Il est reconnu, depuis des années, que la flore intestinale par son équilibre complexe et dynamique joue un rôle essentiel dans la santé humaine. Une des stratégies les plus prometteuses pour la maintenir ou l’améliorer consiste à moduler le microbiome par l’utilisation de bactéries probiotiques ou de sucres prébiotiques. C’est dans ce contexte que s’inscrivent les études structurales et fonctionnelles d’α glucosidases bactériennes développées dans cette thèse. Ces enzymes hydrolysant les liaisons α-(1,4) glucosidiques sont classées, selon la base de données CAZy, dans les familles de glycoside hydrolases (GH) 4, 13, 31, 63, 97 et 122. Ces travaux de thèse, centrés sur trois α-glucosidases issues de Lactobacillus bulgaricus (11842aglu, GH31), Lactococcus lactis (1403aglu, GH13) et Shewanella sp. ANA-3 (SHWaglu, GH97), exposent la mise au point de leurs protocoles de surexpression et de purification. Ils présentent également des études bioinformatiques de 11842aglu et de 1403aglu, ainsi qu’une caractérisation enzymatique préliminaire de cette dernière. Une analyse structurale et fonctionnelle approfondie de SHWaglu a aussi été réalisée. La résolution, par cristallographie aux rayons X, des structures de SHWaglu seule, en complexe avec différents ligands et de mutants, a participé à enrichir les connaissances, jusqu’à présent peu étendues, sur les enzymes de la famille GH97. Ainsi, un motif structural conservé au sein de cette famille a notamment été mis en évidence. Par ailleurs, ces informations structurales combinées aux études enzymatiques ont permis de révéler des déterminants moléculaires de l’activité de cette α-glucosidase et, par conséquent, d’établir les relations structure-fonction-activité de cette enzyme. Ainsi, l’ensemble des données obtenues, couplé à des études d’ingénierie protéique, contribue à ouvrir de nouvelles perspectives industrielles, notamment en suggérant d’optimiser ou de conférer des activités enzymatiques modifiées dans certaines cibles de choix afin de leur faire synthétiser des sucres de type prébiotiques / It is now generally accepted that the gut flora with its complex and dynamic nature plays a vital role in human health. One of the most promising strategies for maintaining or improving health is to modulate the microbiome by the use of probiotics and prebiotics as food supplements. The structure/function/activity relationship studies of bacterial α-glucosidases described in this thesis have been performed within this context. These α-(1,4)-glucosidic bond hydrolyzing enzymes are classified, according to the CAZy database, into glycoside hydrolases families (GH) 4, 13, 31, 63, 97 and 122. This thesis work, has focused on three α-glucosidases from Lactobacillus bulgaricus (11842aglu, GH31), Lactococcus lactis (1403aglu, GH13) and Shewanella sp. ANA-3 (SHWaglu, GH97), and the development of their overexpression and purification protocols. It also presents a bioinformatics studies of 11842aglu and 1403aglu, as well as preliminary enzymatic characterization of the latter. As for SHWaglu, detailed structural and functional studies have been carried out. The crystal structures of SHWaglu in its native state, in complex with different ligands as well as site directed mutants have contributed to increase our knowledge on enzymes from the GH97 family which to date remains relatively limited. Notably, a conserved structural motif in this family has been identified. Overall, the structural- and enzymatic studies and analyses have revealed molecular-and structural determinants governing the activity and broad substrate specificity of this α-glucosidase which is adapted to cold temperatures. Apart from the insight gained from a fundamental research point of view, data described within this work, coupled with protein engineering studies may contribute to open up new industrial perspectives, in particular by suggesting optimized or altered enzyme activities in some attractive enzyme targets with the aim of synthesizing prebiotic compounds

Thesis (MSc)--University of Stellenbosch, 2005. / ENGLISH ABSTRACT: Aspalathus linearis is a leguminous shrub native to the Cedarberg Mountains in the Western Cape, of which the leaves and stems are used for the preparation of rooibos tea. Over the past few decades, rooibos tea and other related products have gained popularity due to their health promoting properties. These beneficial properties can partly be ascribed to the phenolic constituents that are trapped within the cellulolytic plant material of the tea leaves as glycoconjugated aroma and phenolic compounds. Although many fungal species are known for their efficient hydrolysis of plant material, fungal enzymes have not been evaluated for the bioprocessing of rooibos tea to improve its commercial value. It was the objective of this study to identify a specific cocktail of microbial enzymes to enhance the maceration of the rooibos plant material, while retaining the antioxidant content. During this study, 11 fungal species known for the production of hydrolytic enzymes, as well as 12 species isolated from rooibos tea products, were screened for their potential to improve aroma development and/or increased extraction of soluble matter and/or antioxidants from rooibos tea material. After culturing in Potato Dextrose medium, the crude enzyme extracts of the 23 isolates were evaluated on spent rooibos tea for enhanced extraction of soluble solids (SS) and/or total polyphenols (TP). Nine strains increased the yield in SS (improvement varying from 3% to 42%), while 14 strains yielded higher levels of TP (increase varying from 1% to 36%). Little improvement in colour development from green (unfermented) rooibos tea was observed, but the enzyme extracts from Pleurotus ostreatus var. florida, Lentinula edodes, Aspergillus oryzae, Aspergillus tubingensis, Paecilomyces variotti and Trichoderma reesei improved the aroma development from green tea to some extent. Ten-fold concentrated enzyme extracts from four of these isolates were able to release at least an additional 10% in SS from the green tea. The crude enzyme extracts prepared from three food-grade strains, i.e. Aspergillus oryzae, Lentinula edodes and Pleurotus ostreatus var.florida, contained relatively high levels of endoglucanase, xylanase and pectinase activities. Eight different culture media were evaluated for optimal hydrolase and laecase production by these food-grade fungi. MYPG proved to be the best growth medium, while 1% spent grain, 1% wheat straw and 1% pineapple peel gave the best induction of xylanase, cellulase, pectinase and laecase activities for L. edodes. When cultured in the Yeast Peptone (YP) medium + 1% wheat straw, the L. edodes enzyme cocktail showed the best improvement in both the aroma and colour development of green tea and may be considered for shortening of the fermentation time required for green tea processing. Traditional open-air fermentation of rooibos tea can take up to -1-6hours, which results in a significant loss in antioxidants and therefore also in its pharmaceutical and nutraceutical value. The Rhizopus oryzae cocktail prepared in YP + 1% wheat straw showed potential for the development of a quick-draw fermented tea made by infusion, where there is improved colour