The papain-like cysteine protease family (C1 proteases) is highly important because of its involvement in research and industrial applications and its role in various human diseases. Protein inhibitors are an important aspect of C1 protease biology and are relevant to its clinical, industrial and research importance. To study the interaction between the proteases and the inhibitors it is very useful to have accurate structural models of the protease-inhibitor complexes. To this end, a high-throughput pipeline for modelling complexes of papain-like cysteine proteases and protein inhibitors was implemented and tested (Tastan Bishop & Kroon, 2011). The pipeline utilizes a novel technique for obtaining modelling templates by using superpositioning to combine coordinates from separate experimental structures. To test the pipeline, models of complexes with known structures (test set) were modelled using many different templates and the resultant models evaluated to compare the quality of the different templates. It was found that use of the new technique to obtain templates did not introduce significant errors, while allowing closer homologs to be used for modelling - leading to more accurate models. The test set models were also used to evaluate certain steps of the modelling protocol. The effect of Rosetta energy minimization on model accuracy and the use of Rosetta energy and DOPE Z-score values to identify accurate models were investigated. Several complexes were then modelled using the best available templates according to criteria informed by the previous results. A website was built that allows a user to download any of the metrics or models produced in the study. This website is accessible at http://rubi.ru.ac.za/cpmdb

A aprotinina, um inibidor de serinoproteinase ácido resistente de massa molar de 7 kDa, é utilizada como insumo ou medicamento. O objetivo principal deste trabalho foi purificar a aprotinina a partir de pulmão suíno. Três procedimentos foram utilizados. O primeiro procedimento utilizou a coluna de tripsina-agarose, o segundo procedimento utilizou a filtração tangencial e coluna de tripsina-Sepharose. O terceiro procedimento utilizou três cromatografias: filtração em gel, troca-iônica e afinidade (tripsina-agarose). A aprotinina suína foi purificada de pulmão utilizando o terceiro procedimento. A seqüência parcial do gene da aprotinina suína apresentou 74% de identidade com a seqüência do gene da aprotinina bovina. Outros dois inibidores de serinoproteinases ácido resistentes foram purificados, são eles: o fragmento ativo do segundo domínio do inibidor de leucoprotease secretada (SLPI), e um segundo inibidor de alta massa molecular, provavelmente bikunina. O protocolo de purificação utilizado neste trabalho recuperou 85mg de aprotinina suína por kg de pulmão. / Aprotinin, an acid stable serine proteinase inhibitor with a molecular mass of 7 kDa, is used as a reagent or drug. The purification of the aprotinin from porcine lungs was the main objective of this work. Three procedures were used. The first one utilized the trypsin-agarose column. The tangential ultra filtration and trypsin-Sepharose column were used in the second procedure. And finally, the gel filtration, ion-exchange and affinity chromatography were employed in the third procedure. The porcine lung aprotinin was purified using the third procedure. The partial sequence of the aprotinin gene was obtained and showed 74% of the identity with the aprotinin bovine gene sequence. Another two acid stable serine proteinase inhibitors were purified: the active fragment of the secretory leukoprotease inhibitor second domain, and one high molecular mass inhibitor, probably bikunina. The purification protocol used in this work recovered 85mg of the porcine aprotinin from kg of lung.

published_or_final_version / Surgery / Master / Master of Philosophy

published_or_final_version / Chemistry / Doctoral / Doctor of Philosophy

A partial cystatin cDNA from rainbow trout was generated by reverse transcription polymerase chain reaction with two degenerate primers. The partial cystatin PCR product was 168 bp and used to screen trout liver λgt 11 cDNA library. Four positive clones were isolated and designated as cstl, cst2, cst3 and cst4. Only cst2 contained the full-length cystatin cDNA which was 674 bp and included 5' untranslated region and the polyadenylation signal sequence AATAAA in the 3' region. Translation of the cDNA contains 132 amino acid residues. Comparison of the amino acid sequence with those of family II cystatin indicated that the 21 amino acids at N-terminal end is a signal peptide that leads to cystatin secretion, and the 111 amino acids are mature cystatin. Four cysteine residues in the cystatin may form two disulfide bonds for the secondary structure. Cst2 was subcloned into pGEM-3z for Northern and Southern blot experiments. Northern blot indicated that trout cystatin mRNA is about 750 bp. Cystatin is expressed in all tissues examined but at various levels. This difference may reflect the regulation of cysteine proteinase activities. Southern blot of trout genomic DNA showed that the copy number of the trout cystatin gene is probably one per haploid genome. / Graduation date: 1997

