Although the regulation of proteins functions by allosteric interactions has been identified in many subcellular processes, long-range conformational changes in proteins are also known to be induced by molecular switches. A molecular switch based on the cis-trans isomerization of a peptidyl-prolyl bond is capable of inducing a conformational change directly to the protein backbone, which is then propagated throughout the system. However, these switches are elusive and difficult to identify due to their intrinsic dynamics in the biomolecules where they are found. Herein, we explore the conformational dynamics and free energy landscape of the SH2 domain of Interleukin-2-inducible T-Cell Kinase (ITK) to fully understand the conformational coupling between the distal cis-trans molecular switch, and its phosphotyrosine binding pocket. Using multiple microsecond-long all-atom molecular dynamics simulations in explicit water for over a total of 60 μs, we show that the cis-trans isomerization of the Asn286-Pro287 peptidyl-prolyl bond is directly correlated to the dynamics of the phosphotyrosine binding pocket, in agreement with previous NMR studies. While the cis state is localized to a single free energy basin and less dynamic, the trans state samples two distinct conformations of its binding pocket – one that recognizes the phosphotyrosine motif, and another that is similar the cis state. These results provide an atomic-level description of a less-well understood allosteric regulation by a peptidyl-prolyl cis-trans molecular switch that could aid in the understanding of normal and aberrant sub-cellular process and the identification of these elusive molecular switches in other proteins.

Quinoxaline-functionalized, cage-annulated oxa- and thiacrown ethers have been synthesized as possible specific metal host systems. The synthesis and characterization of quinoxaline-functionalized, cage-annulated oxa- and thiacrown ethers have been described. The characterization of these host systems have been fully achieved in solution by using various techniques such as IR, 1H NMR, and 13C NMR spectroscopic methods, high-resolution mass spectrometry (HRMS), elemental microanalysis, and X-ray crystallographic analysis in case of one quinoxaline-functionalized, cage-annulated oxacrown ether compound. The synthesis of the diphosphine ligand 2,3-bis(diphenylphosphino)-N-p-tolylmaleimide (bmi) is described. The substitution of the MeCN ligands in the activated cluster 1,2-Os3(CO)10(MeCN)2 by the diphosphine ligand bmi proceeds rapidly at room temperature to furnish a mixture of bridging and chelating Os3(CO)10(bmi) isomers and the ortho-metalated product HOs3(CO)9[μ-(PPh2)C=C{PPh(C6H4)}C(O)N(tolyl-p)C(O)]. Thermolysis of the bridging isomer 1,2-Os3(CO)10(bmi) under mild conditions gives the chelating isomer 1,1-Os3(CO)10(bmi), whose molecular structure has been determined by X-ray crystallography. The kinetics for the ligand isomerization have been investigated by UV-vis and 1H NMR spectroscopy in toluene solution over the temperature range of 318-348 K. On the basis of kinetic data conducted in the presence of added CO and the Eyring activation parameters, a non-dissociative phosphine migration across one of the Os-Os bonds is proposed. Orthometalation of one of the phenyl groups associated with the bmi ligand is triggered by near-UV photolysis of the chelating cluster 1,1- Os3(CO)10(bmi).

Ce travail traite de la synthèse énantiosélective de composés trifluorométhylés via l’étude de la réaction d’isomérisation rédox d’alcools allyliques trifluorométhylés catalysée par des complexes de ruthénium. Nous avons mis au point la réaction d’isomérisation rédox d’alcools allyliques secondaires β-trifluorométhylés. Une étude du mécanistique réactionnel a mis en évidence que l’étape cinétiquement déterminante de cette réaction pour les substrats β-trifluorométhylés est différente de celle décrite pour les substrats non fluorés, il s’agit de l’étape d’insertion. Cette observation nous a permis de mettre au point une réaction d’isomérisation rédox énantiospécifique permettant un transfert intramoléculaire de chiralité via un processus suprafacial. Cette méthode a été appliquée à la synthèse du (S)-CF3-citronellol. En parallèle, nous avons étudié la réaction tandem : isomérisation rédox – transfert d’hydrogène en partant d’alcools allyliques ou d’énones β-trifluorométhylées permettant l’accès aux alcools saturés correspondants. / This work deals with the enantioselective synthesis of trifluoromethylated compounds via the study of the ruthenium catalyzed redox isomerization reaction of trifluoromethylated allylic alcohols. We have developed optmized conditions for the redox isomerization of β-trifluoromethylated secondary allylic alcohols. A mechanistic study of the reaction revealed that the rate determining step for β-trifluoromethylated substrates is different from that described for the non-fluorinated substrates. This observation allowed us todevelop an enantiospecific redox isomerization reaction with a total transfer of chirality via a suprafacialintramolecular process. This methodology has been applied to thesynthesis of (S)-CF3-citronellol. In parallel, we have studied the tandem reaction : redox isomerization - transfer hydrogenation starting from β-trifluoromethylated allylic alcohols orenones, allowing access to the corresponding saturated alcohols.