release and more than 20% improved extraction of soluble solids without a loss in the TP content. When cultured in Potato Dextrose medium, the L. edodes cocktail can be used for aroma and colour development from green tea, while the R. oryzae cocktail can be used for increasing the antioxidant content in rooibos extracts from green or fermented tea. This was confirmed with small-scale industrial treatments of fermented tea where the L. edodes YP + wheat straw cocktail improved the release in SS by more than 10% and the R. oryzae yP + wheat straw cocktail increased the yield in SS by more than 30% and the TP by more than 20%. / AFRIKAANSE OPSOMMING: Aspalathus linearis is 'n fynbosplant inheems aan die Sederberge in die Wes-Kaap, waarvan die blare en stingels vir die voorbereiding van rooibostee gebruik word. Die afgelope paar dekades het die gewildheid van rooibostee en verwante produkte aansienlik toegeneem weens die gesondheidsvoordele wat dit inhou. Hierdie voordelige eienskappe kan toegeskryf word aan die fenoliese komponente wat binne die sellulolitiese plantweefsel van die teeblare as gekonjugeerde geur- en fenoliese verbindings vasgevang is. Alhoewel verskeie swamspesies vir hul doeltreffende degradering van plantmateriaal bekend is, is fungale ensieme nog nie geëvalueer vir die prosessering van rooibostee om die kommersiële waarde daarvan te verbeter nie. Die doelwit van hierdie studie was om 'n spesifieke kombinasie van mikrobiese hidrolitiese ensieme te identifiseer wat die maserasie van rooibos plantmateriaal sal verhoog met behoud van die anti-oksidant inhoud. Tydens hierdie studie is 11 swamspesies wat bekend is vir die produksie van hidrolitiese ensieme, asook 12 swamspecies wat vanaf rooibostee produkte geïsoleer is, geëvalueer vir hul potensiaalom geurontwikkeling en/of ekstraksie van oplosbare stowwe en/of anti-oksidante vanuit rooibostee materiaal te verbeter. Die kru ensiemekstrakte van die 23 isolate, wat ID Aartappel-Dextrose medium opgegroei is, is op oorskot rooibostee geëvalueer vir verhoogde ekstraksie van oplosbare vastestowwe (SS) en/of totale polifenole (TP). Nege rasse het die opbrengs van oplosbare vastestowwe verhoog (verbetering tussen 3% en 42%), terwyl 14 rasse die totale polifenoliese vlakke laat toeneem het (tot so hoog as 36%). Baie min verbetering in kleurontwikkeling van groen (ongefermenteerde) rooibostee is waargeneem, maar ensiemekstrakte van Pleurotus ostreatus var. florida, Lentinula edodes, Aspergillus oryzae, Aspergillus tubingensis, Paecilomyces variotti en Trichoderma reesei, het wel die aroma ontwikkeling vanaf groen tee tot 'n mate verbeter. Tienvoudig gekonsentereerde ekstrakte van vier van hierdie isolate het 'n verbetering van meer as 10% in die ekstraksie van opgeloste vastestowwe uit groen tee tot gevolg gehad. Die ensiemekstrakte van drie swarnme bekend vir hul gebruik in die voedselindustrie, nl. A. oryzae, L. edodes and P. ostreatus var. florida, het relatief hoë vlakke van endoglukanase, xylanase en pektinase aktiwiteit getoon. Agt verskillende kultuur-media is vir die optimale produksie van hidrolitiese and lakkase ensieme vanaf hierdie voedsel-graad swarnme geëvalueer. MYPG was die beste groeimedium vir L. edodes, -terwyl 1% koringstrooi, 1% oorskot graan en 1% pynappelskil die beste induksie van xylanase, pektinase, endoglukanase en lakkase aktiwiteite vir hierdie organisme getoon het. Lentinula edodes opgegroei in YP medium + 1% koringstrooi, het die beste verbetering in aroma en kleur getoon vanaf groen tee getoon. Hierdie ekstrak kan dus moontlik gebruik word vir die verkorting van die fermentasietyd wat vir groen tee benodig word. Ope-lug fermentasie van groen tee duur gewoonlik tot 16 uur en lei tot 'n aansienlike verlies in antioksidant-inhoud. Die R. oryzae ekstrak het die beste potensiaal vir die vervaardiging van 'n "quick-draw" tee getoon met 'n goeie kleurvrystelling sonder enige verlies in SS en TP opbrengs. Wanneer die swamme in Aartappel-Dextrose medium opggegroei word, kan die L. edodes ensiemekstrak vir aroma en kleurontwikkeling van groen tee aangewend word, terwyl die R. oryzae ensiemekstrak vir die verhoging van die antioksidant-inhoud in rooibos ekstrakte van groen tee of gefermenteerde tee gebruik kan word. Dit is bevestig met die kleinskaalse behandeling van gefermenteerde tee waar die L. edodes YP + 1% koringstrooi ensiemekstrak die vrystelling van SS met meer as 30% en die TP met meer as 20% verbeter het.

Thesis (PhD)--Stellenbosch University, 2014. / ENGLISH ABSTRACT: The development of ―energycane‖ varieties of sugarcane for ethanol production is underway, targeting the use of both sugar juice (first generation ethanol) and bagasse (second generation ethanol). Nevertheless, identification of the preferred varieties represents the biggest challenge to the development of energycane due to large number of samples produced during breeding. In the present study, dilute acid pretreatment, enzymatic hydrolysis and fermentation processes were used to evaluate the processability of bagasse (fibrous residue generated after juice sugar extraction) from different varieties of sugarcane to select preferred varieties with the properties of improving combined ethanol yield (ethanol from juice and bagasse) per hectare. The impact of variety selection on combined ethanol yield (ethanol from juice and bagasse) per hectare was also assessed. In the first part of this study, 115 varieties of sugarcane originated from classical breeding and precision breeding (genetic engineering) were screened based on agronomic data and experimental data from biochemical processes (dilute acid pretreatment and enzymatic hydrolysis) applied to the bagasse fraction of each variety. The results showed wide variations in the chemical composition of bagasse between the varieties. Structural carbohydrates and lignin content ranged from 66.6 to 77.6% dry matter (DM) and 14.4 to 23.1% DM, respectively. The majority of precision breeding varieties showed higher arabinoxylan, lower lignin and lower ash content than most of classical breeding varieties. Combined sugar yield from the bagasse after pretreatment and enzymatic hydrolysis also varied significantly among the varieties. Up to 27.9 g/100g (dry bagasse) difference in combined sugar yield was observed. Combined sugar yield was inversely correlated with lignin as well as ash content, but it correlated positively with structural carbohydrates content. Total potential ethanol yields per hectare, calculated based on cane yield, soluble and non-soluble sugar content also differed significantly among the varieties (8,602−18,244 L/ha). Potential ethanol from bagasse contributed approximately one third of the total potential ethanol yield. Interestingly, some of the varieties had combined properties of high potential ethanol yield per hectare and improved bagasse convertibility. Thus, six varieties (3 from each breeding technology) were selected as preferred varieties for further investigation. To enhance sugar yield from bagasse, optimisation of pretreatment was conducted on the selected varieties. Industrial bagasse was included for comparison purposes. The pretreatment optimisation was based on maximising combined sugar yield from the combined pretreatment-hydrolysis