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Master's Dissertation
DOI
https://doi.org/10.11606/D.76.2023.tde-06102023-114452
Document
Author
Full name
Adriano Alves Furtado
E-mail
Institute/School/College
Knowledge Area
Date of Defense
Published
São Carlos, 2023
Supervisor
Committee
Garratt, Richard Charles (President)
Salinas, Roberto Kopke
Silva, Wanius Jose Garcia da
Title in Portuguese
Estudos estruturais e bioquímicos de 10 enzimas com possível atividade de PET hidrolase oriundas de metagenoma antártico
Keywords in Portuguese
CBM
Cristalografia
Difração de raios X
PET
PETase
Abstract in Portuguese
Até o momento, os plásticos têm sido os produtos com maior acúmulo nos últimos anos e sua fragmentação tem sido um dos maiores poluentes. O polietileno tereftalato (PET) é um dos materiais mais utilizados na fabricação de garrafas descartáveis e tem sido o foco estratégico para decomposição e mitigação da poluição. No entanto, os processos desenvolvidos até agora têm sido ineficientes. Com a descoberta de enzimas que degradam o PET, surge a oportunidade de aplicação biotecnológica para minimizar esses problemas. Neste trabalho, estudamos 11 enzimas recombinantes da Antártica (e uma variação) com potencial atividade catalítica contra o PET, identificadas por metagenômica. Os parâmetros de expressão proteica foram otimizados em diferentes cepas de Escherichia coli e as purificações foram realizadas em duas ou três etapas (Cromatografia de Afinidade, Troca Iônica e Exclusão Molecular) com algumas adaptações. A partir das purificações, isolamos 10 proteínas . Os ensaios de cristalização levaram a cristais para 8 enzimas, das quais obtivemos 4 estruturas cristalográficas resolvidas entre 2,32 Å e 1,2 Å. Análises estruturais das estruturas resolvidas por difração de raios-X e estruturas teóricas geradas pelo AlphaFold2 foram realizadas por meio de docking molecular entre as enzimas e um fragmento de PET. Essas análises revelaram mudanças sequenciais e estruturais críticas. Com a intenção de acumular um maior conhecimento sobre PETase, que poderia ser empregada na melhoria das enzimas para fins biotecnológicos, experimentos biofísicos e bioquímicos foram realizados, onde observamos comportamentos distintos tanto para a estabilidade térmica quanto para atividade.
Title in English
Structural and biochemical studies of 10 enzymes with possible PET hydrolase activity from an Antarctic metagenome
Keywords in English
CBM (Carbohydrate-binding module)
Crystallography
PET (Polyethylene Terephthalate)
PETase
X-ray Diffraction
Abstract in English
Plastics have been the most accumulated products in recent years, and their fragmentation has become one of the major pollutants. Polyethylene terephthalate (PET) is one of the most commonly used materials in the production of disposable bottles and has been a strategic focus for decomposition and mitigation of pollution. However, the processes developed so far have been inefficient. With the discovery of enzymes that degrade PET, there is an opportunity for biotechnological application to minimize these problems. In this study, we investigated 11 recombinant Antarctic enzymes (and a variant) with potential catalytic activity against PET, identified through metagenomics. Protein expression parameters were optimized in different strains of Escherichia coli, and purifications were performed in two or three steps (Affinity Chromatography, Ion Exchange, and Size Exclusion) with some adaptations. From the purifications, we isolated 10 proteins. Crystallization assays resulted in crystals for 8 enzymes, from which we obtained 4 crystal structures resolved at resolutions ranging from 2.32 Å to 1.2 Å. Structural analyses of the resolved structures by X-ray diffraction and theoretical structures generated by AlphaFold2 were performed through molecular docking between the enzymes and a PET fragment. These analyses revealed critical sequential and structural changes. With the aim of accumulating greater knowledge about PETase, which could be employed in the improvement of enzymes for biotechnological purposes, biophysical and biochemical experiments were conducted, where distinct behaviors were observed for both thermal stability and activity.
 
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Publishing Date
2023-10-06
 
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