Vibrio cholerae acquiert les gènes de la toxine cholérique suite à l’infection par le phage CTXphi et devient par la suite une bactérie pathogène. L'infection se déroule en deux étapes : une interaction entre le pilus TCP et le domaine pIIIN2ctx, puis la formation du complexe TolAIIIV.c/pIIIN1ctx. Cette seconde étape est l’étape limitante de l’infection. L’objectif général de ma thèse a été d’étudier les forces motrices associées à cette étape.1) J’ai étudié les mécanismes moléculaires associés à la spécificité phage/bactérie en ciblant les interactions électrostatiques et le feuillet intermoléculaire par RMN et double hybride bactérien.2) J’ai résolu la structure de TolAIIIV.c libre par RMN. La comparaison des structures de cette protéine à l’état libre et liée ont permis de mettre en évidence un changement conformationnel et de proposer un mécanisme moléculaire d’ajustement induit. De plus, l’étude de la flexibilité de la protéine par RMN à haute pression (HP) a montré l’importance de la cavité interne de la protéine TolAIII pour favoriser l’ajustement induit lors de la formation du complexe TolAIIIV.c/pIIIN1CTX.3) J’ai vérifié si l’ajustement induit observé précédemment était lié à la présence de cette cavité d’une manière générale chez les protéines TolAIII. Une étude de dispersion de relaxation et de RMN à HP de la protéine TolAIIIE.c a permis de vérifier l’importance de cette cavité pour le mécanisme d’ajustement induit essentiel à cette famille de protéine. De plus, nous avons corrélée la flexibilité particulière de la protéine TolAIIIE.c à la présence d’une boucle qui lui confère une certaines flexibilité nécessaires pour interagir avec plusieurs partenaires. / Vibrio cholerae becomes a pathogen after CTXphi phage infection. The phagic infection is a wo step mechanism: first TCP pilus binds to pIIIN2ctx, then TolAIIIV.c binds to pIIIN1ctx. The second step is essential for the acquisition of genes of cholera toxins leading to cholera disease. The main goal of my thesis is to study the driving forces associated to the phage infection.First, I studied the molecular mechanism associated to phage/bacteria specificity targeting electrostatic bonds and hydrophobic interactions within the intermolecular sheet. These experiments use NMR and bacterial two hybrids methods. Our results show that electrostatic bonds are essential for the complex formation.Second, I solved the solution structure of TolAIIIV.c using NMR. The comparison of the structures of free and bound states of TolAIIIV.c, shows an associate conformational change and lead us to propose a model for the molecular mechanism of the induced fit. Then the study of the TolAIII flexibility, using high pressure NMR shows the importance of TolAIII cavity to promote the induced fit during TolAIIIV.c/pIIIN1ctx complex formation.Finally, we wanted to show if the induced fit is correlated to the presence of cavity in TolAIII family. A study using NMR relaxation dispersion and high-pressure NMR experiments on TolAIIIE.c shows the importance of this cavity for the induced fit. The presence of a loop at the top of the N-terminal helix in TolAIIIE.c leads to the protein to have several conformations necessary to interact with many partners.

京都大学 / 0048 / 新制・課程博士 / 博士(エネルギー科学) / 甲第22797号 / エネ博第411号 / 新制||エネ||79(附属図書館) / 京都大学大学院エネルギー科学研究科エネルギー基礎科学専攻 / (主査)教授 片平 正人, 准教授 小瀧 努, 教授 森井 孝 / 学位規則第4条第1項該当 / Doctor of Energy Science / Kyoto University / DGAM

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.

京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第19521号 / 理博第4181号 / 新制||理||1600(附属図書館) / 32557 / 京都大学大学院理学研究科化学専攻 / (主査)教授 林 重彦, 教授 谷村 吉隆, 教授 松本 吉泰 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM

京都大学 / 新制・課程博士 / 博士(理学) / 甲第24441号 / 理博第4940号 / 新制||理||1706(附属図書館) / 京都大学大学院理学研究科化学専攻 / (主査)准教授 齊藤 尚平, 教授 依光 英樹, 教授 畠山 琢次 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM

No description available.

Yes / Fluorescence spectroscopy on a series of aqueous solutions of poly(acrylic acid) containing a luminescent label showed that polymers with molar mass, Mn < 16.5 kDa did not exhibit a pH responsive conformational change, which is typical of higher molar mass poly(acrylic acid). Below this molar mass, polymers remained in an extended conformation, regardless of pH. Above this molar mass, a pH-dependent conformational change was observed. Diffusion-ordered nuclear magnetic resonance spectroscopy confirmed that low molar mass polymers did not undergo a conformational transition, although large molar mass polymers did exhibit pH-dependent diffusion. / Engineering and Physical Sciences Research Council (EPSRC) funded CASE award PhD. Part funded by flocculant manufacturer SNF (UK) Ltd.

Yes / Globular proteins are important both as therapeutic agents and excipients. However, their fragile native conformations can be denatured during pharmaceutical processing, which leads to modification of the surface energy of their powders and hence their performance. Lyophilized powders of hen egg-white lysozyme and β-galactosidase from Aspergillus oryzae were used as models to study the effects of mechanical denaturation on the surface energies of basic and acidic protein powders, respectively. Their mechanical denaturation upon milling was confirmed by the absence of their thermal unfolding transition phases and by the changes in their secondary and tertiary structures. Inverse gas chromatography detected differences between both unprocessed protein powders and the changes induced by their mechanical denaturation. The surfaces of the acidic and basic protein powders were relatively basic, however the surface acidity of β-galactosidase was higher than that of lysozyme. Also, the surface of β-galactosidase powder had a higher dispersive energy compared to lysozyme. The mechanical denaturation decreased the dispersive energy and the basicity of the surfaces of both protein powders. The amino acid composition and molecular conformation of the proteins explained the surface energy data measured by inverse gas chromatography. The biological activity of mechanically denatured protein powders can either be reversible (lysozyme) or irreversible (β-galactosidase) upon hydration. Our surface data can be exploited to understand and predict the performance of protein powders within pharmaceutical dosage forms.

