Abstract About one-third of mammalian proteins are secreted proteins and membrane proteins. Most of these proteins contain disulfide bonds in their native state, covalent links formed between the thiol groups of cysteine residues. In many proteins, disulfide bonds play an essential role in folding, stabilizing structure and the function of the protein. Therefore, understanding the pathways of disulfide bond formation is crucial for a wide range of medical processes and therapies. Disulfide bond formation is catalyzed by the Protein Disulfide Isomerase (PDI) family. To date the mechanisms of the PDIs in disulfide bond formation and pathways for disulfide bond formation have not been fully characterized. Here the structure of the substrate binding <b>b’x</b> domain of human PDI was determined. The structure shows that the<b> b'</b> domain has a typical thioredoxin fold and that the <b>x</b> region can interact with the substrate binding site of the <b>b'</b> domain. Specifically, the <b>x</b> region of PDI can adopt alternative conformations during the functional cycle of PDI action and that these are linked to the ability of PDI to interact with folding substrates. In addition, this study showed that two human proteins, GPx7 and GPx8 are involved in disulfide bond formation. The addition of GPx7 or GPx8 to a folding protein along with PDI and peroxide allows the efficient oxidative refolding of a reduced denatured substrate protein. Finally, this thesis includes the development of a system for the efficient production of disulfide bond containing proteins in the cytoplasm of E. coli. It showed that the introduction of Erv1p, a sulfhydryl oxidase and FAD-dependent catalyst of disulfide bond, allows the formation of native disulfide bonds in the cytoplasm of E. coli even without the disruption of genes involved in disulfide bond reduction. Introduction of Erv1p and a disulfide isomerase, e.g. PDI, allows the efficient formation of natively folded eukaryotic proteins with multiple disulfide bonds in the cytoplasm of E. coli. This system is able to express high levels of complex disulfide bonded eukaryotic proteins. / Tiivistelmä Noin kolmasosa kaikista nisäkkäiden proteiineista on solun ulkopuolelle eritettäviä proteiineja ja kalvoproteiineja. Monet näistä proteiineista sisältävät natiivissa konformaatiossaan disulfidisidoksia, jotka ovat kovalenttisia sidoksia kysteiinitähteiden tioliryhmien välillä. Useissa proteiineissa näillä disulfidisidoksilla on keskeinen rooli proteiinin laskostumisessa, kolmiulotteisen rakenteen stabiloinnissa sekä proteiinin toiminnassa. Disulfidisidosten muodostumisen taustalla olevien mekanismien tunteminen onkin tärkeää monien lääketieteellisten prosessien ja hoitomenetelmien kannalta. Disulfidisidosten muodostumista katalysoivat proteiinidisulfidi-isomeraasi (PDI) -perheeseen kuuluvat entsyymit. PDI entsyymien toimintamekanismeja ja disulfidisidosten muodostumisen reaktioreittejä ei kuitenkaan vielä tunneta tarkasti. Tässä väitöskirjassa selvitettiin ihmisen PDI entsyymin substraattia sitovan <b>b’x</b> alayksikön rakenne. Rakenteesta voidaan todeta <b>b’</b> alayksikön laskostuminen tyypilliseen tioredoksiini muotoon sekä <b>x</b> alueen interaktio <b>b’</b> alayksikön substraattia sitovan kohdan kanssa. PDI entsyymin katalysoiman reaktioketjun aikana <b>x</b> alayksikkö voi muuttaa konformaatiotaan mahdollistaen PDI entsyymin interaktion laskostuvien substraattiproteiinien kanssa. Tässä tutkimuksessa osoitettiin myös kahden ihmisen proteiinin, GPx7 ja GPx8 osallistuminen disulfidisidosten muodostumista katalysoiviin reaktioihin. GPx7 ja GPx8 entsyymien lisäys laskostumisreaktioon yhdessä PDI:n ja vetyperoksidin kanssa mahdollistaa pelkistetyn, denaturoidun substraattiproteiinin tehokkaan, hapettaviin reaktioihin perustuvan uudelleenlaskostumisen natiiviin muotoonsa. Osana tätä väitöstutkimusta kehitettiin menetelmä, joka mahdollistaa disulfideja sisältävien proteiinien tehokkaan tuoton E.colin solulimassa. Menetelmässä sulfhydryylioksidaasina ja FAD:sta riippuvana disulfidisidosten muodostumisen katalysaattorina toimiva Erv1p mahdollistaa disulfidisidosten muodostumisen E.colin solulimassa myös ilman solun pelkistävien reaktioreittien geneettistä poistamista. Erv1p yhdessä disulfidi-isomeraasin, kuten PDI, kanssa mahdollistaa oikein laskostuneiden, useita disulfidisidoksia sisältävien eukaryoottisten proteiinien tehokkaan tuotannon E.colin solulimassa. Menetelmällä pystytään tuottamaan suuria määriä monimutkaisia disulfidisidoksellisia proteiineja.

