Zinc-binding proteins represent approximately one tenth of the proteome and a good portion of them are zinc-dependent hydrolases. This thesis focuses on biochemical and structural characterization of glutamate carboxypeptidase II (GCPII) and histone deacetylase 6 (HDAC6), two members of the zinc-dependent metallohydrolase superfamily. We describe here their interactions with natural substrates and inhibitors. GCPII is a homodimeric membrane protease catalyzing hydrolytic cleavage of glutamate from the neurotransmitter N-acetylaspartylglutamate (NAAG) and dietary folates in the central and peripheral nervous systems and small intestine, respectively. This enzyme is associated with several neurological disorders and also presents an ideal target for imaging and treatment of prostate cancer. GCPII inhibitors typically consist of a zinc-binding group (ZBG) linked to an S1' docking moiety (a glutamate moiety or its isostere). As such, these compounds are highly hydrophilic molecules therefore unable to cross the blood-brain barrier and this hampers targeting GCPII to the central nervous system. Different approaches are adopted to alter the S1' docking moiety of the existing inhibitors. As a part of this thesis, we present different strategies relying on replacement of the canonical P1' glutamate residue...

Voltage-gated ion channels play fundamental roles in neural excitability and thus dysfunctional channels can cause disease. Understanding how the voltage-sensor of these channels activate and inactivate could potentially be useful in future drug design of compounds targeting neuronal excitability. The opening and closing of the pore in voltage-gated ion channels is caused by the arginine-rich S4 helix of the voltage sensor domain (VSD) moving in response to an external potential. Exactly how this movement is accomplished is not yet fully known and an area of hot debate. In this thesis I study how the opening and closing in voltage-gated potassium (Kv) channels occurs. Recently, both experimental and computational results have pointed to the possibility of a secondary structure transition from α- to 3(10)-helix in S4 being an important part of the gating. First, I show that the 3(10)-helix structure in the S4 helix of a Kv1.2-2.1 chimera protein is significantly more favorable compared to the α-helix in terms of a lower free energy barrier during the gating motion. Additional I suggest a new gating model for S4, moving as sliding 310-helix. Interestingly, the single most conserved residue in voltage- gated ion channels is a phenylalanine located in the hydrophobic core and directly facing S4 causing a barrier for the gating charges. In a second study, I address the problem of the energy barrier and show that mutations of the phenylalanine directly alter the free energy barrier of the open to closed transition for S4. Mutations can either facilitate the relaxation of the voltage-sensor or increase the free energy barrier, depending on the size of the mutant. These results are confirmed by new experimental data that supports that a rigid, cyclic ring at the phenylalanine position is the determining rate-limiting factor for the voltage sensor gating process. / QC 20110616

