Diss. (sammanfattning) Linköping : Linköpings universitet, 2010. / Härtill 5 uppsatser.

Diss. (sammanfattning) Linköping : Linköpings universitet, 2009. / Härtill 5 uppsatser.

The biosynthetic pathway for the production of the dipeptide antibiotic bacilysin has been the subject of intense research over the past three decades. These studies revealed the role of multiple enzymes in the biosynthesis of this antibiotic. The identification of different enzymes was initially guided by genetic studies on different strains of Bacillus. The functional role of some these enzymes have been validated in vitro in the recent past. Despite this, the in vitro synthesis of bacilysin still remains elusive. The focus of this study was on two oxidoreductases - BacC and BacG. In the course of these studies, several variations to conventional oxidoreductase mechanisms were observed. These studies also provided us an opportunity to examine an oxidoreductase, BacC, at atomic resolution. This thesis describes these structural studies alongside efforts to achieve the biosynthesis of bacilysin in vitro. Chapter 1 provides an introduction to the broad goals of this thesis. First, the diversity of naturally occurring antibiotics is described. This is followed by a description of nonribosomal peptides and their preferred route for antibiotic synthesis. A summary of previous work in this area is provided to place this study in perspective. Earlier studies performed in this laboratory and others provided a framework for understanding the role of BacC and BacG. These studies have been described with an emphasis on the pivotal role of oxidoreductases in this process. In this context, known features of oxidoreductases, classification of the enzyme family, known reaction mechanisms, preferred substrates and cofactors of the enzyme have been summarized in this chapter. Chapter 2 describes the structural and biochemical characterization of B.subtilis BacG. The crystal structures of BacG determined in the apo form and ligand bound states could capture different conformational states of this enzyme. These structures revealed a basis to understand the ping-pong reaction mechanism. The catalytic residues Tyr-Ser-Lys-Asn involved in the proton relay were examined by mutational analysis. These biochemical studies could corroborate our observations derived from structural analysis. Put together, these studies suggest synchronized conformational changes in BacG that can rationalize cofactor specificity and catalytic action on di hydroxyphenyl pyruvate to form tetra hydroxyphenyl pyruvate en route to anticapsin biosynthesis. Bacillus subtilis BacC could be structurally characterized at 1.19Å resolution. The atomic resolution structure formed the basis for the analysis reported in this chapter. The structure revealed aspects of non-covalent interactions that could be unambiguously determined due to the high resolution diffraction data. The atomic resolution structure also enabled us to conduct charge density analysis on this protein. Atomic displacement parameters were used as a tool to explore paths of non-covalent interactions. A commercially available substrate, 3-Quinuclidinone, was used to characterize enzymatic activity. We note that this enzyme follows a rapid equilibrium random mechanism. Furthermore, the kinetic profiles were conclusive to draw inferences on allosteric interactions. A comparison between the NADH-complex and the apo enzyme structure suggests aspects of nuanced atomic displacement that governs the intra structural signal transduction. Taken together, this study provided a template to analyze the role of non-covalent interactions in regulating enzymatic activity. Chapter 4 is based on a survey of oxidoreductases that have been previously described in literature. During this study, we collated the extensive structural and biochemical data in this family of enzymes. However, we noted that the data remains disperse thereby limiting efforts to understand the reaction mechanism from a structural perspective. Here we collate information of known sequences, structures, cofactors, ligand preferences, reaction mechanisms and their influence on higher order association and catalytic activity in this class of enzymes. Chapter 5 summarizes the findings on two oxidoreductases (BacC, BacG). These studies on two closely related oxidoreductases BacC and BacG performing different roles in the same biosynthetic pathway revealed aspects biosynthesis that are often poorly recognized in protein engineering. The role of the reaction mechanism and their influence on the cofactor specificity could be inferred from the studies on these two enzymes. These studies also suggest the feasibility of evaluating aspects of enzyme activity and regulation provided the wealth of a priori information that is currently available. Put together, these studies provide a data-set for protein engineering efforts on oxidoreductases with general inferences for other enzymes in the short-chain dehydrogenases/ reductases (SDR) family. Appendix 1 provides a schematic representation of our efforts to biosynthetically obtain bacilysin in vitro. The identification, mass spectrometry of the products and substrates en route to bacilysin biosynthesis are compiled in this section. Appendix 2 describes the preliminary characterization of B.subtilis BacF. This part of the work describes the cloning, expression and purification of BacF and attempts to obtain suitable diffracting crystals for structural analysis.

