Com o objetivo de estudar a potencialidade do emprego de termolisina como catalisador nas reações de incorporação de N-acil-asparagina a ésteres de aminoácidos e peptídeos, foram sintetizados os seguintes di- e tripeptídeos: Boc-Asn-Ile-OBzl, Z-Asn-Ile-OBzl, Moz-Asn-Ile-OBzl, Boc-Asn-Leu- OBzl, Z-Asn-Leu-OBzl, Moz-Asn-Leu-OBzl, Z-Asn-Leu-OEt, Boc-Asn-Phe-OBzl, Z-Asn-Phe-OBzl, Moz-Asn-Phe-OBzl, Z-Asn-Phe- OEt, Z-Asn-Val-OBzl, Moz-Asp-Val-OBzl, Moz-Asn-Ile-Gly-OBzl, Moz-Asn-Ile-Ala-OBzl, Moz-Asn-Ile-Leu-OBzl e Moz-Asn- Ile-Phe-OBzl. Todos os peptídeos foram obtidos na forma pura, com bom rendimento e foram analisados e caracterizados por cromatografia em camada delgada, ponto de fusão, análise elementar, análise de aminoácidos e ressonância magnética protônica. Entre os grupos protetores de asparagina, benziloxicarbonil e p-metoxibenziloxicarbonil permitiram a obtenção dos dipeptídeos com excelentes rendimentos. Foi observado que os tripeptídeos requerem para a sua síntese menores concentração de enzima e tempo de reação em relação aos dipeptídeos. Não foi possível estabelecer a especificidade secundária da termolisina para o resíduo P\'2 pois os rendimentos dos tripeptídeos sintetizados não apresentaram diferença significativa. Foi também realizado um estudo metodológico para determinar as condições ótimas de síntese de Boc-Asn-Ile-OBzl, que consistiu em analisar a influência do pH, concentração de enzima, concentraçao e volume da solução de acetato de sódio, proporção entre os componentes carboxílico e amínico, temperatura e adição de solvente orgânico ao meio de reação. / With de objective of studying the potential for the use of thermolysin as a catalyst in reactions of incorporation of N-acyl-asparagine into esters of aminoacids and peptides, the following di- and tripeptides were synthesized: Boc-Asn-Ile-OBzl, Z-Asn-Ile-OBzl, Moz-Asn-Ile-OBzl, Boc-Asn-Leu-OBzl, Z-Asn-Leu-OBzI, Moz-Asn-Leu-OBzl, Z-Asn-Leu-OEt, Boc-Asn-Phe-OBzl,Z-Asn-Phe-OBzl, Moz-Asn-Phe-OBzl, Z-Z-Asn-Phe-OEt, Z-Asn-Val-OEt, Moz-Asn-Val-OBzl, Moz-Asn-Ile-Gly-OBzl, Moz-Asn-Ile-Ala-OBzl, Moz-Asn-Ile-Leu-OBzl e Moz-Asn-Ile-Phe-OBzl. All of these peptides were obtained in pure form in good yield and analyzed and characterized by thin layer chromatography, melting point, elemental analysis, aminoacid analysis and proton magnetic resonance. Among the protecting groups of asparagine, benzyloxycarbonyl and p-methoxybenzyloxycarbonyl gave excellent yields of the dipeptides. Relative to the dipeptides, the synthesis of the tripeptides was found to require lower enzyme concentrations and temperatures. Since the yields of the tripeptides failed to exhibit significant differences, it was not possible to establish the existence of a secondary specificity of thermolysin for the residue P\' 2 . A methodological study was also performed to determine the optimum conditions for synthesis of Boc-Asn-Ile-OBzl. This study consisted of an analysis of the influence of pH, enzyme concentration, concentration and volume of the solution of sodium acetate, relative proportions of the carboxyl and amino components, temperature, and addition of organic solvent to the reaction medium.

