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Protein folding is the process during which an extended and unstructured polypeptide converts to its compact folded structure that is most often the functional state. The process has been characterized extensively in dilute buffer in-vitro during the last decades but the actual biological place for this process is the inside of living cells. The cytoplasm of a cell is filled with a plethora of different macromolecules that together occupy up to 40% of the total volume. This large amount of macromolecules restricts the available space to each individual molecule, which has been termed macromolecular crowding. Macromolecular crowding results in excluded volume effects and also increases chances for non-specific interactions. Macromolecular crowding should favor reactions that lead to a decrease in the total occupied volume by all molecules, such as folding reactions. Theoretical models have predicted that the stability of protein folded states should increase in presence of macromolecular crowding due to unfavorable effects on the extended unfolded state. To understand protein folding and function in living systems, we need to have a defined quantitative link between in-vitro dilute conditions (where most biophysical experiments are made) and in-vivo crowded conditions. An important question is thus how macromolecular crowding modifies the biophysical properties of a protein. The work underlying this thesis focused on how macromolecular crowding tunes protein equilibrium stability and kinetic folding processes. To mimic the crowded cellular environment, synthetic sugar-based polymers (Dextrans of different sizes and Ficoll 70) were used as crowding agents (crowders) in controlled in-vitro experiments. In contrast to previous studies which often have focused on one protein and one crowder at a time, the goal here was to make systematic analyses of how size, shape and concentration of the crowders affect both equilibrium and kinetic properties of structurally-different proteins. Three model proteins (cytochrome c, apoazurin and apoflavodoxin) were investigated under crowding by Ficoll 70 and different-size Dextrans, using various spectroscopic techniques such as far-UV circular dichroism and intrinsic tryptophan fluorescence. Thermodynamic models were applied to explain the experimental results. It was discovered that equilibrium stability of all three proteins increased in presence of crowding agents in a crowder concentration dependent manner. The stabilization effect was around 2-3 kJ/mol, larger for the various Dextrans than for Ficoll 70 at the same g/l, but independent of Dextran size (in the range 20 to 70 kDa). To further investigate the cause for the stabilization a theoretical crowding model was applied. In this model, Dextran and Ficoll were modeled as elongated rods and the protein was represented as a sphere, where the folded sphere representation was smaller than the unfolded sphere representation. It is notable that the observed stability changes could be reproduced by this model taking only steric interactions into account. This correlation showed that when using sugar-based crowding agents, excluded volume effects could be studied in isolation and there were no contributions from nonspecific interactions. Time-resolved experiments with apoazurin and apoflavodoxin revealed an increase in the folding rate constants while the unfolding rates were invariant in the presence of crowding agents. For apoflavodoxin and cytochrome c, the presence of crowding agents also altered the folding pathway such that it became more homogeneous (cytochrome c) and it gave less misfolding (apoflavodoxin). These results showed that macromolecular crowding restricts the conformational space of the unfolded polypeptide chain, makes the conformations more compact which, in turn, eliminates access to certain pathways. The results from kinetic and equilibrium measurements on three model proteins, together with available data from the literature, demonstrate that macromolecular crowding effects due to volume exclusion are in the order of a few kJ/mol. Considering the numerous concentration balances and cross-dependent reactions of the cellular machinery, small changes in energetics/kinetics of the magnitudes found here can still have dramatic consequences for cellular fitness. In fact local and transient changes in macromolecular crowding levels may be a way to tune biochemical reactions without invoking gene expression.

Lipid-detergent systems are interesting to study, as the two amphiphiles have very different spontaneous curvature, however readily form mixed micelles in solution. These micelles can be shorter cylindrical micelles or long worm-like micelles. For such a system the size of the micelles varies strongly with solute conditions, being dependent on the total amount of amphiphile in solution, as well as, the lipid to detergent ratio in the micelles. Although the broad phase behaviour of such systems has been studied and is relatively well understood, there are still many open questions remaining. Some of the questions that motivated the work presented are: how the length and composition of the micelles varies within the micellar region, and how the micelles grow? The biologically interesting system under study is lecithin and bile salt, where the equilibrium sizes were experimentally determined for different samples within the micellar region. A model, combining the length of the micelles, with the concentrations of lecithin and bile salt in the system is presented, and is used to calculate the composition of the micelles at equilibrium. The kinetics of the growth of the micelles after a pertubation causing a shift in the equilibrium size has not been studied in detail before. The kinetics of the system are studied using a stopped flow setup, which I specifically designed for neutron scattering experiments. The stopped flow setup allows for the measurement to start 200ms after the initial mixing of the two liquids, after dilution of a solution the micelles relax to a new longer length. The kinetics of this relaxation were studied as a function of the initial and final size of the micelles, as well as, the ionic strength of the solution. The micelles were found to grow through coalescence, where the rate of growth seems to be constant for different sizes of micelles and the time taken for the relaxation depends on the difference between the final and initial lengths of the micelles. The rate of growth is strongly influenced through changing the ionic strength of the solution, indicating the importance of an electrostatic barrier to the fusion of micelles.