The two techniques aqueoustwo-phase partitioning and expanded bed adsorption that bothare suitable for primary protein recovery were studied. Most ofthe work was focused on partition in aqueous two-phase systemsand in particular on the possibility to effect the partitionbehaviour by fusion of short peptide tags or protein domains tothe target protein. The partitioning of fusionproteins between different variants of the domain tag Z and thenaturally occurring protein DNA Klenow polymerase were studiedin Breox/Reppal aqueous two-phase systems. Most studies wereperformed with cell homogenate. The Breox/Reppal system was infocus because if the fusion protein can be partitioned to theBreox-rich top phase the next step can be a thermoseparatingaqueous two-phase system. When the Breox phase is heated to50°C it switches from a one-phase system to a two-phasesystem resulting in an almost pure water rich top phase andhighly concentrated Breox-rich bottom phase. The Breox can thenbe reused and the protein recovered from the water phase. TheZ-domain was genetically modified in different ways to Zbasic1, Zacid2and Ztrp12and fused to the Klenow protein to try toenhance partitioning to the Breox-rich phase. From theexperiments it was not possible to observe any effects on thepartition behaviour irrespectively of tested properties of thedomain tag. Despite the absence of domain tag effects highK-values, i.e. partition to the Breox-rich top phase, wereobserved in the Breox/Reppal system. However, the proteinK-values seemed to be rather sensitive to the cell homogenateload and showed a tendency to decrease with increased cellhomogenate load. Also increased phosphate concentration reducedthe K-values. The partitioning of cell debris also seemed todependent on the cell homogenate load. At higher homogenateload (&lt;=20g DW/L) clear Breox-rich top phases were observedwith the cell debris collected in Reppal-rich bottomphases. Two different tetrapeptides,AlaTrpTrpPro and AlaIleIlePro were inserted near the C-terminusof the protein ZZT0. The Trp-rich peptide unit stronglyincreased both the partitioning of ZZT0 into the poly(ethyleneglycol) (PEG)-rich phase in a PEG/potassium phosphate aqueoustwo-phase system and its retention on PEG and propylhydrophobic interaction chromatographic columns with potassiumphosphate as eluent in isocratic systems. Both the partitioningand the retention increased with increasing number of Trp-richpeptide units inserted into ZZT0. Insertion of Ile-richtetrapeptide units affected the partitioning and retention to amuch lesser extent. Partition and modelling data also indicateda folding of inserted Trp and Ile tetrapeptide units, probablyto minimise their water contact. It was also investigated howto predict the partitioning of proteins in isoelectricPEG/phosphate aqueous two-phase systems. The capture ofß-galactosidase fromE. colicell homogentate (50g DW/L) by metal chelatexpanded bed adsorption was studied. These experiments showedthat capture, with a certain degree of selectivity, andclarification of ß-galactosidase could be achieved from acell homogenate. However, a rather low recovery of about 35 %was obtained at a capacity of 0.25mg/mL of gel. Thus, severalparameters remain to be optimised like the load buffercomposition and the cell homogenate load. <b>Keywords:</b>E. coli, aqueous two-phase systems, fusion proteins,hydrophobic interaction chromatography, expanded bedadsorption, ß-galactosidase, Klenow polymerase, Z-domain,peptide tags / NR 20140805

Renewable lignocellulosic materials are promising green plastic alternatives to fossil fuel-based plastics. However, the hydrophilic nature and poor water resistance of lignocellulosic materials have hindered their practical applications. This study reports a facile metal-ion-modification (MIM) route, swelling with aqueous metal ion solutions, and drying to convert conventional hydrophilic paper and wood pulp into biodegradable hydrophobic paper and tableware without the addition of hydrophobic sizing chemicals/materials. Metal ions such as Fe3+ and Zr4+ can coordinate with pulp fibers’ polar groups (i.e., O.H., C=O, and COOH) that induce self-assembly of their surface fibrillated “hairy” cellulose nanofibrils to form a more compact structure with fewer available O.H. groups for water sorption. The formation of coordination bonds with polar groups (i.e., O.H., C=O, and COOH) decreases the surface energy of pulp fibers and increases their hydrophobicity and water resistance. Only ~3 mg of metal ions is needed to induce the wettability transition in 1 g of kraft pulp, resulting in hydrophobic paper and tableware with water contact angles (WCAs) of 120-140° and displayed wet tensile strengths of up to 9.5 MPa, and low water absorbency, which were comparable to synthetic polymer films. This MIM technique can be integrated into the existing paper-making process for the scalable production of hydrophobic papers and tableware, providing an alternative route for developing sustainable and biodegradable plastic counterparts. The MIM-induced lignocellulose hydrophobization mechanisms were elucidated using X-ray photoelectron spectroscopy (XPS), Fourier transforms infrared spectroscopy (FT-IR), and scanning electron microscopy-energy dispersive spectroscopy (SEM-EDS), and density functional theory (DFT). Furthermore, this MIM technique was also evaluated for its applicability in wood treatment. The treatment effectively tunes the wood surface from hydrophilic to hydrophobic, enhancing its water resistance. The MIM treatment significantly improved the dimensional stability of SYP, red oak, and poplar. For example, the Fe3+ treatment reduced the tangential swelling of SYP, poplar, and red oak by 57%, 50%, and 40%, respectively. Overall, this eco-friendly and facile MIM method holds promise for developing sustainable and biodegradable alternatives to conventional plastics, contributing to a more environmentally friendly future.

