A comparative study of protoheme and heme d catalases : role of the heme and the heme pocket in catalysis and ligand binding

Catalase dismutes H20 2 to O2 and H20. In successive twoelectron reactions H20 2 induces both oxidation and reduction at the heme group. In the first step the protoheme prosthetic group of beef liver catalase forms compound I, in which the heme has been oxidized from Fe3+ to Fe4+=0 and a porphyrin radical has been created. Compound II is formed by the oneelectron reduction of comp I. It retains Fe4+=0 but lacks the porphyrin radical and is catalytically inert. Molecular structures are available for Escherichia coli Hydroperoxidase II, Micrococcus Iysodeiktus, Penicillium vitale and beef liver enzymes, which contain different hemes and heme pockets. In the present work, the pockets and substrate access channels of protoheme (beef liver & Micrococcus) and heme d (HPII of E. coli and Penicillium) catalases have been analysed using Quanta��� and CharmMTM molecular modeling packages on the Silicon Graphics Iris Indigo 2 computer. Experimental studies have been carried out with two catalases, HPII (and its mutants) and beef liver. Fluoride and formate' are inhibitors of both enzymes, and their binding is modulated by the heme and by distal residues N201 & H128. Both HPII and beef liver enzymes form compound I with H202 or peracetate. The reduction of beef liver enzyme compound I to II and the decay of compound II are accelerated by fluoride. The decay of compound II is also accelerated by formate, and this reagent acts as a 2-electron donor towards compound I of both enzymes. It is concluded that heme d enzymes (Penicillium and HPII of E. coli) are formed by autocatalytic transformation of protoheme in a modified pocket which contains a characteristic serine residue as well as a partially occluded heme channel. They are less active than protoheme enzymes but also do not form the inactive compound II species. Binding of peroxide as well as fluoride and formate is prevented by mutation of H128 and modulated by mutation of N201.

Investigations in flow injection analysis (FIA): conventional FIA determination of chloride in water; sequential injection (SI)-FIA determination of mercury in water

Flow injection analysis (FIA) was applied to the determination of both chloride ion and mercury in water. Conventional FIA was employed for the chloride study. Investigations of the Fe3 +/Hg(SCN)2/CI-,450 nm spectrophotometric system for chloride determination led to the discovery of an absorbance in the 250-260 nm region when Hg(SCN)2 and CI- are combined in solution, in the absence of iron(III). Employing an in-house FIA system, absorbance observed at 254 nm exhibited a linear relation from essentially 0 - 2000 Jlg ml- 1 injected chloride. This linear range spanning three orders of magnitude is superior to the Fe3+/Hg(SCN)2/CI- system currently employed by laboratories worldwide. The detection limit obtainable with the proposed method was determin~d to be 0.16 Jlg ml- 1 and the relative standard deviation was determined to be 3.5 % over the concentration range of 0-200 Jig ml- 1. Other halogen ions were found to interfere with chloride determination at 254 nm whereas cations did not interfere. This system was successfully applied to the determination of chloride ion in laboratory water. Sequential injection (SI)-FIA was employed for mercury determination in water with the PSA Galahad mercury amalgamation, and Merlin mercury fluorescence detection systems. Initial mercury in air determinations involved injections of mercury saturated air directly into the Galahad whereas mercury in water determinations involved solution delivery via peristaltic pump to a gas/liquid separator, after reduction by stannous chloride. A series of changes were made to the internal hardware and valving systems of the Galahad mercury preconcentrator. Sequential injection solution delivery replaced the continuous peristaltic pump system and computer control was implemented to control and integrate all aspects of solution delivery, sample preconcentration and signal processing. Detection limits currently obtainable with this system are 0.1 ng ml-1 HgO.