Peptidyl-prolyl isomerization is an important post-translational modification of protein because proline is the only amino acid that can stably exist as cis and trans, while other amino acids are in the trans conformation in protein backbones. This makes prolyl isomerization a unique mechanism for cells to control many cellular processes. Isomerization is a rate-limiting process that requires a peptidyl-prolyl cis/trans isomerase (PPIase) to overcome the energy barrier between cis and trans isomeric forms. Pin1, a key PPIase in the cell, recognizes a phosphorylated Ser/Thr-Pro motif to catalyze peptidyl-prolyl isomerization in proteins. The significance of the phosphorylation-dependent Pin1 activity was recently highlighted for isomerization of ATR (ataxia telangiectasia- and Rad3-related). ATR, a PIKK protein kinase, plays a crucial role in DNA damage responses (DDR) by phosphorylating hundreds of proteins. ATR can form cis or trans isomers in the cytoplasm depending on Pin1 which isomerizes cis-ATR to trans-ATR. Trans-ATR functions primarily in the nucleus. The cis-ATR, containing an exposed BH3 domain, is anti-apoptotic at mitochondria by binding to tBid, preventing activation of pro-apoptotic Bax. Given the roles of apoptosis in many human diseases, particularly cancer, we propose that cytoplasmic cis-ATR enables cells to evade apoptosis, thus addicting cancer cells to cis-ATR formation for survival. But in normal DDR, a predominance of trans-ATR in the nucleus coordinates with a minimal level of cytoplasmic cis-ATR to promote DNA repair while preventing cell death; however, cells can die when DNA repair fails. Therefore, a delicate balance/equilibrium of the levels of cis- and trans-ATR is required to ensure the cellular homeostasis. In this review, we make a case that this anti-apoptotic role of cis-ATR supports oncogenesis, while Pin1 that drives the formation of trans-ATR suppresses tumor growth. We offer a potential, novel target that can be specifically targeted in cancer cells, without killing normal cells, to significantly reduce the adverse effects usually seen in cancer treatment. We also raise important issues regarding the roles of phosphorylation-dependent Pin1 isomerization of ATR in diseases and propose areas of future studies that would shed more understanding on this important cellular mechanism.

