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<p> This thesis describes the ionic strength and ion binding effects on the oxidation reduction properties of cytochrome c and its lysine modified derivatives.</p> <p> Cytochrome c has been modified in two different ways: a complete modification of all lysine residues and specific modification of one lysine residue. Some properties of the modified derivatives are described.</p> <p> Ion binding properties of cytochrome c and its lysine modified derivatives were studied by measuring the apparent equilibrium constant of the reaction between the ferri- form of the protein and potassium ferrocyanide. It was found that unmodified cytochrome c binds one cation (K+, Na+) per molecule, and binding is much stronger to the reduced form of the protein. Binding of cations is not changed upon modification of the lysine residues. For binding of the chloride, there are two binding sites on the cytochrome c molecule, and the binding is much stronger to the oxidized form of the protein. It was shown that upon the modification of the lysine residues in either way the binding of chloride was considerably changed. It was concluded that one of these two binding sites for chloride on cytochrome c involves lysine residue, probably the residue number 13.</p> / Thesis / Master of Science (MSc)

Deux thématiques principales ont été étudiées au cours de cette thèse. La première partie porte sur la synthèse de complexes de manganèse dérivés de porphyrines et de salens. L'activité catalytique de ces complexes a été évaluée dans l'époxydation d'alcènes non-Fonctionnalisés. Suite à cette étude, les propriétés électroniques des ligands ont été étudiées, notamment par le biais de la complexation d'anions. Dans une deuxième étape, nous nous sommes intéressés à la synthèse de phosphines P-Chirogéniques. Afin de trouver un substitut à l'éphédrine, couramment utilisée dans ces synthèses, des dérivés du (1S,2S)-2-Aminocyclohexanol et de la D-Glucosamine ont été synthétisés. L'utilisation de groupements sulfonamides a permis l'obtention aisée d'oxazaphospholidines N-Tosylées. L'un ou l'autre diastéréoisomère de cet hétérocycle peut être obtenu en fonction du degré d'oxydation du réactif phosphoré utilisé. Avec cette stratégie, divers oxydes de phosphines ont été obtenus avec de bons rendements et de bonnes énantiosélectivités / This thesis is divided in two parts. The first part focuses on the synthesis of manganese complexes derived from porphyrins and salens. The catalytic activity of these complexes were evaluated toward the epoxidation of unfunctionalized alkenes. Next, the electronic properties of the ligands were evaluated using their anion binding properties. In a second part, we were interested in the synthesis of P-Chirogenic phosphines. In order to find a surrogate to ephedrine, that is commonly used in those syntheses, derivatives from (1S,2S)-2-Aminocyclohexanol and D-Glucosamine were synthesized. The use of sulfonamides allows the access to N-Tosylated oxazaphospholidines. Both diastereoisomers could be synthesized depending on the oxydation state of the phosphine precursor. Using this strategy, various phosphine oxides were obtained in good yields and enantioselectivities

The periplasmic binding protein (PBP) superfamily is found throughout the genosphere of both prokaryotic and eukaryotic organisms. PBPs function as receptors in bacterial solute transport and chemotaxis systems; however the same fold is also used in transcriptional regulators, enzymes, and eukaryotic neurotransmitter receptors. This versatility has been exploited for structure-based computational protein design experiments where PBPs have been engineered to bind novel ligands and serve as biosensors for the detection of small-molecule ligands relevant to biomedical or defense-related interests. In order to further understand functional adaptation from a structural biology perspective, and to provide a set of robust starting points for engineering novel biosensors by structure-based design, I have characterized the ligand-binding properties and solved the structure of nine PBPs from various thermophilic bacteria. Analysis of these structures reveals a variety of mechanisms by which diverse function can be encoded in a common fold. It is observed that re-modeling of secondary structure elements (such as insertions, deletions, and loop movements), and re-decoration of amino acid side-chains are common diversification mechanisms in PBPs. Furthermore, the relationship between hinge-bending motion and ligand binding is critical to understanding the function of natural or engineered adaptations in PBPs. Three of these proteins were solved in both the presence and absence of ligand which allowed for the first time the observation and analysis of ligand-induced structural rearrangements in thermophilic PBPs. This work revealed that the magnitude and transduction of local and global ligand-induced motions are diverse throughout the PBP superfamily. Through the analysis of the open-to-closed transition, and the identification of natural structural adaptations in thermophilic members of the PBP superfamily, I reveal strategies which can be applied to computational protein design to significantly improve current strategies. / Dissertation