ORGANOSILICON BIOTECHNOLOGY: A BIO-INSPIRED APPROACH TO THE HYDROLYSIS OF ALKOXYSILANES and THE LIPASE-CATALYZED SYNTHESIS OF SILOXANE-CONTAINING POLYESTERS AND POLYAMIDES

The first part of this thesis studied the capacity of amino acids and enzymes to catalyze the hydrolysis and condensation of tetraethoxysilane and phenyltrimethoxysilane. Selected amino acids were shown to accelerate the hydrolysis and condensation of tetraethoxysilane under ambient temperature, pressure and at neutral pH (pH 7��0.02). The nature of the side chain of the amino acid was important in promoting hydrolysis and condensation. Several proteases were shown to have a capacity to hydrolyze tri- and tet-ra- alkoxysilanes under the same mild reaction conditions. The second part of this thesis employed an immobilized Candida antarctica lipase B (Novozym-435, N435) to produce siloxane-containing polyesters, polyamides, and polyester amides under solvent-free conditions. Enzymatic activity was shown to be temperature dependent, increasing until enzyme denaturation became the dominant pro-cess, which typically occurred between 120-130���C. The residual activity of N435 was, on average, greater than 90%, when used in the synthesis of disiloxane-containing polyesters, regardless of the polymerization temperature except at the very highest temperatures, 140-150���C. A study of the thermal tolerance of N435 determined that, over ten reaction cycles, there was a decrease in the initial rate of polymerization with each consecutive use of the catalyst. No change in the degree of monomer conversion after a 24 hour reaction cycle was found.

Tetrathiafulvalene and 2,2'-Bipyridine: Bridging both Worlds in the Pursuit of Novel Molecular Materials

The preparation and characterization of two families of building blocks for molecule-based magnetic and conducting materials are described in three projects. In the first project the synthesis and characterization of three bis-imine ligands LI - L3 is reported. Coordination of LI to a series of metal salts afforded the five novel coordination complexes Sn(L4)C4 (I), [Mn(L4)(u-CI)(CI)(EtOH)h (II), [CU(L4)(u-sal) h(CI04)2 (sal = salicylaldehyde anion) (III), [Fe(Ls)2]CI (IV) and [Fe(LI)h(u-O) (V). All complexes have been structurally and magnetically characterized. X-ray diffraction studies revealed that, upon coordination to Lewis acidic metal salts, the imine bonds of LI are susceptible to nucleophilic attack. As a consequence, the coordination complexes (I) - (IV) contain either the cyclised ligand L4 or hydrolysed ligand Ls. In contrast, the dimeric Fe3+ complex (V) comprises two intact ligand LI molecules. In. this complex, the ligand chelates two Fe(III) centres in a bis-bidentate manner through the lone pairs of a phenoxy oxygen and an imine nitrogen atom. Magnetic studies of complexes (II-V) indicate that the dominant interactions between neighbouring metal centres in all of the complexes are antiferromagnetic. In the second project the synthesis and characterization two families of TTF donors, namely the cyano aryl compounds (VI) - (XI) and the his-aryl TTF derivatives (XII) - (XIV) are reported. The crystal structures of compounds (VI), (VII), (IX) and (XII) exhibit regular stacks comprising of neutral donors. The UV -Vis spectra of compounds (VI) - (XIV) present an leT band, indicative of the transfer of electron density from the TTF donors to the aryl acceptor molecules. Chemical oxidation of donors (VI), (VII), (IX) and (XII) with iodine afforded a series of CT salts that where possible have been characterized by single crystal X -ray diffraction. Structural studies showed that the radical cations in these salts are organized in stacks comprising of dimers of oxidized TTF donors. All four salts behave as semiconductors, displaying room temperature conductivities ranging from 1.852 x 10-7 to 9.620 X 10-3 Scm-I. A second series of CT salts were successfully prepared via the technique of electrocrystallization. Following this methodology, single crystals of two CT salts were obtained. The single crystal X-ray structures of both salts are isostructural, displaying stacks formed by trimers of oxidized donors. Variable temperature conductivity measurements carried out on this series of CT salts reveal they also are semiconductors with conductivities ranging from 2.94 x 10-7 to 1.960 X 10-3 S em-I at room temperature. In the third project the synthesis and characterization of a series of MII(hfac)2 coordination complexes of donor ligand (XII) where M2+ = Co2+, Cu2+, Ni2+ and Zn2+ are reported. These complexes crystallize in a head-to-tail arrangement of TTF donor and bipyridine moieties, placing the metal centres and hfac ligands are located outside the stacks. Magnetic studies of the complexes (XV) - (XVIII) indicate that the bulky hfac ligands prevent neighbouring metal centres from assembling in close proximity, and thus they are magnetically isolated.

