Técnicas de bioinformática aplicadas ao estudo de poligalacturonases de fungos
Autor(a) principal: | |
---|---|
Data de Publicação: | 2012 |
Tipo de documento: | Dissertação |
Idioma: | por |
Título da fonte: | Repositório Institucional da UFSCAR |
Texto Completo: | https://repositorio.ufscar.br/handle/ufscar/6530 |
Resumo: | Plant cell walls are composed of approximately 65% cellulose microfibrils and pectin. The latter is proteolytically degraded by the so-called pectinases enzymes (also known as pectinolytic enzymes). Pectinases may be either depolymerizing. They are produced by plants, filamentous fungi, bacteria, and yeast. Due to the wide commercial use of pectinase, one has testified a growing number of studies devoted to understand the activities of such enzymes. Bioinformatics tools were employed throughout this work in order to study fungal polygalacturonase (PG) under two aspects. Firstly, all stored fungal PG sequences in databases (2093) were analyzed in order to evaluate through searching for sequential motifs and phylogenetic studies the possibility to classifying the enzymes as either Endo- or Exo-PG. After excluding those with less than 70 amino acids, those that corresponded to the hypothetical protein , and those that were neither PG nor fungal PG, there were 957 sequences left. Those sequences were separated according to genus and species. For each group, multiple sequence alignments were made by using ClustalW software. The alignments were analyzed and the sequences displaying 100% identity were then expunged, thus resulting in a database of unique sequences of fungal PG. By means of the alignment, the study of structural motifs, and the construction of phylogenetic trees, one was able to classify all the sequences according to their mode of action in either Endo- or Ex-PG. Throughout the second part of our research, protein homology-modeling methods were employed while constructing a three-dimensional model of a L. gongylophorus fungal polygalacturonase, symbiont of leaf-cutting ant. The model was validated by PROCHECK, VERIFY 3D, and WHAT IF software. By analyzing the 3D model of the L. gongylophorus PG, a catalytic mechanism of the enzyme was outlined, which may take place by inverting the configuration of sugar anomeric carbon (substrate). |
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Santos, Adriana Miranda dosSouza, Dulcina Maria Pinatti Ferreira dehttp://genos.cnpq.br:12010/dwlattes/owa/prc_imp_cv_int?f_cod=K4787362Y3http://lattes.cnpq.br/6845476344714243869845c0-9a86-4182-8788-5d4526867fd12016-06-02T20:36:39Z2012-08-302016-06-02T20:36:39Z2012-04-18SANTOS, Adriana Miranda dos. Técnicas de bioinformática aplicadas ao estudo de poligalacturonases de fungos. 2012. 123 f. Dissertação (Mestrado em Ciências Exatas e da Terra) - Universidade Federal de São Carlos, São Carlos, 2012.https://repositorio.ufscar.br/handle/ufscar/6530Plant cell walls are composed of approximately 65% cellulose microfibrils and pectin. The latter is proteolytically degraded by the so-called pectinases enzymes (also known as pectinolytic enzymes). Pectinases may be either depolymerizing. They are produced by plants, filamentous fungi, bacteria, and yeast. Due to the wide commercial use of pectinase, one has testified a growing number of studies devoted to understand the activities of such enzymes. Bioinformatics tools were employed throughout this work in order to study fungal polygalacturonase (PG) under two aspects. Firstly, all stored fungal PG sequences in databases (2093) were analyzed in order to evaluate through searching for sequential motifs and phylogenetic studies the possibility to classifying the enzymes as either Endo- or Exo-PG. After excluding those with less than 70 amino acids, those that corresponded to the hypothetical protein , and those that were neither PG nor fungal PG, there were 957 sequences left. Those sequences were separated according to genus and species. For each group, multiple sequence alignments were made by using ClustalW software. The alignments were analyzed and the sequences displaying 100% identity were then expunged, thus resulting in a database of unique sequences of fungal PG. By means of the alignment, the study of structural motifs, and the construction of phylogenetic trees, one was able to classify all the sequences according to their mode of action in either Endo- or Ex-PG. Throughout the second part of our research, protein homology-modeling