Les polymères à empreintes moléculaires (MIP) sont des matériaux synthétiques capables de mimer les anticorps biologiques. En effet, ils possèdent deux des principales caractéristiques de ces derniers, à savoir : la capacité de reconnaître et de se lier spécifiquement à des molécules cibles. De plus, leur synthèse facile, leur bas coût de production, leur haute spécificité et stabilité par rapport aux anticorps naturels font des MIP une alternative intéressante. En effet, les propriétés de reconnaissance moléculaire des MIP permettent d'envisager leur utilisation dans une vaste gamme d’applications. Ils sont ainsi largement exploités dans les sciences séparatives pour l'analyse d'échantillons environnementaux ou agro-alimentaires, ou comme élément de reconnaissance dans des biocapteurs. Récemment, des applications de ces matériaux dans les domaines biologiques et biomédicaux ont émergé comme pour la détection, l'extraction et l"élimination de molécules indésirables dans l'organisme, la vectorisation ou l'administration contrôlée des médicaments. Dans nos recherches, nous avons développé des MIP dégradables par voie biochimique ou enzymatique, ayant une application potentielle en tant que système de libération contrôlé de molécules. En général, les MIPs sont synthétisés par polymérisation radicalaire libre en utilisant une formulation composée de monomères fonctionnels, d'agents de réticulation, et d'une molécule cible servant à réaliser l'empreinte moléculaire. Dans ce travail de thèse, nous avons utilisé pour la synthèse de MIP dégradable des agents de réticulation clivables contenant, soit une fonction chimique dégradable par voie chimique ou enzymatique (ponts disulfures et phosphatediester), soit un disaccharide issus d'agro-ressources et pouvant être naturellement hydrolysé par des enzymes. En présence d'un réactif spécifique (agent réducteur ou enzyme), les liaisons dites "sensibles" aux réactifs chimiques ou enzymatiques peuvent être clivées, ce qui entraîne une dégradation de la matrice polymérique. Le polymère perdra alors sa capacité de reconnaissance et de liaison à la molécule cible et permettra la libération de celle-ci. Nous pensons donc, que les nouveaux MIP dégradables pourraient avoir un énorme potentiel comme vecteurs "intelligents" dans des applications médicales tels que les systèmes de libération contrôlée de médicament. Finalement, nous avons étudié la dégradation par des microorganismes de la structure de base de ce type de polymères, en utilisant comme modèles des chaines linéaires et réticulées. / Molecularly imprinted polymers (MIPs) are biomimetic synthetic receptors that possess two of the most important features of biological antibodies – the ability to recognize and bind specific target molecules. Owing to their easier preparation, lower cost, higher specifity and stability compared to antibodies, they have the potential to be widely applied for environemental and food analysis. Recently, MIPs also emerged in the biochemical field as diagnostic tools, chemicals traps to remove undesirable substance from the body, or drug delivery systems, where usually the combination of biocompatibility and degradability after its use is desirable. Here, we developed biochemically or enzymatically degradable MIPs, which have potential applications as activation-modulated drug delivery systems. In general, MIPs are prepared by radical polymerization of functional monomers and cross-linkers in the presence of a target molecule acting as template. Degradable MIPs were synthesized using cleavable cross-linkers containing a degradable group (disulfide bond or phosphate ester bond) or derived from a natural disaccharide. In the presence of a cleaving reagent (reducing agent or enzyme), the chemo or enzyme-sensitive bond could be cleaved, resulting in the degradation of the polymer matrix. The degraded polymers looses the binding sites structure resulting in the loss of recognition and binding capacity towards the target molecules, and thus in the release of bound molecules. These degradable MIPs provide new opportunities as “smart” vectors for controlled delivery of active molecules in biomedical applications. Finally, the biodegradation of the polymer backbone by bacteria was investigated.