The asymmetric reduction of ketones to chiral hydroxyl compounds by alcohol dehydrogenases (ADHs) is an established strategy for the provision of valuable precursors for fine chemicals and pharmaceutics. However, most ADHs favor linear aliphatic and aromatic carbonyl compounds, and suitable biocatalysts with preference for cyclic ketones and diketones are still scarce. Among the few candidates, the alcohol dehydrogenase from Thauera aromatica (ThaADH) stands out with a high activity for the reduction of the cyclic α-diketone 1,2-cyclohexanedione to the corresponding α-hydroxy ketone. This study elucidates catalytic and structural features of the enzyme. ThaADH showed a remarkable thermal and pH stability as well as stability in the presence of polar solvents. A thorough description of the substrate scope combined with the resolution and description of the crystal structure, demonstrated a strong preference of ThaADH for cyclic α-substituted cyclohexanones, and indicated structural determinants responsible for the unique substrate acceptance.

Neste trabalho, enzimas álcool-desidrogenases provenientes de fungos marinhos e a lipase imobilizada de Candida antarctica foram utilizadas para produção de compostos de interesse sintético e biológico. No capítulo 1, enzimas álcool-desidrogenases de fungos isolados da alga marinha Bostrychia radicans foram empregadas em reações de redução de cetonas fluoradas 1-5. Os fungos identificados como Botryosphaeria sp. CBMAI 1197, Eutypella sp. CBMAI 1196, Hidropisphaera sp. CBMAI 1194 e Xylaria sp. CBMAI 119 atuaram como biocatalisadores nestas reações levando à produção de álcoois com elevada pureza enantiomérica. O fungo Botryosphaeria sp. CBMAI 1197 destacou-se frente aos demais microrganismos, produzindo os álcoois (S)-2,2,2-trifluoro-1-feniletanol (1a) e (R)-1-(2,4,5-trifluorofenil)etanol (3a) com excelentes conversões (100% e 97%) e excessos enantioméricos (ee >99%). Este fungo também apresentou enzimas álcool-desidrogenases ativas frente a cetonas dicarboniladas 4-5, produzindo os álcoois 4,4,4-trifluoro-1-fenil-1,3-butanodiol (4a) e 4,4,4-trifluoro-1-(2-naftalenil)-1,3-butanodiol (5a) com 100% de conversão em ambos os casos e com purezas enantioméricas respectivas a 99% e 97%. Este foi o primeiro estudo realizado no Brasil com fluorocetonas dicarboniladas e com os fungos isolados da alga marinha Bostrychia radicans. No capítulo 2, a lipase comercial de Candida antarctica foi o biocatalisador empregado em reações de aminólise entre os ésteres linoleato de etila (1) e salicilato de etila (3), a amina graxa N-dodecilamina (2) e os aminoálcoois (4-9). A amina graxa N-dodecilamina (2) também foi utilizada em reações com o linoleato de etila (1), onde a lipase de Candida antarctica produziu a respectiva amida graxa 10 com rendimentos superiores a 95%. Os aminoálcoois foram selecionados para reações com o salicilato de etila (3), onde a lipase exibiu quimiosseletividade pelo grupo amino, produzindo predominantemente amidas fenólicas (12-19) com rendimentos entre 23-68%. A enzima CALB apresentou quimiosseletividade reduzida na reação com o 5-aminopentanol (6) onde os produtos amida 14 e éster 15 foram obtidos com rendimentos de 44 e 33%, respectivamente. O produto 2-hidroxi-N-(2-hidroxipropil)benzamida (19) foi obtido com rendimento superior a 90% a partir da reação catalisada pela lipase de Candida antarctica. Este produto foi selecionado como intermediário para a síntese de uma molécula hidrofóbica 21 que apresenta o éster oleato de etila em sua constituição. O produto 21 foi obtido com 75% de rendimento. As amidas fenólicas 12-21 produzidas neste trabalho são derivadas do ácido linoleico (ômega 6) e do ácido salicílico, os quais apresentam propriedades emolientes e antioxidantes. Estes compostos são interessantes para a formulação de produtos cosméticos de aplicação cutânea. Neste processo biotecnológico as reações foram conduzidas na ausência de solventes orgânicos, evitando o tratamento de solventes voláteis e a formação de subprodutos. Os compostos foram analisados por Cromatografia líquida de alta eficiência e caracterizados por RMN (1H, 13C), EMAR e IV. A aplicação de reações de biocatálise seja através de células microbianas ou de enzimas isoladas foram muito promissoras na síntese de compostos orgânicos de interesse como álcoois enantiomericamente puros ou amidas graxas. / In this work, alcohol dehydrogenase (ADHs) enzymes from marine fungi and immobilized lipase from Candida antarctica were employed for the production of compounds of biological and synthetic interest. In chapter 1, ADHs of