Heparan sulfate (HS) is a cell-surface sulfated polysaccharide that binds to multiple proteins and has been implicated in cancer, viral infection and Alzheimer's disease. Due to the heterogeneity of HS, the structural requirements for protein binding are ill- defined. Chemical synthesis of structurally-defined HS oligosaccharides, which are tunable in terms of length, order of monosaccharides and sulfation pattern, is required for the investigation of HS-protein binding. Single molecule methods have been utilised in biophysics to study dynamic processes and can allow observation of rare events which would be 'averaged out' in ensemble measurements. Access to fluorescently labelled HS oligosaccharides should allow investigation of interactions with proteins at the single molecule level using methods such as single molecule FRET, providing a method complementary to NMR studies (ensemble) and X-ray crystallography (non-dynamic).This thesis presents the development of a method for the fluorescent labelling of a chemically synthesised HS disaccharide utilising a reducing-end amine tag. Analysis of the fluorescence properties of the labelled disaccharide at ensemble and single molecule level indicated no perturbation of the fluorophore when attached to the sugar. Fluorescence correlation spectroscopy measurements of the fluorescent HS disaccharide with the protein FGF-1 showed no binding, which is attributed to the low concentration (1 nM) of disaccharide required in the experiment. Additional work is presented in this thesis on the development of a method for atom-specific 13C labelling of HS oligosaccharides, which has been initiated by synthesis of a 13C labelled L-iduronate monosaccharide and a 13C labelled disaccharide. New strategies for the synthesis of HS oligosaccharides based on orthogonal thioglycoside-based glycosylations employing S-benzoxazolyl and S-thiazolyl donors have been investigated. Development of a chemoselective glycosylation strategy for HS oligosaccharide synthesis utilising a 'super-disarmed' [2.2.2] L-iduronic lactone is presented.

Oligosaccharides are important biomolecules that are targets and also components of many medical treatments, including treatments for cancer, HIV, and inflammation. While the demand for medically-relevant oligosaccharides is increasing, these compounds have proven difficult to synthesize. Whole-cell oligosaccharide synthesis is a promising method that requires relatively inexpensive substrates and can complete the synthesis in just one step. However, whole-cell oligosaccharide synthesis employing common microorganisms like E. coli have been plagued by low yields. This dissertation investigates an alternative microorganism for oligosaccharide production: Agrobacterium sp. ATCC 31749. This Agrobacterium strain produces high levels of curdlan polysaccharide, demonstrating its natural ability to produce the sugar nucleotide precursor for oligosaccharide production. The two main objectives of this dissertation are 1) to develop biocatalysts for oligosaccharide synthesis by engineering ATCC 31749 and 2) to determine what factors affect poly- and oligosaccharide production in this Agrobacterium strain. ATCC 31749 was engineered to produce two oligosaccharides of medical importance: N-acetyllactosamine and galactose-α 1,3-lactose. Oligosaccharide production in the biocatalyst was further improved with additional metabolic engineering. Substrate uptake was increased through expression of a lactose permease, and availability of the sugar nucleotide substrate improved with gene knockout of the curdlan synthase gene. Both of these engineering efforts led to increased oligosaccharide synthesis in the Agrobacterium biocatalyst. Overall, the engineered Agrobacterium strains synthesized gram-scale quantities of the oligosaccharide products in just one step and requiring only a few inexpensive substrates and cofactors. Additional improvement of the oligosaccharide-producing biocatalysts required further investigation of the factors influencing poly- and oligosaccharide production in ATCC 31749. In this dissertation, several environmental and intracellular factors are identified that affect both oligosaccharide and curdlan production. Sucrose was the preferred carbon source for oligosaccharide synthesis, and the addition of citrate to the synthesis reaction led to significant improvement in oligosaccharide production. To identify the genetic factors and possible mechanisms regulating curdlan production, the genome of ATCC 31749 was sequenced. The genome sequence was utilized for transcriptome analysis of ATCC 31749. In the transcriptome analysis, genes significantly up- and down-regulated during curdlan production were identified. Subsequent gene knockout experiments showed several factors to be important for curdlan synthesis, namely the nitrogen signaling cascade, polyphosphate, and the GTP-derived second messengers (p)ppGpp and c-di-GMP. In addition to the development of biocatalysts for oligosaccharide production, this investigation provides insight into the complex mechanisms regulating exopolysaccharide synthesis.