La conception de surfaces "intelligentes" sensibles aux stimuli externes (lumière, champ électromagnétique, environnement chimique ...) attire un intérêt considérable en raison de leur potentiel pour une large gamme d'applications. Dans ce contexte, nous étudions les propriétés de transfert de photos d'une monocouche de photochromes organiques immobilisés sur des surfaces de silicium.Les groupes Fulgimide sont ancrés par liaison covalente au-dessus de monocouches alkyliques fonctionnalisées greffées sur des surfaces Si (111) exemptes d'oxyde. La composition des monocouches dans les états stationnaires photo EPS-UV et EPS-Vis est déterminée à partir de l'analyse quantitative de l'intensité de la bande infrarouge caractéristique des isomères ouverts (E, Z) et fermés (C). La photocommutation de surface UV-Vis est surveillée par des mesures infrarouge à transformée de Fourier in situ en temps réel lors de l'éclairage UV-Vis. Les études de dépendance temporelle de la photocommutation montrent une diminution de l'efficacité quantique pendant la commutation. Cette diminution de l'efficacité quantique dépend faiblement de la densité de fulgimide et n'est pas observée en solution. Cependant, les mesures de PC en fonction du flux de photons ont permis de déterminer une section efficace de la PC (σ) de la majorité des molécules commutables. Les études de photocommutation dépendantes de la polarisation montrent une forte dépendance de σ par rapport au champ électrique local de la lumière excitante d'isomérisation.Les modèles analytiques et les simulations de Monte Carlo basées sur les interactions des voisins les plus proches sont effectuées pour obtenir une meilleure compréhension des observations expérimentales. Ces simulations expliquent qualitativement la dépendance à la température de la cinétique de commutation, diminuant l'efficacité quantique et la faible densité de surface de la photocommutation.Il a été montré dans cette thèse que σ dépend du champ électrique local. À l'instar de la spectroscopie Raman améliorée en surface, le champ électrique local sur les surfaces augmente en raison du plasmon des nanoparticules d'or. Le plasmon de la monocouche de nanoparticules d'or et ainsi l'amélioration du champ électrique dépend de la longueur d'onde de l'irradiation externe. L'exploitation de cet effet améliore significativement la cinétique de la commutation en fonction de la longueur d'onde de l'irradiation. Cette amplification dépendant de la longueur d'onde de la cinétique de la commutation s'explique par la même amplification dépendante de la longueur d'onde du champ électrique. / The design of “smart” surfaces responsive to external stimuli (light, electromagnetic field, chemical environment…) is attracting considerable interest because of their potential for a wide range of applications. Within this context we are studying the photoswitching properties of a monolayer of organic photochromes immobilized onto silicon surfaces.Fulgimide groups are anchored through covalent linkage atop of functionalized alkyl monolayers grafted on oxide free Si(111) surfaces. The monolayers composition at the photo stationary states PSS-UV and PSS-Vis is determined from quantitative analysis of the infrared band intensity characteristic of open (E,Z) and closed (C) isomers. The UV-Vis surface photocommutation is monitored by in-situ real time FTIR measurements during UV-Vis illumination. Time dependence studies of photocommutation evidence decreasing quantum efficiency during the commutation. This decrease in quantum efficiency only weakly depends on fulgimide density and is not observed in solution. However, PC measurements as a function of photon flux enabled determining a PC cross section (σ) of the majority of switching molecules. Polarization dependent photocommutation studies show the strong dependence of σ with respect to the local electric field of the isomerization-exciting light.Analytical models and Monte Carlo simulations based on nearest neighbor interactions are performed to gain deeper insight in the experimental observations. These simulations qualitatively explain the temperature dependence of the commutation kinetics, decreasing quantum efficiency and weak surface density dependence of the photocommutation.It has been shown in this thesis that σ depends on the local electric field. Similar to the Surface Enhanced Raman Spectroscopy the local electric field at surfaces is increased due to the plasmon of gold nanoparticles. The plasmon of the gold nanoparticle monolayer and thereby the enhancement of the electric field depends on the wavelength of the external irradiation. Exploitation of this effect improves the photo switching kinetics significantly depending on the wavelength of the irradiation. This wavelength dependent amplification of the switching kinetics is explained by the same wavelength dependent enhancement of the electric field.

Isomerization is a synthetically useful technique to form the more stable internal alkene from terminal alkene feedstock. Unfortunately, these transformations form a variety of isomers without catalyst control. Z alkenes are thermodynamically challenging to form compared to their E counterparts but are useful in pharmaceutical, fragrance, and flavor industries, making them sought-after products. Therefore, catalysts targeting specific regio- and stereoisomers, particularly Z alkenes, will benefit many fields. This work analyzes several Mo(0) complexes as Z-2-alkene selective isomerization catalysts. Particular focus has been given to cis-Mo(CO)4(PCy3)(piperidine) due to easy purification and characterization. Substantial improvement to reported Z selectivities have been obtained with this complex, though disadvantages exist. To have a clearer understanding of the mechanism and source of Z selectivity, DFT analysis was completed, and a mechanism proposed. A rare rotation of hydride and carbonyl ligands was found, only reported in one prior Mo complex, that facilitates the isomerization. Key characteristics were discovered that will be applied to develop future iterations with the goal of reducing, or removing, the disadvantages of this system. / Chemistry

京都大学 / 新制・課程博士 / 博士(工学) / 甲第24148号 / 工博第5035号 / 新制||工||1786(附属図書館) / 京都大学大学院工学研究科合成・生物化学専攻 / (主査)教授 杉野目 道紀, 教授 大江 浩一, 教授 中尾 佳亮 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DGAM