methods were employed while constructing a three-dimensional model of a L. gongylophorus fungal polygalacturonase, symbiont of leaf-cutting ant. The model was validated by PROCHECK, VERIFY 3D, and WHAT IF software. By analyzing the 3D model of the L. gongylophorus PG, a catalytic mechanism of the enzyme was outlined, which may take place by inverting the configuration of sugar anomeric carbon (substrate).A parede celular de células de plantas é composta de aproximadamente 65% de rede de celulose e rede de pectato. Essa última é proteoliticamente degradada por enzimas chamadas pectinases ou enzimas pectinolíticas. As pectinases podem ser despolimerizantes ou desesterificantes e são produzidas por plantas, fungos filamentosos, bactérias e leveduras. Impulsionado pelas aplicações comerciais que pectinases representam, é crescente o estudo para o melhor entendimento sobre as atividades dessas enzimas. Ferramentas de bioinformática foram usadas neste trabalho para estudar poligalacturonases (PG) de fungos, sob dois aspectos. Na primeira parte do trabalho, todas as sequências de PG de fungos depositadas em bancos de dados (2093) foram analisadas e avaliadas quanto à possibilidade de classificação das enzimas em Endo- ou Exo-PG através de busca de motivos sequenciais e estudos filogenéticos. Após exclusão daquelas com menos de 70 aminoácidos, das que correspondiam a 'proteína hipotética' e ainda das que não eram PG ou mesmo não eram PG de fungos restaram 957 sequências. Essas sequências foram separadas por gênero e espécie e para cada grupo foram realizados alinhamentos múltiplos de sequências usando o programa ClustalW . Os alinhamentos foram analisados e as sequências com 100% de identidade foram retiradas, resultando em um conjunto de dados com 417 sequências únicas de PG de fungos. Através dos alinhamentos, do estudo de motivos estruturais e da construção de árvores filogenéticas foi possível classificar todas as sequências de acordo com seu modo de ação em Endo- ou Exo-PG. Na segunda parte do trabalho foi usado o método de modelagem por homologia na construção do modelo tridimensional de uma poligalacturonase do fungo L. gongylophorus, simbionte de formigas cortadeiras. O modelo foi validado com os programas PROCHECK, VERIFY 3D e WHAT IF. Através da análise do modelo 3D da PG do L. gongylophorus foi possível propor um mecanismo de ação da enzima, que deve ocorrer com inversão da configuração do carbono anomérico do açúcar (substrato).Financiadora de Estudos e Projetosapplication/pdfporUniversidade Federal de São CarlosPrograma de Pós-Graduação em Química - PPGQUFSCarBRQuímica orgânicaPoligalacturonaseFungosAlinhamento de sequênciasSequência de aminoácidosRelações filogenéticasCIENCIAS EXATAS E DA TERRA::QUIMICA::QUIMICA ORGANICATécnicas de bioinformática aplicadas ao estudo de poligalacturonases de fungosinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/masterThesis-1-170fa011e-1108-4239-97ab-fe5cd4b2d233info:eu-repo/semantics/openAccessreponame:Repositório Institucional da UFSCARinstname:Universidade Federal de São Carlos (UFSCAR)instacron:UFSCARORIGINAL4425.pdfapplication/pdf4096750https://repositorio.ufscar.br/bitstream/ufscar/6530/1/4425.pdfd77921e33ac24b167ed701cea4759eb0MD51TEXT4425.pdf.txt4425.pdf.txtExtracted texttext/plain0https://repositorio.ufscar.br/bitstream/ufscar/6530/4/4425.pdf.txtd41d8cd98f00b204e9800998ecf8427eMD54THUMBNAIL4425.pdf.jpg4425.pdf.jpgIM Thumbnailimage/jpeg8456https://repositorio.ufscar.br/bitstream/ufscar/6530/5/4425.pdf.jpg76855656f1a811cd43474c16a4e3ac62MD55ufscar/65302023-09-18 18:30:39.46oai:repositorio.ufscar.br:ufscar/6530Repositório InstitucionalPUBhttps://repositorio.ufscar.br/oai/requestopendoar:43222023-09-18T18:30:39Repositório Institucional da UFSCAR - Universidade Federal de São Carlos (UFSCAR)false |
dc.title.por.fl_str_mv |
Técnicas de bioinformática aplicadas ao estudo de poligalacturonases de fungos |
title |
Técnicas de bioinformática aplicadas ao estudo de poligalacturonases de fungos |
spellingShingle |
Técnicas de bioinformática aplicadas ao estudo de poligalacturonases de fungos Santos, Adriana Miranda dos Química orgânica Poligalacturonase Fungos Alinhamento de sequências Sequência de aminoácidos Relações filogenéticas CIENCIAS EXATAS E DA TERRA::QUIMICA::QUIMICA ORGANICA |
title_short |
Técnicas de bioinformática aplicadas ao estudo de poligalacturonases de fungos |
title_full |
Técnicas de bioinformática aplicadas ao estudo de poligalacturonases de fungos |