Visando dar continuidade ao estudo de incorporação de N-acil-asparagina a derivados de aminoácidos e a peptídeos mediante catálise por termolisina, foi estudada a viabilidade de síntese dos peptídeos Z-Asn-Cys(S-Bzl)-OBut e Moz-Asn-Cys(S-Bzl)-Pro-Leu-Gly-NH2. Durante a síntese do pentapeptídeo Moz-Asn-Cys(S-Bzl)-Pro-Leu-Gly-NH2 foi constatada a formação de um subproduto cuja estrutura foi elucidada a partir da comparação ao padrão autêntico Moz-Asn-Leu-Gly-NH2. Para a obtenção deste padrão, sintetizamos o tripeptídeo Moz-Asn-Leu-Gly-OEt a partir de Moz-Asn-OH e H-Leu-Gly-OEt na presença de termolisina. A recristalização deste peptídeo em MeOH/H2 O levou à transformação do mesmo em Moz-Asn-Leu-Gly-OMe, confirmada pelo isolamento e caracterização do produto por espectrometria de massa e ressonância magnética protônica, análise elementar e de aminoácidos e por determinação do tempo de retenção por HPLC. Estudos posteriores demonstraram o envolvimento do íon Ca(II) no processo e nos permitiram sugerir um modelo da ligação deste íon ao peptídeo e da sequência de reação da transesterificação estudada. Também foi investigada a possibilidade de diversos ésteres de peptídeos e de peptidilresinas de Merrifield sofrerem transesterificação quando incubados em metanol na presença de Ca(II). Para tanto, os tripeptídeos Z-Asn-Leu-Gly-OEt, Boc-Asn-Leu-Gly-OEt, Moz-Asn-Leu-Gly-OBzl, Moz-Asn-Leu-Gly-OBu Moz-Gln-Leu-Gly-OEt, Moz-Asn-Ile-Gly-OEt e Moz-Asn-Leu-Ala-OEt foram sintetizados mediante catálise por termolisina. Também foram testados vários outros peptídeos disponíveis no laboratório e Boc-Leu-Gly-Res e Moz-Asn-Leu-Gly-Res. Com exceção dos ésteres terc-butílicos, todos sofreram transesterificação em soluções metanólicas de acetato de cálcio. / The main obJective was the study of thermolysin catalyzed incorporation of N-acyl-asparagine into amino acid and peptide derivatives. Both Z-Asn-Cys(S-Bzl)-OBut and Moz-Asn-Cys(S-Bzl)-Pro-Leu-Gly-NH2 syntheses have been studied. The formation of a by-product occurred during the synthesis of the later pentapeptide. By comparison with an authentic standard this by-product was identified as Moz-Asn-Leu-Gly-NH2. The standard Moz-Asn-Leu-Gly-NH2 was obtained by aminolYSlS of Moz-Asn-Leu-Gly-OEt. This peptide was synthesized by coupling Moz-Asn-OH with H-Leu-Gly-OEt using thermolysin as catalyst. During the recrystallization in MeOH/H2O, the transformation of Moz-Asn-Leu-Gly-OEt to its methyl-ester was obtained. This observation has been confirmed by purification and caracterization of the peptide by: Mass Spectroscopy, Nuclear Magnetic Ressonance, Amino Acid and Elemental Analysis and HPLC. Later studies have shown that the Ca(II) ion participates in the process. A model for the binding of this ion to the peptide and for the transesterification reaction has been suggested. Further studies have been performed with (1) the newly synthesized peptides Z-Asn-Leu-Gly-OEt, Boc-Asn-Leu-Gly-OEt, Moz-Asn-Leu-Gly-OBzl, Moz-Asn-Leu-Gly-OBut, Moz-Gln-Leu-Gly-OEt, Moz- Asn-Ile-Gly-OEt and Moz-Asn-Leu-Ala-OEt; (2) several other peptides available in our laboratory; and (3) Boc-Leu-Gly-Res and Moz-Asn-Leu-Gly-Res. With the exception of t-butyl-esters, all peptides tested have transesterified in methanolic calcium acetate solutions.

Structural biology is a branch of science related to biochemistry, biophysics, and molecular biology that deals with the molecular structures of biological macromolecules, in particular nucleic acids and proteins. Structure-guided drug design uses three-dimensional knowledge of protein structures to design small molecules which block the action of specific proteins. When crystals of theses macromolecules and their complexes can be obtained, their crystal structures can be determined by using isomorphous differences between a native structure and a derivative structure. This allows crystallographers to determine the coordinates of a small number of heavy atoms which provide initial phases for macromolecules. The advent of synchrotron radiation allowed determination of a heavy atom substructure by use of anomalous differences using either multiple wavelengths (MAD) or a single wavelength (SAD); the latter has become the most common phasing method in crystallography and is the method used in this study. The use of SeMet has been by far the most successful method employed in SAD. However, in some cases production of SeMet proteins is not possible thus necessitating additional options, for example, xenon. Noble gases such as xenon may be used in SAD experiments by binding to various, non-specific sites. Advances in noble gas pressurization systems like the Hampton Research Xenon Chamber have greatly eased the production of noble gas derivatives, xenon itself being a prime candidate with a very strong anomalous signal when compared to lighter noble gases like krypton and argon. Investigation of the phasing properties of xenon was carried out on test proteins hen egg white lysozyme (HEWL), thermolysin, glucose isomerase, and thaumatin II. Phases were successfully determined for all four proteins including thaumatin II which did not bind xenon but was successful due to the anomalous signal from 17 native sulfurs. The three remaining proteins showed varying occupancies and numbers of sites including xenon sites in thermolysin and glucose isomerase which have not been observed previously. This document will serve as a guide for the preparation of xenon derivative crystals and provides a strategy for the collection and processing of data from xenon derivatives.