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Hydrophobic coatings find application in various sectors of the economy including to electronics, textiles, optical devices, and in scientific and commercial equipment. These different applications demand that different hydrophobic coatings posses a range of properties that may include smoothness or roughness, thicknesses on the order of a monolayer or a micron, robustness or the ability to dissolve quickly, transparency or opacity, water resistance or water permeability, electrical conductivity, oleophobicity, etc. However, whatever the final/desired properties, deposition via dry-deposition processes offers significant advantages, including greater reproducibility, increased environmental friendliness, and cost effectiveness on an industrial scale. Herein I explore the chemical vapor deposition of silanes and the characterization of a commercial, hydrophobic coating to better prepare and understand hydrophobic coatings on different materials. One of the characterization techniques I used frequently in these studies is X-ray photoelectron spectroscopy (XPS). Accordingly, in Chapter 2 of this thesis I discuss this technique vis-à-vis the chemical shifts it detects, which reflect the oxidation states of materials being probed. In particular, I discuss a recommendation made over a decade ago by Gion Calzaferri for 'fixing' the problem of oxidation numbers as applied to organic materials and show how XPS confirms his suggestion. In Chapter 3 I introduce hydrogen as an etch/cleaning gas for silicon wafers. I first show that, like argon and oxygen plasmas, hydrogen plasmas will effectively clean silicon wafers. However, I then show that hydrogen plasma treatment leads to a silicon surface that is chemically different than those prepared with the other plasmas and that undergoes silanization to a greater extent -- the resulting surfaces have higher water contact angles and thicknesses. In Chapter 4 I study the deposition of a potential barrier layer for water, which was prepared from an aza silane: N-n-butyl-aza-2,2-dimethoxysilacyclopentane (1) in a molecular layer deposition (MLD)-like process using either water or ammonium hydroxide as the second half reactant. This molecule has the interesting property of undergoing self-limiting growth, where the termination of this growth is accelerated by use of an ammonium hydroxide catalyst. Interestingly, films of 1 are considerably thicker on nylon than on silicon, which is explained by nylon acting as a water reservoir in the reaction. In Chapter 5 I show the careful characterization of the hydrophobic coating on an Apple iPod nano, which was probed by ToF-SIMS, wetting, and XPS. I could identify that the coating is only applied to the touchscreen of the device. SIMS suggested that the fluorinated coating contains oxygen, which should add to its biodegradability. Finally, in Chapter 6 I make recommendation for future work in these areas.

Return liquor from thermal hydrolysis process (THP) can significantly add to the nitrogen load of a wastewater treatment plant (WWTP) and introduce UV quenching substances to the wastewater stream when recycled. While there are mature technologies in place to handle the inorganic nitrogen produced due to the thermal pretreatment, organic nitrogen remains a parameter of concern for utilities employing THP pretreatment. The impact of operating conditions of the THP on dissolved organic nitrogen (DON) and UV absorbance in return liquor was investigated. Operating conditions studied were (1) operating temperature (2) solids retention time (SRT) in the anaerobic digester (3) THP flash pressure (4) the effect of co-digestion of sewage sludge with food waste and, (5) polymer conditioning. Operating temperature and polymer dose had the most significant impact on DON and UV quenching. It was found that an increase in operating temperature resulted in an increase in DON, which was primarily contributed by the hydrophilic fraction. An increase in temperature also resulted in increased UV254 absorbance. However, this trend was not linear and the increase was more pronounced when the temperature was increased from 150 C to 170 C. Increasing flash pressure from 25 psi to 45 psi did not have a significant impact on the return liquor. However, increasing the flash pressure to 75 psi increased the DON and UV254 absorbing compounds. Co-digesting the sludge with food waste resulted in a slight increase in DON and a decrease in dissolved organic carbon (DOC) and UV quenching compounds. Increasing the SRT from 10 days to 15 days resulted in a slight decrease in DON but did not have any impact on UV254 absorbance. Overall, it can be concluded that optimizing operating conditions of thermal hydrolysis process can result in decreased DON and UV quenching compounds in the recycle stream. / Master of Science

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