow process. Analysing the input (mRNA) and output (protein) of translation, we find that local protein structure information is encoded in the mRNA nucleotide sequence. The Coding Sequence and Structure (CSandS) database developed in this work provides a detailed mapping between over 4000 solved protein structures and their mRNA. CSandS facilitates a comprehensive analysis of codon usage over many organisms. In assigning translation speed, we find that relative codon usage is less informative than tRNA concentration. For all speed measures, no evidence was found that domain boundaries are enriched with slow codons. In fact, genes seemingly avoid slow codons around structurally defined domain boundaries. Translation speed, however, does decrease at the transition into secondary structure. Codons are identified that have structural preferences significantly different from the amino acid they encode. However, each organism has its own set of ‘significant codons’. Our results support the premise that codons encode more information than merely amino acids and give insight into the role of translation in protein folding.
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spelling pubmed-29652302010-10-28 Synonymous codon usage influences the local protein structure observed Saunders, Rhodri Deane, Charlotte M. Nucleic Acids Res Structural Biology Translation of mRNA into protein is a unidirectional information flow process. Analysing the input (mRNA) and output (protein) of translation, we find that local protein structure information is encoded in the mRNA nucleotide sequence. The Coding Sequence and Structure (CSandS) database developed in this work provides a detailed mapping between over 4000 solved protein structures and their mRNA. CSandS facilitates a comprehensive analysis of codon usage over many organisms. In assigning translation speed, we find that relative codon usage is less informative than tRNA concentration. For all speed measures, no evidence was found that domain boundaries are enriched with slow codons. In fact, genes seemingly avoid slow codons around structurally defined domain boundaries. Translation speed, however, does decrease at the transition into secondary structure. Codons are identified that have structural preferences significantly different from the amino acid they encode. However, each organism has its own set of ‘significant codons’. Our results support the premise that codons encode more information than merely amino acids and give insight into the role of translation in protein folding. Oxford University Press 2010-10 2010-06-08 /pmc/articles/PMC2965230/ /pubmed/20530529 http://dx.doi.org/10.1093/nar/gkq495 Text en © The Author(s) 2010. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.5 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Structural Biology
Saunders, Rhodri
Deane, Charlotte M.
Synonymous codon usage influences the local protein structure observed
title Synonymous codon usage influences the local protein structure observed
title_full Synonymous codon usage influences the local protein structure observed
title_fullStr Synonymous codon usage influences the local protein structure observed
title_full_unstemmed Synonymous codon usage influences the local protein structure observed
title_short Synonymous codon usage influences the local protein structure observed
title_sort synonymous codon usage influences the local protein structure observed
topic Structural Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2965230/
https://www.ncbi.nlm.nih.gov/pubmed/20530529
http://dx.doi.org/10.1093/nar/gkq495
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