Dissertations / Theses: 'Β Peptide'

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Das, Chittaranjan. "Designed β-Hairpin, β-Sheet And Mixed α-β Structures In Synthetic Peptides." Thesis, Indian Institute of Science, 2000. http://hdl.handle.net/2005/263.

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Synthetic construction of protein molecules has been widely pursued over the last two decades. A primary goal behind de novo protein design has been to build minimal systems by capturing the essential features of protein structures. Such minimal models can be used to understand underlying principles governing folding, structure, and function of proteins molecules. Several approaches envisioning successful construction of synthetic proteins have been described over the years, some of them being admirably successful (DeGrado et al, 1999; Richardson et al> 1992; Baltzer, 1998). Specific patterning of polar and apolar residues in synthetic sequences has been widely used to achieve designed polypeptide structures like helix bundles (DeGrado et ah, 1999) and (3-sheets (Smith and Regan, 1997; Lacroix et a/., 1998), with reliance on hydrophobic driving forces for folding. Our laboratory has been pursuing a distinctly alternative approach, that employs stereochemically constrained amino acids to generate specific secondary structures which can then be assembled into composite structures by appropriately chosen linking segments. This approach, which involves linking prefabricated modules of secondary structures can be termed as a "Meccano set" approach to protein design (Balaram, 1992). The studies embodied in the present thesis describe attempts at construction of synthetic polypeptide motifs using the stereochemically directing influence of conformationally constrained amino acid residues, such as DPro or Aib (α-aminoisobutyric acid). This thesis is subdivided into 8 chapters, with Chapter 1 providing a perspective of the field of protein design. Subsequent chapters (2-8) describe studies directed towards the specific goal of construction of polypeptide motifs. Chapter 2 describes synthesis and conformational characterization of two octapeptides Boc-Leu-Val-Val-DPro-LAla-Leu-Val-Val-OMe (1) and Boc-Leu-Val-Val-DPro-DAla-Leu-Val-Val-OMe (2), designed to investigate the effect of specific β-turn stereochemistry on β-hairpin structures. 500 MHz NMR studies establish that both peptides 1 and 2 adopt predominantly β-hairpin conformations in chloroform and methanol solutions, with interstrand registry established by observation of long-range nuclear Overhauser effects (NOEs). Specific NOEs provide evidence for a type II' β-turn conformation for the DPro-LAla segment in 1, while the NMR data suggest that a type I' DPro-DAla β-turn conformation predominates in the peptide 2. The crystal structure of 1 reveals two independent molecules in the crystallographic asymmetric unit, both of which adopt β-hairpin conformations nucleated by a type II’ β-turn across DPro-LAla and stabilized by 3 cross strand hydrogen bonds. These designed β-hairpins with defined tight turns produce characteristic vibrational circular dichroism (VCD) patterns, demonstrating the utility of VCD as a probe for conformational analysis of β-hairpins. In Chapter 3, we present conformational analysis on designed β-hairpin sequences incorporating a 'Phe-Phe' residue pair at a non-hydrogen bonding position. Two octapeptides Boc-Leu-Phe-Val-DPro-Gly-Leu-Phe-Val-OMe and Boc-Leu-Phe-Val-DPro-Ala-Leu-Phe-Val-OMe were synthesized and conformationally characterized by 500 MHz NMR spectroscopy. Specific NOEs observed in solution provide conclusive evidence favoring specific orientation effects pertaining to the 'Phe-Phe' pair. The peptides exhibited anomalous electronic CD, which has been explained in terms of aromatic contributions by the side chain chromophores. Interestingly, the VCD patterns obtained for these peptides were almost identical to those obtained for other β-hairpins, described in Chapter 2. Chapter 4 describes the synthesis and conformational analysis of designed decapeptide sequences with centrally located DPro-Xxx β-trun segments. Two sequences Boc-Met-Leu»Phe-Val'DPro-Ala-Leu-Val-Val-Phe-OMe (1) and Boc-Met-Leu-Val-Val-^ro-Gly-Leu-Val-Val-Phe-OMe (2) were designed to study the effect of chain length elongation, of β-strands, on designed β-hairpin structures. 500 MHz NMR studies establish β-hairpin folds in both these sequences, with strand segments aligned even at the termini of the structures. Multi-stranded, antiparallel β-sheet structures can be generated by successive placement of β-hairpin sequences in a single polypeptide chain. The successful construction of three stranded β-sheet structures is described in Chapter 5 of this dissertation. A 14-residue peptide Boc-Leu-Phe-Val-DPro-Gly-Leu-Val-Leu-Ala-DPro-Gly-Phe-Val-Leu-OMe (LFV14) was designed such that it is composed of three strand segments linked by two DPro-Gly turn segments. The peptide showed excellent solubility in apolar media, permitting detailed conformational analysis by 500 MHz NMR spectroscopy in organic solvents. Observation of long-range, interstrand NOEs, diagnostic of multiple hairpin structures, provides conclusive evidence for a predominantly populated three stranded β-sheet structure in solution. Extension of this strategy has been described in which an 18-residue peptide, Arg-Gly-Thr-Ile-Lys-DPro-Gly-Val-Thr-Phe-Ala-DPro-Ala-Thr-Lys-Tyr-Gly-Arg, was designed with enhanced solutility in water to probe (β-sheet structure formation in aqueous and mixed aqueous-methanol systems. NMR data provided conclusive evidence in favor of the desired structure being significantly populated in methanol and methanol-water mixtures (50 %, v/v). In water, spectroscopic evidence suggests that the long-range order expected of a three-stranded structure is lost, possibly due to water invading the interstrand hydrogen bonds. Successful construction of a four-stranded antiparallel β-sheet structure has been demonstrated in Chapter 6. A 26-residue peptide Arg-Gly-Thr-Ile-Lys»DPro-Gly-Ile-Thr- Phe-Ala-DPro-Ala-Thr-Val-Leu-Phe-Ala-Val-DPro-Gly-Lys-Thr-Leu-Tyr-Arg was designed to have four strand segments linked by three DPro-Xxx turn segments. The peptide exhibited excellent NMR properties permitting structure determination by analysis of NOE data, which revealed that a four stranded β-sheet structure is indeed populated in methanol. Structural studies on this peptide in mixed methanol-water established that the four stranded β-sheet is appreciably populated at a composition of 50 % (v/v) methanol-water mixture, with the β-sheet structure still detectable even at a composition of 70 % water-30 % methanol. In a completely aqueous environment, the β-sheet structures is significantly disrupted, presumably due to solvent invasion. The nucleating β-turns, however, appear to have retained their structural integrity even in this competitive environment. Chapter 7 describes the insertion of L-Lactic acid (Lac), a hydroxy acid, into polypeptide helices stabilized by a-aminoisobutyricacid (Aib). This study was undertaken to investigate the effect of hydrogen bond deletion on peptide helices. Crystal structure determination of three oligopeptides containing Lac residues has been performed. Peptide 1, Boc-Val-Ala-Leu-Aib-Val-Lac-Leu-Aib-Val-Ala-Leu-OMe, and peptide 2, Boc-Val-Ala-Leu-Aib-Val-Lac-Leu-Aib-Val-Leu-OMe adopt completely helical conformations in the crystalline state, with the Lac(6) residue comfortably accommodated in the center of a helix. NMR studies of peptide 1 and its all amide analog 4, Boc-Val-Ala-Leu-Aib-Val-Ala-Leu-Aib-Val-Ala-Leu-OMe, provide firm evidence for a continuous helical segment in both the cases. In a 14-residue peptide 3, Boc-Val-Ala-Leu-Aib- Val- Ala-Leu- Val- Ala-Leu- Aib-Val-Lac-Leu-OMe, residues Val( 1 )-Leu( 10) adopt a helical conformation, which is terminated by formation of a Schellman motif, with Aib(ll) as the site of chiral reversal. The loss of the hydrogen bond at the C-terminus appears to facilitate the chiral reversal at Aib(l 1). In the final section of this thesis, Chapter 8, successful construction of a synthetic motif containing two distinct elements of secondary structure, a (β-hairpin and a helix, has been described. The design of a 17-residue peptide Boc-Val-Ala-Leu-Aib-Val-Ala-Leu-Gly-Gly-Leu-Phe-Val-DPro-Gly-Leu-Phe-Val-OMe, BH17, is based on a modular approach, in which previously characterized β-hairpin (Leu-Phe-Val-DPro-Gly-Leu-Phe-Val) and helix (Val-Ala-Leu-Aib-Val-Ala-Leu) modules are linked by a Gly-Gly linker. The positioning of the achiral Gly residue at position 8 facilitates termination of the potential helical segment (residues 1-7) by formation of a Schellman motif. Gly(9) is anticipated to be the sole conformationally flexible residue. NMR studies on BH17 indicated the presence of both the helix (residues 1-7) and the β-hairpin (residues 10-17) structures in the sequence, with four major conformational possibilities at the linking segment. Crystal structure determination of BH17 revealed that the two elements of structure are approximately arranged in an orthogonal fashion. The crystal structure validates the original premise that a modular assembly strategy may be viable for the construction of larger synthetic structures. Chapter 9 summarises the major results of this thesis. (For formulae, please refer "pdf" format)

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Chiricotto, Mara. "Hydrodynamic effect on β-amyloid peptide aggregation." Thesis, Sorbonne Paris Cité, 2016. http://www.theses.fr/2016USPCC136/document.