title_fullStr |
Técnicas de bioinformática aplicadas ao estudo de poligalacturonases de fungos |
title_full_unstemmed |
Técnicas de bioinformática aplicadas ao estudo de poligalacturonases de fungos |
title_sort |
Técnicas de bioinformática aplicadas ao estudo de poligalacturonases de fungos |
author |
Santos, Adriana Miranda dos |
author_facet |
Santos, Adriana Miranda dos |
author_role |
author |
dc.contributor.authorlattes.por.fl_str_mv |
http://lattes.cnpq.br/6845476344714243 |
dc.contributor.author.fl_str_mv |
Santos, Adriana Miranda dos |
dc.contributor.advisor1.fl_str_mv |
Souza, Dulcina Maria Pinatti Ferreira de |
dc.contributor.advisor1Lattes.fl_str_mv |
http://genos.cnpq.br:12010/dwlattes/owa/prc_imp_cv_int?f_cod=K4787362Y3 |
dc.contributor.authorID.fl_str_mv |
869845c0-9a86-4182-8788-5d4526867fd1 |
contributor_str_mv |
Souza, Dulcina Maria Pinatti Ferreira de |
dc.subject.por.fl_str_mv |
Química orgânica Poligalacturonase Fungos Alinhamento de sequências Sequência de aminoácidos Relações filogenéticas |
topic |
Química orgânica Poligalacturonase Fungos Alinhamento de sequências Sequência de aminoácidos Relações filogenéticas CIENCIAS EXATAS E DA TERRA::QUIMICA::QUIMICA ORGANICA |
dc.subject.cnpq.fl_str_mv |
CIENCIAS EXATAS E DA TERRA::QUIMICA::QUIMICA ORGANICA |
description |
Plant cell walls are composed of approximately 65% cellulose microfibrils and pectin. The latter is proteolytically degraded by the so-called pectinases enzymes (also known as pectinolytic enzymes). Pectinases may be either depolymerizing. They are produced by plants, filamentous fungi, bacteria, and yeast. Due to the wide commercial use of pectinase, one has testified a growing number of studies devoted to understand the activities of such enzymes. Bioinformatics tools were employed throughout this work in order to study fungal polygalacturonase (PG) under two aspects. Firstly, all stored fungal PG sequences in databases (2093) were analyzed in order to evaluate through searching for sequential motifs and phylogenetic studies the possibility to classifying the enzymes as either Endo- or Exo-PG. After excluding those with less than 70 amino acids, those that corresponded to the hypothetical protein , and those that were neither PG nor fungal PG, there were 957 sequences left. Those sequences were separated according to genus and species. For each group, multiple sequence alignments were made by using ClustalW software. The alignments were analyzed and the sequences displaying 100% identity were then expunged, thus resulting in a database of unique sequences of fungal PG. By means of the alignment, the study of structural motifs, and the construction of phylogenetic trees, one was able to classify all the sequences according to their mode of action in either Endo- or Ex-PG. Throughout the second part of our research, protein homology-modeling methods were employed while constructing a three-dimensional model of a L. gongylophorus fungal polygalacturonase, symbiont of leaf-cutting ant. The model was validated by PROCHECK, VERIFY 3D, and WHAT IF software. By analyzing the 3D model of the L. gongylophorus PG, a catalytic mechanism of the enzyme was outlined, which may take place by inverting the configuration of sugar anomeric carbon (substrate). |
publishDate |
2012 |
dc.date.available.fl_str_mv |
2012-08-30 2016-06-02T20:36:39Z |
dc.date.issued.fl_str_mv |
2012-04-18 |
dc.date.accessioned.fl_str_mv |
2016-06-02T20:36:39Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/masterThesis |
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masterThesis |
status_str |
publishedVersion |
dc.identifier.citation.fl_str_mv |
SANTOS, Adriana Miranda dos. Técnicas de bioinformática aplicadas ao estudo de poligalacturonases de fungos. 2012. 123 f. Dissertação (Mestrado em Ciências Exatas e da Terra) - Universidade Federal de São Carlos, São Carlos, 2012. |
dc.identifier.uri.fl_str_mv |
https://repositorio.ufscar.br/handle/ufscar/6530 |
identifier_str_mv |
SANTOS, Adriana Miranda dos. Técnicas de bioinformática aplicadas ao estudo de poligalacturonases de fungos. 2012. 123 f. Dissertação (Mestrado em Ciências Exatas e da Terra) - Universidade Federal de São Carlos, São Carlos, 2012. |
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Universidade Federal de São Carlos |
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Universidade Federal de São Carlos |
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