Com o objetivo de estudar a potencialidade do emprego de termolisina como catalisador nas reações de incorporação de N-acil-asparagina a ésteres de aminoácidos e peptídeos, foram sintetizados os seguintes di- e tripeptídeos: Boc-Asn-Ile-OBzl, Z-Asn-Ile-OBzl, Moz-Asn-Ile-OBzl, Boc-Asn-Leu- OBzl, Z-Asn-Leu-OBzl, Moz-Asn-Leu-OBzl, Z-Asn-Leu-OEt, Boc-Asn-Phe-OBzl, Z-Asn-Phe-OBzl, Moz-Asn-Phe-OBzl, Z-Asn-Phe- OEt, Z-Asn-Val-OBzl, Moz-Asp-Val-OBzl, Moz-Asn-Ile-Gly-OBzl, Moz-Asn-Ile-Ala-OBzl, Moz-Asn-Ile-Leu-OBzl e Moz-Asn- Ile-Phe-OBzl. Todos os peptídeos foram obtidos na forma pura, com bom rendimento e foram analisados e caracterizados por cromatografia em camada delgada, ponto de fusão, análise elementar, análise de aminoácidos e ressonância magnética protônica. Entre os grupos protetores de asparagina, benziloxicarbonil e p-metoxibenziloxicarbonil permitiram a obtenção dos dipeptídeos com excelentes rendimentos. Foi observado que os tripeptídeos requerem para a sua síntese menores concentração de enzima e tempo de reação em relação aos dipeptídeos. Não foi possível estabelecer a especificidade secundária da termolisina para o resíduo P\'2 pois os rendimentos dos tripeptídeos sintetizados não apresentaram diferença significativa. Foi também realizado um estudo metodológico para determinar as condições ótimas de síntese de Boc-Asn-Ile-OBzl, que consistiu em analisar a influência do pH, concentração de enzima, concentraçao e volume da solução de acetato de sódio, proporção entre os componentes carboxílico e amínico, temperatura e adição de solvente orgânico ao meio de reação. / With de objective of studying the potential for the use of thermolysin as a catalyst in reactions of incorporation of N-acyl-asparagine into esters of aminoacids and peptides, the following di- and tripeptides were synthesized: Boc-Asn-Ile-OBzl, Z-Asn-Ile-OBzl, Moz-Asn-Ile-OBzl, Boc-Asn-Leu-OBzl, Z-Asn-Leu-OBzI, Moz-Asn-Leu-OBzl, Z-Asn-Leu-OEt, Boc-Asn-Phe-OBzl,Z-Asn-Phe-OBzl, Moz-Asn-Phe-OBzl, Z-Z-Asn-Phe-OEt, Z-Asn-Val-OEt, Moz-Asn-Val-OBzl, Moz-Asn-Ile-Gly-OBzl, Moz-Asn-Ile-Ala-OBzl, Moz-Asn-Ile-Leu-OBzl e Moz-Asn-Ile-Phe-OBzl. All of these peptides were obtained in pure form in good yield and analyzed and characterized by thin layer chromatography, melting point, elemental analysis, aminoacid analysis and proton magnetic resonance. Among the protecting groups of asparagine, benzyloxycarbonyl and p-methoxybenzyloxycarbonyl gave excellent yields of the dipeptides. Relative to the dipeptides, the synthesis of the tripeptides was found to require lower enzyme concentrations and temperatures. Since the yields of the tripeptides failed to exhibit significant differences, it was not possible to establish the existence of a secondary specificity of thermolysin for the residue P\' 2 . A methodological study was also performed to determine the optimum conditions for synthesis of Boc-Asn-Ile-OBzl. This study consisted of an analysis of the influence of pH, enzyme concentration, concentration and volume of the solution of sodium acetate, relative proportions of the carboxyl and amino components, temperature, and addition of organic solvent to the reaction medium.