Heparin glycosaminoglycans mediate a range of biological events, including anticoagulation as well as a diversity of cell proliferation and differentiation processes. Heparin saccharides have been shown to act as inhibitors against angiogenesis and metastasis of tumour cells. This thesis describes work developing chemistry towards varying length oligosaccharide sequences with potential to offer variable sulfation patterns. The main synthetic components to this work were contribution to developing scalable syntheses of an orthogonally protected L-Iduronic acid unit and a differentially protected D-glucosamine unit. The synthetic work also evaluated a recently reported diazo transfer reagent, which allowed for earlier placement of azide protection over that of previously developed routes within the group. This provided a cheaper, more atom efficient route towards protected D-glucosamine building blocks. Glycosylation of the developed D-GlcN donor units with the L-Ido acceptor allowed the production of key disaccharides which facilitated an efficient iterative glycosylation strategy towards longer oligosaccharides, ultimately providing a differentially protected pentasaccharide. The project evaluated methods towards generating various dimeric heparin type systems through forming new O4 ether linkages between GlcN residues across various short linker fragments. The most successful of these dimerisations used a methallyl dichloride core which allowed for further derivatisation towards dihydroxylated species, the analysis of which highlighted some interesting proton NMR data. The final aspect of this project began development of chemistry towards non-reducing end-labelled oligosaccharide sequences by implementation of a masked aldehyde unit on the C4 hydroxyl of GlcN synthesised from the allylated GlcN precursor via dihydroxylation chemistry. Incorporation of this moiety (protected as a 1,2-dibenzyl glycol) within both a trisaccharide and a pentasaccharide was achieved. Further development of this chemistry should allow for late step oxidative cleavage to reveal the reactive aldehyde, potentially allowing for attachment of various amine functionalised fluorophores via reductive amination. Radiolabelling of such a species should also be possible through sodium borotritide reduction for example.

<p>The intricate interplay of biomolecules acting together, rather than alone, provides insight into the most basic of cellular functions, such as cell signaling, metabolism, defense, and, ultimately, the creation of life. Inherent in each of these processes is an evolutionary tendency towards increased efficiency by means of biolgocial synergy-- the ability of individual elements of a system to produce a combined effect that is different and often greater than the sum of the effects of the parts. Modern biochemists are challenged to find model systems to characterize biological synergy.</p><p>We discuss the multicomponent, enzyme complex the cellulosome as a model system of biological synergy. Native cellulosomes comprise numerous carbohydrate-active binding proteins and enzymes designed for the efficient degradation of plant cell wall matrix polysaccharides, namely cellulose. Cellulosomes are modular enzyme complexes, comparable to enzyme "legos" that may be readily constructed into multiple geometries by synthetic design. Cellulosomal enzymes provide means to measure protein efficiency with altered complex geometry through assay of enzymatic activity as a function of geometry.</p><p>Cellulosomes are known to be highly efficient at cellulose depolymerization, and current debates on the molecular origins of this efficiency suggest two related effects provide this efficiency: i) substrate targeting, which argues that the localization of the enzyme complex at the interface of insoluble cell wall polysaccharides facilitates substrate depolymerization; and ii) proximity effects, which describe the implicit benefit for co-localizing multiple enzymes with divergent substrate preferences on the activity of the whole complex.</p><p>Substrate targeting can be traced to the activity of a single protein, the cellulosomal scaffoldin cellulose binding module CBM3a that is thought to uniquely bind highly crystalline, insoluble cellulose. We introduce methods to develop a molecular understanding of the substrate preferences for CBM3a on soluble and insoluble cellulosic substrates. Using pivaloylysis of cellulose triacetate, we obtain multiple soluble cello-oligosaccharides with increasing degree of glucose polymerization (DP) from glucose (DP1) to cellodecaose (DP10) in high yield. Using calorimetry and centrifugal titrations, cello-oligosacharides were shown to not bind Clostridial cellulolyticum CMB3a. We developed AFM cantilever functionalization protocols to immobilize CBM3a and then probe the interfacial binding between CBM3a and a cellulose nanocrystal thin film using force spectroscopy. Specific binding at the interface was demonstrated in reference to a control protein that does not bind cellulose. The results indicate that i) CBM3a specifically binds nanocrystalline cellulose and ii) specific interfacial binding may be probed by force spectroscopy with the proper introduction of controls and blocking agents.</p><p>The question of enzyme proximity effects in the cellulosome must be answered by assaying the activity of cellulosomal cellulases in response to cellulosome geometry. The kinetic characterization of cellulases requires robust and reproducible assays to quantify functional cellulase content of from recombinant enzyme preparations. To facilitate the real-time routine assay of cellulase activity, we developed a custom synthesis of a fluorogenic cellulase substrate based on the cellohexaoside of Driguez and co-workers (vide infra). Two routes to synthesize a key thiophenyl glycoside building block were presented, with the more concise route providing the disaccharide in four steps from a commercial starting material. The disaccharide building blocks were coupled by chemical activation to yield the fully protected cellohexaoside over additional six steps. Future work will include the elaboration of this compound into an underivatized FRET-paired hexasaccharide and its subsequent use in cellulase activity assays.</p><p>This dissertation also covers an experimental system for the evaluation of methonium desolvation thermodynamics. Methonium (-N+Me3, Am) is an organic cation widely distributed in biological systems. The appearance of methonium in biological transmitters and receptors seems at odds with the large unfavorable desolvation free energy reported for tetramethylammonium (TMA+), a frequently utilized surrogate of methonium. We report an experimental system that facilitates incremental internalization of methonium within the molecular cavity of cucurbit[7]uril (CB[7]).</p><p>Using a combination of experimental and computational studies we show that the transfer of methonium from bulk water to the CB[7] cavity is accompanied by a remarkably small desolvation enthalpy of just 0.5±0.3 kcal*mol-1, a value significantly less endothermic than those values suggested from gas-phase model studies (+49.3 kcal*mol-1). More surprisingly, the incremental withdrawal of methonium surface from water produces a non- monotonic response in desolvation enthalpy. A partially desolvated state exists, in which a portion of the methonium group remains exposed to solvent. This structure incurs an increased enthalpic penalty of ~3 kcal*mol-1 compared to other solvation states. We attribute this observation to the pre- encapsulation de-wetting of the methonium surface. Together, our results offer a rationale for the wide biological distribution of methonium and suggest limitations to computational estimates of binding affinities based on simple parameterization of solvent-accessible surface area.</p> / Dissertation