京都大学 / 0048 / 新制・課程博士 / 博士(工学) / 甲第19003号 / 工博第4045号 / 新制||工||1622(附属図書館) / 31954 / 京都大学大学院工学研究科分子工学専攻 / (主査)教授 白川 昌宏, 教授 佐藤 啓文, 教授 梶 弘典 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DGAM

No description available.

No description available.

Cerca de 20 % dos casos familiares de esclerose lateral amiotrófica (ELAf) são causados por mutações na enzima Cu,Zn-superóxido dismutase (SOD1). Inicialmente se supôs que as enzimas mutantes teriam a atividade SOD comprometida, entretanto isto não foi comprovado. Atualmente, considera-se que as enzimas mutantes adquiram propriedades tóxicas. Quais seriam estas propriedades e como levariam à degeneração do neurônio motor são questões ainda não respondidas. Neste trabalho, comparamos neuroblastomas humanos transfectados com SOD1 G93A associada à ELAf (SH-SY5YG93A), e SOD1 selvagem (SH-SY5YWT) com células parentais (SH-SY5Y) em relação ao crescimento, viabilidade, produção basal de oxidantes, atividades SOD e peroxidásica e modificações estruturais da SOD. As células transfectadas apresentaram aumento na taxa de crescimento e na produção basal de oxidantes. As células SH-SY5YWT e SH-SY5YG93A mantiveram a expressão de SOD1 e atividade consistente com o aumento esperado de duas vezes, em estágios iniciais de cultura. A atividade peroxidásica do homogenato da célula SH-SY5YG93A foi maior. Após quatro semanas, a linhagem SH-SY5YG93A manteve a expressão de SOD1, mas as atividades dismutásica e peroxidásica diminuíram. A expressão de SOD1 aumentou a proporção de formas alteradas de SOD1, como enzima reduzida, multímeros formados por ponte dissulfeto e formas insolúveis em detergente, particularmente na linhagem SH-SY5YG93A. Entre estas formas insolúveis, identificamos um dímero covalente de SOD. Estas formas alteradas provavelmente são responsáveis pela ativação do proteassomo e estresse do retículo endoplasmático, verificados nas células transfectadas. Concluindo, a superexpressão da SOD1 foi suficiente para elevar as formas imaturas e oligomerizadas de SOD1 e a oxidação basal, e a mutação G93A ressaltou estes processos. / Some familial ALS (fALS) are caused by mutations in the Cu,Zn-superoxide dismutase enzyme (SOD1). It was thought that the mutated enzymes would have impaired SOD activity, but this has not been corroborated so far. Presently, it is more accepted that the mutated enzymes acquire a new toxic function. What this new toxic function is and how it relates to the degeneration of motor neurons remains debatable. Here, we compared human neuroblastoma cells transfected with fALS mutant G93A (SH-SY5YG93A) or wild-type SOD1 (SH-SY5YWT) with parent cells (SH-SY5Y) in regard to growth, viability, basal oxidant production, SOD and peroxidase activities, and SOD forms. Transfected cells presented increased growth rate and basal oxidant production. SH-SY5YWT and SH-SY5YG93A cells in early culture stage showed SOD expression and activity consistent with the expected two-fold increase; SH-SY5YWT homogenates showed increased peroxidase activity. After four weeks, SH-SY5YG93A maintained SOD1 expression levels but peroxidase and dismutase activities were lower. SOD1 expression increased the levels of altered SOD1 forms such as the reduced enzyme, disulfide multimers and detergent-insoluble forms, particularly in SH-SY5YG93A cells. Among the insoluble forms a covalent SOD dimer was identified. These altered SOD forms are probably responsible for proteasome activation and endoplasmatic reticulum stress response verified in transfected cells. In conclusion, SOD1 over-expression was sufficient to increase intracellular immature and oligomerized SOD1 forms and basal oxidation and the G93A mutation enhanced these processes.

