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  • 1.
    Bengtsson, Linda
    KTH, Skolan för kemivetenskap (CHE).
    Odorant binding protein and olfactory receptors: plausible role as detectors in an odorant biosensor2011Independent thesis Advanced level (degree of Master (Two Years)), 20 poäng / 30 hpOppgave
    Abstract [en]

    The development of an inexpensive, portable, stable, sensitive and selective biosensor for detection of odorants is a daunting task. Here, we hypothesized the development of a detector layer composed of the protein groups; the olfactory receptors (ORs) and the odorant binding proteins (OBPs), known to bind odorants in animal sensing. We report the design of 13 OR gene-vector constructs, and their subsequent transformation into

    Escherichia (E.) coli (BL21 (DE3)-STAR-pLysS) strain. Moreover, we report the expression of several ORs into an in vitro wheat germ extract using three separate detergent mixes for protein solubilization.

     

    In addition, we describe the design of an odorant binding protein from the Aenopheles gambiae mosquito PEST strain (OBP-PEST) gene-vector construct under an IPTG (Isopropyl β-D-1-thiogalactopyranoside) inducible promoter. OBP-PEST was heterologously expressed in E.coli with an 8 amino acid long sequence (WSPQFEK) attached C-terminally, via a thrombin cleavage site and a flexible linker (GSSG). The WSPQFEK sequence, commonly referred to as a Strep-tag, enabled subsequent affinity chromatography purification of the protein, via binding to an engineered Streptavidin equivalent. Surprisingly, the OBP-PEST was found to contain a signal sequence leading to its truncation and secretion when expressed in E.coli.

     

    Biophysical analyses were established using Circular Dichroism (CD) for the analysis of two lipocalins: Beta-lactoglobulin (BLG) and OBP-PEST. We studied the solubility, refoldability and the conformational transitions of BLG, as a result of change in solvent, pH and temperature. The secondary structure of OBP-PEST and its thermal stability was investigated.

     

    In conclusion, this thesis work has enabled biophysical analyses of OBP-PEST and future analogs of interest to the development of a stable protein detector layer. Although further experiments are needed to fully characterize the biophysical properties, and to find odorant substrates of OBP-PEST, it was found to be a suitable alternative to ORs in a biosensor detector layer application. More importantly, an inherent OBP-PEST signal sequence was found to mediate protein secretion when expressed heterologously in E.coli. To the best of our knowledge this is the first lipocalin discovered to be secreted upon heterologous expression in E.coli.

     

    We hypothesize that this signal peptide could be used as a means for targeted secretion and, hence, efficient protein purification.

  • 2.
    Fauquet, Germain
    KTH, Skolan för kemivetenskap (CHE).
    Reconnaissance biomoléculaire, Comparaison de l'impact du soufre et de l'oxygène dans la liaison glycosidique2011Independent thesis Advanced level (degree of Master (Two Years)), 20 poäng / 30 hpOppgave
    Abstract [en]

    Interactions between carbohydrates and proteins play a key role in many biological processes. Cell-cell interactions, cell communication and cell proliferation are examples of processes based on highly specific interactions between proteins and complex oligosaccharides. The synthesis of carbohydrate mimics is essential for the study and understanding of such recognition processes, and has therefore become increasingly popular over the latest decades. In synthesis, thiol derivatives have several advantages. Thus, the combined nucleophilicity and chemical stability of sulfhydryl groups render thiol carbohydrate analogs as excellent building blocks for glycosylation processes. The objectives of the present project were to investigate the differences between naturally occurring oligosaccharides and their sulfur-analogs in biomolecular interactions with specific proteins. Convenient methodologies to the synthesis of a range of D-mannopyranose thioanalogs were developed. These strategies allows for the access to 1,2- and 1,6-linked dimannosides by glycosylation. A carbohydrate-protein interaction methodology to test the developed compounds against a mannose-specific lectin (Concanavalin A) using quartz crystal microbalance (QCM) methodology was furthermore developed.

  • 3.
    Fouilland, Laura
    KTH, Skolan för kemivetenskap (CHE).
    Synthesis of novel 1.10-phenanthrolins and cyclic analogs, a potential anticancer and antimalarial agents2011Independent thesis Advanced level (degree of Master (Two Years)), 20 poäng / 30 hpOppgave
    Abstract [en]

    The potential antimalarial and anticancer effect of molecules containing 1,10-phenanthroline skeleton has been suspected on several previous studies. It is why the goal of this project is to synthesize novel 1,10-phenanthrolines and cyclic analogs.

    The originality of this project is the synthesis way of these novel compounds. Indeed, these structures will be obtained through an original redox approach developed in the SMITH laboratory using the tetrakis(dimethylamino)ethylene (TDAE) reagent.

         The TDAE is an electron rich organic molecule which is an effective reducing agent capable of generating an anion from halogenated derivatives under mild conditions via a single electron transfer (SET). From the different substrate we will work with, the TDAE will generate an anion which will be additioned on the 1,10-phenanthroline-5,6-dione.

    These different substrates will be aromatic and heterocyclic nitro-benzylic, and quinonic derivates as well as bromodifluoromethyl heteroarylated substrates.

    A one pot two step (reduction, dehydration) reaction will be done on these addition products, in order to obtain a cyclised product.