2024 / Within the chaos of intracellular signaling pathways, scaffold proteins serve as the control boards to organize the comings and goings of a variety of signals and proteins. There are over 300 known scaffold proteins, which act as switchboards that lessen this chaos of the cellular “soup” and enable proper cellular responses. While the terms scaffold, adaptor, docking, and anchoring protein have sometimes been used interchangeably, this dissertation focuses on scaffolds as a distinct class of proteins that are central to enhancing signaling cascades, have multiple interaction domains to facilitate higher order complex formation, and are highly conserved. In addition, scaffold proteins are not simply inert or passive platforms. Rather, there are multiple examples of scaffolds that, while catalytically inactive, are dynamic in their mechanism of action. Studying these dynamic roles is critical to our understanding of signaling cascades and how signaling-related disease states occur. NF-κB Essential Modulator (aka NEMO or IKK gamma) is a scaffold protein that has a pivotal role in the NF-κB signaling pathway. In this dissertation, NEMO is examined both for its changes in activity upon mutation and the mechanical/structural effects of mutations within a highly conserved central region termed the intervening domain (IVD). The IVD of NEMO is essential for proper function of the protein and for the coordination of phosphorylation of the inhibitor IκBα in the activation of canonical NF-κB pathway. The proper structural organization of NEMO is required for cytokine-induced activation of IκB kinase (IKK), and the impact that the IVD has on this structural organization is demonstrated. Mutations within the conserved IVD core are detrimental to the activation of the canonical NF-κB pathway and reduce the ability of NEMO to form ubiquitin-induced liquid-liquid phase separated droplets in vitro. The effects of the IVD mutations also correlate with a reduced ability of NEMO to form signal-induced puncta in vivo. Thermal and chemical denaturation studies of truncated NEMO variants indicate that the IVD affects the stability of the full-length NEMO molecule, due to conflicting structural demands of this region on upstream and downstream domains. This conformational strain in the IVD mediates allosteric communication between N- and C-terminal regions of NEMO. Overall, these findings support the hypothesis that the IVD of NEMO participates in signal-induced activation of the IKK/NF-κB pathway by acting as a mediator of conformational change in NEMO. These findings demonstrate the importance of conformational change for scaffold protein function and provide new information about how clinical mutations in scaffolds can affect function and can serve as targets for therapeutic intervention.

Molecular Biology has allowed the characterization and manipulation of the molecules of life in the wet lab. Also the structures of those macromolecules are being continuously elucidated. During the last decades of the past century, there was an increasing interest to study how the different genes are organized into different organisms (‘genomes’) and how those genes are expressed into proteins to achieve their functions. Currently the sequences for many genes over several genomes have been determined. In parallel, the efforts to have the structure of the proteins coded by those genes go on. However it is experimentally much harder to obtain the structure of a protein, rather than just its sequence. For this reason, the number of protein structures available in databases is an order of magnitude or so lower than protein sequences. Furthermore, in order to understand how living organisms work at molecular level we need the information about the interaction of those proteins. Elucidating the structure of protein macromolecular assemblies is still more difficult. To that end, the use of computers to predict the structure of these complexes has gained interest over the last decades. The main subject of this thesis is the evaluation of current available computational methods to predict protein – protein interactions and build an atomic model of the complex. The core of the thesis is the evaluation protocol I have developed at Service de Conformation des Macromolécules Biologiques et de Bioinformatique, Université Libre de Bruxelles, and its computer implementation. This method has been massively used to evaluate the results on blind protein – protein interaction prediction in the context of the world-wide experiment CAPRI, which have been thoroughly reviewed in several publications [1-3]. In this experiment the structure of a protein complex (‘the target’) had to be modeled starting from the coordinates of the isolated molecules, prior to the release of the structure of the complex (this is commonly referred as ‘docking’). The assessment protocol let us compute some parameters to rank docking models according to their quality, into 3 main categories: ‘Highly Accurate’, ‘Medium Accurate’, ‘Acceptable’ and ‘Incorrect’. The efficiency of our evaluation and ranking is clearly shown, even for borderline cases between categories. The correlation of the ranking parameters is analyzed further. In the same section where the evaluation protocol is presented, the ranking participants give to their predictions is also studied, since often, good solutions are not easily recognized among the pool of computer generated decoys. An overview of the CAPRI results made per target structure and per participant regarding the computational method they used and the difficulty of the complex. Also in CAPRI there is a new ongoing experiment about scoring previously and anonymously generated models by other participants (the ‘Scoring’ experiment). Its promising results are also analyzed, in respect of the original CAPRI experiment. The Scoring experiment was a step towards the use of combine methods to predict the structure of protein – protein complexes. We discuss here its possible application to predict the structure of protein complexes, from a clustering study on the different results. In the last chapter of the thesis, I present the preliminary results of an ongoing study on the conformational changes in protein structures upon complexation, as those rearrangements pose serious limitations to current computational methods predicting the structure protein complexes. Protein structures are classified according to the magnitude of its conformational re-arrangement and the involvement of interfaces and particular secondary structure elements is discussed. At the end of the chapter, some guidelines and future work is proposed to complete the survey.