Výzkum v této práci byl zaměřen na přípravu a charakterizaci blokových kopolymerů typu polypropylen-blok-poly(propylenu-co-ethylenu) (dále jen PP-blok-EPR). Tyto materiály jsou považovány za účinné kompatibilizátory mezi semi-krystalickou polypropylenovou (PP) matricí a amorfními doménami statistického kopolymeru propylenu a etylenu (EPR) v rázuvzdorném sekvenčním kopolymeru (ICP) a proto byl výzkum zaměřen na zkoumání vlivu přídavku blokového kopolymeru PP-blok-EPR na vlastnosti komerčního ICP. Blokové kopolymery byly připraveny za použití techniky „stopped-flow“. Pro tento účel byla zkonstruována vysokotlaká polymerační „stopped-flow“ aparatura, která umožňuje syntézu kopolymerů PP-blok-EPR za podmínek blízkých podmínkám v průmyslových reaktorech pro výrobu komerčních ICP materiálů. Aparatura umožňuje vyrábět PP-blok-EPR polymer v množství dostačující na jeho charakterizaci a následnou přípravu směsí s komerčním ICP. Velmi krátké polymerační časy (obvykle kolem 0.2 s) kterých bylo dosaženo v kapilárním reaktoru aparatury „stopped-flow“ zajišťuje, že aktivní centra Ziglorova-Nattova katalyzátoru produkují polymer řetězce skládající se z bloku semikrystalického polypropylenu a bloku amorfního EPR kopolymeru. Takovéto molekuly jsou v literatuře popsány jako „skutečné blokové kopolymery PP-blok-EPR“. Kopolymery syntetizované v aparatuře „stopped-flow“ byly frakcionovány preparativní TREF (Temperature Rising Elution Fractionation) metodou a získané frakce byly následně analyzovány pomocí DSC, 13C-NMR a GPC/SEC. Tyto analýzy odhalily přítomnost amorfního EPR ve vysoce krystalické frakci (100-140 °C). Toto zjištění potvrdilo, že významná část polymerních řetězců, připravených v aparatuře „stopped-flow“ jsou blokové kopolymery skládající se z bloku semikrystalického PP homopolymeru a bloku amorfního EPR kopolymeru v jednom polymerním řetězci. Kopolymery získané metodou „stopped-flow" byly v tavenině smíchány s komerčním rázuvdorným kopolymerem ICP. U takto připravených směsí byly vyhodnoceny mechanické vlastnosti, DTMA a reologické vlastnosti a výsledky byly srovnány s vlastmi původního komerčního ICP kopolymeru. Dále byly studovány rozdíly v morfologii a umístění EPR domén v matrici PP prostřednictvím SEM. Zřetelný vliv kopolymeru PP-blok-EPR na vlastnosti ICP byl pozorován zejména v morfologických změnách EPR domén dispergovaných v PP matrici. Tyto změny mají pozitivní vliv na rovnováhu mezi modulem v ohybu a rázovou pevností ICP materiálu. Vliv kopolymeru PP-blok-EPR na reologické vlastnosti ICP byl nevýznamný. Podobně také v případě DTMA nebyl pozorován významný vliv kopolymeru PP-blok-EPR na vlastnosti ICP.