African animal trypanosomosis or nagana is a disease in livestock caused by various species of protozoan parasites belonging to the genus Trypanosoma particularly T. congolense, T. vivax and T. b. brucei. Nagana is the most important constraint to livestock and mixed crop-livestock farming in tropical Africa. Trypanosomes undergo part of their developmental life in their insect vector, the tsetse fly and part in their mammalian host. Measures for eradicating the continent of the tsetse fly vector include insecticidal spraying, targeting and trapping. Vaccine development has been hampered by the generation of an inexhaustible collection of variant surface glycoproteins that trypanosomes possess and allow for evasion of the host immune system. Anti-disease vaccines aimed at reducing the symptoms of the disease rather than killing the parasite itself have been demonstrated as an alternative approach. Trypanotolerant cattle are able to protect themselves from the disease-associated symptoms. They are able to mount a better antibody response to the CATL-like cysteine peptidase, TcoCATL, compared to trypanosusceptible breeds. Bovine trypanosomosis, however, continues to be controlled primarily by trypanocidal compounds such as isometamidium chloride, homidium and diaminazene that have been developed more than 50 years ago and consequently drug resistance is widespread. Trypanosomal cysteine peptidases have also been proven to be effective targets for chemotherapeutics. TcrCATL, inhibited by the vinyl sulfone pseudopeptide inhibitor K11777, was effective in curing or alleviating T. cruzi infection in preclinical proof-of-concept studies and has now entered formal preclinical drug development investigation. Understanding enzymatic as well as structural characteristics of pathogenic peptidases is the first step towards successful control of the disease. To date no such characterisation of the major cysteine peptidases from T. vivax has been conducted. Although the major cysteine peptidase from T. vivax, TviCATL, has not been proven as a pathogenic factor yet, its high sequence identity with the pathogenic counterparts such as TcrCATL and TcoCATL hold much speculation for TviCATLs role in pathogenocity. In the present study, native TviCATL was isolated from T. vivax Y486, purified and characterised. TviCATL showed to have a general sensitivity to E-64 and cystatin and has a substrate specificity defined by the S2 pocket. TviCATL exhibited no activity towards the CATB-like substrate, Z-Arg-Arg-AMC but was able to hydrolyse Z-Phe-Arg-AMC, the CATL-like substrate. Leu was preferred in the P2 position and basic and non-bulky hydrophobic residues were accepted in the P1 and P3 positions respectively. Similar findings were reported for TcoCATL. The substrate specificity of TviCATL and TcoCATL does argue for a more restricted specificity compared to TcrCATL. This was based on the Glu333 in TcrCATL substituted with Leu333 in TviCATL and TcoCATL. In the case of TcrCATL, the Glu333 allows for the accommodation of Arg in the P2 position. Like other trypanosomal cysteine peptidases, TviCATL was inhibited by both chloromethyl ketones, Z-Gly-Leu-Phe-CMK and H-D-Val-Phe-Lys-CMK. Determining further structural and functional characteristics as well as whether TviCATL, like the T. congolense homolog, TcoCATL, acts as a pathogenic factor, would be important information to the designing of specific chemotherapeutic agents. To date, TcrCATL and TbrCATL (from T. b. rhodesiense) are the only trypanosomal CATL-like cysteine peptidases been crystallised and their tructures solved. This advantage has allowed for the directed design of synthetic peptidase inhibitors. The crystal structure of TcoCATL will be of major significance to the design of specific chemotherapeutic agents. Furtherrmore, understanding the dimeric conformation of TcoCATL is important for vaccine design as immune responses are likely to recognise the dimer specific epitopes. In the current study, the catalytic domain of TcoCATL and TviCATL, were recombinantly expressed in Pichia pastoris and purified to homogeneity. The T. congolense cysteine peptidase pyroglutamyl peptidase (PGP), also proven to be pathogenic in T. b. brucei, was recombinantly expressed in E. coli BL21 (DE3) cells and also purified to homogeneity. Purified cysteine peptidases along with previously purified TcoCATL dimerisation mutants, TcoCATL (H43W) and TcoCATL (K39F; E44P), possessing mutated residues involved in TcoCATL dimerisation, as well as the mutant proenzyme TcoCATL (C25A), were screened for crystallisation conditions using the Rigaku robotic crystallisation suite. One-dimensional needle-like crystals were found for TcoCATL (K39F; E44P). Optimisation of the TcoCATL (K39F; E44P) crystals were analysed for X-ray diffraction. The poor diffraction pattern prompted further optimisations for better crystal quality, which is presently underway. The crystal structure of TcoCATL, with some of the residues involved in dimerisation mutated, will be pivotal in understanding the dimerisation model. Furthermore, the information about the structure will be valuable for vaccine design and chemotherapeutics development. / Thesis (M.Sc.)-University of KwaZulu-Natal, Pietermaritzburg, 2011.

