The purine bias of coding sequences is determined by physicochemical constraints on proteins

Detalhes bibliográficos
Autor(a) principal: Ponce de Leon, Miguel
Data de Publicação: 2014
Outros Autores: Miranda, Antonio Basilio de, Alvarez-Valin, Fernando, Carels, Nicolas
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da FIOCRUZ (ARCA)
Texto Completo: https://www.arca.fiocruz.br/handle/icict/10104
Resumo: Nicolas Carels - Fundação Oswaldo Cruz. Centro de Desenvolvimento Tecnológico em Saúde. Rio de Janeiro, RJ, Brasil. Documento produzido em parceria ou por autor vinculado à Fiocruz, mas não consta a informação no documento.
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spelling Ponce de Leon, MiguelMiranda, Antonio Basilio deAlvarez-Valin, FernandoCarels, Nicolas2015-04-22T14:23:10Z2015-04-22T14:23:10Z2014PONCE DE LEON, Miguel et al. The purine bias of coding sequences is determined by physicochemical constraints on proteins. Bioinformatics and Biology Insights, n. 8, p. 93-108, 2014.1177-9322https://www.arca.fiocruz.br/handle/icict/101040.4137/BBI.S13161Nicolas Carels - Fundação Oswaldo Cruz. Centro de Desenvolvimento Tecnológico em Saúde. Rio de Janeiro, RJ, Brasil. Documento produzido em parceria ou por autor vinculado à Fiocruz, mas não consta a informação no documento.This research was supported by the Brazilian agencies CAPES/UDELAR number 029/2007 to ABM and FAV.CNPq and FIOCRUZ/CAPES (CDTS) providing a researcher fellowships to NC.Urugayan agency ANII providing a research fee to FAV.Universidad de la República. Facultad de Ciencias. Sección Biomatemática. Montevideo, Uruguay.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Genômica Funcional e Bioinformática. Rio de Janeiro, RJ, Brasil.Universidad de la República. Facultad de Ciencias. Sección Biomatemática. Montevideo, Uruguay.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Genômica Funcional e Bioinformática. Rio de Janeiro, RJ, Brasil.For this report, we analyzed protein secondary structures in relation to the statistics of three nucleotide codon positions. The purpose of this investigation was to find which properties of the ribosome, tRNA or protein level, could explain the purine bias (Rrr) as it is observed in coding DNA. We found that the Rrr pattern is the consequence of a regularity (the codon structure) resulting from physicochemical constraints on proteins and thermody-namic constraints on ribosomal machinery. The physicochemical constraints on proteins mainly come from the hydropathy and molecular weight (MW) of secondary structures as well as the energy cost of amino acid synthesis. These constraints appear through a network of statistical correlations, such as (i) the cost of amino acid synthesis, which is in favor of a higher level of guanine in the first codon position, (ii) the constructive contribution of hydropathy alternation in proteins, (iii) the spatial organization of secondary structure in proteins according to solvent accessibility, (iv) the spatial organization of sec-ondary structure according to amino acid hydropathy, (v) the statistical correlation of MW with protein secondary structures and their overall hydropathy, (vi) the statistical correlation of thymine in the second codon position with hydropathy and the energy cost of amino acid synthesis, and (vii) the statistical correlation of adenine in the second codon position with amino acid complexity and the MW of secondary protein structures. Amino acid physicochemical properties and functional constraints on proteins constitute a code that is translated into a purine bias within the coding DNA via tRNAs. In that sense, the Rrr pattern within coding DNA is the effect of information transfer on nucleotide composition from protein to DNA by selection according to the codon positions. Thus, coding DNA structure and ribosomal machinery co-evolved to minimize the energy cost of protein coding given the functional constraints on proteins.engLibertas AcademicaThe purine bias of coding sequences is determined by physicochemical constraints on proteinsinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleGenomicsAncestral codonPurine biasSecondary structureHelixSheetTurn