Au niveau moléculaire, les fonctions des motifs hélicoïdaux sont souvent associées à la stabilité de cesarchitectures. Par exemple, lorsqu’une hélice α est isolée de la structure tertiaire des protéines, celle-cidevient alors flexible et perd son activité. Afin de contrôler la rigidité de ces architectures, différentesapproches ont été proposées dont la construction d’édifices moléculaires repliés de façon contrôlée : lesfoldamères. Notre équipe s’intéresse aux foldamères d’oligoamide aromatique hélicoïdaux et à l’heureactuelle plusieurs études ont déjà été menées afin de comprendre les facteurs influant la stabilité de telleshélices: la longueur de l’oligomère, le solvant et l’effet de l’introduction d’un espaceur aliphatique dans laséquence. Lors de ce travail nous nous sommes tout d’abord intéressés à la capacité de repliement de cinqmonomères aromatiques couramment utilisés pour la préparation de foldamères. Leur contribution dans lastabilité hélicoïdale du système a été évaluée par RMN, diffraction des rayons-X et HPLC chirale dynamique.Inspirés par le rôle des ponts disulfure dans les protéines, nous avons décidé d’explorer l’effet d’une telleliaison sur la stabilité des hélices d’oligoamide aromatique. Deux composés contenant une liaison disulfureintramoléculaire ou deux liaisons intermoléculaires ont été synthétisés et leur stabilité étudiée par RMN, HPLCChiral et Dichroïsme circulaire.Enfin, la synthèse d’hélices moléculaires de grandes dimensions (assimilables à celles de polymèresmonodisperses) a été réalisée par une approche convergente de triplement de longueur de segment via laformation de liaisons anhydrides entre blocs oligomériques. / At the molecular level, the functions of helical patterns are often directly associated with the stability of thesearchitectures, (in α-helices). For example, upon removal of such an entity from the protein’s tertiary structure,the peptidic helix becomes flexible and thus inactive. In order to control the rigidity of these architectures,several strategies have been used and the construction of completely artificial well folded molecules known asfoldamers is one them. Our group mainly focuses on helical aromatic oligoamide foldamers and to dateseveral studies have been carried out to investigate factors affecting the helical stability; the influence ofoligomer length, solvent effects and the effect of aliphatic linkers within a helical aromatic sequence.In the present study we investigate the helical propensity of five commonly used aromatic monomers infoldamer synthesis and by using NMR spectroscopy, X-ray crystallography and dynamic chiral HPLC weevaluate their contribution in helical stability. Additionally, inspired by the role of disulfide bonds in proteins wedecided to explore their effect on helical stability. For this reason intra- and inter-molecularly disulfide bondedcompounds were designed and synthesized. Their stability was studied using NMR spectroscopy, chiral HPLCand CD experiments.Finally, the synthesis of mono-disperse helical strings of polymeric dimensions through a convergent, segmenttripling strategy has been developed. This protection/deprotection free synthesis was carried out byconnecting oligomeric blocks via a labile anhydride functionality.