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Un fait marquant et essentiel de la maladie neurodégénérative d’Alzheimer est la formation de plaques amyloïdes dans le cerveau, résultat de l’agrégation des protéines amyloïde-β (Aβ1-40/1-42). Le développement de nouveaux médicaments requiert la compréhension des mécanismes de formation des fibres amyloïdes et la connaissance de la structure et dynamique des oligomères métastables qui sont les vecteurs principaux de la neurotoxicité. Parce que les simulations atomistiques en solvant explicite ne peuvent pas être réalisées sur de grands systèmes pour des temps très longs, nous avons opté pour un modèle protéique gros grain (CG) avec un solvant implicite. Nous nous sommes intéressés dans ces travaux de thèse à clarifier le rôle d’interactions hydrodynamiques(HI) dans la dynamique de formation des agrégats du peptide Aβ(16-22), connu pour former également des fibres amyloïdes. Ces interactions sont essentielles pour modéliser,dans un solvant implicite, les processus se produisant dans des environnements cellulaires très encombrés. Notre approche est basée sur une méthode multi-échelle et multi-physique qui couple les techniques Lattice Boltzmann et de dynamique moléculaire(LBMD). Dans notre système, les interactions médiées par le solvant aqueux sont incluses naturellement. Pour le système moléculaire, nous avons choisi le modèle gros grain à haute résolution OPEP (Optimized Potential for Efficient Protein structure prediction). Pour la première fois, nous avons effectué des simulations quasi tout-atome pour de très grands systèmes contenant des milliers de peptides Aβ ( 16-22). Après avoir correctement réglé le paramètre clé de notre couplage afin d’obtenir la diffusivité expérimentale des monomères et des oligomères du peptide Aβ ( 16-22), nous avons démontré que les HI accélèrent le processus d’agrégation pour des systèmes de taille moyenne (100 Aβ (16-22) peptides) et grande (1000 Aβ (16-22) peptides). Une caractérisation détaillée de la taille des clusters et de l’organisation structurelle des peptides est présentée. Enfin,nous avons examiné comment la concentration affecte la première phase d’agrégation des peptides et leurs structures
The self-assembly of misfolded amyloid-β (Aβ 1-40/1-42) proteins into insoluble fibrils is strongly linked to the pathogenesis of Alzheimer’s disease (AD). The development of new drugs requires the understanding of the mechanisms leading to fibril formation, and the knowledge of the dynamics and structures of the early metastable oligomers which are the main neurotoxic species. Because atomistic simulations in explicit solvent cannot be performed on very large systems for a significant time scale, we resort to a coarse grained (CG) protein model with an implicit solvent. Our investigation enlightens the role of hydrodynamic interactions (HI) in the kinetics of β-amyloidogenesis, interactions which are essential, when an implicit solvent is used, to model processes occurring in highly crowded like-cell environments, among others.Our approach is based on a multi-scale and multi-physics method that couples Lattice Boltzmann and Molecular Dynamics (LBMD) techniques. In our scheme the solvent- mediated interactions are included naturally. As a first step, we focus on Aβ (16-22) peptide, known to form amyloid fibril alone, and we adopt the high resolution CG OPEP (Optimized Potential for Efficient Protein structure prediction) model, developed in our laboratory. For the first time, we have performed quasi-all-atom simulations for very large systems containing thousands of Aβ (16-22) peptides. After the correct tuning of the key parameters of our coupling in order to obtain the experimental diffusivity of Aβ (16-22) monomer and small oligomers, we have demonstrated that HI speed up the aggregation process of medium (100 peptides) and large (1000 peptides) systems. A detailed characterization of the fluctuating clusters along the trajectories is presented in terms of their sizes and the structural organization of the peptides. Finally, we have investigated how changes in the concentration affect the early aggregation phase of the peptides and their structures

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Newby, Francisco Nicolas. "Structural studies of the Alzheimer's amyloid β peptide." Thesis, University of Cambridge, 2013. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.607712.

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Liu, Yong-Peng. "Total Synthesis of Microsclerodermin D." Thesis, université Paris-Saclay, 2020. http://www.theses.fr/2020UPASF024.

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La microsclerodermine D est un peptide macrocyclique d’origine marine qui comporte six amino acides, dont deux sont disponibles commercialement : la glycine (Gly) et la sarcosine (Sar). Les quatre autres amino acides : l’acide (R)-γ-amino-β-hydroxybutyrique (GABOB), le D-6-chlorotryptophane (6-Cl-Trp), un β-amino acide polyhydroxylé (APTO) et l’acide 3-amino-4-hydroxypyrrolidinoacetique (PyrrAA) seront préparés via de nouvelles voies de synthèse. Notre objectif est de développer une voie de synthèse de la microsclerodermine D modulable et qui permettrait la synthèse d’autres membres de la famille des microsclerodermines et d’analogues. Nos nous intéresserons également à de potentielles études permettant d’évaluer leurs propriétés biologiques et leur potentiel en tant qu’agent anticancéreux
Microsclerodermin D is a macrocyclic peptide of marine origin which contains six amino acids, of which two are commercially available: glycine (Gly) and sarcosine (Sar). The four other amino acids: (R)-γ-amino-β-hydroxybutyric acid (GABOB), D-6-chlorotryptophan (6-Cl-Trp), a polyhydroxylated β-amino acid (APTO) and 3-amino-4-hydroxypyrrolidinoacetic acid (PyrrAA) will be accessible by new synthetic routes. Our goal is to develop a modular synthetic route to microsclerodermin D that could be applicable for the preparation of other microsclerodermin family members and analogues thereof. We are also looking forward to make some investigations on their biological activities or potential as anticancer drug

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Österlund, Nicklas. "Gas phase studies of the Amyloid-β peptide : Peptide oligomerization and interactions with membrane mimetics." Thesis, Stockholms universitet, Institutionen för biokemi och biofysik, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-155009.

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The amyloid-β peptide is an amphiphilic peptide that exhibits self-aggregating properties, forming the amyloid fibrils that can be found in the brains of Alzheimer patients. Today it is believed that it is the soluble Aβ oligomers rather than the mature fibrils that are the main neurotoxic species. These small peptide assemblies are known to associate with lipid membranes and form pores that can transport Ca2+ into the cell, which in part could be responsible for their neurotoxic properties. However, most biophysical methods that have been developed to study Aβ target either the monomer or the mature fibrils, and not the low abundance and polydisperse oligomers. In this work, a soft ionization mass spectrometry method that retains non-covalent oligomer interactions in the gas phase has been developed. Using this method, monomeric and oligomeric Aβ (1-40) from dimers up to octamers, except heptamers, were detected in vitro. It was also possible to detect and study the effects of peptide modifications such as methionine-35 oxidation. As mass spectrometry is a non-averaging technique the aggregation kinetics for reduced and oxidized peptides are followed simultaneously, and the results showed that the oxidized form of Aβ(1-40) aggregates slower and forms lower amounts of soluble oligomers than the reduced form. Additionally, Aβ(1-40) interactions with zwitterionic SB3-14 detergent micelles were studied in the gas phase, and it was demonstrated that Aβ-micelle complexes can survive in the mass spectrometer and be identified. Detergent head group charges seem to be essential for peptide-micelle interaction, both in the gas phase and in solution as no structure induction is observed upon addition of the non-ionic detergent DDM. Overall gas phase and solution properties agree well, which is encouraging for future gas phase studies of Aβ interactions with membrane mimetics.

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Klementieva, Oxana. "Influence of Cu(II) and Glycodendrimers on Amyloid-beta-Peptide Aggregation." Doctoral thesis, Universitat Internacional de Catalunya, 2012. http://hdl.handle.net/10803/78910.

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La malaltia d’Alzheimer es caracteritza per l’acumulació de plaques extracel.lulars amiloides, formades pels anomenats pèptids amiloides (Aβ40). L’homeòstasi del coure (Cu) es veu afectada en l’etiologia de la malaltia d’Alzheimer, encara que el seu rol és un fet controvertit. Per a l’estudi de la influència del Cu(II) en l’agregació del pèptid amiloide, la morfologia i l’estructura secundària dels agregats amiloides formats en presència de Cu(II) s’han utilitzat AFM, TEM, SEM, SAXS, FTIR i espectrometria de fluorescència. A més, els efectes tòxics d’aquests agregats s’han estudiat en cèl.lules neuronals. Els resultats obtinguts mostren que aquests agregats són amorfos i presenten una toxicitat més alta que les fibres. Per a l’estudi dels dendrímers de maltosa com a possibles moduladors de l’agregació i de la toxicitat del pèptide amiloide. S’ha confirmat que aquests dendrimers no són tòxics en cèl.lules neuronals i que són capaços de modular l’agregació i toxicitat del pèptid amiloide. Aquests resultats permeten considerar als dendrimers de maltosa com a possibles eines per a reduir la toxicitat dels pèptids amilodies.
Senile plaques of Alzheimer’s disease patients are composed primarily of the amyloid-β-peptide (Aβ). Recent studies implicate Cu(II) in the aetiology of AD. The role of Cu(II) in ADis currently highly disputed. Influence of Cu(II) on Aβ aggregation and amyloidogenic properties of glycodendrimers were investigated in this thesis. AFM, TEM, SEM, SAXS, FTIR and fluorescence spectroscopy were used to study a morphology and a secondary structure of Aβ-Cu(II) aggregates. The toxic effects of Aβ40-Cu(II) amorphous aggregates was confirmed for neuronal cell lines. It was shown that maltose glycodendrimers can be efficiently used to modulate Alzheimer’s amyloid peptide aggregation and inhibit cell toxicity by facilitating the clustering of amyloid fibrils. These results show that glycodendrimers are promising non-toxic agents in the search for anti-amyloidogenic compounds. It was also suggested that fibril clumping may be anti-amyloid toxicity strategy.

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Guivernau, Almazán Biuse 1988. "Modulation of Amyloid-β peptide aggregation and neurotoxicity in Alzheimer's disease." Doctoral thesis, Universitat Pompeu Fabra, 2016. http://hdl.handle.net/10803/585932.

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Aggregation of the amyloid-β (Aβ) peptide to form oligomers and amyloid fibrils is a central event in the pathogenesis of Alzheimer’s disease (AD). This thesis aims to provide a better understanding of Aβ toxicity and the impact of changes in Aβ aggregation, both relevant to AD. We have found that Aβ nitrotyrosination inhibits fibril formation, which favours the stabilization of small oligomers. We show that nitro-Aβ oligomers strongly bind to dendrites, altering N-methyl-D-aspartate receptor (NMDAR) physiological function and leading to neuronal dysfunction and cell death. Furthermore, we propose a model for Aβ fibril assembly, according to which fibril elongation is interrupted upon nitrotyrosination, due to the destabilization of interprotofibrillar contacts. Additionally, using a genome-wide screen in Saccharomyces cerevisiae, we have identified novel modulators of Aβ toxicity that are potential targets for the development of new AD therapeutic approaches.
L’agregació del pèptid b-amiloide (Aβ) en forma d’oligòmers i fibres és un esdeveniment central en la patogènesi de la malaltia d’Alzheimer. Aquesta tesi pretén aprofundir en els coneixements actuals sobre la toxicitat causada per l’Aβ així com en l’impacte que tenen els canvis en l’agregació d’aquest, tots dos rellevants per la malaltia d’Alzheimer. Els nostres resultats indiquen que la nitrotirosinació de l’Aβ inhibeix la formació de fibres, afavorint l’estabilització d’oligòmers. Demostrem que els oligòmers d’Aβ nitrat s’uneixen a les dendrites, alterant la funció fisiològica dels receptors d’N-metil- D-aspartat (NMDAR) i provocant disfuncions neuronals i la mort cel·lular. A més, proposem un model d’assemblatge per a les fibres d’Aβ, segons el qual la nitrotirosinació interromp l’elongació de la fibra a causa de la desestabilització dels contactes entre protofibres. Addicionalment, utilitzant un cribratge genòmic en Saccharomyces cerevisiae, hem identificat nous moduladors de la toxicitat causada per Aβ, que podrien ser clau per al desenvolupament de noves estratègies terapèutiques de la malaltia Alzheimer.

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Lindberg, Hanna. "Engineering of Affibody molecules targeting the Alzheimer’s-related amyloid β peptide." Doctoral thesis, KTH, Proteinteknologi, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-173864.

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Moore, Claire E. J. "Investigation into glucagon like peptide-1 signalling in pancreatic β-cells." Thesis, University of Leicester, 2008. http://hdl.handle.net/2381/29965.