process. A central composite design (CCD) was applied to investigate the effects of temperature, acid concentration and residence time on the responses and was later used to determine the maximum combined sugar yield. Pretreatment optimisation was conducted at gram scale (22.9 ml reactor) and at bench scale (1000 ml reactor). Significant differences in sugar yields (xylose, glucose, and combined sugar) between the varieties were observed. The combined sugar yields from the best performing varieties and industrial bagasse at optimal pretreatment-hydrolysis conditions differed by up to 34.1% and 33% at gram and bench scale, respectively. A high ratio of carbohydrates to lignin and low ash contents increased the release of sugar from the substrates. At mild pretreatment conditions, the differences in bioconversion efficiency between varieties were greater than at severe conditions. This observation suggests that under less severe conditions the conversion efficiency was largely determined by the properties of the biomass. Furthermore, it was demonstrated that the pretreatment conditions with temperature ranged from 184 to 200 °C and varying residence time to provide a severity factor between 3.51 and 3.96 was observed to be the area in common where 95% of maximum combined sugar yield could be obtained. Simultaneous Saccharification and Fermentation (SSF) was performed on the unwashed pressed-slurry from bagasse pretreatment at conditions for maximum combined sugar yield at bench scale. Batch and fed-batch SSF feeding strategy at different solid loadings and enzyme dosages were used aiming to reach an ethanol concentration of at least 40 g/L. The results revealed significant improvement in overall ethanol yield after SSF for the selected varieties (84.5–85.6%) compared to industrial bagasse (74.8%). The maximum ethanol concentration from the best performing varieties was 48.6−51.3 g/l and for poor performing varieties was 37.1−38.3 g/l. Ethanol concentration in the fermentation broth was inversely correlated with lignin content and the ratio of xylose to arabinose, but it showed positive correlation with glucose yield from pretreatment-enzymatic hydrolysis. The overall assessment of the varieties showed greater improvement in combined ethanol yields per hectare (71.1–90.7%) for the best performing varieties with respect to industrial sugarcane. The performance in terms of ethanol yields of selected varieties from a number harvest years was evaluated. The results showed considerable variations in ethanol yields across harvests. The results showed that the best variety in terms combined ethanol yield was not maintained across harvests. The differences in ethanol yields were greater among the varieties than across the harvests. Prolonged severe drought significantly affected the ethnol yields of all varieties represented by lower and intermediate lignin content for cane yield compared to that which had highest lignin content. However, carbohydrates content in the bagasse and sugar yield/recovery between the harvest years did not change for the most of the varieties. In summary, the present study provides evidence of the impact of cultivar selection and pretreatment optimisation in increasing conversion efficiency of bagasse. The results demonstrate that varieties with lower lignin and ash content, as well as highly substituted xylan resulted in higher sugar and ethanol yields. These results suggest that lower process requirements can be achieved without adversely affecting juice ethanol and cane yield per hectare. Nonetheless, an attempt to reduce lignin content in the bagasse, to reduce processing requirements for ethanol production, can also target the improvement of crop tolerance toward severe drought conditions. / AFRIKAANSE OPSOMMING: Die ontwikkeling van ―energie-riet‖ rasse vir etanol produksie is goed op dreef, waar beide die sap (eerste generasie etanol) en die bagasse (tweede generasie etanol) geteiken word. Die groot aantal monsters wat tydens teling geproduseer word, bied egter die grootste uitdaging vir die identifisering van nuwe rasse ten einde energie-riet te ontwikkel. In die huidige studie is verdunde suurvoorbehandeling, ensiematiese hidrolise en fermentasie-prosesse gebruik om die verwerkbaarheid van bagasse (veselagtige residu gegenereer na sap suiker ekstraksie) van verskillende suikerrietrasse te evalueer om nuwe variëteite te selekteer wat eienskappe van verbeterde gekombineerde etanolopbrengs (etanol van sap en bagasse) per hektaar toon. Die impak van variëteit-seleksie op gekombineerde etanol opbrengs (etanol van sap en bagasse) per hektaar is ook beoordeel. In die eerste deel van hierdie studie het uit ‗n siftingsproses van 115 suikerriet rasse bestaan wat deur klassieke en presisie (geneties gemodifiseerde) teling gegenereer is. Die sifting was op agronomiese data gebaseer, asook op data van verdunde suur voorafbehandeling en ensimatiese hidrolise eksperimente wat op die bagasse fraksie van elke ras uitgevoer is. Die resultate het op groot variasie in die chemiese samestelling van die bagasse van verskillende rasse gedui. Die strukturele koolhidrate het tussen 66.6 en 77.6% droë massa (DM) gewissel, terwyl die lignien inhoud ‗n variasie van 14.4 en 23.1% DM getoon het. Verder het meeste van die presisie-teling variëteite ‗n hoër arabinoxilaan, maar ‗n laer lignien en as-inhoud as meeste van die klassieke teling rasse gehad. Die gekombineerde suikeropbrengs (GSO) van die bagasse na voorafbehandeling en ensimatiese hidrolise het ook beduidend tussen rasse gewissel, waar ‗n verskil van tot 27.9 g/100g (droë bagasse) waargeneem is. Daar was ‗n omgekeerde korrelasie tussen die gekombineerde suikeropbrengs en die lignien en as-inhoud gewees, maar die opbrengs het ‗n sterk positiewe korrelasie met die strukturele koolhidrate getoon. Die totale potensiële etanol opbrengs per hektaar wat vanaf die suikerriet se oplosbare en nie-oplosbare suikerinhoud bereken is, het ook beduidend tussen rasse verskil (8,602−18,244 L/ha), waar die potensiële etanol opbrengs van die bagasse gedeelte ongeveer een derde van die totale potensiële etanol opbrengs beslaan het. Interessante bevindinge het op sommige rasse met gekombineerde eienskappe van hoë potensiële opbrengs per hektaar asook ‗n hoë omskakelingsvermoë gedui. Derhalwe is ses variëteite (drie van elke telingstegnologie) as voorkeurvariëteite vir verdere studie gekies. Om die etanol opbrengs vanaf die bagasse te verbeter was voorafbehandeling van die voorkeurvariëteite geoptimeer, en waar industriële bagasse vir vergelykingsdoeleindes ingesluit was. Vir die optimering was dit ten doel gestel om die gekombineerde suikeropbrengs van die gekombineerde voorafbehandeling-hidrolise proses te maksimeer. ‗n Sentrale saamgestelde ontwerp (SSO) is gebruik om die effek van temperatuur, suurkonsentrasie en residensietyd op die responsveranderlikes vas te stel wat uiteindelik gebruik is om die maksimum gekombineerde suikeropbrengs te bepaal. Die optimering van die voorafbehandeling is op gram-skaal in ‗n 22.9 ml reaktor, asook op bank-skaal in ‗n 1000 ml reaktor uitgevoer. Beduidende verskille in die suikeropbrengs (xilose, glukose en gekombineerde suiker) is tussen die voorkeurrasse waargeneem. Tussen die rasse wat die