O objetivo deste trabalho foi estudar in vivo e in vitro a ação de inibidores de proteinase (IPs) de soja sobre o desenvolvimento e atividade das proteinases intestinais de lagartas da broca-da-cana (Diatraea saccharalis) (Fabr., 1794). Foram identificadas e caracterizadas as principais enzimas digestivas de (Diatraea saccharalis). As propriedades antimetabólicas dos IPs de soja, do tipo Kunitz e Bowman-Birk, foram determinadas in vivo e in vitro, antes e após a incorporação em dieta artificial, com avaliação do potencial de crescimento de populações da broca da cana. Baseando-se na hidrólise de substratos sintéticos específicos, dois picos de atividade tríptica (pH 8,0 e 9,0) e a presença de um pico de atividade quimotríptica (pH 9,0) foram observados em lagartas de último ínstar. Conforme observado em outros lepidópteros, D. saccharalis apresentou pH ótimo alcalino para estas proteinases. A inibição da atividade da tripsina e da quimotripsina in vitro pelos IPs de soja sugeriu que ambos, Kunitz e Bowman-Birk, poderiam ter um efeito antimetabólico quando ingeridos pela lagarta. A incorporação dos IPs de soja, parcialmente purificados em dieta artificial de lagartas recém-eclodidas na concentração de 0,5% (p/p), reduziu significativamente o crescimento e desenvolvimento da broca refletindo no aumento do número e duração dos ínstares, além da redução do peso larval e do alongamento das fases larval e pupal. No entanto, a ingestão dos IPs não influenciou a sobrevivência nem a segunda geração das lagartas mantidas em dieta artificial contendo estes inibidores. Além disso, houve um aumento na atividade tríptica e redução da porcentagem de inibição das mesmas pelos IPs, in vitro. Foi observado também que o valor nutricional da dieta afeta a resposta do inseto ao inibidor. Por meio de estudos de tabela de vida de fertilidade, menores valores da taxa líquida de reprodução (Ro), capacidade inata de aumentarem número (Rm), ) razão finita de aumento (λ), maiores durações de média de uma geração (T) e tempo para a população duplicar (Dt) foram obtidas para adultos provenientes de dieta contendo os IPs. As diferenças observadas refletem na redução do crescimento da população, indicando um alto potencial dos IPs na proteção de plantas de cana-de-açúcar contra os danos provocados pela broca da cana / The objective of the present study was to evaluated, in vivo and in vitro, the action of soybean proteinase inhibitor (SPI) on the development and midgut proteinase activities of the sugarcane borer (Diatraea saccharalis) (Fabr., 1794). The major proteinase activities of D. saccharalis were characterized. The antímetabolic properties of the SPI, Kunitz and Bowman-Birk in vitro, before and after incorporation into artificial diet, in vivo, and its interference on population increase potential of the pest have been evaluated. Based on hydrolysis of the synthetic substrates, two major trypsin activities were identified (pH 8.0 and 9.0) and also a chymotrypsin activity with an optimum pH at 9.0. D. saccharalis trypsin and chymotrypsin display aIkaline pH optima, as observed to most Lepidoptera insects. The inhibition of trypsin and chymotrypsin activities in vitro,by SPI suggested that either, Kunitz and Bowman-Birk, could have a potential antimetabolic effect when ingested by these insect larvae. The incorporation of semi-purified extract SPI into an artificial diet of neonate larvae at 0.5% (w/w), significantly reduced the growth and development of the insect, reflecting an increase of the instar number and duration, and a significantly lower average weight. However, ingestion of SPI did not influence larval survival and the second generation of larvae fed SPI diet. In addition, there was an increase of the leveI of tryptic activity and a decrease of inhibition by the SPI in vitro. It was also observed that the diet nutrition value affect the insect susceptibility to the inhibitor. Studies on the fertility life table showed that lower net reproduction rates ((Ro), instantaneous rate of increase (Rm), and finite ratio of increase (λ), and the higher mean generation time (T) and the doubling time (Dt) were obtained from adults reared on diet supplemented with SPI. The observed differences potentially translate into large differences in population growth, indicating a potential value of SPI for protecting sugarcane plants against damage by D. saccharalis