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Glucagon like peptide-1 (GLP-1) is a GS-coupled receptor agonist that exerts multiple effects on pancreatic beta-cells, including the stimulation of insulin gene expression and secretion, growth and survival. A number of kinases are activated in response to GLP-1R activation, including extracellular regulated kinases (Erk1/2), phosphatidylinositol 3-kinase (PI3K), protein kinase B (PKB) and mammalian target of rapamycin mTOR, all of which contribute in regulating various aspects of beta-cell function. However, the mechanism by which GLP-1 activates these signalling pathways in pancreatic beta-cells is not fully understood. Therefore, the objectives of this thesis were to investigate how GLP-1 signals to Erk1/2. PI3K/PKB and mTOR. It has previously been reported that GLP-1 stimulated Erk1/2 activation is dependent on the influx of Ca2+ specifically through L-Type VGCC. In this thesis I provide evidence that this increase in Ca2+ activates the Ca2+ dependent phosphatase, calcineurin which in turn activates IKK leading to the activation of the MEK kinase, Tp12. Ca2+ entry through L-Type VGCC also plays a key role in stimulating insulin secretion which I show is responsible for glucose stimulated PI3K activation and PKB phosphorylation. In contrast, GLP-1 can activate PI3K independent of insulin secretion which is unable to couple to PKB. Interestingly, GLP-1 is able to potentiate glucose stimulated mTOR activation via a PI3K leading to the phosphorylation of rpS6 on Ser240/244. Moreover, GLP-1 can stimulate the phosphorylation of rpS6 on Ser235/236 which is not dependent on mTOR activation or the two currently known S6Ks, S6K1/2 or p90RSK.

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Höger, Geralin. "Self-Organization of β-Peptide Nucleic Acid Helices for Membrane Scaffolding." Doctoral thesis, Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2019. http://hdl.handle.net/21.11130/00-1735-0000-0003-C187-A.

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VILARDO, ELISA. "Il microRNA-101 regola la proteina precursore del peptide β-amiloide." Doctoral thesis, Università degli Studi di Roma "Tor Vergata", 2010. http://hdl.handle.net/2108/1175.

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Nella patogenesi della malattia di Alzheimer, il livello di espressione della proteina precursore del peptide β-amiloide (APP) riveste un ruolo determinante. E’ stato evidenziato che mutazioni che incrementano la sintesi proteica di APP, inclusa la duplicazione genica del locus di APP in alcune famiglie e nella trisomia del cromosoma 21, che contiene il gene APP, sono sufficienti per indurre lo sviluppo della patologia in forma precoce. Per questo motivo, la regolazione del gene APP è stata oggetto di intensi studi riguardanti sia la caratterizzazione del promotore, che le regioni 5’ e 3’ non tradotte dell’RNA messaggero. Negli ultimi anni, il meccanismo di regolazione post-trascrizionale dell’espressione genica mediato dai microRNA è stato estesamente indagato in diversi meccanismi biologici e in vari tipi cellulari. I microRNA modulano finemente la traduzione di proteine necessarie alla risposta a stimoli di origine extracellulare, ed in altri casi definiscono spazialmente e temporalmente i profili di espressione di geni coinvolti nello sviluppo e differenziamento. Lo svolgimento di questa tesi sperimentale ha trovato il suo avvio nella domanda se il sistema dei microRNA fosse coinvolto in maniera significativa nella regolazione dell’espressione dell’APP. Tramite RNAi, è stata silenziato il gene Argonauta 2, componente fondamentale del complesso ribonucleoproteico che media l’azione dei microRNA, ed è stato osservato un aumento della proteina APP. Mediante analisi bioinformatica sono stati individuati i possibili microRNA interagenti con APP ed è stato scelto il miR-101, arricchito nel sistema nervoso. Tramite analisi dei profili di espressione in ippocampo di ratto, tra gli 8 giorni e i 6 mesi di età, è stata osservata una correlazione inversa tra i livelli di miR-101, che aumenta, e APP, che diminuisce nel corso del tempo. Utilizzando un costrutto reporter, è stata dimostrata la capacità del miR-101 di inibire la traduzione di APP attraverso l’interazione diretta con il 3’UTR del messaggero. Bloccando l’azione del miR-101 in colture primarie ippocampali, è stato osservato un significativo aumento della proteina APP endogena, confermando l’azione regolatoria del microRNA nel contesto neuronale fisiologico, mentre la over-espressione del miR-101 si è rivelata efficace nell’indurre una repressione a livello post-trascrizionale dell’APP. E’ stato inoltre osservato che la stimolazione di neuroni ippocampali con Interleuchina-1β, principale mediatore della neuroinfiammazione e fattore di rischio per AD, induce una modulazione coordinata nel tempo di APP e del miR-101. I dati ottenuti dimostrano quindi l’esistenza di un’attività repressiva del miR-101 sull’APP in condizioni fisiologiche, mentre la perturbazione di tale regolazione è sufficiente ad indurre un aumento della proteina APP, condizione associata alla patologia di Alzheimer. Considerando studi recenti, in cui il miR-101 è stato visto down-regolato in cervelli di casi sporadici di malattia di Alzheimer, e i dati qui ottenuti, miR-101 può essere visto come un regolatore con attività protettiva verso una eccessiva produzione del precursore del peptide β-amiloide. La caratterizzazione della via di trasduzione del segnale, neuroinfiammatorio, che coinvolge il miR-101, e la sua possibile associazione con la patologia di Alzheimer potrebbero aprire nuovi scenari nella eziopatogenesi di questa malattia neurodegenerativa.
In the pathogenesis of Alzheimer's disease, the expression level of the β-amyloid precursor protein (APP) plays a crucial role. It has been shown that mutations which increase APP protein synthesis, including the duplication of the locus of APP gene in certain families and trisomy of chromosome 21 (containing the APP gene), are sufficient to induce the early form of pathology. Therefore APP gene regulation has been extensively studied and both the promoter and 5’ and 3’ untranslated regions of mRNA have been charachterised. In recent years, the post-transcriptional mechanism of gene expression mediated by microRNAs has been discovered and investigated in several biological mechanisms and cell types. MicroRNAs have been shown to finely modulate the translation of proteins needed for the response to extracellular stimuli, and to define the spatial and temporal expression profiles of genes involved in neuronal development and differentiation. This experimental thesis focused on the question whether microRNAs are significantly involved in APP regulation. Through RNAi , Argonauta-2 gene, a key component of the ribonucleoprotein complex mediating the action of microRNAs, was silenced and APP protein increase was observed. Through bioinformatic analysis, microRNAs potentially interacting with APP have been identified and miR-101, which is enriched in the nervous system, was further investigated. Through expression analysis in rat hippocampus, from 8 days up to 6 months of age, it was observed an inverse correlation between miR-101 levels, which increase, and APP expression, which decreases over time. Using a reporter construct, the ability of miR-101 to inhibit the translation of APP through direct interaction with the messenger 3’UTR was demonstrated. Through inhibition of miR-101 in hippocampal primary cultures, a significant increase of endogenous APP protein was observed, confirming the miRNA regulatory function in the neuronal context. Instead miR-101 over-expression was effective in inducing APP repression at post-transcriptional level. It was also observed that stimulation of hippocampal neurons with IL-1, the first player of neuroinflammation and risk factor for Alzheimers Disease, induces coordinated modulation of APP and miR-101. These data demonstrate the repressive effect of miR-101 on APP under physiological conditions, while the alteration of this regulation is sufficient to induce an increase of APP protein, a condition which is associated to familial Alzheimer’s disease. In view of previous studies, in which miR-101 was shown to be down-regulated in the brains of sporadic cases of Alzheimer's disease, and of data obtained in this work, miR-101 may be a protective regulator of excessive production of β-amyloid precursor protein. The characterization of the signal transduction pathway activated by neuroinflammation, involving miR-101, and the relationship between this pathway and Alzheimer's disease might open a new perspective on the pathogenesis of this neurodegenerative disease.

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Pahlke, Denis. "Synthesis, characterisation and sensor-functionalisation of transmembrane β-peptides." Doctoral thesis, Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2018. http://hdl.handle.net/21.11130/00-1735-0000-0003-C180-1.

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13

Hu, Zilun. "CONSTRAINED β–PROLINES: I. METHANOPYRROLIDINE β-AMINO ACIDS: SYNTHESIS AND CHARACTERIZATION OF NOVEL C6- SUBSTITUTED ANALOGUES AND PEPTIDE OLIGOMERS II. SYNTHESIS OF 2,2-DISUBSTITUTED PYRROLIDINE-3-CARBOXYLIC ACIDS." Diss., Temple University Libraries, 2015. http://cdm16002.contentdm.oclc.org/cdm/ref/collection/p245801coll10/id/339315.

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Chemistry
Ph.D.
In the study of structurally restricted cyclic β-amino acids and peptides, methanopyrrolidine-5-carboxylic acids (MetPyr-5-acids), or 5-syn-carboxy-2-azabicyclo[2.1.1] hexanes, and derivatives were investigated. MetPyr-5-acids are a series of highly conformationally constrained β-proline derivatives, which belong to a novel category of β-amino acids utilized as building blocks for the synthesis of β-peptides. These β-peptides lack the backbone hydrogen bonds necessary for folding in the usual manner. Substituents and functional groups in this ring system were envisioned to impact the folding properties and functionalities of the corresponding β-peptides. In the present study, the analogues of MetPyr-5-acids with C6- substitutions were prepared, and the folding properties of their peptides were explored. To introduce different functionalities at C6 in MetPyr-5-acids, 6-syn-hydroxymethyl substituted derivatives were synthesized and were used as key intermediates. In the synthesis of this core structure, the major steps in their preparation included the Michael addition of benzyloxymethyl allyl amine to 3-butynone, followed by UV light irradiation of the diene to afford 5-acetyl-6-benzyloxymethyl-2-azabicyclo[2.1.1]hexane. Haloform (Br2/NaOH) oxidation of the acetyl group leads to the 6-substituted MetPyr-5-acid. Resolution of the racemate was achieved either by resolving (±)-6-syn-benzyloxymethyl-MetPyr-5-acid via a classical crystallization resolution method using (S)-(-)-α-methylbenzylamine, or by chiral preparative HPLC separation of (±)-6-syn-benzyloxymethyl-MetPyr-5-acid methyl ester. The absolute stereochemistry was confirmed by X-ray crystallography of a derivative. Novel analogs with a range of functionalities incorporated at the C6 position in MetPyr-5-acid were synthesized from 6-syn-hydroxymethyl-MetPyr-5-acid methyl ester, and include hydrophilic groups such as hydroxyl, amino, methyl ether, and hydrophobic groups, such as substituted phenyl groups and triazole. From the protected C6-substituted analogs of MetPyr-5-acids, peptide oligomers of C6-benzyloxymethyl-2,4-methanopyrrolidine-b-amino acid were prepared up to the length of octomer in high yields. This series of oligomers were characterized by circular dichroism (CD) and indicated enhanced order of folding uniformity for the tetramer and up, with increasing ordered folding for longer oligomers. The octomer exhibited minimal solvent effects, and was stable with increasing temperature up to 80 °C. Analysis by NMR of the iso-butyric amide capped monomer indicated a mixture of cis/trans conformation favoring the cis conformation. This was slightly different from the C6 unsubstituted iso-butyric amide derivative, which favored the trans conformation. For the dipeptide, the C6-benzyloxymethyl substitution increased the percentage of cis conformation of the dipeptide amide bond, but the major peptide had the trans conformation. This demonstrated that C6 substitutions could shift the cis/trans equilibrium towards the cis conformation. Longer oligomers showed ordered secondary folding structure as demonstrated by the increase in ellipticity per amino acid unit, but was too complicated to be determined by NMR analysis. Both the CD patterns and molecular model calculation predicted that the longer oligomers (tetramer and above) favor the trans conformation. This preference was driven by the backbone dipole effect. II. SYNTHESIS OF 2,2-DISUBSTITUTED PYRROLIDINE-3-CARBOXYLIC ACIDS Due to the perceived steric influence of 2,2-disubstitution in the pyrrolidine-3-carboxylic acid, it is believed that the adjacent amide/peptide bonds should result in a trans amide bond conformation. Because of the difficulty in introducing disubstitution at the hindered C2 position, the synthesis of such derivatives has not been successful. For this reason a new method was introduced to prepare novel derivatives, at the N- and C- termini of protected 2,2-dimethyl pyrrolidine-3-carboxylic acid, i.e., benzyloxycarbonyl protected 2,2-dimethylpyrrolidine-3-carboxylate. This procedure included the Michael addition of 2-nitropropane to dimethyl fumarate, followed by ring closure of the amino ester derived from reduction of the nitro ester providing the pyrrolidinone. Reduction of the pyrrolidinone to the pyrrolidine with borane finished 2,2-dimethylpyrrolidine-3-carboxylate in moderate overall yield. A preliminary set of two amides, iso-butyric amide and 3,5-dichlorobenzamide of this 2,2-dimethylpyrrolidine-3-carboxylate, were also prepared. NMR analysis of this pyrrolidine derivative suggested the amide bonds adopted the trans conformation. It was concluded that steric bulk of the 2,2-disubstitution favorably influenced the trans amide conformation. This demonstrated that trans amide conformation control of a β-proline amide was possible.
Temple University--Theses

