A esquistossomose humana, doença causada pelo S. mansoni e com 6 milhões de infectados somente no Brasil, possui uma única estratégia terapêutica eficiente atualmente disponível. Esta se baseia na utilização de praziquantel e relatos de cepas resistentes à essa droga tem despertado o interesse da comunidade científica sobre o desenvolvimento de novas estratégias terapêuticas. Uma melhor caracterização dos processos metabólicos do parasita podem auxiliar nestas buscas. Diante desse contexto, nosso grupo tem trabalhado na caracterização estrutural e funcional das enzimas que compõem a via de salvação de purinas e pirimidinas deste parasita, com dez enzimas já caracterizadas. Uma das enzimas remanescentes é a uridina fosforilase (UP) (EC 2.4.2.3), cujo a qual o genoma do parasita apresenta duas isoformas, a smUPa e smUPb (92% de identidade entre elas). Com o objetivo de caracterizar estruturalmente estas enzimas, ambas foram obtidas via expressão heteróloga, purificadas e submetidas a ensaios de cristalização e co-cristalização (para obtenção das estruturas interagindo com diferentes ligantes). Após coleta de dados de difração de raio-x, processamento e refinamento adequado foram obtidas seis estruturas da smUPa (smUPaapo, smUPa+Timidina, smUPa+timina, smUPa+uracil, smUPa-5fluorouracil) e duas da smUPb (smUPbapo e smUPb+citrato). A análise das estruturas revela que as duas isoformas apresentam essencialmente a mesma estrutura, no entanto, apesar das poucas divergências em nível de sequência de aminoácidos, existem diferenças significativas entre os sítios ativos. A smUPa apresenta o sítio com as mesmas características de UPs conhecidas, em contrapartida a smUPb apresenta duas mudanças significativas que elimina a capacidade de interagir com a base nitrogenada (Q201L) e a cavidade que acomoda a base nitrogenada (G126D), o que torna as smUPs um caso único de isoformas de UP em um mesmo organismo conhecidas. É plausível que a smUPb não seja capaz de catalisar a fosforólise reversível da uridina, sendo ou um pseudogene ou alguma outra enzima com atividade catalítica diferente da UP. Para a completa caracterização destas enzimas, testes de atividade enzimática serão realizados e deverão auxiliar a determinar a real função da smUPb. / Human schistosomiasis, a disease caused by Schistosoma sp., is estimated to affect six million individuals in Brazil alone and there is currently only one therapeutic strategy available. This is based on the use of praziquantel and reports of the appearance of strains resistant to the drug has motivated the scientific community towards the search for new possible therapies. Biochemical characterization of the parasites metabolism is essential for the rational development of new therapeutic alternatives. Based on this,reasoning our group has been working on the structural and functional characterization of the enzymes involved in the pyrimidine and purine salvage pathways of S. mansoni. One of the remaining enzymes to be characterized is uridine phosphorylase (UP) (EC 2.4.2.3), for which there are two isoforms present in the parasite genome, smUPa and smUPb, which share 92% sequence identity. In order to structurally characterize these enzymes, both smUPs were produced by heterologous expression, purified and submitted to crystallization e co-crystallization assays, in the latter case in order to obtain the structure of different enzyme-ligand complexes. After data collection, processing and refinement, five structures of smUPa (smUPaapo, smUPa+Timidina, smUPa+timina, smUPa+uracil and smUPa+5fluorouracil) and two structures of smUPb (smUPbapo and smUPb+citrato) were obtained. Analysis of the structures revealed that the isoforms have the same fold, but despite the high sequence identity, significant differences are observed at the active site probably profoundly affecting enzyme activity. Whilst SmUPa presents an active site similar to that of other known UPs, smUPb is predicted to lack the ability to interact with the nucleoside base due to the presence of a leucine in place of a glutamine at position 201 and an aspartatic acid in place of glycine at position 126. These differences turn the smUPs into a unique case of UP isoforms. It is plausible that smUPb is unable to catalyze the reversible phosphorolysis of uridine and could be either a pseudogene or a different enzyme altogether of unknown catalytic activity. A complete functional characterization in vitro will be necessary in order to determine its real function.