beste gevaar het, asook die industriële bagasse, het die gekombineerde suikeropbrengs by optimale voorafbehandeling-hidrolise toestande onderskeidelik met tot 34.1% en 33% op gram-skaal en bank-skaal gevarieer. ‗n Hoë verhouding van koolhidrate tot lignien, asook ‗n lae as-inhoud het tot ‗n toename in die vrystelling van suiker uit die substraat gelei. By matige voorafbehandelingstoestande was die verskille in omskakelingseffektiwiteit tussen rasse groter as onder hewige toestande, wat daarop gedui het dat omskakelingseffektiwiteit grotendeels deur die eienskappe van die biomassa bepaal is. Verder is daar ook gedemonstreer dat die voorbehandelingsomstandighede met temperatuur tussen 184 en 200ºC en verandering van die residensietyd om 'n hewigheidsfaktor van tussen 3.51 en 3.96 te verskaf, 'n gemeenskaplike area gelewer het waar 95% van maksimum gekombineer suiker opbrengs (GSO) verkry kon word. Gelyktydige versuikering en fermentasie (GVF) is na voorafbehandeling op ongewaste, gepersde bagasse substraat by toestande vir die maksimum gekombineerde suikeropbrengs op bank-skaal uitgevoer. Bondel en voerbondel SSF voerstrategie by verskillende vaste ladings en ensiemdoserings is gebruik om 'n etanol konsentrasie van ten minste 40 g/L te bereik. Ná GVF was die algehele etanol opbrengs vir die voorkeurvariëteite (84.5–85.6%) beduidend beter relatief tot die industriële bagasse (74.8%). Die maksimum etanol opbrengs na SSF van die rasse met die beste prestasie was 48.6-51.3 g/L en 37.1-38.3 g/L vir rasse wat swak presteer het. Die etanol konsentrasie in die fermentasiesop was omgekeerd met lignien en die verhouding van xilose tot arabinose gekorreleer, maar was duidelik positief met die glukose opbrengs vanaf voorafbehandeling-hidrolise gekorreleer. ‗n Algemene assessering het op ‗n duidelike verbetering van die voorkeurvariëteite in terme van gekombineerde etanol opbrengs per hektaar gedui (71.1–90.7%), relatief tot die industriële suikerriet. Die prestasie in terme van etanol opbrengs van geselekteerde variëteite is oor 'n reeks oesjare ge-evalueer. Die resultate het aansienlike variasies in etanol opbrengs oor oesjare getoon. Die resultate het gewys dat die beste variëteite in terme van gekombineerde etanol opbrengs nie volhou is oor oeste nie. Die verskille in etanol opbrengste tussen variëteite was groter as die verskille oor oesjare. Verlengde ernstige droogte het die etanol opbrengs van alle variëteite met laer en intermediere lignien inhoud vir rietopbrengs aansienlik beinvloed, in vergelyking met dié wat die hoogste lignien inhoud gehad het. Die koolhidraatinhoud in die bagasse en suiker opbrengs/lewering tussen die oesjare het vir die meeste variëteite egter nie gewissel nie. Ter opsomming, die huidige studie verskaf bewyse van die impak van kultivarseleksie en voorbehandelings optimisering op die verhoging van die omskakelings-doeltreffendheid van bagasse. Die resultate wys dat variëteite met laer lignien- en asinhoud, en hoogs-gesubstitueerde xilaan hoër suiker- en etanol opbrengs gelewer het. Hierdie resultate stel voor dat verminderde voorbehandelingsvereistes bereik kan word sonder om die sap etanol en rietopbrengs per hektar te benadeel. Nieteenstaande, 'n poging om die lignien inhoud van die bagasse te verminder om die verwerkingsvereistes vir etanolproduksie te verminder, kan ook die verbetering van gewas-toleransie tov ernstige droogte-toestande teiken.

In all sequenced genomes, a large fraction of predicted genes encodes proteins of unknown biochemical function and up to 15% of the genes with ‘‘known’’ function are mis-annotated. Several global approaches are being employed to predict function, including sequence similarity searches, analysis of gene expression, protein interaction, and protein structure. Enzymes comprise a group of target proteins that require experimental characterization for accurate functional annotations. Here I applied enzyme genomics to identify new enzymes by screening individually purified proteins for enzymatic activity under relaxed reaction conditions, which allowed me to identify the subclass or sub-subclasses of enzymes to which the unknown protein belongs. Further biochemical characterization of proteins was facilitated by the application of secondary screens with natural substrates (substrate profiling). Application of general enzymatic screens and substrate profiling greatly sped up the identification of biochemical function of unknown proteins and the experimental verification of functional predictions produced by other functional genomics approaches. As a test case, I used this approach to characterize the members of the haloacid dehalogenase (HAD)-like hydrolase superfamily, which consists mainly of uncharacterized enzymes, with a few members shown to possess phosphatase, beta-phosphoglucomutase, phosphonatase, and dehalogenase activities. Low sequence similarity between the members of the HAD superfamily precludes the computational prediction of their substrates and functions. Using a representative set of 80 phosphorylated substrates I characterized the phosphatase activities of 21 soluble HADs from Escherichia coli and seven soluble HADs from Saccharomyces cerevisiae. E. coli HADs show broad and overlapping substrate specificity against a wide range of phosphorylated metabolites. The yeast enzymes were more specific, and one protein also showed protein phosphatase activity. Comparison of HAD substrate profiles from two model organisms showed several “functional niches” that are occupied by HADs, which include hydrolysis of nucleotides, phosphoglycolate, phosphoserine, and pyridoxal phosphate. I proposed the cellular function for a number of HADs from both organisms based on substrate specificities. The physiological relevance of the phosphatase activity with the preferred substrate was validated in vivo for one of the HADs, E. coli YniC.

The pyrimidine salvage enzyme, nucleoside hydrolase, is catalyzes the irreversible hydrolysis of nucleosides into the free nucleic acid base and D-ribose. Nucleoside hydrolases have varying degrees of specificity towards purine and pyrimidine nucleosides. In E. coli, three genes were found that encode homologues of several known nucleoside hydrolases in protozoa. All three genes (designated yaaF, yeiK, and ybeK) were amplified by PCR and cloned. Two of the gene products (yeiK and ybeK) encode pyrimidine-specific nucleoside hydrolases, while the third (yaaF) encodes a nonspecific nucleoside hydrolase. All three were expressed at low levels and had different modes of regulation. As a comparative analysis, the homologous genes of Pseudomonas aeruginosa and P. fluorescens (designated nuh) were cloned. Both were determined to encode nonspecific nucleoside hydrolases. The nucleoside hydrolases of the pseudomonads exhibited markedly different modes of regulation. Both have unique promoter structures and genetic organization. Furthermore, both pseudomonad nucleoside hydrolase were found to contain an N-terminal extension of 30-35 amino acids that is shown to act as a periplasmic-signaling sequence. These are the first two nucleoside hydrolases, to date,that have been conclusively demonstrated to be exported to the periplasmic space. The physiological relevance of this is explained.