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14

Valls, Comamala Victòria 1987. "Targeting aging and Alzheimer's disease : from GM1 ganglioside to amyloide-β peptide." Doctoral thesis, Universitat Pompeu Fabra, 2018. http://hdl.handle.net/10803/664938.

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Aging is the main challenge that humanity will face on the near future. Brain aging is associated with cognitive deficiencies and is the main risk factor for Alzheimer’s Disease (AD). AD is the most common neurodegenerative disease leading to dementia caused by the aggregation of amyloid-β peptide (Aβ). In this thesis, we have shown that neuronal aging leads to alteration in the ganglioside membrane content. Specifically, increased levels of GM1 ganglioside in membrane leads to a decrease in the calcium entry through NMDA receptors and a reduction of dendritic spines. Overall, pointing a role in the alterations in learning and memory associated to aging. On the other hand, we have showed the inhibitory effect of the human gamma immunoglobulins (IgG) in Aβ aggregation through the antigen-binding fragment (Fab), which binds to Aβ blocking fibrillation progression.
L’envelliment de la població és i serà un gran repte per la nostra societat en els pròxims anys. L’envelliment cerebral està associat amb deficiències cognitives i és el principal factor de risc pel desenvolupament de la malaltia d’Alzheimer. L’Alzheimer és la malaltia neurodegenerativa que més freqüentment provoca demència i és causada per l’agregació del pèptid β-amiloide (Aβ). En aquesta tesis hem demostrat que l’envelliment neuronal condueix a alteracions en el contingut de gangliòsids de les membranes. Particularment, l’increment del gangliòsid GM1 en la membrana condueix a una disminució en l’entrada de calci a través dels receptors de NMDA i a una reducció de les espines dendrítiques. En conjunt, indicant el rol de GM1 en les alteracions en l’aprenentatge i la memòria que es produeixen en l’envelliment. Per una altra banda, hem demostrat l’efecte inhibitori de gamma immunoglobulina humana (IgG) en la inhibició de l’agregació de l’Aβ a través del contacte del fragment d’unió a l’antigen (Fab). Fab s’uneix a Aβ inhibint la progressió de la fibril·lació.

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Wahlström, Anna. "NMR studies on interactions between the amyloid β peptide and selected molecules." Doctoral thesis, Stockholms universitet, Institutionen för biokemi och biofysik, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-60346.

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Alzheimer’s disease is an incurable neurodegenerative disorder linked to the amyloid β (Aβ) peptide, a 38-43 residue peptide. The detailed molecular disease mechanism(s) is (are) unknown, but oligomeric Aβ structures are proposed to be involved. In common for the papers in this thesis is interactions; interactions between Aβ(1-40) and selected molecules and metal ions. The purpose has been to find out more about the structural states that Aβ can adopt, in particular the β-sheet state, which probably is linked to the oligomeric structures. The methods used have been nuclear magnetic resonance (NMR), circular dichroism (CD) and fluorescence spectroscopy using Thioflavin T (ThT). Upon addition of SDS/LiDS detergent or Congo red (CR) to Aβ(1-40), the initial random coil/PII-helix state was transformed into β-sheet and, in the case of detergent, a final α-helical state. In contrast to SDS/LiDS and CR, the dimeric Affibody molecule locks monomeric Aβ(1-40) in a β-hairpin state. It was found that by truncating the flexible N-terminal end of the Affibody molecule its affinity to Aβ was improved. The aggregation of Aβ(1-40) was further studied in the presence of a β-cyclodextrin dimer by a kinetic assay using ThT. Although having a weak dissociation constant in the millimolar range, the β-cyclodextrin dimer modified the aggregation pathways of Aβ. Finally Aβ(1-40) was studied in presence of Cu2+ and Zn2+ at physiological and low pH. Cu2+ was observed to maintain its specific binding to Aβ when decreasing the pH to 5.5 while Zn2+ behaved differently. This could be of importance in the Alzheimer’s disease brain in which the environment can become acidic due to inflammation. In conclusion the results show that Aβ(1-40) is very sensitive to its environment, responding by adopting different conformations and aggregating in aqueous solutions. The β-sheet state is induced by varying molecules with different properties, properties that govern the final Aβ state.
At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 4: Manuscript. Paper 5: Manuscript.

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Chen, Chen. "SINGLE-MOLECULE ANALYSIS OF ALZHEIMER'S β-PEPTIDE OLIGOMER DISASSEMBLY AT PHYSIOLOGICAL CONCENTRATION." UKnowledge, 2014. http://uknowledge.uky.edu/chemistry_etds/31.

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The diffusible soluble oligomeric amyloid β-peptide (Aβ) has been identified as a toxic agent in Alzheimer’s disease that can cause synaptic dysfunction and memory loss, indicating its role as potential therapeutic targets for AD treatment. Recently an oligomer-specific sandwich biotin-avidin interaction based assay identified the Aβ oligomer dissociation potency of a series of dihydroxybenzoic acid (DHBA) isomers. Because the sandwich assay is an ensemble method providing limited size information, fluorescence correlation spectroscopy (FCS) was employed to provide single molecule resolution of the disassembly mechanism. Using FCS coupled with atomic force microscopy, we investigated the size distribution of fluorescein labeled synthetic Aβ oligomers at physiological concentrations, and monitored in real time the change of size and mole fraction of oligomers in the presence of dissociating agents or conditions. The higher-order dissociation process caused by DHBA isomers produced no transient oligomeric intermediates, a desirable feature for an anti-oligomer therapeutic. Urea and guanidine hydrochloride, in contrast, produced a linear dissociation with a progressive decrease of size and mole fraction of oligomers. FCS allows the facile distinction of small molecule Aβ oligomer dissociators that do not produce stable potentially toxic oligomeric Aβ intermediates.

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17

Meisch, Jeffrey P. "Human β-defensin 3 peptide is increased and redistributed in Crohn’s ileitis." Case Western Reserve University School of Graduate Studies / OhioLINK, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=case1270735950.

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18

Abelein, Axel. "Modulation of Alzheimer's amyloid β peptide self-assembly : Insights into molecular mechanisms of peptide aggregation associated with Alzheimer's disease." Doctoral thesis, Stockholms universitet, Institutionen för biokemi och biofysik, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-114172.

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Misfolding of proteins and peptides is closely linked to several neurodegenerative disorders, among them Alzheimer's disease (AD), the most prominent example of brain diseases. The self-assembly of the amyloid β peptide (Aβ) into amyloid fibrils is one histologic hallmark of AD. A detailed knowledge about the underlying mechanism(s) of Aβ aggregation is crucial for advances toward a fundamental understanding of the disease, which may promote the search for and design of efficient therapeutics. The work presented in this thesis deals with modulation of the aggregation process by various compounds, i.e. small organic molecules (e.g. lacmoid and Congo red), surfactants and metal ions. These results provide insight into the molecular mechanism of modulator interactions and interference with Aβ and its aggregation pathways. Applying a combination of kinetic and dynamic studies as well as structural investigations we characterized the molecular interactions between Aβ and aggregation modulators in terms of microscopic rate constants, conformational preferences and thermodynamics. An important conclusion is that these modulators form highly dynamic complexes with Aβ, with life-times on the timescale of milliseconds. Despite the similar exchange dynamics, the effect on peptide aggregation is modulator-specific and fibril formation can be accelerated, retarded or inhibited by their interactions. In summary, Aβ self-assembly is governed by microscopic kinetic and dynamic processes that can be altered by aggregation modulators. Further elucidation of these mechanisms is beneficial for the understanding and therapeutic intervention of amyloid diseases.

At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 4: Manuscript.

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Selim, Erik. "Solid-phase synthesis of Avian β-Defensin 8." Thesis, Linnéuniversitetet, Institutionen för kemi och biomedicin (KOB), 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:lnu:diva-32076.

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Differences in the expression of antimicrobial peptides in vivo have been proposed as underlying factors influencing susceptibility to infection. In this context, the role of avian b-defensins in inhibiting avian influenza infections is a study object in an ongoing collaboration with the Zoonotic Ecology and Epidemiology group at Lnu. In this report, an attempt to synthesize two variants of the peptide Anas Platyrhynchos AvBD-8, using Fmoc-based SPPS, is described. The length of AvBD-8 (43 aa) necessitated peptide synthesis in two segments to subsequently be ligated using native chemical ligation. The first component of a 19 aa segment was thus a Dbz-linker, which would allow to ligate this end with a second segment (24 aa). Halfway through the synthesis of this larger segment the batch was split into two pots, allowing the synthesis of two segments differing by one single amino acid (R for W). The composition of these segments were: Dbz-HDTSCTGGAQKCQVANNPA (Dbz-segment), SVVTRCCPIGQKCWGFARTNPPPC(boc) (W-segment), and SVVTRCCPIGQKCRGFARTNPPPC(boc) (R-segment). Crude product yields were 284,5 mg; 67,6% (Dbz-segment), 137,6 mg; 52,3% (W-segment), and 166,3 mg; 64,2%. Preliminary mass spectrometric analysis on the crude products did not indicate the presence of the desired segments in major mass peaks. Further product purification is necessary in order to allow definite conclusions, but it appears as if the synthesis has not worked. Possible explanations are either impure or degraded reactant(-s), folding or shielding effects of the growing peptide chain at some point inhibiting synthesis, or experimental errors during one or more of the many steps involved in the synthesis.