Animals without Borders: Farmed Animal Resistance in New York

While billions of farmed animals are immobilized within agribusiness, every year some of these animals manage to break free. This thesis examines the stories of those who flee slaughterhouses and the public response to these individuals. My objective is to understand how animals resist and the role that their stories play in disrupting the ways that humans, particularly as consumers, are distanced from the violence of animal enterprises. Included are six vignettes that allow for an in-depth case study of those who have escaped within New York State. Located in the interdisciplinary field of critical animal studies, my inquiry draws upon new animal geographies, transnational feminisms, and critical discourse analysis. This contribution provides discussion of farmed animal resistance in particular and compares experiences and representations of their resistance from both the ���view from below,��� which is learned through the animals��� caretakers, and a ���view from above,��� which is gleaned from their representations in corporate-driven mainstream media.

Lipase-Mediated Enzymatic Catalysis For The Synthesis of New Chiral Polymers

Immobilized lipase B from Candida antarctica (N435) was investigated as a potential biocatalyst to generate silicone-based chiral polymers from monomers derived from the enzymatic dihydroxylation of bromobenzene. Several conditions and parameters have been investigated for this purpose and lipase transesterification preference to each of the free secondary alcohols in the chiral monomers was documented. The N435 was challenged with a series of substrates where the free alcohol moieties were systematically protected in order to study the substrate preference(s) for the transesterification reactions.

Cyclotetrasiloxane Frameworks for the Chemoenzymatic Synthesis of Oligoesters

Immobilized lipase B from Candida antarctica (Novozym�� 435, N435) was utilized as part of a chemoenzymatic strategy for the synthesis of branched polyesters based on a cyclotetrasiloxane core in the absence of solvent. Nuclear magnetic resonance spectroscopy and matrix-assisted laser desorption ionization time-of-flight mass spectrometry were utilized to monitor the reactions between tetraester cyclotetrasiloxanes and aliphatic diols. The enzyme-mediated esterification reactions can achieve 65��� 80% consumption of starting materials in 24���48 h. Longer reaction times, 72���96 h, resulted in the formation of cross-linked gel-like networks. Gel permeation chromatography of the polymers indicated that the masses were Mw �� 11 400, 13 100, and 19 400 g mol 1 for the substrate pairs of C7D4 ester/ octane-1,8-diol, C10D4 ester/pentane-1,5-diol and C10D4 ester/octane-1,8-diol respectively, after 48 h. Extending the polymerization for an additional 24 h with the C10D4 ester/octane-1,8-diol pair gave Mw �� 86 800 g mol 1. To the best of our knowledge this represents the first report using lipase catalysis to produce branched polymers that are built from a cyclotetrasiloxane core.

The Ligand and Membrane-binding Behaviour of the Phosphatidylinositol Transfer Proteins (PITPa & PITPb)