Aliando reações enzimáticas a compostos orgânicos de silício, objetivou-se explorar o potencial destes substratos em reações biocatalisadas. A intenção era ampliar o escopo de substratos e desbravar novas transformações. Inicialmente foram abordados os trabalhos relativos ao uso de hidrolases em reações envolvendo organossilanos, cujo uso de lipases foi o foco da nossa contribuição. Nela, a resolução cinética enzimática (RCE) de alcoóis quirais benzílicos contendo silício e outros heteroátomos (fósforo e estanho) foi explorada e transesterificações enantiosseletivas eficientes foram alcançadas, em que tanto os produtos acetilados e os alcoóis remanescentes foram obtidos em excelentes excessos enantioméricos (e.e. >99% em todos os casos). Considerações sobre a relação estrutura/atividade das reações catalisadas por lipase foram feitas, e foi possível perceber que os compostos contendo silício reagiram mais rapidamente que aqueles contedo fósforo e estanho. Em seguida, numa extensão natural da RCE, buscou-se realizar a resolução cinética dinâmica (RCD). Diversos experimentos de RCD foram realizados utilizando lipase e dois tipos de catalisadores de racemização diferentes: complexos de rutênio e uma resina de troca catiônica. Embora tenham sido encontrados indícios de que a racemização utilizando os catalisadores de rutênio estava acontecendo no meio reacional, a inativação do catalisador durante o processo foi uma dificuldade que, nos estudos realizados, não foi possível contornar. Foi então que uma resina de troca catiônica foi utilizada como alternativa de racemização, e dependendo do substrato utilizado foi possível realizar eficientes RCDs (rendimento até 93% e e.e. até 96%) através de uma esterificação enzimática empregando um acilante de cadeia longa. O último trabalho empregando hidrolases foi na acilação de silanóis. A partir dos resultados interessantes envolvendo a acilação de um silanol arílico (conversão de 75% para o acetoxissilano derivado usando a CAL-B), tentou-se acilar um silanol benzílico racêmico e, embora o substrato tenha sido acetilado enzimaticamente (conversão de até 47% para o acetoxissilano derivado nas condições estudadas), a reação se deu sem enantiosseletividade. Nas reações envolvendo oxidorredutases, tanto mono-oxigenases quanto enzimas provenientes da bactéria Arthrobacter sp., foram empregadas como biocatalisadores. Na tentativa de se realizar a oxidação da ligação C-Si utilizando BVMOs (Baeyer-Villiger mono-oxigenases), foi possível concluir que a instabilidade dos silanos e alcoxissilanos nas reações em meio aquoso poderia configurar um entrave no desenvolvimento da metodologia. Por outro lado, evidências de oxidação enzimática da ligação Si-H foram observadas em dois substratos arílicos, que podem servir de direcionamento para futuros projetos envolvendo este tema. Por fim, células íntegras da bactéria Arthrobacter sp. foram utilizadas em reações de desracemização aeróbica (R)-seletiva de alcoóis e redução anaeróbica (S)-seletiva de cetonas, ambas utilizando substratos contendo silício, fósforo, estanho e boro. Transformações com elevada enantiosseletividade foram encontradas, provando a versatilidade da Arthrobacter sp. em mediar reações enantiocomplementares. / By combining both enzymatic reactions and organosilicon compounds, we aimed to explore the potential of these substrates in biocatalytic reactions. The main goal was to expand the scope of substrates and breakthrough new transformations. Initially the study was based on the use of hydrolases in reactions involving organosilanes, in which lipases were the focus of our contribution. Thus, enzymatic kinetic resolution (EKR) of chiral benzylic alcohols containing silicon and other heteroatoms (phosphorus and tin) was explored and efficient enantioselective transesterifications were achieved, in which both acetylated products and remaining alcohols were obtained in excellent enantiomeric excesses (e.e. > 99% in all cases). Considerations about the structure/activity relationship of lipase-catalyzed reactions were done, and it was found out that silicon-containing compounds can react faster than those phosphorus- or tin-containing analogues. Then, an extension of EKR was the dynamic kinetic resolution (DKR). Several experiments were performed using lipase and different racemization catalysts: ruthenium complexes and a cation exchange resin. Although racemization by ruthenium catalysts have been found, in our studies inactivation of the catalyst during the process was a problem that was not possible to be solved. A cation exchange resin was used in racemization, and depending on the substrate it was possible to perform efficient DKRs (yield up to 93% and e.e. up to 96%) via an enzymatic esterification using an acylating agent with long chain. Another work with hydrolases was the enzymatic acylation of silanols. From the interesting results involving the acylation of an aryl-silanol (75% conversion to the acetoxy-silane derivative, by CAL-B), the acylation of a racemic benzyl-silanol was performed and although the substrate has been successfuly acetylated by a series of lipases (up to 47% conversion to the acetoxy-silane derivative under the conditions studied), the reaction occurred without any enantioselectivity. In reactions involving oxidoreductases, both mono-oxygenases and enzymes from the bacterium Arthrobacter sp., were used as biocatalysts. In an attempt to carry out the oxidation of the C-Si bond using BVMOs, it was found out that the instability of the substrates in aqueous media could set an obstacle in the development of the methodology. Moreover, evidence of enzymatic oxidation of Si-H bond were observed for two aryl substrates, which can serve as guidance for future projects involving the topic. Finally, whole cells of the bacterium Arthrobacter sp. were used for (R)- selective deracemization of alcohols and (S)-selective reduction of ketones, both using silicon-, phosphorus-, tin- and boron-containing substrates. Transformations with high enantioselectivity were achieved, showing the versatility of Arthrobacter sp. in mediating enantiocomplementary reactions.