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20

Huez, Philippe. "Synthèses et analyses conformationnelles de macrocycles aza-β³-peptidiques contenant des atomes d'azote chirogéniques." Thesis, Rennes 1, 2014. http://www.theses.fr/2014REN1S072/document.

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Le travail présenté dans ce mémoire est consacré à la synthèse de cycles pseudopeptidiques construits à partir d'aza-β³-aminoacides, et à la détermination des conformations adoptées par ces cycles. Le travail réalisé a permis de montrer que les cycles obtenus à 8, 16 et 24 liaisons adoptent des conformations privilégiées dans lesquelles la configuration relative des atomes d'azote chiraux est fixée en dépit du phénomène d'inversion pyramidale associé à la structure électronique de cet élément chimique, en réponse à des contraintes structurelles qui varient selon la taille du macrocycle. Ces cycles existent alors sous la seule forme de deux invertomères en équilibre. La constante de vitesse de cet équilibre, qui est indiscernable de la barrière d'inversion pyramidale des atomes d'azote, est maintenue à des valeurs étonnamment faibles par les contraintes conformationnelles. L'étude de ces macrocycles originaux dans le domaine de la chiralité a permis d'apporter en particulier des résultats nouveaux concernant l'influence de l'encombrement stérique des chaînes latérales sur la vitesse d'inversion pyramidale des atomes d'azote, mais aussi sur le transfert de chiralité d'éléments d'asymétrie exocycliques vers la séquence chirale du squelette, et enfin de montrer également l'intérêt des nouveaux cycles à 8 chaînons à travers l'étude de leur conformation
The work depicted here is devoted to the synthesis of pseudopeptides built from aza-β³-aminoacid units, and to their conformational analysis. The results show that the cycles with 8, 16, and 24 bonds each adopt a ground conformation where the relative configuration of the chiral nitrogen atom is fixed in response to specific structural constraints, and despite the nitrogen pyramidal inversion phenomenon. The cycles just undergo equilibrium between two invertomeric forms, and the energetic barrier associated with the macrocycle inversion reveals surprisingly slow considering the size of the compounds. The influence of steric crowding of the side chains on the inversion rate has been carefully studied, but also the transfer of chirality from exocylic elements towards chirotopic nitrogen atoms inside the backbone. A specific chapter is devoted to the 8-membered rings, that reveal the interest of these newly described compounds in the domain of nitrogen chirality

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21

Abelein, Axel. "Modulation of amyloid β peptide self-assembly : Aggregation mechanisms associated with Alzheimer's disease." Licentiate thesis, Stockholms universitet, Institutionen för biokemi och biofysik, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-89078.

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22

Tran, Thi Thuy Linh. "Étude théorique de peptides amyloidogènes : Ensemble conformationnel, oligomérisation et inhibition par des ligands peptidomimétiques." Thesis, Université Paris-Saclay (ComUE), 2016. http://www.theses.fr/2016SACLS518.

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De nombreuses protéines associées aux maladies neurodégénératives humaines sont intrinsèquement désordonnées. Ce sont des protéines qui sont dépourvues de structure tertiaire ou secondaire stable dans des conditions physiologiques. Plus précisément, les protéines intrinsèquement désordonnées (IDPs) subissent diverses changements conformationnels entre la pelote aléatoire, des conformations hélicoïdales et des structures en feuillet-β, ces deux dernières étant généralement impliquées dans la reconnaissance protéine-protéine. Parmi une vingtaine de peptides amyloïdogènes connus liés aux maladies dégénératives humaines, notre étude porte sur deux protéines désordonnées: le peptide Amyloïde-β (Aβ) associé à la maladie d'Alzheimer et l'Islet Amyloid Polypeptide (IAPP) impliqué dans le diabète de type II. Aβ possède deux alloformes courants de 40 et 42 résidus, tandis que IAPP est une hormone peptidique de 37 résidus. Les agrégats de Aβ sont toxiques pour les cellules du cerveau, tandis que la fibrillisation de IAPP affecte les cellules-β du pancréas. Le mécanisme d'agrégation de ces deux peptides reste encore mal connu, mais il a été proposé qu’en solution, ces peptides visitent différentes conformations, l'une d'entre elles étant riche en feuillets-β. Cela conduirait à l’oligomérisation de ces peptides, par le biais d’interactions feuillet-β / feuillet-β et, éventuellement, à la formation de fibrilles. Le but de notre étude est de mieux caractériser la dynamique conformationnelle de ces deux peptides, dans leur forme monomérique et oligomérique. Comprendre les premières étapes de leur agrégation est crucial pour le développement de nouvelles molécules thérapeutiques efficaces contre ces protéines amyloïdes
Many proteins associated with human neurodegenerative diseases are intrinsically disordered. They are proteins which lack stable tertiary or secondary structure under physiological conditions. More specifically, intrinsically disordered proteins (IDPs) undergo various structural conversions between random coil, helical conformations and β-strand structures, these two latter being generally involved in protein-protein recognition. Among about twenty known amyloidogenic peptides related to human degenerative diseases, we focus our study on two disordered proteins: the Amyloid-β peptide (Aβ) associated to the Alzheimer’s disease and the Islet Amyloid Polypeptide (IAPP) involved in type II diabetes. Aβ has two common alloforms of 40 and 42 residues in length, meanwhile IAPP is a 37-residues peptide hormone. Aggregates of Aβ are toxic to the brain cells, meanwhile IAPP fibrillization affects the pancreatic β-cells. The aggregation mechanism of these two peptides is not known in detail, but it was proposed that in solution, these peptides visit various conformations, one of them being rich in β-strands. This would lead to peptide oligomerization, through β-strand / β-strand interactions and eventually to the fibril formation. The aim of our study is to provide insights into the conformational dynamics of these two peptides in monomeric and oligomeric forms. Understanding the early steps of their aggregation is crucial for the development of new effective therapeutic molecules against these amyloid proteins.De nombreuses protéines associées aux maladies neurodégénératives humaines sont intrinsèquement désordonnées. Ce sont des protéines qui sont dépourvues de structure tertiaire ou secondaire stable dans des conditions physiologiques. Plus précisément, les protéines intrinsèquement désordonnées (IDPs) subissent diverses changements conformationnels entre la pelote aléatoire, des conformations hélicoïdales et des structures en feuillet-β, ces deux dernières étant généralement impliquées dans la reconnaissance protéine-protéine. Parmi une vingtaine de peptides amyloïdogènes connus liés aux maladies dégénératives humaines, notre étude porte sur deux protéines désordonnées: le peptide Amyloïde-β (Aβ) associé à la maladie d'Alzheimer et l'Islet Amyloid Polypeptide (IAPP) impliqué dans le diabète de type II. Aβ possède deux alloformes courants de 40 et 42 résidus, tandis que IAPP est une hormone peptidique de 37 résidus. Les agrégats de Aβ sont toxiques pour les cellules du cerveau, tandis que la fibrillisation de IAPP affecte les cellules-β du pancréas. Le mécanisme d'agrégation de ces deux peptides reste encore mal connu, mais il a été proposé qu’en solution, ces peptides visitent différentes conformations, l'une d'entre elles étant riche en feuillets-β. Cela conduirait à l’oligomérisation de ces peptides, par le biais d’interactions feuillet-β / feuillet-β et, éventuellement, à la formation de fibrilles. Le but de notre étude est de mieux caractériser la dynamique conformationnelle de ces deux peptides, dans leur forme monomérique et oligomérique. Comprendre les premières étapes de leur agrégation est crucial pour le développement de nouvelles molécules thérapeutiques efficaces contre ces protéines amyloïdes

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23

Kil, Hyun Joo. "Design & Synthesis of Peptidomimetics Adopting Secondary Structures for Inhibition of p53/MDM2 Protein-protein Interaction and Multiple Myeloma Cell Adhesion." Scholar Commons, 2014. https://scholarcommons.usf.edu/etd/5051.

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The protein-protein interactions (PPIs) occur when two or more proteins are bound together. Also, this protein-protein interactions (PPIs) cause the various biological processes in the body. Due to this reason, abilities of controlling or inhibiting PPIs can give us promising advantages like (1) better understanding of biological systems, (2) development of new diagnostic approaches for health or disease, and (3) establishment of novel molecular therapeutics. Many proteins adopt the secondary structures, where most of protein-protein interactions take place. -Helices and -sheets are the prevalent secondary conformations, but there are extended secondary structures such as -hairpins, -turns, 310 helix, and so on. As a result, construction of molecules mimicking these protein secondary structures is tractable target for drug design. Moreover, in drug discovery, designing peptidomimetics or non-peptidic mimetics is a popular strategy instead using peptides or truncated peptides because peptides or truncated peptides are prone to proteolysis and degraded in the body. Also, peptidomimetics and non-peptidic mimetics have not only the similar topology as peptides but also resistance to proteolysis. Due to these advantages, in this study, peptidomimetics or non-peptidic mimetics were synthesized and tested for different targets: (1) synthesis of non-peptidic -helical mimetics for p53-MDM2 inhibition, (2) solution-phase synthesis of -hairpin peptide for the inhibition of multiple myeloma cells (MM) adhesion, and (3) synthesis of -hairpin peptoid-peptide hybrids. The synthesis in all three different studies was succeeded, but they still need some improvements. For instance, non-peptidic -helical mimetics, terpyrimidyl derivatives, were synthesized successfully, but they did not show any bioactivity against p53-MDM2. Also, they have a solubility problem. Based on these results, it is necessary to improve the pharmacokinetic properties and bioactivity by changing the substituents on the rings or structures. The -hairpin peptide for the second case already showed good bioactivity against multiple myeloma (MM). For the next level of bio-study, the considerable amount of a -hairpin peptide was demanded. In order to make the substantial -hairpin peptide, the solution phase peptide synthesis was chosen instead of the solid phase peptide synthesis because of the cost-effect. Two methodology were tried for the solution-phase peptide synthesis: (1) segment ligation and (2) continuous synthesis. In the former case, the -hairpin peptide synthesis was successful, but, in the latter case, it is necessary to investigate the appropriate coupling reagents for each step. Peptoid-peptide hybrids has been one of the popular peptidomimetics in the last two decades. Also, mimicking the peptide secondary structure in peptoids has been studied extensively these days. The combination of these two factors was the goal for the third case. Because peptoid-peptide hybrids with a secondary structure can be recognizable by native proteins and resistant to proteolysis. So far, three sets of peptoid-peptide hybrids were synthesize and checked the secondary structure formation by using NMR. However, there was no indication of the secondary structure formation in the three sets of peptoid-peptide hybrids. This result suggests that it is necessary to introduce the more constrained components in peptoid-peptide hybrids. In the above three chapters, it has been tried to find the new drug candidates by synthesizing peptidomimetics or non-peptidic mimetics. Even though the synthesis was successful, some intended results such as the bioactivity or the secondary structure formation were not obtained. However, these results can give us the inspirations to improve properties of peptidomimetics or non-peptidic mimetics for a certain purpose, which leads to earn the intended results and eventually find new drug candidates.