Invasive fungal infections are prevalent and often deadly in immunocompromised patients. There continues to be a pressing need for the development of novel antifungal compounds since there are currently only 13 compounds licensed for the treatment of invasive fungal infections and antibiotic-resistant strains have been emerging. CAY-1 is an antifungal steroidal saponin which was isolated from the fruit of the cayenne pepper plant in 0.1% yield. In Vitro studies of CAY-1 have shown it to be an effective antifungal agent against sixteen pathogenic fungal strains and it showed no cytotoxicity toward mammalian cells up to 100 ìg/mL. The development of a practical synthesis of CAY-1 will potentially allow for further exploration of its medicinal utility and provide the opportunity to synthesize derivatives of CAY-1 which could be investigated in structure-activity relationship studies. To this end, methods for the preparation of they CAY-1 aglycone and pentasaccharide moieties have been investigated. Through this work, several partially protected stereoisomers of the CAY-1 aglycone have been prepared which can be used for the synthesis of saponin derivatives of CAY-1 for structure-activity relationship studies. Definitive characterization of one of these isomers, 3á-hydroxy-(22S, 25R)-5á-spirostan-2â-yl acetate, was achieved by X-ray crystallography. Furthermore, a quantitative inversion of the C-3 stereochemical configuration of this compound was achieved via an acetate group migration of the corresponding mesylate. The possibility of competition between the acetate migration and substitution mechanisms with various nucleophiles was explored. The results, however, indicate that this inversion only occurs via the acetate migration. Additionally, the CAY-1 pentasaccharide synthesis poses two significant challenges. First, these results demonstrate that the central 2, 3-branched portion can be synthesized efficiently from a partially protected glucopyranosyl acceptor since the C-2 and C-3 alcohols differ in their reactivity in glycosylation reactions. The second challenge is the ƒÀ-(1¨4) linkage to the galactosyl acceptor which significantly increases the complexity of the synthesis as compared to literature reported syntheses of other branched oligosaccharides. Nonetheless, this ƒÀ-(1¨4) linkage was achieved using a disarmed trichloroacetimidate glucosyl donor.