coilRibosomeTranslationEnergy costinfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZLICENSElicense.txttext/plain1914https://www.arca.fiocruz.br/bitstream/icict/10104/1/license.txt7d48279ffeed55da8dfe2f8e81f3b81fMD51ORIGINALantonio_mirandaetal_IOC-2014.pdfapplication/pdf6011074https://www.arca.fiocruz.br/bitstream/icict/10104/2/antonio_mirandaetal_IOC-2014.pdf22a1fae47d8842ca6b4a3d60220ab4d7MD52TEXTantonio_mirandaetal_IOC-2014.pdf.txtantonio_mirandaetal_IOC-2014.pdf.txtExtracted texttext/plain81046https://www.arca.fiocruz.br/bitstream/icict/10104/3/antonio_mirandaetal_IOC-2014.pdf.txte8c7b5eaddf77bbd72cd2dc5a2151f7fMD53icict/101042023-07-28 10:55:52.136oai:www.arca.fiocruz.br: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ório InstitucionalPUBhttps://www.arca.fiocruz.br/oai/requestrepositorio.arca@fiocruz.bropendoar:21352023-07-28T13:55:52Repositório Institucional da FIOCRUZ (ARCA) - Fundação Oswaldo Cruz (FIOCRUZ)false
dc.title.en_US.fl_str_mv The purine bias of coding sequences is determined by physicochemical constraints on proteins
title The purine bias of coding sequences is determined by physicochemical constraints on proteins
spellingShingle The purine bias of coding sequences is determined by physicochemical constraints on proteins
Ponce de Leon, Miguel
Genomics
Ancestral codon
Purine bias
Secondary structure
Helix
Sheet
Turn coil
Ribosome
Translation
Energy cost
title_short The purine bias of coding sequences is determined by physicochemical constraints on proteins
title_full The purine bias of coding sequences is determined by physicochemical constraints on proteins
title_fullStr The purine bias of coding sequences is determined by physicochemical constraints on proteins
title_full_unstemmed The purine bias of coding sequences is determined by physicochemical constraints on proteins
title_sort The purine bias of coding sequences is determined by physicochemical constraints on proteins
author Ponce de Leon, Miguel
author_facet Ponce de Leon, Miguel
Miranda, Antonio Basilio de
Alvarez-Valin, Fernando
Carels, Nicolas
author_role author
author2 Miranda, Antonio Basilio de
Alvarez-Valin, Fernando
Carels, Nicolas
author2_role author
author
author
dc.contributor.author.fl_str_mv Ponce de Leon, Miguel
Miranda, Antonio Basilio de
Alvarez-Valin, Fernando
Carels, Nicolas
dc.subject.en.pt_BR.fl_str_mv Genomics
Ancestral codon
Purine bias
Secondary structure
Helix
Sheet
Turn coil
Ribosome
Translation
Energy cost
topic Genomics
Ancestral codon
Purine bias
Secondary structure
Helix
Sheet
Turn coil
Ribosome
Translation
Energy cost
description Nicolas Carels - Fundação Oswaldo Cruz. Centro de Desenvolvimento Tecnológico em Saúde. Rio de Janeiro, RJ, Brasil. Documento produzido em parceria ou por autor vinculado à Fiocruz, mas não consta a informação no documento.
publishDate 2014
dc.date.issued.fl_str_mv 2014
dc.date.accessioned.fl_str_mv 2015-04-22T14:23:10Z
dc.date.available.fl_str_mv 2015-04-22T14:23:10Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.citation.fl_str_mv PONCE DE LEON, Miguel et al. The purine bias of coding sequences is determined by physicochemical constraints on proteins. Bioinformatics and Biology Insights, n. 8, p. 93-108, 2014.
dc.identifier.uri.fl_str_mv https://www.arca.fiocruz.br/handle/icict/10104
dc.identifier.issn.none.fl_str_mv 1177-9322
dc.identifier.doi.pt_BR.fl_str_mv 0.4137/BBI.S13161
identifier_str_mv PONCE DE LEON, Miguel et al. The purine bias of coding sequences is determined by physicochemical constraints on proteins. Bioinformatics and Biology Insights, n. 8, p. 93-108, 2014.
1177-9322
0.4137/BBI.S13161
url https://www.arca.fiocruz.br/handle/icict/10104
dc.language.iso.fl_str_mv eng
language eng
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Libertas Academica
publisher.none.fl_str_mv Libertas Academica
dc.source.none.fl_str_mv reponame:Repositório Institucional da FIOCRUZ (ARCA)
instname:Fundação Oswaldo Cruz (FIOCRUZ)
instacron:FIOCRUZ
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reponame_str Repositório Institucional da FIOCRUZ (ARCA)
collection Repositório Institucional da FIOCRUZ (ARCA)
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