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Sadek, Muheeb. "Synthesis and Investigation of Nucleobase Functionalized β-Peptide as SNAREs Model System for Membranefusion." Doctoral thesis, Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2015. http://hdl.handle.net/11858/00-1735-0000-0022-605D-6.

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25

Zhu, Maximillian. "Computational studies of the Alzheimer's amyloid-β peptide : from structural ensembles to therapeutic leads." Thesis, University of Cambridge, 2013. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.608056.

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26

Khamsing, Dany. "Mécanisme d’activation neuronale de mTORC1 et de son altération par le peptide amyloïde β." Thesis, Sorbonne Paris Cité, 2017. http://www.theses.fr/2017USPCB090.

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MTOR est une sérine/thréonine kinase appartenant au complexe mTORC1 (mTOR Complexe 1), un régulateur clé de la traduction. Ce complexe joue un rôle au sein de la LTP (Potentialisation à Long Terme), une forme de plasticité synaptique qui requiert la synthèse de nouvelles protéines pour renforcer la transmission synaptique. La première partie de ma thèse porte sur les mécanismes de régulation de la voie mTORC1 dans les neurones. Dans les cellules non neuronales, cette voie de signalisation est classiquement régulée par deux voies distinctes. D’une part, les acides aminés induisent le recrutement du complexe mTORC1 à la membrane des endo-lysosomes où la protéine Rheb est enrichie et favorisent ainsi l’activation de mTORC1. D’autre part, les facteurs de croissance activent mTORC1 en stimulant la voie PI3K/Akt/TSC/Rheb. Nos résultats indiquent que les neurones sont capables d’ "utiliser" le mécanisme responsable de la translocation de mTORC1 en réponse à la supplémentation en acides aminés pour coupler l’induction de la plasticité synaptique à l’activation de mTORC1. En effet, les récepteurs NMDA et le BDNF, deux acteurs centraux de la LTP, augmentent le recrutement de mTORC1 à la membrane des endo-lysosomes même en absence d’acides aminés, et activent mTORC1. Par des stratégies induisant la translocation de mTORC1 à la membrane des endo-lysosomes, nous avons montré que ce mécanisme est important pour l’activation de mTORC1 mais n’est pas suffisant : il faut également une activation de la protéine Rheb. Le second aspect de mon projet porte sur la régulation de mTORC1 dans le cadre de la maladie d’Alzheimer, une maladie neurodégénérative caractérisée par une perte progressive de la mémoire. Les déficits cognitifs s’accompagnent d’un dysfonctionnement progressif des synapses suivi par la perte neuronale, tous deux causés par une accumulation anormale du peptide amyloïde β (Aβ). Les données de la littérature montrent que les oligomères toxiques du peptide Aβ (AβO) inhibent la plasticité synaptique dans les stades précoces de la maladie. Cependant, les mécanismes restent obscurs. Plusieurs études mettent en évidence une altération de la voie mTORC1. Nos résultats montrent que les AβO inhibent le recrutement de mTORC1 à la membrane des endo-lysosomes. Ce mécanisme est rétabli par une inhibition pharmacologique de l’AMPK. Ainsi, ces données indiquent que les AβO inhibent l’adressage de mTORC1 aux compartiments endo-lysosomaux via l’AMPK. Cela aurait pour conséquence une inhibition de la synthèse protéique décrite dans la littérature et contribuerait ainsi au dysfonctionnement synaptique
MTOR is a serine/threonine kinase that belongs to mTORC1 (mTOR complex 1), a key regulator of translation. This complex is involved in LTP (Long Term Potentiation), a form of synaptic plasticity requiring new protein synthesis to reinforce synaptic transmission. The first part of my thesis investigates the mechanism of mTORC1’s regulation in neurons. In non-neuronal cells, mTORC1 pathway is commonly activated by two distinct pathways. On the one hand, amino acids induce mTORC1 recruitment to the membrane of endo-lysosomes where Rheb is enriched and can thus promote mTORC1 activation. On the other hand, growth factors activate mTORC1 via the PI3K/Akt/TSC/Rheb pathway. Our results indicate that neurons are capable of “using” amino acid-induced translocation of mTORC1 to connect synaptic plasticity induction to mTORC1 activation. Indeed, NMDA receptors and BDNF, two main actors of synaptic plasticity, increase mTORC1 recruitment to the membrane of endo-lysosomes even in the absence of amino acids, and activate mTORC1. Using strategies targeting mTORC1 to endo-lysosomes, we show that this mechanism promotes activation of mTORC1 but is not sufficient: Rheb activation is also required. The second part of my project is focused on the regulation of mTORC1 in Alzheimer’s disease, a neurodegenerative pathology characterized by a progressive memory loss. Cognitive deficits are widely believed to result from a progressive dysfunction of synapses, followed by a loss of neurons, both caused by an abnormal accumulation of the amyloid β peptide (Aβ). Data from others show that toxic Aβ oligomers (AβOs) inhibit synaptic plasticity at early stages of the disease. However, the mechanisms remain poorly understood. Several studies indicate an alteration of the mTORC1 pathway. Our results show that AβOs inhibit mTORC1 recruitment to the membrane of endo-lysosomes and that this effect can be rescued by a pharmacological inhibition of AMPK. Thus our data indicate that AβOs inhibit mTORC1 translocation to endo-lysosomal compartments via AMPK. This could lead to the impairment of protein synthesis reported in other studies and thus alter synaptic function

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Ratté, Gabriel. "Interaction entre un peptide de β-lactoglobuline bovine (β-lg f1-8) et les protéines du lactosérum : le cas de l’a-lactalbumine." Master's thesis, Université Laval, 2013. http://hdl.handle.net/20.500.11794/24544.

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Des observations préliminaires ont montré que l’auto-assemblage d’un peptide issu de l’hydrolyse trypsique de la β-lactoglobuline (β-lg f1-8) modifiait la composition de mélanges de protéines de lactosérum, particulièrement en α-lactalbumine (α-la) soluble. Le but du présent travail était de démontrer l’occurrence d’interactions entre le peptide β-lg f1-8 et l’α-la. L’étude de l’auto-assemblage du peptide β-lg f1-8 en présence d’α-la à 25 et 55 °C a permis d’observer que l’ajout d’α-la à un hydrolysat trypsique permettait de retarder la floculation du peptide à 55 °C. La mise en contact d’α-la avec le peptide β-lg f1-8 a permis de modifier le profil de solubilité de la protéine à différents pH, mais pas son profil de dénaturation thermique obtenu par calorimétrie différentielle à balayage (DSC). Ces observations suggèrent que le peptide β-lg f1-8 interagit avec l’α-la par le biais d’interactions hydrophobes et qu’il pourrait être utilisé dans le développement de nouvelles stratégies de fractionnement de mélanges protéiques.
Preliminary observations showed that the self-assembly capacity of a β-lactoglobulin peptide obtained from trypsin hydrolysis (β-lg f1-8) could modify the composition of whey protein mixtures, mainly by reducing the amount of soluble α-lactalbumin (α-la). The goal of this study was to demonstrate the occurrence of interactions between β-lg f1-8 peptide and α-la. A study of the peptide self-assembly process in presence of α-la at 25 and 55 °C showed that the addition of α-la to the original tryptic hydrolysate delays the flocculation of peptide β-lg f1-8 at 55 °C. Adding β-lg f1-8 peptide to α-la modified the solubility profile of the protein at various pH, but its thermal unfolding profile obtained by differential scanning calorimetry (DSC) remained unchanged. All of these observations suggest that the peptide β-lg f1-8 can interact with the α-la via hydrophobic interactions and could be used for developing new strategies for the fractionation of protein mixtures.

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Di, Scala Coralie. "Rôle du cholestérol dans l'oligomérisation des peptides β-amyloïdes responsables de la maladie d'Alzheimer." Thesis, Aix-Marseille, 2014. http://www.theses.fr/2014AIXM4361.

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La maladie d'Alzheimer est la maladie neurodégénérative la plus fréquente dont la prévalence augmente avec l'âge. Elle résulte d'un excès de peptide β-amyloïde (Aβ) capable de s'agréger, de s'insérer dans la membrane plasmique des cellules et de s'organiser en pores perméables au calcium. Cette insertion est modulée par la composition lipidique de la membrane dont le cholestérol. Alors que plusieurs études indiquent que le cholestérol interagit avec le peptide Aβ et module sa toxicité, les mécanismes moléculaires sous-jacents demeurent mal compris.A l'aide d'approches expérimentales multiples nous avons évalué le rôle du cholestérol dans l'insertion du peptide Aβ à la membrane ainsi que dans le processus d'oligomérisation responsable de la formation de pore. Notre étude identifie le domaine 22-35 du peptide Aβ comme domaine d'interaction avec le cholestérol au sein duquel deux acides aminés sont essentiels : la Val24 et la Lys28. Ce petit fragment s'organise en pore dans la membrane plasmique et déclenche une entrée massive de calcium dans les cellules. Cet effet n'est plus observé lorsque les cellules ont moins de cholestérol dans leur membrane ou en présence de zinc, un inhibiteur des pores amyloïdes. Le cholestérol maintient le peptide de façon oblique et en hélice α. Cette orientation favorise l'établissement d'une liaison hydrogène entre l'Asp27 d'un peptide et la Lys28 d'un peptide voisin, qui stabilise le pore. Enfin, notre étude montre que le bexarotène, un composé anti-Alzheimer dont le mécanisme d'action est controversé, prévient l'insertion du peptide dans des membranes et empêche la formation de pores dans la membrane plasmique des cellules nerveuses
Alzheimer's disease is the most common neurodegenerative disease whose prevalence increases with age. It is the result of excess β-amyloid peptide (Aß), which self-organizes. This peptide is able to insert into the plasma membrane of cells where their organization in calcium permeable pores triggers the early stages of toxicity. This insertion is directly modulated by the lipid composition of the membrane especially cholesterol. Whereas several studies indicate that cholesterol interacts with and modulates Aß toxicity, the underlying molecular mechanisms remain poorly understood.Using computational, physico-chemical and cellular approaches, we evaluated the role of cholesterol in the insertion of the Aß peptide in the membrane and in the oligomerization process responsible for pore formation. Our study identifies the 22-35 fragment of Aβ as a functional cholesterol-binding domain in which two amino acids are essential: Val24 and Lys28. When incubated with SH-SY5Y cells, the minimal Aβ22-35 peptide caused an increase of Ca2+ entry. This effect was no longer observed in cholesterol-depleted cells and was inhibited by zinc, a classical blocker of amyloid channels. Cholesterol specifically induced a tilted alpha-helical topology of Aβ22-35 which appeared to facilitate the oligomerization process through the establishment of a hydrogen bond network involving Asn27 and Lys28. Finally, our study showed that bexarotene, an anti-Alzheimer compound whose mechanism of action is still under debate, competitively inhibited Aβ insertion into cholesterol-containing membranes and prevented calcium-permeable amyloid pore formation in the plasma membrane of neural cells

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Bosson, Anthony. "Impact du peptide amyloïde β sur la signalisation calcique astrocytaire et les interactions neurone-glie." Thesis, Université Grenoble Alpes (ComUE), 2016. http://www.theses.fr/2016GREAV029/document.