     

         It is the first time we try these reactions on these kind on molecules, it is why this project needs a lot of optimization and that the yield obtained are medium or equal to zero. However, we observed that the addition reaction with TDAE worked with 4 substrates out of 6.

    We tried the cyclisation reaction on only one addition product and we think that after some improvement of the reaction conditions and the work-up, we will be able to obtain the product with a good yield.

  • 4.
    Heid, Berenice
    KTH, Skolan för kemivetenskap (CHE).
    Enantioselective Preparation of ω-Functionalized O-Acylated Cyanohydrins2011Independent thesis Advanced level (degree of Master (Two Years)), 20 poäng / 30 hpOppgave
    Abstract [en]

    A minor enantiomer recycling one-pot process usingω-functionalized prochiral aldehydes as starting materials and two reinforcing catalysts has been reported. The desired aldehyde for these process studies was 5-bromo-1-pentanal.

    In a two-phase solvent system, enzyme-catalyzed hydrolysis of the minor enantiomer regenerates continuously the prochiral starting material and Lewis acid catalysed addition of acetyl cyanide provides the O-acetylated cyanohydrins. The minor enantiomer recycling process has been studied and improved for 5-bromo-1-pentanal to receive high enantiomeric excess and yield of the expected O-acetylated cyanohydrin.

  • 5.
    Mirmohades, Mohammad
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Fysikalisk kemi. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Molekylär biomimetik.
    Towards a Novel Donor-Sensitizer-Catalyst Triad Entirely Composed of Earth Abundant Elements2011Independent thesis Advanced level (degree of Master (Two Years)), 20 poäng / 30 hpOppgave
  • 6.
    Saur, Ann-Kathrin
    KTH, Skolan för kemivetenskap (CHE).
    Synthesis of α1,2- and α1,6, linked Dimannosides for Analysis of Protein Carbohydrate Interactions2011Independent thesis Advanced level (degree of Master (Two Years)), 20 poäng / 30 hpOppgave
    Abstract [en]

    The aim of the project was to synthesize α1,2-linked and α1,6-linked dimannosides linked through either an oxygen-atom or a sulphur-atom, and subsequently test the binding properties of the dimannosides to lectins with known specificity towards mannose-containing glycans. Thedimannosides were prepared by a glycosylation reaction using selectively protected monosaccharides containing a thiol or alcohol nucleophilic glycosyl acceptor and a series of different glycosyl donors. The synthetic routes to the different building blocks were designed to efficiently make use of common intermediate compounds to streamline the synthesis. The glycosyl acceptors used forthe synthesis of α1,2-linked as well as α1,6-linked dimannosides were synthesized in few steps and diversified only in the last steps of the synthesis. The glycosyl donors used in the study were synthesized from commercially available starting material in a straightforward and convenientsynthesis in 7 to 8 steps.

  • 7.
    Song, Yan
    KTH, Skolan för kemivetenskap (CHE).
    Regio- and Stereoselectivity in Glycosyl Disulfide Desulfurization. Generation of S-linked Disaccharides2011Independent thesis Advanced level (degree of Master (Two Years)), 20 poäng / 30 hpOppgave
    Abstract [en]

    This report describes the synthesis of thiomonosaccharides and the subsequent oxidation to carbohydrate disulfides followed by evaluation of a desulfurization reaction with the aim of developing a facile method for production of S-linked oligosaccharides. The carbohydrate disulfides were synthesized in few steps from commercially available starting materials. Small and simple disulfides were used to evaluate the desulfurization process yielding important information about choice of solvent, catalyst and temperature required for the desulfurization to occur. The optimized conditions were then applied to the carbohydrate disulfides. Results showed that the reactivity of the carbohydrate disulfides depends a lot on the position of the disulfide. One of the carbohydrate disulfides was efficiently desulfurized giving the thioether linked disaccharide, as determined by mass spectrometry. However, more work is needed to develop a general procedure for the desulfurization working on many different carbohydrate disulfides.

  • 8.
    Widing, Joakim
    KTH, Skolan för kemivetenskap (CHE).
    Preparation of Affinity Based Probes to Elucidate the Mode of Action of y-Secretase Modulators2011Independent thesis Advanced level (degree of Master (Two Years)), 20 poäng / 30 hpOppgave
    Abstract [en]

    γ-Secretase is an enzyme that takes part of the breakdown of amyloid precursor protein (APP) into amyloid-β (Aβ) peptides. Aβ-peptides from this process can be linked to Alzheimer’s disease. γ-Secretase modulators (GSMs) have been reported in the literature to reduce the potentially dangerous variant of Aβ-peptides. However, the mechanism of the binding site for these modulators is poorly understood. In this report substances of affinity based probes (AfBPs) have been prepared that can be used as a method to extract the binding site. The AfBPs were constituted of a cross-linking group, a biotinyl group and a γ-secretase modulator. Different variants of the biotin probe were prepared to investigate if the activity of the original modulator could be retained. The report will show that this could be done.

    In the future, the synthesised affinity based probes could be used to understand the mode of action of γ-secretase modulators. For instance the modulator could be incubated with the enzyme and the crosslinking group, when activated, covalently bind to a residue near the binding site. The complex could then be captured on avidin and the binding site be determined.

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