This thesis covers different topics in the field of synthetic organic chemistry combined with the field of surface science and glycobiology. First, the text presents a series of orthogonally protected oligosaccharides (tri-, penta-, and heptasaccharides) of varying length and structures, which are synthesized with the aim of developing novel heterobifunctional biocompatible cross-linkers. Successful conjugation with different chemical handles is also described and used to illustrate the potential implementation of defined carbohydrate based compounds have potential use in biosensing applications. The results of incubation experiments using living cells indicate that the linker is incorporated into cell surfaces and enriched in microdomains. Second, synthesis of various saccharide-terminated alkane thiols immobilized on gold surfaces is reported. The protein adsorption and antifouling characteristics of these surfaces were investigated using model proteins and the common fouling organisms, Ulva linza and Balanus amphitrite. Further, oligo(lactose)-based thiols (di-, tetra-, and hexasaccharides) were synthesized and immobilized on gold nanoparticles to investigate how well these rigid, rod-like oligosaccharides can stabilize such nanoparticles for future use in constructing hybrid nanoparticles. Finally, the thesis describes synthesis of a systematic series of oligo(ethylene) glycols possessing either hydrogen- or methyl-terminated groups. Investigation of the fundamental characteristics of self-assembled monolayers, will give important insights into the design of protein repellant surfaces.

No description available.

La glycosylation des protéines est une modification co/post-traductionnelle, localiséeprincipalement dans l’appareil de golgi, impliquée dans divers processus physiologiques. Àl’inverse de la synthèse des protéines et des nucléotides, celle des sucres est plus complexe,en partie, à cause des nombreux branchements structuraux et de la diversité stéréochimiquedes glycannes. Les glycosyltransférases sont les enzymes responsables de la biosynthèse desoligo- et polysaccharides. Cependant, il existe différents procédés permettant de réaliser lasynthèse in vitro d’oligosaccharides tels que des procédés chimiques, enzymatiques ouchimio-enzymatiques. La Core 2 β(1,6)-N-acétylglucosaminyltransférase I (C2GnT-I) est uneglycosyltransférase (GT) transmembranaire de type II qui crée une liaison β1,6 entre une Nacétylglucosamine(GlcNAc) et la N-acétylgalactosamine (GalNAc) d’un noyau Core 1,formant ainsi une structure branchée de type Core 2. Une fois le branchement Core 2 initié,au moins trois réactions successives de transfert peuvent avoir lieu, impliquant les β(1,4)-galactosyltransférases, les α(2,3)-sialyltransférases et les α(1,3)-fucosyltransférases. Il estadmis que les GTs sont réparties séquentiellement dans les compartiments cis, médian ettrans de l’appareil de Golgi selon leur ordre d’intervention et le type cellulaire. Nous avonsmis au point un procédé de reconstitution membranaire, comportant des glycoprotéinesgolgiennes, dont les GTs, par l’intermédiaire d’une lectine, la wheat germ agglutinin (WGA).Il est admis que la WGA interagit avec les composants de la membrane plasmique et ceux del’appareil de Golgi. L’étude de notre système membranaire reconstitué a mis en évidence uneactivité élevée de la C2GnT-1 in vitro, et son efficacité à synthétiser des oligosaccharidesbranchés Core 2, par glycosylation séquentielle. / Protein glycosylation is a co/posttranslational modification, localized in the Golgi apparatus,involved in various physiological processes. Sugar synthesis is more complex than that ofproteins and nucleic acids, in part because of the glycosidic bond and glycan stereochemistrydiversity. Glycosyltransferases are enzymes responsible of oligo- and polysaccharidesbiosynthesis. Various methods are used for the synthesis of oligosaccharides, in vitro, suchas chemical, enzymatic or chemo-enzymatic. Core 2 β(1,6)-N-acetylglucosaminyltransferase I(C2GnT-I) is a type-II transmembrane glycosyltransferase (GT). This enzyme create a β1,6bond between N-acetylglucosamine (GlcNAc) and Core 1 N-acetylgalactosamine (GalNAc),forming a Core 2 branched structure. Once the Core 2 branch is initiated, at least threesuccessive transfer reactions can take place, involving β(1,4)-galactosyltransferases, α(2,3)-sialyltransferases and α(1,3)-fucosyltransferases. It is known that GT are distributedsequentially in the cis, medial and trans Golgi apparatus in order of intervention andaccording to cell type. We have developed a membrane reconstitution process comprisinggolgi glycoproteins, including GT, by the use of a lectin, the wheat germ agglutinin (WGA). Itis known that WGA interacts with plasma membrane and Golgi apparatus components. Ourreconstituted membrane system showed a high C2GnT-1 activity in vitro and its effectivenessin synthesizing Core2 branched oligosaccharides by sequential glycosylation.