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La maladie d'Alzheimer est une maladie neurodégénérative associée à une perte progressive des fonctions mnésiques et cognitives, qui font suite à des dysfonctions synaptiques. Ces dysfonctions sont en partie dues à la présence d’oligomères solubles du peptide amyloïde β (Aβo). Chez l’homme ces oligomères sont déjà présents durant la phase asymptomatique de la maladie et semblent expliquer la perte synaptique et les dysfonctions caractéristiques de la maladie. Cependant, les mécanismes clés qui initient ce dysfonctionnement et cette perte synaptique restent inconnus. Il est actuellement admis que la synapse compte un 3ème partenaire qui joue un rôle majeur dans l'intégrité structurale et fonctionnelle de la synapse, l’astrocyte. Grâce à leurs prolongements, les astrocytes peuvent enrober la plupart des synapses et contribuer activement aux changements morphologiques et fonctionnels observés durant l'activité synaptique. Cependant leur implication a été peu étudiée dans le contexte de la maladie d'Alzheimer.Le but de ces travaux de thèse, était d’étudier de quelle manière Aβo modifie l’activité calcique astrocytaire et quelles peuvent en être les répercussions sur l’activité synaptique. Ainsi, nous avons mis en évidence sur tranche aigue d’hippocampes de souris, une hyperactivité calcique généralisée, au sein du réseau astrocytaire et au niveau des prolongements fins astrocytaires. Cette hyperactivité s’est révélée être dépendante d’un canal membranaire récemment identifié au niveau astrocytaire, le canal TRPA1. Cette hyperactivité calcique dépendante de TRPA1, se manifeste également très précocement, avant l’apparition de plaques amyloïdes, dans un modèle de souris transgénique pour la maladie d’Alzheimer. Au niveau neuronal, nous avons observé une augmentation de la transmission synaptique basale en présence d’Aβo. De manière intéressante, l’inhibition pharmacologique de TRPA1 permet de bloquer l’hyperactivité calcique induite par Aβo et de rétablir l’activité synaptique précédemment perturbée par l’Aβo. Dans leur ensemble, nos résultats suggèrent que les astrocytes soient une cible privilégiée d’Aβo lors des phases asymptomatiques de la maladie d’Alzheimer, et que le blocage de l’hyperactivité calcique astrocytaire puisse garantir l’intégrité synaptique en présence d’Aβo
Alzheimer’s disease is a neurodegenerative disorder associated with a progressive loss of cognitive functions following synaptic dysfunctions. These synaptic alterations are mainly due to oligomeric forms of amyloid β peptide (Aβo). In humans, these oligomers are already present during the silent phase of the disease and seem to explain synaptic loss and synaptic dysfunctions. However, key mechanisms that initiate synaptic loss and synaptic dysfunctions remain unknown. It is now well established that there is a third component of the synapse, playing major role in morphological and functional synaptic integrity, the astrocyte. Thanks to their processes, astrocytes can enwrap most of synapses and actively participate to morphological and functional changes observed during synaptic activity. Still, their involvement in Alzheimer’s disease is under-investigated.The aim of these thesis works, was to evaluate how Aβo modify astrocytic calcium activity and what could be the repercussions on synaptic activity. We have observed on mice hippocampal acute brain slices a global calcic hyperactivity, within the astrocytic network and inside fine processes. This hyperactivity was dependent on a recently identified astrocytic channel, the TRPA1 channel. This TRPA1-dependent calcic hyperactivity shows up also very early, before amyloid plaques formation, in a transgenic mouse model of Alzheimer’s disease. On the neuronal side, glutamatergic synaptic transmission was increased by Aβo. Interestingly, pharmacological inhibition of TRPA1 could block astrocytic calcium hyperactivity and restore glutamatergic synaptic activity previously disturbed by Aβo. Overall, our data suggests that the astrocyte is a frontline target of Aβo during the prodromal phase of Alzheimer’s disease, and that blockade of astrocytic calcium hyperactivity could preserve synaptic integrity even when Aβo is applied

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Fischer, Sabrina [Verfasser], and Armin [Akademischer Betreuer] Geyer. "β-Hairpin-Peptide zur Erkennung von Antikörpern gegen rheumatoide Arthritis / Sabrina Fischer. Betreuer: Armin Geyer." Marburg : Philipps-Universität Marburg, 2015. http://d-nb.info/1068315679/34.

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31

Allan, Laura Elizabeth. "Investigating the effects of the Alzheimer's disease-associated amyloid β-peptide on intracellular calcium homeostasis." Thesis, University of Cambridge, 2010. https://www.repository.cam.ac.uk/handle/1810/283857.

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I investigated the effects of Aβ₄₂ on the Ca²⁺ signalling capacity of human neuroblastoma SH-SY5Y cells and primary hippocampal cultures. I developed an in vitro model system of dissociated hippocampal neurons and glial cells in order to reflect as closely as possible the mature hippocampus. Extensive characterisation of the culture revealed that functional neuronal networks were established by day in vitro 11, as demonstrated by the occurrence of spontaneous oscillations in both membrane potential and intracellular Ca²⁺ levels. Neurons exhibited functional ionotropic and metabotropic signalling systems which, in turn, rendered them sensitive to cell death induced by excitotoxic stimuli. Samples of synthetic Aβ₄₂ were prepared according to two published protocols. One protocol produced Aβ₄₂ samples which exhibited highly dynamic aggregation kinetics, the other produced homogeneous Aβ₄₂ oligomers which were stable in their conformational state for up to 24 hours. While both Aβ₄₂ preparations impaired cell viability following 24-hour treatment, only Aβ₄₂ oligomers elicited robust Ca²⁺ responses following their extracellular application to cells. Aβ₄₂ oligomers elicited distinct but different effects on the Ca²⁺ signalling capacity of SH-SY5Y cells and primary hippocampal neurons, respectively. in SH-SY5Y cells, Aβ₄₂ oligomers acted to deplete the content of the intracellular ER Ca²⁺ store, in part through InsP₃ receptors and in part through an as yet unidentified leak pathway. In primary hippocampal neurons, the application of Aβ₄₂ oligomers resulted in a sustained and elevated increase in intracellular Ca²⁺ concentrations. It is postulated that these early cellular events, although distinct, will ultimately converge on a common pathway resulting in dysregulation of Ca²⁺ homeostasis and cell death. Thus, the findings of this thesis support the mounting body of evidence implicating the role of Ca²⁺ dysregulation in mediating the neurotoxic effects of Aβ₄₂ oligomers.

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Yao, Jun. "Modulateurs et médiateur dans la pathogénie du peptide β- amyloïde dans la maladie d' Alzheimer." Paris 6, 2006. http://www.theses.fr/2006PA066134.

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33

Jain, Priyesh. "Design and Synthesis of Beta-Hairpin Peptidomimetics for Modulating Integrin Mediated Cell Adhesion, Abeta Fibrillogenesis and p53-MDM2 Protein-Protein Interactions." Scholar Commons, 2010. http://scholarcommons.usf.edu/etd/3458.

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Inhibiting therapeutically important protein-protein interactions has been a tremendous challenge for medicinal chemists. The folded 3D structures of peptides and proteins, mainly comprise secondary structural elements i.e α-helices and β-sheet have created an opportunity to design small molecules and peptidomimetic inhibitors of protein-protein interaction (PPI). Hence, information about the formation and stabilization of these secondary structures is vital for designing future drugs. In this dissertation, several cyclic beta-hairpin peptidomimetics that mimic the recognition surface have been designed and synthesized as inhibitors for different targets such as integrin mediated extracellular matrix -cell adhesion in multiple myeloma, p53-MDM2 PPI, amyloid beta fibrillogenesis inhibitor. Cyclization of linear peptides to restrict the number of conformations available to the linear peptide can increase its affinity for the target as well as increase its proteolytic resistance. In this study, different beta turn promoters that increase the propensity of cyclic peptides to adopt beta-sheet structures have been designed and synthesized. Chapter two discusses the design and synthesis of several cyclic III (Integrin Interaction Inhibitor) peptides that block adhesion of integrins to extracellular matrix components in Multiple Myeloma tumor cells. These cyclic peptides, as assayed by TOPRO 3 assay were more potent than the parent linear peptide with a bio-activity of 1.08 μM. We have also studied structure activity relationships (SAR) of these cyclic III peptide analogs to increase the potency and bioavailability of these peptides. Chapter three describes the application of cyclic beta-hairpin peptidomimetics to inhibit abeta fibrillogenesis that is responsible for Alzheimer’s disease. We have successfully designed and synthesized cyclic peptides that target the hydrophobic region (17-21) of abeta fibril which is believed to cause self aggregation and plaque formation. We have also successfully explored these cyclic beta-hairpin peptides to disrupt p53-MDM2 interactions. Chapter five discusses the design and synthesis of novel cysteine based Peptide Nucleic Acid (PNA) monomers that are aimed to increase cellular uptake by introducing positively charged species attached to the cysteine side chain. We have successfully synthesized CPNA monomers and made efforts to make PNA oligomers.

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RIZZA, FABIO. "Structural modelling of biological macromolecules: the cases of neurofibromin, bifurcating Electron Transferring Flavoprotein and Amyloid-β (1-16) peptide." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2021. http://hdl.handle.net/10281/310480.