Visando dar continuidade ao estudo de incorporação de N-acil-asparagina a derivados de aminoácidos e a peptídeos mediante catálise por termolisina, foi estudada a viabilidade de síntese dos peptídeos Z-Asn-Cys(S-Bzl)-OBut e Moz-Asn-Cys(S-Bzl)-Pro-Leu-Gly-NH2. Durante a síntese do pentapeptídeo Moz-Asn-Cys(S-Bzl)-Pro-Leu-Gly-NH2 foi constatada a formação de um subproduto cuja estrutura foi elucidada a partir da comparação ao padrão autêntico Moz-Asn-Leu-Gly-NH2. Para a obtenção deste padrão, sintetizamos o tripeptídeo Moz-Asn-Leu-Gly-OEt a partir de Moz-Asn-OH e H-Leu-Gly-OEt na presença de termolisina. A recristalização deste peptídeo em MeOH/H2 O levou à transformação do mesmo em Moz-Asn-Leu-Gly-OMe, confirmada pelo isolamento e caracterização do produto por espectrometria de massa e ressonância magnética protônica, análise elementar e de aminoácidos e por determinação do tempo de retenção por HPLC. Estudos posteriores demonstraram o envolvimento do íon Ca(II) no processo e nos permitiram sugerir um modelo da ligação deste íon ao peptídeo e da sequência de reação da transesterificação estudada. Também foi investigada a possibilidade de diversos ésteres de peptídeos e de peptidilresinas de Merrifield sofrerem transesterificação quando incubados em metanol na presença de Ca(II). Para tanto, os tripeptídeos Z-Asn-Leu-Gly-OEt, Boc-Asn-Leu-Gly-OEt, Moz-Asn-Leu-Gly-OBzl, Moz-Asn-Leu-Gly-OBu Moz-Gln-Leu-Gly-OEt, Moz-Asn-Ile-Gly-OEt e Moz-Asn-Leu-Ala-OEt foram sintetizados mediante catálise por termolisina. Também foram testados vários outros peptídeos disponíveis no laboratório e Boc-Leu-Gly-Res e Moz-Asn-Leu-Gly-Res. Com exceção dos ésteres terc-butílicos, todos sofreram transesterificação em soluções metanólicas de acetato de cálcio. / The main obJective was the study of thermolysin catalyzed incorporation of N-acyl-asparagine into amino acid and peptide derivatives. Both Z-Asn-Cys(S-Bzl)-OBut and Moz-Asn-Cys(S-Bzl)-Pro-Leu-Gly-NH2 syntheses have been studied. The formation of a by-product occurred during the synthesis of the later pentapeptide. By comparison with an authentic standard this by-product was identified as Moz-Asn-Leu-Gly-NH2. The standard Moz-Asn-Leu-Gly-NH2 was obtained by aminolYSlS of Moz-Asn-Leu-Gly-OEt. This peptide was synthesized by coupling Moz-Asn-OH with H-Leu-Gly-OEt using thermolysin as catalyst. During the recrystallization in MeOH/H2O, the transformation of Moz-Asn-Leu-Gly-OEt to its methyl-ester was obtained. This observation has been confirmed by purification and caracterization of the peptide by: Mass Spectroscopy, Nuclear Magnetic Ressonance, Amino Acid and Elemental Analysis and HPLC. Later studies have shown that the Ca(II) ion participates in the process. A model for the binding of this ion to the peptide and for the transesterification reaction has been suggested. Further studies have been performed with (1) the newly synthesized peptides Z-Asn-Leu-Gly-OEt, Boc-Asn-Leu-Gly-OEt, Moz-Asn-Leu-Gly-OBzl, Moz-Asn-Leu-Gly-OBut, Moz-Gln-Leu-Gly-OEt, Moz- Asn-Ile-Gly-OEt and Moz-Asn-Leu-Ala-OEt; (2) several other peptides available in our laboratory; and (3) Boc-Leu-Gly-Res and Moz-Asn-Leu-Gly-Res. With the exception of t-butyl-esters, all peptides tested have transesterified in methanolic calcium acetate solutions.

京都大学 / 0048 / 新制・課程博士 / 博士(農学) / 甲第18316号 / 農博第2041号 / 新制||農||1020(附属図書館) / 学位論文||H26||N4823(農学部図書室) / 31174 / 京都大学大学院農学研究科食品生物科学専攻 / (主査)教授 保川 清, 教授 安達 修二, 教授 伏木 亨 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DFAM

京都大学 / 0048 / 新制・論文博士 / 博士(農学) / 乙第12878号 / 論農博第2805号 / 新制||農||1028(附属図書館) / 学位論文||H26||N4877(農学部図書室) / 31596 / (主査)教授 保川 清, 教授 安達 修二, 教授 伏木 亨 / 学位規則第4条第2項該当 / Doctor of Agricultural Science / Kyoto University / DFAM