Two studies were conducted to determine the relative effect of various combinations of antioxidants on vitamin A oxidation and isomerization in nonfat dry milk (NDM). In the first study, one lot of pasteurized unfortified skim milk was divided, fortified with vitamins A and D and one of 11 antioxidant treatments, and spray dried. A control batch from the same lot was also fortified with vitamins A and D and spray dried. Samples were analyzed for total vitamin A bioactivity after zero, one, and two weeks of storage. After two weeks at 50°C, the only NDM samples that did not experience significant vitamin A loss were those treated with butylated hydroxytoluene, either alone at 0.57 ppm or at 0.29 ppm in combination with 250 ppm ascorbic acid. The control sample was significantly different from both of these treatments, and retained only 17% of its original retinol activity equivalents. Isomer composition changed over the two weeks of storage, with an increase of the 13-cis, 9,13-di-cis and the 9-cis isomers as well as a decrease in the all-trans isomer. In the second study, two lots of pasteurized, vitamin A & D fortified, condensed skim milk were divided into four batches, three of which were spiked with an antioxidant treatment: 250 ppm ascorbic acid + 1 ppm propyl gallate, 250 ppm ascorbic acid + 1 ppm butylated hydroxyanisole, or 2 ppm propyl gallate; the fourth batch was a control. Each of the eight batches was homogenized, spray dried and stored in the absence of light at 30°C for 3 months. Vitamin A and riboflavin were analyzed before spray drying, and after 0, 1, 2, 4, 6, 8, 10, and 12 weeks. Two treatments had significant higher vitamin A than the control, the 250 ppm ascorbic acid + 1 ppm butylated hydroxyanisole treatment and the 2 ppm propyl gallate treatment. Limited vitamin A degradation occurred in all samples during the study timeframe, although the overall degree of retinol isomerization began and remained high in all samples, with cis isomers accounting for approximately 23% of the total μg of retinol after 12 weeks. There were no significant differences in riboflavin content between any of the antioxidant treatments and no significant degradation in riboflavin over time. Antioxidants appear to be an effective means of reducing vitamin A oxidation and isomerization in nonfat dry milk. Butylated hydroxytoluene in combination with ascorbic acid was the most effective antioxidant blend observed. Antioxidants may be less effective at protecting against degradation of vitamin A if isomerization has already taken place.

<p> A kinetic and mechanistic study on catalytic decomposition of n- and sec-butyl acetate was carried out. The catalysts were silica-alumina and synthetic zeolites including type A, X, Y and mordenite. The reactions were performed in the temperature region of 140° to 290°C at atmospheric pressure using a fixed-bed flow reactor.</p> <p> The esters decomposed to acetic acid and n-butenes. The isomerization of butenes occurred consecutively. The mechanism of ester decomposition was different from that of pyrolysis. The catalytic activity was effected by acidity, cations and pore size. The Langmuir-Hinshelwood rate equation corresponding to the surface reaction on dual-sites correlated data satisfactorily. Strong adsorption of acetic acid, crystal collapse and the blocking of pores with organic deposit caused aging of catalysts.</p> / Thesis / Doctor of Philosophy (PhD)

Fortified and unfortified soymilk were produced from the same production batches for comparative evaluation. Fortification included a comprehensive array of micronutrients of interest to community and humanitarian nutrition programs. The effects of time after fortification prior to cooling, cooling method, and light or dark refrigerated storage on the stability of 5 vitamins (vitamin A, vitamin C, thiamine, riboflavin, and folate) were investigated for both fortified and unfortified soymilk. Significant vitamin C loss (6%) and mild vitamin A isomerization occurred while soymilk was hot immediately following fortification. Cooling bottled soymilk in an ambient water bath or ice water bath made no difference in the levels of any of the vitamins measured. Significant loss of riboflavin (18%) and significant vitamin A isomerization to cis isomers other than 13-cis, resulting in loss of bioactivity, occurred during 12 days of light-exposed refrigerated storage. An increase of 13-cis isomer was observed in dark refrigerated storage but with no significant loss of vitamin A bioactivity. No significant degradation of any other vitamins occurred during 12 days of dark refrigerated storage. Sensory evaluation by a panel of youth and children revealed no significant preferences between fortified and unfortified soymilk excepting colour, for which property there was a slight preference for unfortified soymilk. Acceptable vitamin stability and sensory characteristics can be achieved in comprehensively fortified soymilk produced in small-scale batch processes with appropriate management of production and storage conditions.