As plantas sintetizam inibidores de proteinases (IPs) como um dos mecanismos de defesa contra o ataque de insetos-praga. Esses inibidores atuam ligando-se às proteinases digestivas localizadas no aparelho digestivo dos insetos fitófagos, impedindo sua atividade proteolítica. Como conseqüência, ocorre uma redução da disponibilidade de aminoácidos levando a um quadro de deficiência nutricional. Portanto, os IPs são considerados agentes anti-metabólicos. Heliothis virescens (Fabr.,1781) é um inseto-praga de polifagia acentuada, atacando várias culturas de importância econômica. Na tentativa de estudar os efeitos de IPs produzidos pelo fumo e de plantas transgênicas de fumo expressando um IP de batata sobre o desenvolvimento da lagarta desta espécie, foram realizados ensaios biológicos nos quais lagartas foram criadas em dieta artificial (sem inibidor), em plantas de fumo transgênicas (expressando o IP do tipo 2 de batata conhecido como PIN2) e em plantas fumo normais (controle). Os ensaios biológicos mostraram que as lagartas de H. virescens apresentaram crescimento e desenvolvimento normais quando em presença do PIN2. A fim de estudar a adaptação das lagartas à presença dos IPs, foram realizados ensaios bioquímicas envolvendo a caracterização das proteinases intestinais das lagartas. A combinação de técnicas de separação de proteínas pelo peso molecular via eletroforese em gradiente de poliacrilamida (SDS-PAGE) e estudos cinéticos, mostraram a expressão de quatro enzimas do tipo das tripsinas (TI- T4) nos homogeneizados do tubo digestivo de lagartas alimentadas com plantas de fumo (transgênicas ou não) com as seguintes propriedades: T1 (Km= 0,27 mM, PM= 70 kDa),T2 (Km= 0,35 mM, PM= 67 kDa), T3 (Km= 2,4 mM, PM= 29 kDa), T4 (Km= 15 mM, PM= 17 kDa). No entanto, lagartas alimentadas em dieta sem inibidor apresentaram apenas uma tripsina majoritária (Km= 2,9 mM, PM= 29 kDa), o que está de acordo com o peso molecular das tripsinas normalmente encontradas nas lagartas de lepidópteros. Além das tripsinas, foram detectadas uma quimotripsina (26 kDa) para os três tratamentos e uma elastase (35 kDa) para os homogeneizados de lagartas alimentadas à base de folhas. Eletroforese nativa em diferentes concentrações de géis de poliacrilamida mostrou que T1 e T2 ocorreram em lagartas alimentadas com folhas (selvagens ou transgênicas), ao passo que a filtração em gel, na presença ou ausência de SDS, revelou ainda que T3 e T4 podem originar TI e T2. Estes resultados sugerem que a presença de IPs nas folhas de fumo permite a expressão de novas moléculas de tripsina com uma superfície hidrofóbica, a qual favorece a formação de oligômeros. Acredita-se que os oligômeros sejam menos afetados pelos IPs por que se ligam melhor ao substrato diminuindo a afinidade dos IPs, ou ainda por hidrolisá-los. O Papel da elastase na adaptação é incerto / not available

More than half of the recognized genera of positive strand RNA viruses employ polyprotein processing as one of the strategies for their genome expression. Normally, this processing is mediated by virus-encoded proteinases that belong to the trypsin-like or papain-like family. In particular, papain-like, leader proteinases were found in diverse families of human, animal, plant, and fungal positive strand RNA viruses. In addition to autocatalytic processing, these proteinases play a variety of roles in the virus life cycle. In plant potyviruses, a papain-like helper component-proteinase (HC-Pro) was implicated in genome amplification, cell-to-cell movement, long distance transport, and suppression of host defense. The p29 proteinase encoded by a fungal hypovirus CHV1 was found to be dispensable for virus replication, but it was identified as a major determinant of viral pathogenicity. In an animal equine aterivirus (EAV), a papain-like proteinase nspl was demonstrated to possess a putative zinc finger domain, which functions in subgenomic RNA synthesis, although it is not essential for virus replication. The Lab proteinase of the foot and mouse disease virus (FMDV) is involved in inhibition of cellular mRNA translation and in virus spread in infected animals. In general, it appears that functional plasticity of the papain-like leader proteinases played an important role in the evolution of viral diversity. Here, we examined the functions of a papain-like leader proteinase (L-Pro) in the life cycle of the beet yellows closterovirus (BYV). It was found that L-Pro is required for autoproteolytic processing, genome amplification, virus invasiveness and cell-to-cell movement for BYV. The gene swapping experiments involving several closterviruses, a potyvirus, as well as CHV1, FMDV, and EAV revealed complex functional profiles of the papain-like leader proteinases. The possible mechanisms that underlie L-Pro functions are discussed. / Graduation date: 2002

Thesis (Ph. D.)--University of Hong Kong, 2009. / Includes bibliographical references (leaves 165-168). Also available online.