京都大学 / 0048 / 新制・課程博士 / 博士(農学) / 甲第19017号 / 農博第2095号 / 新制||農||1029(附属図書館) / 学位論文||H27||N4899(農学部図書室) / 31968 / 京都大学大学院農学研究科食品生物科学専攻 / (主査)教授 保川 清, 教授 安達 修二, 教授 入江 一浩 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DFAM

Protein misfolding is considered to be the major pathogenic mechanism in homocystinuria due to cystathionine beta-synthase (CBS) deficiency. The aim of this work was to study molecular mechanisms underlying protein misfolding of CBS mutants. Firstly, we studied spatial arrangement of normal human CBS protein. Using data from differential covalent labeling of solvent-exposed aminoacid residues, we identified interdomain contact area between the catalytic core and the regulatory domain in human CBS, and we subsequently generated the structural model of the full-length CBS. In the next step, we studied evolutionary divergence of CBS protein structures. We performed phylogenetic analysis that revealed unique spatial arrangement of CBS enzyme in nematodes; the domain architecture of CBS in Caenorhabditis elegans was studied experimentally in more detail. Finally, we determined conformational properties of a representative set of human CBS mutants that exhibited in various extent affected formation of tetramers and decreased catalytic activity. Using thermolysin-based proteolytic techniques for analysis of nine mutants expressed in E.coli, we found that an unfolded structure is a common intermediate occurring in CBS misfolding. The importance of protein unfolding for pathogenesis of CBS deficiency was...

Dans ce travail, nous nous sommes intéressés au développement d’un nouveau biocapteur enzymatique ultrasensible pour la détection conductimétrique d’une mycotoxine, l’ochratoxine A (OTA). Une peptidase, la thermolysine (TLN), a été choisie comme élément de reconnaissance. Le biocapteur proposé est basé sur l’immobilisation de la TLN dans une matrice d’alcool polyvinylique (PVA)/polyéthylènimine (PEI) contenant des nanoparticules d’or et réticulée à la surface de microélectrodes interdigitées à l’aide de vapeurs de glutaraldéhyde. Dans les conditions optimales (35 min de réticulation, mesure à pH 7 et 25°C), la réponse du biocapteur est linéaire jusqu’à 60 nM et la limite de détection est de 1 nM. Cette valeur est 700 fois plus basse que celle obtenue en utilisant une méthode d’immobilisation basée sur la co-réticulation de la TLN en présence d’albumine de sérum bovin (BSA). La matrice PVA/PEI crée un environnement aqueux favorable à l’enzyme. Par ailleurs, les interactions entre les groupements amines protonés du PEI et les charges négatives des nanoparticules citratées et de la TLN améliore leur dispersion dans la matrice et favorise la stabilisation de l’enzyme et son accessibilité au substrat (OTA). Le biocapteur conductimétrique développé est très reproductible et stable pendant 30 jours lorsqu’il est stocké à 4°C dans du tampon phosphate 20 mM pH7 entre 2 mesures. Le biocapteur a ensuite été évalué sur des échantillons d’huile d’olive commerciale dopée. Aucun prétraitement de l’échantillon n’a été nécessaire et des taux de recouvrement proches de 100% ont été obtenus, démontrant l’absence d’effet de matrice / A new ultrasensitive enzymatic biosensor for the direct conductometric detection of ochratoxin A (OTA) has been developed in this work. Thermolysin (TLN), a peptidase, was chosen as recognition element. The proposed biosensor is based on TLN immobilization into a polyvinyl alcohol (PVA)/polyethylenimine (PEI) matrix containing gold nanoparticles (AuNPs) and cross-linked at the surface of gold interdigitated microelectrodes using glutaraldehyde vapor. Under optimal conditions (35 min cross-linking time, working pH of 7 and temperature of 25◦C), the biosensor response was linear up to 60 nM OTA and the limit of detection was 1 nM. This value was 700 times lower than the detection limit obtained using the more classical method based on enzyme cross-linking in the presence of bovine serum albumin (BSA). PVA/PEI hydrogel creates a very favorable aqueous environment for the enzyme. In addition, interactions between protonated amino groups of PEI and negative charges of both citrated AuNPs and thermolysin improve their dispersion in the polymer blend, favoring enzyme stabilization and accessibility to the substrate (OTA). The developed OTA biosensor was very reproducible and stable over a 30 days period when stored at 4◦C in 20 mM phosphate buffer between two measurements. The method was further evaluated using commercial doped olive oil samples. No pretreatment of the sample was needed for testing and no matrix effect was observed. Recovery values were close to 100%, demonstrating the suitability of the proposed method for OTA screening in olive oil