fungi isolated from the marine alga Bostrychia radicans were used in reduction reactions of fluorinated ketones 1-5. The fungi identified as Botryosphaeria sp. CBMAI 1197, Eutypella sp. CBMAI 1196, Hidropisphaera sp. CBMAI 1194 and Xylaria sp. CBMAI 119 acted as biocatalysts in these reactions leading to production of alcohols with high enantiomeric purity. The fungus Botryosphaeria sp. CBMAI 1197 presented highlighted compared to other microorganisms producing the alcohols (S)-2,2,2-trifluoro-1-phenylethanol (1a) and (R) -1 - (2,4,5-trifluorophenyl) ethanol (3a) with excellent conversions (100% and 97%) and enantiomeric excesses (ee > 99%). This fungus also exhibited ADHs enzymes active with dicarbonylateds ketones, leading to the production of the alcohols 4,4,4-trifluoro-1-phenylbutane-1,3-diol (4a) and 4,4,4-trifluoro-1-(naphthalen-2-yl)butane-1,3-diol -1,3-butanediol (5a) with conversions of 100% in both cases and enantiomeric excess of 99%-97%, respectively. This was the first study conducted with dicarbonilated fluoroketones 4-5 and with fungi isolated from the marine alga Bostrychia radicans in Brazil. In chapter 2, immobilized lipase from Candida antarctica was used as biocatalyst in the aminolysis reaction between esters of ethyl linoleate (1) and ethyl salicylate (3), the fatty amine N-dodecylamine (2) and the aminoalcohols (4-8). Six aminoalcohols were selected for reactions with ethyl salicylate (3), where the lipase exhibited chemoselectivity by the amino groups, producing predominantly phenolic amides in yields of 23-63%. The CALB exhibited um reduction in chemoselectivity in the reaction with 5-aminopentanol (6) where the amide 14 and ester 15 products were obtained with 44% and 33% yields. The product 2-hydroxy-N-(2-hydroxypropyl) benzamide (19) was obtained in yield greater than 90% from the reaction catalyzed by lipase from Candida antarctica. This product was selected as reagente for the synthesis of a hydrophobic molecule 21 presenting ester ethyl oleate in its constitution. The product 21 was obtained in 75% yield. The phenolic amides 12-21 produced in this work are derived from linoleic acid (omega 6) and salicylic acid, which presents emollient and antioxidants properties. These compounds are interesting for the formulation of cosmetic products for skin application. In this biotechnological process, the reactions were carried out under solvent-free conditions and vacum, avoiding the treatment of volatile solvents and by-product formation. The compounds were analyzed by high performance liquid chromatography and characterized by NMR (1H, 13C), IR and HRMS. Applying biocatalysis reactions, either through microbial cells or isolated enzymes were promising for the synthesis of organic compounds such as enantiomerically pure alcohols and fatty phenolic amides.

No description available.

Neste trabalho, enzimas álcool-desidrogenases provenientes de fungos marinhos e a lipase imobilizada de Candida antarctica foram utilizadas para produção de compostos de interesse sintético e biológico. No capítulo 1, enzimas álcool-desidrogenases de fungos isolados da alga marinha Bostrychia radicans foram empregadas em reações de redução de cetonas fluoradas 1-5. Os fungos identificados como Botryosphaeria sp. CBMAI 1197, Eutypella sp. CBMAI 1196, Hidropisphaera sp. CBMAI 1194 e Xylaria sp. CBMAI 119 atuaram como biocatalisadores nestas reações levando à produção de álcoois com elevada pureza enantiomérica. O fungo Botryosphaeria sp. CBMAI 1197 destacou-se frente aos demais microrganismos, produzindo os álcoois (S)-2,2,2-trifluoro-1-feniletanol (1a) e (R)-1-(2,4,5-trifluorofenil)etanol (3a) com excelentes conversões (100% e 97%) e excessos enantioméricos (ee >99%). Este fungo também apresentou enzimas álcool-desidrogenases ativas frente a cetonas dicarboniladas 4-5, produzindo os álcoois 4,4,4-trifluoro-1-fenil-1,3-butanodiol (4a) e 4,4,4-trifluoro-1-(2-naftalenil)-1,3-butanodiol (5a) com 100% de conversão em ambos os casos e com purezas enantioméricas respectivas a 99% e 97%. Este foi o primeiro estudo realizado no Brasil com fluorocetonas dicarboniladas e com os fungos isolados da alga marinha Bostrychia radicans. No capítulo 2, a lipase comercial de Candida antarctica foi o biocatalisador empregado em reações de aminólise entre os ésteres linoleato de etila (1) e salicilato de etila (3), a amina graxa N-dodecilamina (2) e os aminoálcoois (4-9). A amina graxa N-dodecilamina (2) também foi utilizada em reações com o linoleato de etila (1), onde a lipase de Candida antarctica produziu a respectiva amida graxa 10 com rendimentos superiores