A esquistossomose humana, doença causada pelo S. mansoni e com 6 milhões de infectados somente no Brasil, possui uma única estratégia terapêutica eficiente atualmente disponível. Esta se baseia na utilização de praziquantel e relatos de cepas resistentes à essa droga tem despertado o interesse da comunidade científica sobre o desenvolvimento de novas estratégias terapêuticas. Uma melhor caracterização dos processos metabólicos do parasita podem auxiliar nestas buscas. Diante desse contexto, nosso grupo tem trabalhado na caracterização estrutural e funcional das enzimas que compõem a via de salvação de purinas e pirimidinas deste parasita, com dez enzimas já caracterizadas. Uma das enzimas remanescentes é a uridina fosforilase (UP) (EC 2.4.2.3), cujo a qual o genoma do parasita apresenta duas isoformas, a smUPa e smUPb (92% de identidade entre elas). Com o objetivo de caracterizar estruturalmente estas enzimas, ambas foram obtidas via expressão heteróloga, purificadas e submetidas a ensaios de cristalização e co-cristalização (para obtenção das estruturas interagindo com diferentes ligantes). Após coleta de dados de difração de raio-x, processamento e refinamento adequado foram obtidas seis estruturas da smUPa (smUPaapo, smUPa+Timidina, smUPa+timina, smUPa+uracil, smUPa-5fluorouracil) e duas da smUPb (smUPbapo e smUPb+citrato). A análise das estruturas revela que as duas isoformas apresentam essencialmente a mesma estrutura, no entanto, apesar das poucas divergências em nível de sequência de aminoácidos, existem diferenças significativas entre os sítios ativos. A smUPa apresenta o sítio com as mesmas características de UPs conhecidas, em contrapartida a smUPb apresenta duas mudanças significativas que elimina a capacidade de interagir com a base nitrogenada (Q201L) e a cavidade que acomoda a base nitrogenada (G126D), o que torna as smUPs um caso único de isoformas de UP em um mesmo organismo conhecidas. É plausível que a smUPb não seja capaz de catalisar a fosforólise reversível da uridina, sendo ou um pseudogene ou alguma outra enzima com atividade catalítica diferente da UP. Para a completa caracterização destas enzimas, testes de atividade enzimática serão realizados e deverão auxiliar a determinar a real função da smUPb. / Human schistosomiasis, a disease caused by Schistosoma sp., is estimated to affect six million individuals in Brazil alone and there is currently only one therapeutic strategy available. This is based on the use of praziquantel and reports of the appearance of strains resistant to the drug has motivated the scientific community towards the search for new possible therapies. Biochemical characterization of the parasites metabolism is essential for the rational development of new therapeutic alternatives. Based on this,reasoning our group has been working on the structural and functional characterization of the enzymes involved in the pyrimidine and purine salvage pathways of S. mansoni. One of the remaining enzymes to be characterized is uridine phosphorylase (UP) (EC 2.4.2.3), for which there are two isoforms present in the parasite genome, smUPa and smUPb, which share 92% sequence identity. In order to structurally characterize these enzymes, both smUPs were produced by heterologous expression, purified and submitted to crystallization e co-crystallization assays, in the latter case in order to obtain the structure of different enzyme-ligand complexes. After data collection, processing and refinement, five structures of smUPa (smUPaapo, smUPa+Timidina, smUPa+timina, smUPa+uracil and smUPa+5fluorouracil) and two structures of smUPb (smUPbapo and smUPb+citrato) were obtained. Analysis of the structures revealed that the isoforms have the same fold, but despite the high sequence identity, significant differences are observed at the active site probably profoundly affecting enzyme activity. Whilst SmUPa presents an active site similar to that of other known UPs, smUPb is predicted to lack the ability to interact with the nucleoside base due to the presence of a leucine in place of a glutamine at position 201 and an aspartatic acid in place of glycine at position 126. These differences turn the smUPs into a unique case of UP isoforms. It is plausible that smUPb is unable to catalyze the reversible phosphorolysis of uridine and could be either a pseudogene or a different enzyme altogether of unknown catalytic activity. A complete functional characterization in vitro will be necessary in order to determine its real function.

Abstract The aim of this PhD-study was to address some of the overlapping bottlenecks in protein engineering and metagenomics by developing or applying new tools which are useful for both disciplines. Two enzymes were studied as an example: Triosephosphate Isomerase (TIM) and Uridine Phosphorylase (UP). TIM is an important enzyme of the glycolysis pathway and has been investigated via means of protein engineering, while UP is a key enzyme in the pyrimidine-salvage pathway. In this thesis TIM was used to address protein engineering aspects, while UP was used in regards to some metagenomic and bioinformatic aspects. The aspects of a structural driven rational design approach and its implications for further engineering of monomeric TIM variants are discussed. Process development based on a new technology, EnBase®, addresses the relative instability of new variants, compared to its ancestors, for further studies. EnBase® is then applied for the production of 15N isotope labeling of a monomeric TIM variant, A-TIM. Systematical function- and engineering studies on dimeric TIM and monomeric TIM in regards to the hinges of the catalytic loop-6 were conducted to investigate enzyme activity and stability. Both the A178L and P168A were proposed to induce loop-6 closure, a wanted feature for A-TIM variants. The P168A mutants are hardly active, but gave great insight into the catalytic machinery, while the A178L mutants did induce partial loop-6 closure, however in addition, monomeric A178L was destabilized. Homology driven genome mining and subsequent isolation- high throughput (HTP) overexpression of a thermostable UP from the Archaea Aeopyrum pernix was carried out as an example for the production of recombinant proteins. In addition an alternative kinetic method to study the kinetics of UP by means of NMR directly from cell lysate is discussed. The combination of expression libraries and EnBase® in a HTP manner may relieve up the gene-to-product bottleneck. The structural aspects of A. pernix UP are explored by means of simple bioinformatic tools in the last section of this thesis. A thermostable, truncated version of UP was created and its use for protein engineering in the future is explored. The long N-terminal and C-terminal ends of A. pernix UP seem to be involved in stabilizing the dimeric and hexameric structures of UP. However, deletion of the N-terminal end of A. pernix UP yielded a thermostable protein. Overall, the finding in regards to process optimization and HTP expression and optimization and the underlying methods used in the TIM studies and the UP studies are interchangeable.