A busca por substâncias benéficas à saúde humana tem impulsionado o desenvolvimento de pesquisas visando o estudo de enzimas e seus produtos através da otimização de bioprocessos. Um dos principais componentes utilizados como base para a indústria de alimentos funcionais são carboidratos denominados frutooligossacarídeos (FOS) derivados da sacarose. Estes são sintetizados por enzimas denominadas frutosiltransferases que podem ser encontradas em plantas, bactérias e fungos. Os FOS têm atraído grande interesse da indústria, devido às suas características fisiológicas e biomoduladoras. Por serem polissacarídeos prebióticos não-digeríveis, têm a capacidade de estimular seletivamente o crescimento de bifidobactérias e lactobacilos, auxiliando na prevenção da cárie dentária e câncer de cólon em humanos. Podem também contribuir na diminuição do colesterol total e triglicerídeos no sangue, promover a reabsorção de cálcio e magnésio e serem utilizados em dietas com restrições alimentares, por serem açúcares de baixo valor calórico e elevado valor nutricional. Tendo em vista a existência de diferentes formas de FOS sintetizados por diferentes mecanismos, o presente trabalho buscou realizar a caracterização estrutural e funcional de um conjunto de 13 frutosiltransferases de bactérias e fungos. Os genes alvo foram clonados e as enzimas expressas e purificadas. Ensaios estruturais e de atividade enzimática, incluindo de hidrólise e polimerização da sacarose, foram conduzidos para a melhor compreensão das bases moleculares envolvidas no reconhecimento do substrato. Oito enzimas, duas β-frutofuranosidases de B. adolescentis, três sucrose-6-phosphate hydrolase de B. licheniformis e L. gasseri e uma invertase de A.niger foram cristalizadas e as enzimas de B. adolescentis e de L. gasseri tiveram suas estruturas resolvidas e seus sítios catalíticos mapeados. Estas apresentam em sua estrutura uma região β-propeller, local identificado como sítio catalítico, conectada à um módulo β-sanduíche. Ambas as enzimas apresentaram atividade hidrolítica da sacarose e a enzima de L. gasseri apresentou a formação dos FOS nistose e 1-cestose com concentrações de 1 M de sacarose bem como em tempos de 8 e 12 horas de incubação. Estes estudos, somados às análises das outras enzimas, permitirão o melhoramento na produção em larga escala, além da otimização e o controle destes processos de obtenção de FOS. / The search for beneficial substances to human health has driven the development of researches on the study of enzymes and their products through bioprocess optimization. One of the main components used as a basis for functional food industry are carbohydrates called fructooligosaccharides (FOS) derived from sucrose. These are synthesized by enzymes called fructosyltransferases which can be found in plants, bacteria and fungi. The FOS has attracted great interest of the industry due to its physiological and biomodulator properties. Because it is non-digestible polysaccharides prebiotics, have the ability to selectively stimulate the growth of bifidobacteria and lactobacilli, assisting in the prevention of tooth decay and colon cancer in humans. They can also contribute to decrease total cholesterol and triglycerides in the blood, to promote the absorption of calcium and magnesium and can be used in diets with dietary restrictions, because they are low-calorie sugars presenting high nutritional value. Considering there are different forms of FOS synthesized by different mechanisms, the present work attempts to make structural and functional characterization of a set of 13 fructosyltransferases of bacteria and fungi. The target genes were cloned and the enzymes were expressed and purified. Structural testing of X-ray crystallography and enzymatic activity, including sucrose hydrolysis and polymerization were carried out for a better understanding of the molecular basis involved in substrate recognition. Eight enzymes, two β-frutofuranosidases B. adolescentis, three sucrose-6-phosphate hydrolase of B. licheniformis and L. gasseri and A. niger invertase, were crystallized and the enzymes from B. adolescentis and from L. gasseri had their structures determined and their catalytic site mapped. These are similar to each other and present in their structure one β-propeller region which was identified as catalytic site, connected to one β-sandwich module. Both enzymes showed hydrolytic activity of the sucrose and L. gasseri showed the formation of FOS, 1-kestose and nystose with 1 M sucrose concentrations and times of 8 and 12 hours of incubation. These studies together with the analysis of other enzymes will enable the improvement in large-scale production, besides the optimization and control of these processes for the production of FOS.

Os fungos filamentosos são microrganismos explorados devido ao potencial biotecnológico de seus produtos, nos quais as enzimas têm papel de destaque. Apesar de serem utilizadas em diversos segmentos industriais, as enzimas compõem um mercado que esta em franca expansão e em busca de melhores níveis de produção, de novas atividades enzimáticas, e outros. Os fungos filamentosos possuem mecanismos refinados de resposta a alterações exógenas. Sendo assim, os estudos proteômicos têm se tornado uma excelente ferramenta para explorar proteínas produzidas em resposta às variações ambientais, tais como, pH, fontes de nitrogênio e carbono, temperatura e tipos de bioprocessos. Um grupo especialmente afetado por estas variações é a produção de enzimas biotecnológicas. Neste trabalho, os perfis de proteínas intracelulares e/ou de enzimas secretadas foram identificados nos bioprocessos com Fusarium oxysporum URM 7401 e Myceliophthora thermophila, submetidos a diferentes condições de cultivo. As proteínas intracelulares de Fusarium oxysporum URM 7401, cultivado em bioprocesso submerso com diferentes pH ou fontes de nitrogênio, foram extraídas do micélio e fracionadas por eletroforese bidimensional (2DE). Os spots proteicos foram selecionados e identificados por espectrometria de massas MALDI- TOF/TOF-MS/MS. As proteínas secretadas foram avaliadas quanto às suas atividades enzimáticas utilizando substratos adequados para: peptidase, lipase, amilase, ?-glicosidase, CMCase, FPase, invertase, pectinase, xilanase e lacase. As proteínas presentes nos secretomas de Fusarium oxysporum URM 7401, cultivado em bioprocesso submerso com caseína e farinha de pena, e de Myceliophthora thermophila, cultivado em bioprocesso sólido com resíduos agroindustriais, foram identificadas por espectrometria de massas LC-ESI-MS/MS e também avaliadas quanto ao potencial de sacarificação de resíduos agroindustriais (farelo de trigo, palha de arroz e palha de soja). As proteínas selecionadas e identificadas, das diferentes condições de cultivo com Fusarium oxysporum URM 7401, em conjunto com os dados de produção enzimática demonstram a influência dos parâmetros dos bioprocessos no metabolismo de compostos, crescimento celular, síntese de nutrientes, estresse oxidativo, entre outros. Além do destaque na produção de enzimas, os extratos dos cultivos com caseína e farinha de pena foram capazes de degradar resíduos agroindustriais. A capacidade lignocelulolítica, conjugada a indução da via das fosfopentoses, sugerem que Fusarium oxysporum URM 7401 também tem potencial para a realização de bioprocesso consolidado e, consequentemente, para a produção de bioetanol. As proteínas do secretoma de Myceliophthora thermophila, quantificadas em ensaios enzimático e identificadas por espectrometria de massas LC-ESI-MS/MS, reforçaram o potencial hidrolítico e oxidativo deste microrganismo, com destaque especial para o grande número de enzimas ativas sobre carboidratos (CAZy) e oxirredutases. A ação deste arsenal enzimático também foi confirmada nos ensaios de degradação com resíduos agroindustriais; e indicaram um elevado potencial para sacarificação de resíduos ii lignocelulósicos. A compreensão dos mecanismos de produção e/ou secreção de proteínas pode ser auxiliada pela proteômica. Estes mecanismos, complementados pela identificação de enzimas biotecnológicas, podem elucidar as rotas metabólicas desencadeadas pelo microrganismo; e também na elaboração de estratégias que propiciem resultados satisfatórios nos bioprocessos. / Filamentous fungi are very exploited due to biotechnological potential of their products, which enzymes play a prominent role. Although they have been using in several industrial segments, the enzymes belong to an expansion market, that looking for a better levels of production, novel enzymatic activities and other. Filamentous fungi have a refined mechanisms for response to exogenous alterations. Thus, the proteomic studies have been become an excellent tool to explore proteins, which are produced in response to environmental changes, such as pH, nitrogen and carbon sources, temperature and kind of bioprocesses. A protein group that can be influenced by these variations is biotechnological enzymes. In this work, the profiles of intracellular proteins and/or of secreted enzymes were identified in the bioprocesses with Fusarium oxysporum URM 7401 and Myceliophthora thermophila, submitted to different culture conditions. The intracellular proteins from Fusarium oxysporum URM 7401, cultured in submerged bioprocess with various pH values or nitrogen sources, were extracted from mycelium and fractionated by bidimentional electrophoresis (2DE). The spots were selected and identified by MALDI-TOF/TOF-MS/MS mass spectrometry. The secreted proteins were evaluated, for their enzyme activities, using suitable substrates for peptidase, lipase, amylase, ?