The canonical Wnt pathway is a vitally important signalling pathway that plays an important role in cell proliferation, differentiation and fate decisions in embryonic development and in the maintenance of adult tissues. The twelve Armadillo (ARM) repeat-containing protein beta-catenin acts as the signal transducer in this pathway and is continuously degraded in the cytosol by the beta-catenin destruction complex (BDC). Upon receiving the Wnt signal the BDC is inactivated, allowing beta-catenin to accumulate in the cytosol and be transported to the nucleus where it binds to the TCF/LEF family of transcription factors, inducing the expression of cell cycle promotor genes. In this Thesis I describe investigations into the roles of leucine-rich repeat kinase 2 (LRRK2) and the transcription factor TCF7L2 within this signalling pathway. LRRK2 is a large multi-domain protein with strong links to Parkinson’s disease and suggested to play a role in inactivating the BDC in response to the Wnt signal. A recent paper proposed that the previously uncharacterised regions of LRRK2 contain a series of tandem repeat sub-domains. I began an investigation into these sub-domains but I was unable to produce soluble protein constructs despite the use of a range of common techniques, and so I was forced to conclude this project early. The main body of this thesis focuses on the interaction between the intrinsically disordered TCF7L2 and the repeat protein beta-catenin, a very long interface of approximately 4800 Å2 that spans from the third to the eleventh ARM repeat of beta-catenin and residues 12 to 50 of TCF7L2, as determined by X-ray crystal structures. First, a fluorescence reporter system for the binding interaction was developed and used to determine the kinetic rate constants for the association and dissociation of the wild-type construct using stopped-flow fluorescence spectroscopy and time-dependent fluorescence spectroscopy. It was found that association of TCF7L2 and beta-catenin was rapid (7.3 ± 0.1 x107 M-1s-1) with only a single phase was observed, whereas dissociation was biphasic and slow (5.7 ± 0.4 x10-4 s-1, 15.2 ± 2.8 x10-4 s-1). Using either of these two dissociation rate constants the calculated Kd value obtained is much lower than the values previously reported in the literature (8 ± 1 / 20 ± 2 pM compared with 16 nM). This reporter system was then used to investigate the striking variability between three crystal structures previously obtained for the TCF7L2-beta-catenin complex, in which different regions of TCF7L2 show different elements of secondary structure. Mutational analysis revealed that the interface residues on TCF7L2 identified in these structures make little or no contribution to the overall binding affinity, pointing to a transient nature of these contact in solution and suggesting that the observed differences between the structures are due to differences in crystal packing. Further experiments into the effect of osmolarity on the binding equilibrium and kinetics supported this conclusion and suggest a change in the association/dissociation mechanism as a function of ionic strength. Lastly, further mutational analysis of TCF7L2 revealed two regions that contribute particularly strongly to the binding kinetics, suggesting that TCF7L2-beta-catenin assembly proceeds via a two-site avidity mechanism. Some of the most destabilising variants display two additional dissociation phases, indicating the presence of an alternative dissociation pathway that is inaccessible to the wild-type. In summary, the results presented here provide insights into the kinetics of molecular recognition of a long intrinsically disordered region with an extended repeat protein surface, a process shown to involve multiple routes with multiple steps in each.

Stopped-flow experiments in which the NAD-malic enzyme was preincubated with different reactants at near saturating substrate concentrations suggest a slow isomerization of the E:NAD:Mg complex. The lag is eliminated by preincubation with Mg˙² and malate suggesting that the formation of E:Mg:Malate either bypasses or speeds up the slow isomerization step. Circular dichroic spectral studies of the secondary structural changes of the native enzyme in the presence and absence of substrates supports the existence of conformational changes with NAD˙ and malate. Thus, a slow conformational change of the E:NAD:Mg complex is likely one of the rate-limiting steps in the pre-steady state.

京都大学 / 新制・課程博士 / 博士(理学) / 甲第23031号 / 理博第4708号 / 新制||理||1675(附属図書館) / 京都大学大学院理学研究科化学専攻 / (主査)教授 寺嶋 正秀, 教授 林 重彦, 教授 渡邊 一也 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM

This thesis is focused on the determination of the propene polymerization kinetics on phthalate and nonphthalate diester Ziegler-Natta MgCl2-supported catalysts under the industrial conditions. The kinetic profiles were determined by various laboratory techniques for propene polymerization. For assessing the profiles were utilized batch gas and liquid polymerization modes in 2-litre and 4-litre reactors. Finally, the results were complemented with the runs performed in a unique Stopped-Flow apparatus, which allows polymerization of liquid propene at very short polymerization times. The kinetics profiles of both catalysts were determined and compared by combination of experimental data of these techniques. The basic properties of the synthesized polymeric powders were measured, such as the melt flow index, bulk density and amount of polypropene fraction soluble in cold xylene.