Cerca de 20 % dos casos familiares de esclerose lateral amiotrófica (ELAf) são causados por mutações na enzima Cu,Zn-superóxido dismutase (SOD1). Inicialmente se supôs que as enzimas mutantes teriam a atividade SOD comprometida, entretanto isto não foi comprovado. Atualmente, considera-se que as enzimas mutantes adquiram propriedades tóxicas. Quais seriam estas propriedades e como levariam à degeneração do neurônio motor são questões ainda não respondidas. Neste trabalho, comparamos neuroblastomas humanos transfectados com SOD1 G93A associada à ELAf (SH-SY5YG93A), e SOD1 selvagem (SH-SY5YWT) com células parentais (SH-SY5Y) em relação ao crescimento, viabilidade, produção basal de oxidantes, atividades SOD e peroxidásica e modificações estruturais da SOD. As células transfectadas apresentaram aumento na taxa de crescimento e na produção basal de oxidantes. As células SH-SY5YWT e SH-SY5YG93A mantiveram a expressão de SOD1 e atividade consistente com o aumento esperado de duas vezes, em estágios iniciais de cultura. A atividade peroxidásica do homogenato da célula SH-SY5YG93A foi maior. Após quatro semanas, a linhagem SH-SY5YG93A manteve a expressão de SOD1, mas as atividades dismutásica e peroxidásica diminuíram. A expressão de SOD1 aumentou a proporção de formas alteradas de SOD1, como enzima reduzida, multímeros formados por ponte dissulfeto e formas insolúveis em detergente, particularmente na linhagem SH-SY5YG93A. Entre estas formas insolúveis, identificamos um dímero covalente de SOD. Estas formas alteradas provavelmente são responsáveis pela ativação do proteassomo e estresse do retículo endoplasmático, verificados nas células transfectadas. Concluindo, a superexpressão da SOD1 foi suficiente para elevar as formas imaturas e oligomerizadas de SOD1 e a oxidação basal, e a mutação G93A ressaltou estes processos. / Some familial ALS (fALS) are caused by mutations in the Cu,Zn-superoxide dismutase enzyme (SOD1). It was thought that the mutated enzymes would have impaired SOD activity, but this has not been corroborated so far. Presently, it is more accepted that the mutated enzymes acquire a new toxic function. What this new toxic function is and how it relates to the degeneration of motor neurons remains debatable. Here, we compared human neuroblastoma cells transfected with fALS mutant G93A (SH-SY5YG93A) or wild-type SOD1 (SH-SY5YWT) with parent cells (SH-SY5Y) in regard to growth, viability, basal oxidant production, SOD and peroxidase activities, and SOD forms. Transfected cells presented increased growth rate and basal oxidant production. SH-SY5YWT and SH-SY5YG93A cells in early culture stage showed SOD expression and activity consistent with the expected two-fold increase; SH-SY5YWT homogenates showed increased peroxidase activity. After four weeks, SH-SY5YG93A maintained SOD1 expression levels but peroxidase and dismutase activities were lower. SOD1 expression increased the levels of altered SOD1 forms such as the reduced enzyme, disulfide multimers and detergent-insoluble forms, particularly in SH-SY5YG93A cells. Among the insoluble forms a covalent SOD dimer was identified. These altered SOD forms are probably responsible for proteasome activation and endoplasmatic reticulum stress response verified in transfected cells. In conclusion, SOD1 over-expression was sufficient to increase intracellular immature and oligomerized SOD1 forms and basal oxidation and the G93A mutation enhanced these processes.

Sample preparation as an essential step in mass spectrometry-based analysis, plays a critical role in proteomics studies. Magnetic nanoparticles (MNPs) have been widely used in protein and peptide sample preparation due to their magnetic properties, biocompatibility, easy synthesis and surface functionalization. MNPs loaded with analyte or analyte modification reagent can be easily separated from the reaction medium by an externally applied magnetic field. The small size of MNPs provides high analyte loading and extraction capacity. Additionally, MNP can be decorated with different functional groups to achieve selective modification or extraction of analyte. In this study we have utilized silica coated iron oxide magnetic nanoparticles (Fe3O4@SiO2 MNPs) for protein and peptide sample preparation. Fluorescence-based methods were utilized for quantitative and qualitative characterization of N-hydrosucccinimidyl (NHS) ester groups on the surface of Fe3O4@SiO2 MNPs. Fluorophore Dansylcadaverine was conjugated to NHS ester functional groups. Fluorometric measurement of cleaved dansylcadaveine was employed to determine the number of NHS ester groups per MNPs that was found to be 2.6 × 102 and 3.4 × 103for 20 nm and 100 nm Fe3O4@SiO2 MNPrespectively. The efficiency of labeling native bovine serum albumin (BSA) by NHS ester coated Fe3O4@SiO2 MNPs was also explored in terms of maximizing the number of MNPs conjugated per BSA molecule or maximizing the number of BSA molecules conjugated per each MNP. Lysine residues of apolipoprotein B-100 (apoB-100) on the surface of intact human low density lipoprotein (LDL) were labeled by NHS ester modified Fe3O4@SiO2 MNPs in aqueous solvents at room temperature. The MNP labeledapoB-100 was treated by SDS to remove lipids and then digested using trypsin. Tryptic peptides were eluted from MNPs by cleaving disulfide linkage between labeled peptides and MNPs. LC-MS/MS analysis found 28 peptides containing labeled lysine residues. These lysine residues should be on the solvent exposed surface of LDL since the large size of MNPs prevents contact of the labeling reagent to those lysines embedded inside the structure of LDL. TCEP- immobilized Fe3O4@SiO2MNPs were fabricated and utilized for reduction of disulfide bonds in bovine pancreas insulin and two different cyclic peptides. Disulfide bonds were efficiently cleaved at room temperature in both organic and aqueous solvents confirmed by LC-MS/MS analysis of reduced/alkylated protein and peptides. Disulfide reduction and alkylation reactions was performed in one step and the reducing agent was simply separated from peptide and protein solution by magnetic separation.

No description available.