-glucosidase, CMCase, FPase, invertase, pectinase, xylanase and laccase. The proteins in secretomes from Fusarium oxysporum URM 7401, cultured in submerged bioprocess with casein and feather meal, and from Myceliophthora thermophila, cultured in solid state bioprocess with agroindustrial residues, were identified by LC-ESI-MS/MS mass spectrometer and they were also evaluated for saccharification potential of the agroindustrial residues (wheat bran, rice straw and soybean straw). The selected and identified proteins from Fusarium oxysporum URM 7401, obtained from different culture conditions, in addition to the enzyme production showed that bioprocess parameters influence the metabolism of compounds, cell growth, synthesis of nutrient, oxidative stress, among other. Besides this prominence in enzymes production, the extracts with casein or feather meal were able to degrade agroindustrial residues. The lignocellulolytic ability, conjugated to induction of the phosphopentoses pathways, suggest that Fusarium oxysporum URM 7401 also has potential for performing consolidated bioprocess and, consequently, for bioethanol production. The secretome proteins from Myceliophthora thermophila, quantified in enzymatic assays and identified by mass spectrometer LC-ESI-MS/MS, reinforce the hydrolytic and oxidative potential from this microorganism, with special emphasis for a great number of carbohydrate-active enzymes (CAZy) and oxidoreductases. The action of this enzymatic arsenal was also confirmed by agroindustrial residue degradation assays; and indicated a high potential for lignocellulosic residue saccharifications. The understanding about protein production and/or secretion mechanisms can be supported by proteomics. These mechanisms, complemented by the identification of biotechnological enzymes, can elucidate the metabolic pathways triggered by the microorganism; and can help to design better performing bioprocesses

As hidrolases de glicosídeos (GHs) exercem papéis fundamentais em vários processos biomédicos e aplicações industriais. A maioria destas enzimas possui vários domínios funcionais ligados entre si por peptídeos conhecidos como linkers. Informações sobre organização estrutural destas enzimas e sua mobilidade, posições e orientações mútuas de domínios individuais, bem como mudanças conformacionais introduzidas por ligantes ou por mudanças de condições bioquímicas (pH e T) podem ser muito informativas. Por esse motivo, é muito importante determinar a organização estrutural de GHs em termos de posição e orientação de seus domínios individuais e compreender a interação entre estes domínios em condições próximas às fisiológicas. Entretanto, atualmente, a conformação, dinâmica e função dos GHs com múltiplos domínios ainda não são totalmente compreendidas. Assim, o principal objetivo deste projeto foi conduzir estudos de hidrolases de glicosídeos em solução, usando SAS. Um grande número de GHs foi clonado e expresso em laboratório sob a direção do Prof. Dr. Igor Polikarpov (Grupo de Biotecnologia Molecular, IFSC / USP), seguindo protocolos já estabelecidos na literatura, para sua expressão e purificação. Experimentos SAXS foram realizados em colaboração com o Dr. Evandro Ares de Araújo (USP, São Carlos) e com o Prof. Dr. Mário de Oliveira Neto (UNESP, Botucatu). Para estudar as hidrolases de glicosídeos, foi utilizado o método de espalhamento a baixo ângulo, e em adição ao trabalho experimental, foi desenvolvido um novo pacote de software SAXSMoW2 para processar os dados do SAXS. Este pacote permite obter rapidamente os principais parâmetros estruturais de moléculas de proteínas, calcular o peso molecular e o estado oligomérico. Também foi aperfeiçoado e aplicado o método de acoplamento estatístico (statistical coupling analysis) , para complementar os dados estruturais experimentais, em especial para xiloses isomerases. Este método pode permitir uma melhor compreensão da relação entre as características estruturais evolutivas e sua funcionalidade biológica. Além disso, métodos de bioinformática foram desenvolvidos para complementar e compreender melhor as informações estruturais obtidas nos experimentos de SAXS. O primeiro foi um método para separar sequências de GH7 em duas categorias, exo e endogluconases. É útil analisar cada tipo de proteína dentro da família separadamente e estudar o papel dos loops funcionais - características estruturais que influenciam significativamente a atividade biológica. Outro método foi desenvolvido para encontrar o centro de atividade na nova enzima Xilose Isomerase obtida, usando uma estrutura relacionada, bem conhecida, da mesma família. Este método foi aplicado a enzimas cujas estruturas foram estudadas pela técnica de cristalografia em nosso laboratório no IFSC / USP. Inspirado pelo SCA, um método de detecção de comunidades difusas de aminoácidos em proteínas foi desenvolvido. Essa informação também pode complementar os resultados do SCA, indicando conjuntos fortemente correlacionados de aminoácidos na enzima. Outro novo método desenvolvido é uma estimativa de afinidade nas famílias de enzimas ativas em carboidratos utilizando similaridade dos modelos escondidos de Markov e bancos de dados open access de sequências de proteínas. / The Glycoside Hydrolases (GHs) play a key role in a number of biomedical processes and industrial applications. Most of these enzymes are multidomain proteins composed of different functional domains connected by linker peptides. Thus, it is very important to determine structural organization of glycoside hydrolases in terms of positions and orientations of their individual domains and comprehend the interplay between their multiple domains under close-to physiological conditions. To study the glycoside hydrolases, in this work a small-angle scattering method has been used. Currently, the conformation, dynamics and function of GHs with multiple domains are not fully understood. This is why the information on their structural organization and mobility; mutual position and orientation of the individual domains and conformational changes induced by interaction with the substrates or difference in biochemical conditions might be very informative. A large number of GHs have been cloned and expressed in the lab under direction of Prof. Dr. Igor Polikarpov (Molecular Biotechnology group, IFSC/USP) and we follow already established protocols for their expression and purification. SAXS experiments have been carried out in collaboration with Dr. Evandro Ares de Araujo (USP, São Carlos) and Prof. Dr. Mario de Oliveira Neto (UNESP, Botucatu). Additionally to experimental work, a new software package SAXSMoW2 for SAXS data processing has been developed. The software allows to obtain rapidly main structural parameters of the protein molecule, calculate molecular weight and oligomeric state. To supplement an structural data, the method of statistical coupling analysis (SCA) has been significantly improved and applied. The method allows a better understanding of interconnection between evolutionary caused structural features and their biological functionality. Also, various bioinformatic methods were developed to complete and understand better structural information obtained in SAXS experiments. The first one is a method for separating sequences from GH7 into the two bins of exo- and endogluconases. It is helpful to analyze each type of proteins inside the family separately and study the role of functional loops -- structural features that significantly influence on biological activity. Other developed method is for finding of activity center in the new obtained Xylose Isomerase enzyme using related well-known structure from the same family. This method was applied to the enzyme whose structure was studied using crystallography technique in our laboratory at IFSC/USP. Inspired by SCA, a method of aminoacid fuzzy communities detection in proteins has been developed as well. This information also can complete SCA results showing strong correlated sets of aminoacids in the enzyme. Another one new developed method is an estimation of carbohydrate-active family affiliation of unknown proteins using Markov hidden model similarities and open access databanks of protein sequences.