Poly(ADP-ribosyl)ation, a covalent modification of proteins catalyzed by poly(ADP-ribose) polymerases (PARPs), plays a crucial role in regulating DNA repair, DNA replication, and cell death. Poly(ADP-ribose) Polymerase-1 (PARP-1) is a nuclear zinc-finger DNA-binding protein that is the most extensively studied member of the PARP family. The activation of PARP-1 depends on the N-terminal DNA-binding domain, which consists of two unusually long zinc finger-like motifs (termed FI and FII) of the form CX₂CX₂₈/₃₀HX₂C and a newly discovered zinc-ribbon motif (FIII). Though zinc is indispensible for PARP-1 activity, the metal binding affinities of the unusual zinc fingers of PARP-1 is not yet known. In this dissertation, the second zinc finger of PARP-1 was used as a model peptide to study the binding properties of several divalent metal ions (Co²⁺, Cd²⁺, Zn²⁺, and Pb²⁺). Metal-induced protein folding was investigated by circular dichroism, and the effects of the metal ions on PARP-1 activity were investigated by poly(ADP-ribosyl)ation activity assays. This study represents the first detailed biochemical characterization of the PARP zinc fingers. The functional role of each zinc finger in DNA damage recognition is critical for understanding how PARP-1 is involved in DNA repair. Thus, we constructed a series of PARP-1 zinc finger variant proteins and investigated their DNA binding properties and their effects on PARP activity. Using a combination of southwestern blotting and activity assays, we demonstrated that FII is more important for DNA binding, while FI and FIII seem to facilitate PARP activity. The DNA sequence-independent binding properties of PARP-1 were further characterized using DNA probes bearing defined secondary structures. Together, our results indicate that the zinc fingers help position the enzyme at specific DNA damage sites, and also help to activate the catalytic domain upon DNA binding. PARP-1 is involved in caspase-independent apoptosis, and the translocation of apoptosis inducing factor (AIF) out of the mitochondrial matrix has been shown to require PARP-1 activity. However, it is not readily apparent how the catalytic activity of PARP-1 (a nuclear protein) triggers the release of AIF from the mitochondrial matrix. In an attempt to understand the relationship between PARP-1 activity and caspase-independent apoptosis, we demonstrate here that AIF is an in vitro protein substrate for PARP-1. The possible implications of this finding will be discussed. / text

Peanut, a major allergenic food, has life-threatening potential and is difficult to be totally avoided due to its common use in processed foods. Thermal processing can influence the allergenic properties of peanuts. However, the kinetics of the reactions caused by thermal processing has not been characterized. In our study, kinetics of the commonly used thermal processing methods on a commercial peanut cultivar (Virginia) using five time intervals was conducted. Water-soluble and SDS-sample buffer soluble proteins were extracted sequentially, and analyzed by sodium-dodecyl-sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and western-blot using human plasma containing IgE antibodies. The relationships between thermal processing (time) and log transformed water-soluble/total extractable major allergen content could be explained by a simple linear regression kinetic model for most of the processing methods (except high-pressure steaming). Among all the methods with optimal processing point, frying for 6 min had relatively lower IgE binding (linear epitopes) ratio may be due to the fact that this processing condition causing break down, cross-linking and aggregation of Ara h 2, and relatively lower solubility. Besides thermal processing, enzymatic processing also is considered to be an effective method in the allergenicity of peanuts. Eleven peanut lines (Coded MS-1~MS-11, MS-9 is the check and a common cultivar namely Valencia) were pre-screened from 122 peanut lines harvested in 2015 for allergen levels. These pre-screened lines were re-planted in 2016 for further analysis. One line, MS-7, was selected for lower Ara h 1 (8.5-9.5% of total protein) and Ara h 2 (4.2-6.6% of total protein) content in 2015 and 2016. Roasted MS-9 (check) peanut powders were used for enzymatic treatment for enzyme selection. A first order kinetic reaction model was conducted to describe the relationship between enzyme concentration (0-400AzU/g) and IgE-binding property reduction. Among eight food-grade enzymes, bromelain, papain and ficin hydrolysates had lower IgE-binding properties in terms of high IgE-binding property reducing rate (K, ≥ 0.4) and were selected for the following study. MS-7 (selected) & MS-9 (at level of 200AzU/g) hydrolyzed by three selected enzymes (200AzU/g) were used for IgE binding property comparison, TGase crosslinking and functional properties study. After hydrolyzed by the selected enzymes (200 AzU/g), the emulsion and foaming stabilities were decreased. Emulsion and foaming stabilities were increased in TGase (5U/g protein) crosslinked hydrolysates, which were even higher than soy protein isolate (SPI). The IgE-binding properties of TGase treated hydrolysates were similar to the hydrolysates without TGase treatment. MS-7 hydrolysates (with/without TGase) possessed less IgE-binding properties and similar functionality as compared with MS-9 hydrolysates.