Variable-temperature stopped-flow (VT-SF) electronic spectroscopy (-85 to -50°C) was utilized to study the reactivity properties of a family of synthetic mononuclear and binuclear non-heme iron enzyme active site analogs. This technique was used to investigate the mechanisms of interactions of two diiron complexes, the diferrous [FeII2(H2Hbamb)2(NMI)2] and the mixed valent [FeII,FeIII(H2Hbamb)2]+, with either oxygen-atom donor (OAD) molecules or the mechanistic probe peroxide, 2-methyl-1-phenylprop-2-yl hydroperoxide (MPPH), and substrates containing weak C-H and O-H bonds. Single turnover studies with 9,10-dihydroanthracene (9,10-DHA) and the deuterated analog, d4-9,10-DHA allowed for the determination of kinetic isotope effects (KIE) which show an inverse KIE and evidence of a disproportionation mechanism. Previous investigations showed the rate of catalytic oxidation of cyclohexane to cyclohexanol by [FeII2(H2Hbamb)2(NMI)2] and MPPH decreased over time. Current VT-SF data show evidence of product inhibition by means of a pre-equilibrium process that inhibits the reaction of the oxidant with the [FeII,FeII] complex. Also examined is the ability of the [FeII,FeIII(H2Hbamb)2]+ complex to catalytically oxidize phenols to phenoxyl radicals via a putative [FeIV=O] species. The reactivity properties of substituted phenols that vary in their oxidation potentials and bond dissociation energies (BDE) was investigated by VT-SF electronic spectroscopic studies to gain insight into the mechanism of oxidation by the [FeII,FeIII] complex. Mechanistic studies were also performed utilizing a mononuclear non-heme iron complex [FeII(N2O1)(CH3OH)Cl2], which can bind alpha-keto acids (e.g. alpha-ketoglutarate, benzoylformate) in a bidentate fashion. Reactivity studies utilizing O2 shows coupled decarboxylation of the alpha-keto acid with catalytic oxidation of the methanol solvent formaldehyde (285 turnovers). In non-reactive solvents, the [FeII(N2O1)(alpha-KG)] adduct complex is capable of catalytically oxidizing a variety of substrates such as 9,10-dihydroanthracene, 2,4-di-tert-butyl phenol, cyclohexene, and cyclooctane at 25°C utilizing O2 as the oxidant. Investigations to the binding of alpha-keto acids to the mononuclear iron complex in the absence of O2 by VT-SF as well as binding studies with NO are discussed. Finally, VT-SF studies were performed to probe the reaction of O2 with [FeII(N2O1)(alpha-KG)(CH3OH)] and the proposed mechanism is discussed. The relevance of these data to non-heme iron enzymes like soluble Methane Monooxygenase, Ribonucleotide Reductase, and Taurine Dioxygenase is discussed.

La puissance de la biopile enzymatique à glucose/oxygène est limitée par sa partiecathodique. Afin de contourner cette limitation, nous avons étudié les enzymescathodiques : les Bilirubine oxydases (BODs). Dans le but de mieux appréhender ces BODs, lemécanisme réactionnel, la nature de l’étape limitante et l’effet des sels ont alors été étudiés.Deux mécanismes différents sont retrouvés en fonction du mode de transfert des protons etdes électrons (4 fois 1H+/1e- ou 2 fois 2H+/2e-). De plus, nous avons démontré que l’étapelimitante est l’oxydation du substrat pour les trois substrats testés et que les sels agissent auniveau du cuivre T1. Les principales limitations des BODs sont leur stabilité à 37 °C ainsi queleur inhibition par le NaCl. Deux techniques ont alors été utilisées pour identifier des BODsplus résistantes. La première méthode est l’extraction de nouvelles enzymes à partird’organismes extremophiles. Elle a permis d’isoler la BOD d’Anaerophaga thermohalophilaqui possède une bonne résistance au NaCl mais une densité de courant faible. Dans unsecond temps, afin de reconstruire des séquences ancestrales, la phylogénie de la familledes Bacillus Bacterium a été effectuée. Cette technique a permis l’identification de troisBODs possédant des caractéristiques très intéressantes : la BOD de Bacillus nakamurai etdeux BODs ancestrales (Noeud 10 et Noeud 13). Par exemple, après une heure à 37°C et 140mM de NaCl, le Noeud 10 possède une meilleure densité de courant que la BOD de Bacilluspumilus, qui est l’enzyme utilisée comme base de la phylogénie. La seconde technique estdonc une méthode de choix permettant la découverte de nouvelles enzymes à la fois plusstables et plus résistantes que les enzymes actuelles. Elle ouvre de grandes perspectivespour l’utilisation des BODs comme enzymes cathodiques ou pour d’autres applicationsbiotechnologiques. Enfin, nous avons montré que l’immobilisation de la BOD de B. pumilusdans le matériau Si-(HIPE) permet la décoloration cyclique de colorants chimiques surplusieurs mois. / Power of glucose/oxygen enzymatic biofuel cell is limited by the cathodic part. In order to prevent this limitation, we studied cathodic enzymes: Bilirubin oxidases (BODs). For this purpose, the kinetic mechanism, rate-limiting step and salts effect were determined. Two different mechanisms are observed depending on the electron/proton transfer (4 times1H+/1e- or 2 times 2H+/2e-). We also demonstrated that the rate-limiting step is the substrate oxidation for the three substrates tested and salts act around the T1 copper. Main BODs limitations are their stability at 37°C and their inhibition by NaCl. Two methods were used toidentify the most resistant BODs. The first one was the identification of new enzymes from extremophile organisms. It allows to isolate BOD from Anaerophaga thermohalophila whichhas good NaCl resistance but low current density. In addition, in order to reconstructancestral sequences, phylogeny of Bacillus Bacterium family was performed. This methodidentified three BODs with interesting features: BOD from Bacillus nakamurai and twoancestral BODs (Noeud 10 and Noeud 13). For example, after one hour at 37°C and 140 mMNaCl, Noeud 10 has a better current density than the BOD from Bacillus pumilus, which is theenzyme used as basis for the phylogeny. This second method allowed the discovery of newenzymes that were both more stable and more resistant than actual enzymes. Thistechnique opens up valuable prospects for the use of BODs as cathodic enzymes or for otherbiotechnological applications. In the end, we demonstrated that BOD from B. pumilusimmobilization in Si-(HIPE) materials allows cyclic discoloration of chemical dyes duringseveral months.