Phenylalanine hydroxylase (PAH, EC: 1.14.16.1) is a non-heme iron tetrahydropterin-dependent monooxygenase that maintains phenylalanine (L-Phe) homeostasis via conversion of L-Phe to L-Tyr. PAH is an allosteric enzyme that converts from an inactive T-state to an active R-state upon addition of substrate, L-Phe. Allosteric activation is correlated with physical and structural changes within the enzyme and a large activation energy. Crystal structures of PAH have not identified the location of the allosteric effector binding site. Herein, we report computational protein mapping efforts using the FTmap algorithm and experimental site-directed mutagenesis studies designed to define and screen possible L-Phe allosteric binding sites. Mass spectroscopic analysis of PAH proteolytic fragments obtained after photo-crosslinking with 2-azido-3-phenylpropanoate overlapped with one computationally derived allosteric binding pocket containing residues 110-120 and 312-317. Ligand docking studies, fluorescence measurements, binding affinity and activity assays on wild-type and mutant enzymes further characterized the shape and specificity of this pocket. Thermodynamic studies using surface acoustic wave (SAW) biosensing determined the affinity of L-Phe for the allosteric site. Two L-Phe binding sites were observed upon SAW titrations, corresponding to the active and allosteric sites respectively ( K D,app^on 113 ± 12 µM active site, K D,app^on 680 ± 20 µM allosteric site). Site-directed mutagenesis was performed to prepare mutant enzymes containing a single tryptophan (L-Trp) residue. The fluorescence signatures of each of the three native L-Trp residues in PAH were determined by titrations with L-Phe. Trp187 primarily reports L-Phe induced allosteric conformational changes, while Trp120 reports active site L-Phe binding. Trp326 reports small signals of both active and allosteric site changes. Variable temperature stopped-flow fluorescence kinetic studies elucidated a working mechanism for L-Phe allosteric activation of PAH. Fluorescent signals from wild-type, single, and double L-Trp PAH mutants have been used to build kinetic mechanisms for the L-Phe binding in each subunit and subsequent active site reorganization or allosteric conformational change. In these mechanisms, the enzyme has reduced activity (1-2% of wtPAH) until both L-Phe induced active and allosteric site conformational changes have occurred. Failure of either activation step prevents enzyme turnover and is the chemical-based cause of the metabolic condition phenylketonuria.

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Le monoxyde d'azote est exclusivement synthétisé chez les mammifères par une famille d’hémoprotéines, les NO-Synthases. Le cœur de l’activité des NO-Synthases est l’activation de l’oxygène c'est-à-dire l’activation de l’intermédiaire réactionnel FeIIO2. Cette étape est contrôlée par la réactivité intrinsèque du fer, par les transferts de proton et les transferts d’électron. Elle doit être parfaitement maîtrisée car elle contrôle le chemin catalytique emprunté et la nature du produit final. Comprendre l’étape d’activation de l’oxygène est essentiel à la compréhension du rôle biologique et/ou pathologique de la NO-Synthase de mammifère. Cette question s'étend aux NO-Synthases bactériennes pour lesquelles on ne connait ni le mécanisme moléculaire ni la fonction biologique. Ce manuscrit propose une analyse approfondie de l’étape d’activation de l’oxygène de la NO-Synthase. Dans un premier temps, nous avons étudié l’influence de l’environnement proximal sur la réactivité intrinsèque du fer et l’activation de l’oxygène. Nous avons généré des protéines mutées qui modifient les propriétés électroniques de la liaison proximale de l’hème. Ces protéines mutées ont été caractérisées par différentes spectroscopies (résonance paramagnétique électronique, Raman de résonance). Dans un second temps nous avons directement étudié le complexe FeIIO2, en présence d’analogues de substrat, grâce à des analyses de cinétique rapide en flux continu et en flux arrêté (stopped-flow). Dans un troisième temps, le rôle du cofacteur tetrahydrobioptérine dans le transfert de proton et d’électron a été étudié par une méthode de piégeage à des temps très courts : le freeze-quench. L'ensemble de nos résultats montrent que l’activation de l’oxygène est régulée par les propriétés électro-donneuses du ligand proximal et par le réseau de liaisons H distal. Nous mettons en évidence des différences dans le rôle redox du cofacteur tetrahydrobioptérine entre la NO-Synthase de mammifère et la NO-Synthase bactérienne. La difficulté majeure pour comprendre l’étape d’activation de l’oxygène de la NO-Synthase réside dans la complexité et la rapidité de la réaction catalytique. Dans ce contexte, nous avons cherché à adapter une méthodologie qui a prouvé son efficacité dans le cas des cytochromes P450 : la cryo-réduction couplée à des sauts en température. / Nitric oxide is exclusively synthesized by NO-Synthases in mammals. The heart of the NO-synthase activity is oxygen activation, which corresponds to the activation of the FeIIO2 intermediate. This step depends on the heme electronic properties and on the electron and proton transfers. Oxygen activation has to be well mastered to control exactly the nature of the end-product. Understanding the oxygen activation step is necessary to better understand the biological/pathological role of the mammalian NO-Synthases. Furthermore, bacterial NO-Synthases function and oxygen activation mechanism are unknown. This PhD work proposes a deep analysis of the oxygen activation step in NO-Synthases. First, proximal environment has been studied with mutated proteins. These mutations impact the electronic properties of the heme proximal bond. Spectroscopic analyses of these mutants have been done by electron paramagnetic resonance and resonance Raman. Then, we have studied the FeIIO2 intermediate with substrate analogs which has necessitated continuous flow and stopped-flow analyses. Finally, the role of the tetrahydrobiopterin cofactor in the electron and proton transfer has been studied and clarified thanks to a very fast trapping method : the freeze-quench. Our results show that the oxygen activation step is elaborately controlled by the proximal bond electron donation and the distal H bond network. At the same time we show some differences between mammalian and bacterial NO-Synthases concerning the redox role of the tetrahydrobiopterin cofactor. The major obstacle to understand the oxygen activation step resides in the complexity of the active site chemistry and the rate of catalytic reactions. For this reason, we propose to adapt an already successful protocol to trap some intermediates in the cytochromes P450 mechanism : cryo-reduction coupled with temperature jumps.