by Wong Ping Shing. / Thesis (M.Phil.)--Chinese University of Hong Kong, 1995. / Includes bibliographical references (leaves 97-112). / ACKNOWLEDGMENTS --- p.i / ABSTRACT --- p.ii / ABBREVIATIONS --- p.viii / Chapter 1. --- INTRODUCTION --- p.1 / Chapter 1.1 --- General properties of zinc / Chapter 1.1.1 --- Biochemistry of zinc --- p.2 / Chapter 1.1.2 --- Distribution of zinc in body --- p.3 / Chapter 1.1.3 --- Roles of zinc in protein function --- p.4 / Chapter 1.2 --- Zinc and zinc-binding proteins in brain / Chapter 1.2.1 --- Distribution of zinc in brain --- p.7 / Chapter 1.2.2 --- Metabolism of zinc in brain --- p.9 / Chapter 1.2.3 --- Compartments of zinc in brain --- p.10 / Chapter 1.2.4 --- Zinc-binding proteins in brain --- p.12 / Chapter 1.3 --- Pathological conditions of brain in relation to zinc --- p.15 / Chapter 1.4 --- Aim of the project --- p.20 / Chapter 2. --- MATERIALS AND METHODS --- p.22 / Chapter 2.1 --- Detection of zinc-binding proteins / Chapter 2.1.1 --- Sodium-Dodecyl Sulphate Polyacrylamide Gel Electrophoresis (SDS-PAGE) --- p.22 / Chapter 2.1.2 --- Electroblotting --- p.24 / Chapter 2.1.3 --- Radioactive zinc blotting --- p.25 / Chapter 2.1.4 --- Autoradiography --- p.25 / Chapter 2.2 --- Subcellular fractionation of porcine brain --- p.26 / Chapter 2.3 --- Purification and structural characterization of a 19 kDa zinc-binding protein / Chapter 2.3.1 --- Purification of a 19 kDa protein --- p.27 / Chapter 2.3.2 --- Sequencing of N-terminal blocked 19 kDa protein --- p.30 / Chapter 2.4 --- Characterization of the binding and biological properties of the 19 kDa zinc-binding protein / Chapter 2.4.1 --- Effect of divalent metal ions on zinc binding to the 19 kDa protein --- p.33 / Chapter 2.4.2 --- Effect of pH on the dissociation of radioactive zinc from the19 kDa protein --- p.34 / Chapter 2.4.3 --- Radioactive calcium blotting --- p.34 / Chapter 2.4.4 --- Interaction of radioactive zinc and radioactive calcium binding to the 19 kDa protein --- p.35 / Chapter 2.4.5 --- Calmodulin activity assay --- p.35 / Chapter 3. --- RESULTS / Chapter 3.1 --- Specificity of radioactive zinc-blot on zinc-binding protein detection --- p.38 / Chapter 3.2 --- Zinc-binding proteins in porcine brain --- p.38 / Chapter 3.3 --- Purification and identification of a cytosolic 19 kDa zinc- binding protein in porcine brain / Chapter 3.3.1 --- Zinc-dependent hydrophobic interaction chromatography --- p.44 / Chapter 3.3.2 --- N-terminal amino acid sequencing --- p.51 / Chapter 3.3.3 --- High pH native gel electrophoresis of 19 kDa protein --- p.51 / Chapter 3.4 --- The zinc and calcium binding properties of the 19 kDa protein / Chapter 3.4.1 --- Effect of pre-exposure to divalent cations on zinc binding --- p.54 / Chapter 3.4.2 --- Competition by divalent cations for zinc binding --- p.56 / Chapter 3.4.3 --- pH dependency of zinc dissociation --- p.56 / Chapter 3.4.4 --- Effect of zinc on radioactive calcium binding --- p.61 / Chapter 3.5 --- The biological activity of the 19 kDa protein / Chapter 3.5.1 --- Effect of the 19 kDa protein on the activity of calmodulin- dependent phosphodiesterase --- p.66 / Chapter 3.5.2 --- Effect of zinc on calmodulin-dependent phosphodiesterase activity --- p.69 / Chapter 3.5.4 --- "Effect of zinc on calcium-deficient, calmodulin-dependent phosphodiesterase activity" --- p.72 / Chapter 4. --- DISCUSSION / Chapter 4.1 --- Detection and Purification of zinc-binding proteins / Chapter 4.1.1 --- Strategy for the detection of zinc-binding proteins --- p.77 / Chapter 4.1.2 --- Purification of zinc-binding protein --- p.79 / Chapter 4.2 --- Amino acid sequencing of the 19 kDa protein --- p.82 / Chapter 4.3 --- Binding properties of the 19 kDa zinc-binding protein --- p.86 / Chapter 4.4 --- Effect of zinc and 19 kDa zinc-binding protein on calmodulin dependent phosphodiesterase --- p.92 / Chapter 4.5 --- Effect of zinc on the properties of calmodulin --- p.90 / Chapter 4.6 --- Significance of the ability of zinc to affect calmodulin activity --- p.94 / Chapter 5. --- CONCLUSION --- p.95 / Chapter 6. --- REFERENCES --- p.97