Human Class I phosphatidylinositol transfer proteins (PITPs) exists in two forms: PITP�� and PITP��. PITPs are believed to be lipid transfer proteins based on their capacity to transfer either phosphatidylinositol (PI) or phosphatidylcholine (PC) between membrane compartments in vitro. In Drosophila, the PITP domain is found to be part of a multi-domain protein named retinal degeneration B (RdgB��). The PITP domain of RdgB�� shares 40 % sequence identity with PITP�� and has been shown to possess PI and PC binding and transfer activity. The detailed molecular mechanism of ligand transfer by the human PITPs and the Drosophila PITP domain remains to be fully established. Here, we investigated the membrane interactions of these proteins using dual polarization interferometry (DPI). DPI is a technique that measures protein binding affinity to a flat immobilized lipid bilayer. In addition, we also measured how quickly these proteins transfer their ligands to lipid vesicles using a fluorescence resonance energy transfer (FRET)-based assay. DPI investigations suggest that PITP�� had a two-fold higher affinity for membranes compared to PITP��. This was reflected by a four-fold faster ligand transfer rate for PITP�� in comparison to PITP�� as determined by the FRET assay. Interestingly, DPI analysis also demonstrated that PI-bound human PITPs have lower membrane affinity compared to PC-bound PITPs. In addition, the FRET studies demonstrated the significance of membrane curvature in the ligand transfer rate of PITPs. The ligand transfer rate was higher when the accepting vesicles were highly curved. Furthermore, when the accepting vesicles contained phosphatidic acid (PA) which have smaller head groups, the transfer rate increased. In contrast, when the accepting vesicles contained phosphoinositides which have larger head groups, the transfer rate was diminished. However, PI, the favorite ligand of PITPs, or the presence of anionic lipids did not appear to influence the ligand transfer rate of PITPs. Both DPI and FRET examinations revealed that the PITP domain of RdgB�� was able to bind to membranes. However, the RdgB�� PITP domain appears to be a poor binder and transporter of PC.

Role of Phosphorylation of the Oxysterol Binding Protein (OSBP) in (PI(4)P) and Sterol-Containing Membrane Recognition and Binding

Studies have demonstrated that the oxysterol binding protein (OSBP) acts as a phosphatidylinositol phosphate (PIP)-sterol exchanger at membrane contact sites (MCS) of the endoplasmic reticulum (ER) and Golgi. OSBP is known to pick up phosphatidylinositol-4-phosphate (PI(4)P) from the ER, transfer it to the trans-Golgi in exchange for a cholesterol molecule that is then transferred from the trans-Golgi to the ER. Upon further examination of this pathway by Ridgway et al. (1), it appeared that phosphorylation of OSBP played a role in the localization of OSBP. The dephosphorylation state of OSBP was linked to Golgi localization and the depletion of cholesterol at the ER. To mimic the phosphorylated state of OSBP, the mutant OSBP-S5E was designed by Ridgway et al. (1). The lipid and sterol recognition by wt-OSBP and its phosphomimic mutant OSBP-S5E were investigated using immobilized lipid bilayers and dual polarization interferometry (DPI). DPI is a technique in which the protein binding affinity to immobilized lipid bilayers is measured and the binding behavior is examined through real time. Lipid bilayers containing 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and varying concentrations of PI(4)Ps or sterols (cholesterol or 25-hydroxycholesterol) were immobilized on a silicon nitride chip. It was determined that wt-OSBP binds differently to PI(4)P-containing bilayers compared to OSBP-S5E. The binding behavior suggested that wt-OSBP extracts PI(4)P and the change in the binding behavior, in the case of OSBP-S5E, suggested that the phosphorylation of OSBP may prevent the recognition and/or extraction of PI(4)P. In the presence of sterols, the overall binding behavior of OSBP, regardless of phosphorylation state, was fairly similar. The maximum specific bound mass of OSBP to sterols did not differ as the concentration of sterols increased. However, comparing the maximum specific bound mass of OSBP to cholesterol with oxysterol (25-hydroxycholesterol), OSBP displayed nearly a 2-fold increase in bound mass. With the absence of the wt-OSBP-PI(4)P binding behavior, it can be speculated that the sterols were not extracted. In addition, the binding behavior of OSBP was further tested using a fluorescence based binding assay. Using 22-(N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)amino)-23,24-bisnor-5-cholen-3��-ol (22-NBD cholesterol), wt-OSBP a one site binding dissociation constant Kd, of 15 �� 1.4 nM was determined. OSBP-S5E did not bind to 22-NBD cholesterol and Kd value was not obtained.