Tuberculosis (TB) affects nearly a third of the world’s population and has been termed a ‘Global Emergency’ by the WHO. The emergence of multi/extensively drug resistant (M/XDR) strains of Mycobacterium tuberculosis (Mtb), the causative agent of TB, and the increasing incidences of azole drug resistant sterol demethylases (CYP51) from pathogenic fungi has propelled studies to understand mechanisms of azole drug resistance on the drug target CYP51. Since Mtb is devoid of a sterol biosynthetic pathway, the presence and study of CYP51B1 and 19 other Cytochrome P450s in its genome is important to clarify host-pathogen mechanism of infection and the potential of using azole drugs to treat TB. In this study, CYP51B1 from Mtb was used as the model enzyme to study CYP51 mutants from Candida albicans fluconazole-resistant clinical strains. By protein engineering methods, F89H, L100F, S348F, G388S and R391K CYP51B1 mutants were made and azole drug binding properties were investigated using stopped-flow kinetics and static equilibrium methods. Dissociation constant (Kd) values were derived for a range of commercially available azole drugs by fitting the equilibrium binding data to a hyperbolic equation. Kd values for stopped-flow kinetics were derived by plotting observed binding rates (kobs) across different azole drug concentrations against time, followed by fitting multiple kobs data to a linear equation to derive azole drug de-binding (koff) and binding (kon) rate constants – the Kd was obtained by koff/kon. Extinction coefficient for heme b content in mutants and Wild Type (WT) CYP51B1 were an average of ɛ419 = 96.1 mM-1 cm-1. Biochemical characterisation of the mutants were carried out using established experiments on CYP51 – reduction of Fe(III)-heme to Fe(II)-heme, NO binding to Fe(III)-heme, rates of CO-Fe(II) adduct formation and rates of collapse of the P450 to P420 species in the presence of CO and estriol with redox partners from Mtb. In order to elucidate the effects of the above mutations on the iron-heme catalytic region, electron paramagnetic resonance (EPR) experiments were carried out with and without azole drugs. Circular dichroism (CD), differential scanning calorimetry (DSC) and multi-angled laser light scattering (MALLS) analysis confirmed that F89H, R391K and L100F mutants were stable and homogeneous. Crystallogenesis was successful for the above mentioned mutants and atomic structures were obtained for all mutants and WT CYP51B1 (in ligand-bound and substrate-free forms), except for S348F and G388S mutants which were expressed as inclusion bodies and 60% holoenzyme, respectively. Reconstituted catalytic assays to determine the sterol demethylating propensity of the mutants were carried out using redox partners from Mtb or E. coli, and with lanosterol and dihydrolanosterol as the surrogate substrates. Redox potentiometry showed similar potentials to WT for all mutants except for the G388S mutant which was relatively positive (–102 mV). Redox cycling experiments followed by EPR analysis for mutants and WT resulted in a novel P450 high-spin species at g value 5.84 (80 %) which gradually collapsed to the initial low spin state over 48 h. Expression trials were concurrently carried out on two other Mtb P450 genes – CYP123 (Rv0744c) and CYP136 (Rv3059) products of which may have similar functions to CYP51B1 or may share similar redox partners. CYP123 is located on the same operon as CYP51B1 while CYP136 has a 29% sequence identity to another CYP51 from a marine slime bacterium. Although further work is necessary, in this study CYP123 was expressed totally as inclusion bodies while CYP136 was expressed as soluble apoprotein fused with trigger factor chaperone.

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.