a 95%. Os aminoálcoois foram selecionados para reações com o salicilato de etila (3), onde a lipase exibiu quimiosseletividade pelo grupo amino, produzindo predominantemente amidas fenólicas (12-19) com rendimentos entre 23-68%. A enzima CALB apresentou quimiosseletividade reduzida na reação com o 5-aminopentanol (6) onde os produtos amida 14 e éster 15 foram obtidos com rendimentos de 44 e 33%, respectivamente. O produto 2-hidroxi-N-(2-hidroxipropil)benzamida (19) foi obtido com rendimento superior a 90% a partir da reação catalisada pela lipase de Candida antarctica. Este produto foi selecionado como intermediário para a síntese de uma molécula hidrofóbica 21 que apresenta o éster oleato de etila em sua constituição. O produto 21 foi obtido com 75% de rendimento. As amidas fenólicas 12-21 produzidas neste trabalho são derivadas do ácido linoleico (ômega 6) e do ácido salicílico, os quais apresentam propriedades emolientes e antioxidantes. Estes compostos são interessantes para a formulação de produtos cosméticos de aplicação cutânea. Neste processo biotecnológico as reações foram conduzidas na ausência de solventes orgânicos, evitando o tratamento de solventes voláteis e a formação de subprodutos. Os compostos foram analisados por Cromatografia líquida de alta eficiência e caracterizados por RMN (1H, 13C), EMAR e IV. A aplicação de reações de biocatálise seja através de células microbianas ou de enzimas isoladas foram muito promissoras na síntese de compostos orgânicos de interesse como álcoois enantiomericamente puros ou amidas graxas. / In this work, alcohol dehydrogenase (ADHs) enzymes from marine fungi and immobilized lipase from Candida antarctica were employed for the production of compounds of biological and synthetic interest. In chapter 1, ADHs of fungi isolated from the marine alga Bostrychia radicans were used in reduction reactions of fluorinated ketones 1-5. The fungi identified as Botryosphaeria sp. CBMAI 1197, Eutypella sp. CBMAI 1196, Hidropisphaera sp. CBMAI 1194 and Xylaria sp. CBMAI 119 acted as biocatalysts in these reactions leading to production of alcohols with high enantiomeric purity. The fungus Botryosphaeria sp. CBMAI 1197 presented highlighted compared to other microorganisms producing the alcohols (S)-2,2,2-trifluoro-1-phenylethanol (1a) and (R) -1 - (2,4,5-trifluorophenyl) ethanol (3a) with excellent conversions (100% and 97%) and enantiomeric excesses (ee > 99%). This fungus also exhibited ADHs enzymes active with dicarbonylateds ketones, leading to the production of the alcohols 4,4,4-trifluoro-1-phenylbutane-1,3-diol (4a) and 4,4,4-trifluoro-1-(naphthalen-2-yl)butane-1,3-diol -1,3-butanediol (5a) with conversions of 100% in both cases and enantiomeric excess of 99%-97%, respectively. This was the first study conducted with dicarbonilated fluoroketones 4-5 and with fungi isolated from the marine alga Bostrychia radicans in Brazil. In chapter 2, immobilized lipase from Candida antarctica was used as biocatalyst in the aminolysis reaction between esters of ethyl linoleate (1) and ethyl salicylate (3), the fatty amine N-dodecylamine (2) and the aminoalcohols (4-8). Six aminoalcohols were selected for reactions with ethyl salicylate (3), where the lipase exhibited chemoselectivity by the amino groups, producing predominantly phenolic amides in yields of 23-63%. The CALB exhibited um reduction in chemoselectivity in the reaction with 5-aminopentanol (6) where the amide 14 and ester 15 products were obtained with 44% and 33% yields. The product 2-hydroxy-N-(2-hydroxypropyl) benzamide (19) was obtained in yield greater than 90% from the reaction catalyzed by lipase from Candida antarctica. This product was selected as reagente for the synthesis of a hydrophobic molecule 21 presenting ester ethyl oleate in its constitution. The product 21 was obtained in 75% yield. The phenolic amides 12-21 produced in this work are derived from linoleic acid (omega 6) and salicylic acid, which presents emollient and antioxidants properties. These compounds are interesting for the formulation of cosmetic products for skin application. In this biotechnological process, the reactions were carried out under solvent-free conditions and vacum, avoiding the treatment of volatile solvents and by-product formation. The compounds were analyzed by high performance liquid chromatography and characterized by NMR (1H, 13C), IR and HRMS. Applying biocatalysis reactions, either through microbial cells or isolated enzymes were promising for the synthesis of organic compounds such as enantiomerically pure alcohols and fatty phenolic amides.