The purine bias of coding sequences is determined by physicochemical constraints on proteins
Autor(a) principal: | |
---|---|
Data de Publicação: | 2014 |
Outros Autores: | , , |
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. |
id |
CRUZ_2b33e3cc4d3fb69b91a0359f0d3572af |
---|---|
oai_identifier_str |
oai:www.arca.fiocruz.br:icict/10104 |
network_acronym_str |
CRUZ |
network_name_str |
Repositório Institucional da FIOCRUZ (ARCA) |
repository_id_str |
2135 |
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 |
instname_str |
Fundação Oswaldo Cruz (FIOCRUZ) |
instacron_str |
FIOCRUZ |
institution |
FIOCRUZ |
reponame_str |
Repositório Institucional da FIOCRUZ (ARCA) |
collection |
Repositório Institucional da FIOCRUZ (ARCA) |
bitstream.url.fl_str_mv |
https://www.arca.fiocruz.br/bitstream/icict/10104/1/license.txt https://www.arca.fiocruz.br/bitstream/icict/10104/2/antonio_mirandaetal_IOC-2014.pdf https://www.arca.fiocruz.br/bitstream/icict/10104/3/antonio_mirandaetal_IOC-2014.pdf.txt |
bitstream.checksum.fl_str_mv |
7d48279ffeed55da8dfe2f8e81f3b81f 22a1fae47d8842ca6b4a3d60220ab4d7 e8c7b5eaddf77bbd72cd2dc5a2151f7f |
bitstream.checksumAlgorithm.fl_str_mv |
MD5 MD5 MD5 |
repository.name.fl_str_mv |
Repositório Institucional da FIOCRUZ (ARCA) - Fundação Oswaldo Cruz (FIOCRUZ) |
repository.mail.fl_str_mv |
repositorio.arca@fiocruz.br |
_version_ |
1798324769191362560 |