Cyclic peptides constitute an attractive class of compounds for drug development, however the numerous problems associated with their synthesis have limited their applicability. The cyclisation step itself is particularly problematic, with solution phase cyclisations being required to be conducted under very high dilution to promote cyclisation over unwanted side reactions such as oligomerisation. In addition, epimerisation, leading to the loss of chiral integrity at the terminal residues is a major concern. Attention is now turning to biochemical cyclisation strategies, such as SICLOPPS and sortase mediated ligation, although these also come with their own inherent disadvantages, for example, in the case of sortase mediated ligation, there is significant “scarring” of the target due to the presence of a four amino acid long recognition sequence. Cyclisation using ribosomally synthesised post translationally modified enzymes is also gaining popularity. One such family of enzymes is the patellamides. PatGmac is capable of performing cyclisations on linear peptide substrates with minimal scarring compared to the aforementioned alternatives and, importantly, with no epimerisation and could constitute a greener and more facile route to cyclic peptides. The work herein details some of the investigations designed to define the range of synthetic utility and test the flexibility of the enzymes. This was done qualitatively, by designing a variety of linear peptide analogues of the natural product, homophymine A, featuring unique structural moieties and evaluating their compatibility with the enzyme. It was also done quantitatively, using an LCMS based semi-quantitative strategy, to assess differences between similar, but different, enzymes and to assess whether there were differences in how different substrates are processed by the same enzyme. In addition to this, a variety of these substrates were also assessed for their proclivity to cyclise under standard chemical conditions for comparison. Lastly, with the increasing appearance cyclic peptides and non-peptidic macrocycles in the libraries of compounds being considered for clinical trials, there is now a growing need for computational modelling of these structures. Herein, a 3D v structure for the natural product callipetin N is proposed for the first time, determined using a combination of computational and NMR techniques.

Mes travaux de thèse ont été réalisés dans le cadre du projet Européen METAEXPLORE, visant à découvrir de nouvelles enzymes d’intérêt industriel à partir des communautés microbiennes environnementales via les approches dites de « métagénomique ». Je me suis personnellement focalisé sur la recherche de chitinases dans les communautés bactériennes du sol, en particulier celui de la station expérimentale de Rothamsted (Royaume-Uni). Des approches de séquençage en 454 ont été réalisées afin de caractériser les bactéries dégradant la chitine au travers d’une stratégie d’enrichissement du sol en microcosme. J’ai également pu réaliser des criblages génétiques de banque de clones fosmidiques afin d’identifier des gènes d’intérêt potentiel. J’ai également été impliqué dans le développement d’un nouvel outil biotechnologique appelé « Genefish », dont le but est la capture de séquences d’ADN environnementales d’intérêt sur un plasmide à l’aide d’une souche E. coli ultra-recombinogène. Mes travaux seront présentés sous la forme de trois chapitres, reprenant successivement :- Chapitre 1 : Une synthèse bibliographique du contexte scientifique- Chapitre 2 : La recherche de nouvelles chitinases via des approches métagénomiques- Chapitre 3 : Le développement et l’utilisation de l’outil « Genefish / I realized my PhD in the frame of the European project METAEXPLORE, which aims to discover new enzymes of industrial interest from the environmental microbial communities through the metagenomic approaches. I was personally focused on finding new chitinases within the soil bacterial communities, with a particular emphasis on the Park Grass soil from Rothamsted research station (U.K). Pyrosequencing approaches were applied in order to characterize chitin degrading bacteria through a soil enrichment strategy in microcosm. I was also involved in genetic screening of fosmid clone library for identifying potential genes of interest. Furthermore, I participated to the development of a new biotechnological tool called “Genefish”, which aims to capture environmental DNA sequence of interest into a plasmid thanks an hyper-recombineering E. coli strain. My PhD work will be presented in 3 chapters:- Chapter 1: A literature review of the scientific context- Chapter 2: The search for new chitinases through metagenomic approaches- Chapter 3: The development and the use of the “Genefish” tool

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Pollen grains are ubiquitous triggers of allergic asthma and seasonal rhinitis. Proteolytic enzymes in pollen as well as other sources are capable of disrupting airway epithelial integrity in vivo and in vitro. This provides a plausible mechanism for the initiation of sensitisation of the respiratory immune system to inhaled pollen allergens, comparable to that suggested for Group 1 allergens from house dust mites and cat dander, which are known to possess intrinsic proteolytic activity. This thesis explores the relationship between pollen allergens and proteolytic enzymes. It describes the different strategies used for the characterisation, purification and identification of immunogenic and proteolytic proteins in the complex mixtures of pollen diffusates. The peptidases in the diffusates of Kentucky blue grass, ryegrass and Bermuda grass pollens were characterised by a sensitive fluorescence assay and gelatin zymography. Among these, Bermuda grass pollen demonstrated the presence of a serine peptidase at Mr ~30,000 Da, which corresponded to an intense band by Western blotting using a monoclonal antibody to the timothy grass (Phleum pratense) group 1 allergen, Phl p 1. Purification of this enzyme from Bermuda grass was complicated by the low levels of the enzyme present in the diffusate, as well as by its autohydrolysis. Partial purification of the serine peptidase activity by affinity chromatography using Concanavalin A Sepharose demonstrated that the diffusate contained a trypsin-like peptidase, detected by the fluorescent assay, in addition to the ~30,000 Da serine endopeptidase, detected on gelatin zymography. Proteomic analysis of the ~30,000 Da protein using one- and two-dimensional electrophoresis and mass spectrometry identified it as the major pollen allergen of Bermuda grass, Cyn d 1. The studies reported here provide, for the first time, evidence that a pollen allergen may possess intrinsic proteolytic activity. This activity may play a role in the initiation of airway inflammation and allergic sensitisation.

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Bibliography: leaves 133-157. / xiii, 157, [22] leaves, [31] leaves of plates : ill. (some col.) ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / The principle aim of the work described in this thesis was to use protein engineering to increase the thermostability of barley (1->3,1->4)-B-glucanases / Thesis (Ph.D.)--University of Adelaide, Dept. of Plant Science, 2000