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In questa tesi sono stati affrontati tre progetti indipendenti, accomunati dall’uso della modellistica molecolare e in particolare della dinamica molecolare. Nel primo progetto è stato studiato il dominio Sec14-PH della neurofibromina (NF1). I domini sec14 sono stati scoperti in numerose proteine dai procarioti all’uomo come scambiatori di lipidi tra membrane, per mezzo di una tasca la cui apertura è legata al movimento di una specifica alpha-elica (elica lid). La struttura cristallina del dominio Sec14 di NF1 (sia del wild type sia di mutanti associati all’insorgenza della patologia neurofibromatosi) ha rivelato la sua particolarità di essere strutturalmente accoppiato ad un dominio PH che interagisce fortemente con l’elica lid tramite un suo loop (detto lid-lock loop). Su questa base è stato formulato un meccanismo di apertura della tasca del Sec14 che coinvolgerebbe un movimento concertato del lid-lock loop, ma questo movimento non è mai stato osservato o dimostrato. Guidati da dati sperimentali sulla denaturazione termica del Sec14-PH di NF1, sia del wild type sia di alcuni mutanti, diverse simulazioni ad alta temperatura sono state effettuare per comparare la dinamica del dominio wild type con un mutante patologico associato all’insorgenza della patologia neurofibromatosi. Con le nostre simulazioni è stato possibile proporre un meccanismo di funzionamento dell’apertura dell’elica lid e fornire delle basi strutturali e dinamiche dell’insorgenza della patologia nel caso del mutante specifico studiato. Nel secondo progetto è stato affrontato lo studio di una proteina chiamata EtfAB che catalizza un processo recentemente scoperto noto come biforcazione elettronica basata sulle flavine. Questo meccanismo è sfruttato solo da alcuni microrganismi anerobici come terza via di accoppiamento energetico e finora si conoscono quattro famiglie di proteine, evolutivamente non correlate, in grado di catalizzarlo. Una di queste è EtfAB, della quale non è chiaro come possa avvenire il trasferimento elettronico tra le due molecole di FAD ad essa legate. Infatti, la distanza tra questi due FAD osservata nella struttura cristalline di EtfAB è di 18 Å, mentre si ritiene più plausibile che i trasferimenti elettronici in biologia non avvengano a distanze maggiori di 14 Å. Per questo è stato suggerito un possibile meccanismo che potrebbe avvicinare le due molecole di FAD. Usando la dinamica molecolare è stato possibile testare, e smentire, il meccanismo proposto. Inoltre, con il Density Functional Theory (DFT), è stato possibile fornire un’interpretazione ad alcuni dati spettroscopici riguardo il possibile trasferimento elettronico tra le due molecole di FAD. Nel terzo progetto, ho collaborato con il Prof. Luca Bertini ad un progetto sulla produzione e propagazione di alcune specie reattive dell’ossigeno (ROS) nel contesto del peptide amiloide beta coinvolto nella patogenesi dell’Alzheimer. Nell’ambito dell’ipotesi amiloide sull’insorgenza della patologia di Alzheimer, un ruolo importante è stato attribuito ai danni causati dai ROS, prodotti da un complesso metallico all’interno del peptide amiloide stesso, in particolare dal radicale ossidrilico (OH.-). Tuttavia, i dettagli su come questi radicali propaghino e reagiscano non sono ancora stati chiariti. Mentre i calcoli DFT del Prof. Bertini affrontavano le capacità ossidative del radicale ossidrilico e i possibili prodotti di reazione nel contesto del peptide amiloide beta, con i miei calcoli di dinamica molecolari è stata fornita una panoramica su quali possibili bersagli del radicale ossidrilico, coordinato allo ione Cu del complesso, possano effettivamente reagire entrando in contatto con il radicale ossidrilico a causa dei moti dinamici del peptide.
In this thesis, three independent projects were addressed, sharing the computational approach based on molecular modeling and in particular molecular dynamics. In the first project, the Sec14-PH domain of neurofibromin (NF1) was investigated. The Sec14 domains have been identified in many different proteins, from prokaryotes to humans, serving as exchangers of lipid molecules between membranes, by means of a pocket whose opening is allowed by the motion of a specific alpha-helix (called lid helix). The crystal structure of the NF1-Sec14 domain (of both the wild type and some mutants associated with the onset of neurofibromatosis pathology) has revealed its peculiarity of being structurally coupled to a PH domain that strongly interacts with the lid helix through a long loop (called lid-lock loop). On this basis, a mechanism for the opening of the Sec14 lipid pocket was formulated which would involve a concerted movement of the lid-lock loop, but this movement has actually never been shown. Guided by available experimental data on the thermal denaturation of Sec14-PH domain of NF1, both on the wild type and some neurofibromin-related mutants, several simulations at high temperature were carried out to compare the dynamics of the wild type domain with a pathological mutant associated with the onset of neurofibromatosis. Our simulations lead us to suggest an opening mechanism for the lid helix and provide a hypothesis for the structural and dynamic basis of the onset of the disease in the case of the specific mutant. The second project addressed the study of a protein called EtfAB which catalyzes a recently discovered process known as Flavin-Based Electron Bifurcation (FBEB). This mechanism is only exploited by some anaerobic microorganisms as a third way of energy coupling. So far, four unrelated protein families are known that are able to catalyze FBEB. Among these, EtfAB, catalyzes the electron transfer between the two FAD molecules bound to it. Surprisingly, the distance between these two FADs, as observed in the crystal structure of EtfAB, is 18 Å, whereas biological electron transfer is considered more likely to occur at a maximal distance of 14 Å. To explain this, a possible mechanism has been suggested that could bring the two FAD molecules closer together. Using molecular dynamics, it was possible to test, and discard, the proposed mechanism. Furthermore, with the Density Functional Theory (DFT), it was possible to provide an interpretation to some spectroscopic data regarding the possible electron transfer between the two FAD molecules. In the third project, I collaborated with Prof. Luca Bertini on a project on the production and propagation of some reactive oxygen species (ROS) in the context of the amyloid-beta peptide involved in the pathogenesis of Alzheimer's. In the amyloid hypothesis on the onset of Alzheimer's disease, an important role has been attributed to the damage caused by ROS, produced by a metal ion coordinated to the amyloid peptide itself, in particular by the hydroxyl radical (OH.-). However, the details of how these radicals propagate and react have not yet been clarified. While Prof. Bertini's DFT calculations addressed the oxidative capacities of the hydroxyl radical and the possible reaction products in the context of the amyloid-beta peptide, my molecular dynamics simulations provided an overview on which possible targets of the hydroxyl radical, coordinated to the ion Cu of the complex, could actually react with the hydroxyl radical due to the dynamic motions of the peptide.

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Bosch, Morató Mònica 1986. "The Role of intracellular amyloid β-peptide in the pathophysiology of GNE myopathy and Alzheimer's disease." Doctoral thesis, Universitat Pompeu Fabra, 2015. http://hdl.handle.net/10803/650351.

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The Amyloid β-peptide (Aβ) is accumulated in several diseases including GNE myopathy and Alzheimer’s disease (AD). GNE myopathy is a skeletal muscle disorder caused by biallelic mutations in the UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase (GNE) gene, which codifies for a key enzyme in sialic acid biosynthesis. The mutated GNE gene encodes a hypofunctional enzyme causing a decrease in cellular sialic acid. We have found that hyposialylation favors Aβ endocytosis in skeletal muscle cells, which is dependent on clathrin and heparan sulfate proteoglycan. Furthermore, we have observed that intracellular Aβ induces apoptosis in skeletal muscle cells through the impairment of Akt signaling pathway. Accordingly, Akt phosphorylation is reduced and apoptosis is enhanced in GNE myopathy myoblasts. Finally, through a genome-wide screen in Saccharomyces cerevisiae we have identified novel modulators of Aβ toxicity including components of the mitochondrial respiratory chain and members of the Ca2+ signaling pathways. In conclusion, this study provides a better understanding of the Aβ relevance in the pathophysiology of GNE myopathy and AD.
El pèptid β-amiloide (Aβ) s’acumula en diverses malalties com la miopatia de GNE i la Malaltia d’Alzheimer (MA). La miopatia de GNE és una malaltia del múscul esquelètic causada per mutacions al gen UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase (GNE), que codifica un enzim clau en la biosíntesis de l’àcid siàlic. El GNE mutat produeixen un enzim hipofuncional i una conseqüent disminució de l’àcid siàlic cel·lular. Hem vist que la hiposialització afavoreix l’endocitosi de l’Aβ en cèl·lules musculars, la qual és dependent de clatrina i de l’heparà sulfat proteoglicà. A més, hem observat que l’Aβ intracel·lular indueix l’apoptosi en cèl·lules musculars mitjançant la inhibició de l’Akt. Així, la fosforilació de l’Akt es troba reduïda i l’apoptosi induïda en mioblasts d’un pacient amb la miopatia de GNE. Finalment, a través d’un cribratge del genoma complert de Saccharomyces cerevisiae, hem identificat nous moduladors de la toxicitat per Aβ que inclouen components de la cadena respiratòria mitocondrial i membres de la via de senyalització del Ca2+. En resum, aquest estudi ofereix una millor comprensió del rol de l’Aβ en la miopatia de GNE i la MA.

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Wan, Yang. "Synthesis of β,γ-diamino acids and their use to design new analogues of the antimicrobial peptide Gramicidin Septide antimicrobien, la Gramicidine S." Thesis, Université Paris-Saclay (ComUE), 2017. http://www.theses.fr/2017SACLS407/document.

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Dans notre groupe, nous nous intéressons au développement de peptides contenant des acides γ-aminés. Comme d’autres peptides contenant des acides aminés non naturels, ils ont montré leur capacité à posséder des conformations stables et/ou des propriétés biologiques intéressantes. De plus, ces peptides sont généralement résistant à la protéolyse. Dans l’objectif de synthétiser des acides -diaminés sous la forme d’un seul stéréoisomère, nous avons développé une voie de synthèse reposant sur une réaction de Blaise suivie d’une réduction diastéréosélective. En appliquant cette méthode, nous avons synthétisé des acides β,γ-diaminés dérivés de la D-phénylalanine et de l’acide L-glutamique. Le premier a été utilisé pour concevoir des analogues d’un peptide antimicrobien, la gramicidine S. Comparé à la molécule parent, les analogues ont montré une cytotoxicité beaucoup moins importante pour les cellules hôtes tout en conservant une activité antibactérienne intéressante. Cette étude nous a donné de meilleures connaissances pour développer d’autres analogues de la gramicidine S ainsi que d’autres peptides antimicrobiens. Nous avons également effectué de nombreuses optimisations pour synthétiser de façon efficace des acides β,γ-diaminés cycliques à partir de l’acide L-glutamique. Les oligomères incorporant ces acides β,γ-diaminés et des acides α-aminés ont montré un fort potentiel pour l’adoption de conformations stables. Ces études vont être poursuivies
In our group, we are interested in developing peptides containing β,γ-diamino acids . Along with many other peptides containing unnatural amino acids, they have shown the ability to possess stable conformations and/or interesting biological activities. Moreover, those peptides are usually more resistant to proteolysis. In order to synthesize stereopure γ-amino acids, we have developed a synthetic route using Blaise reaction and subsequent diastereoselective reduction as key reactions. Through applying this method, we have synthesized β,γ-diamino acids derived from D-phenylalanine and L-glutamic acid. The former β,γ-diamino acid was used for designing antimicrobial peptide gramicidin S analogues. Compared with mother molecule, the analogues exerted much less host cell cytotoxicity while remaining interesting antibacterial activity. Meanwhile, it gave us more knowledge for further developing analogues of gramicidin S as well as other antimicrobial peptides. We also paid lots of effort to efficiently synthesize cyclic β,γ-diamino acids starting from L-glutamic acid. Interestingly, when oligomers incorporating this β,γ-diamino acids and α-amino acids, they have shown the potential to adopt stable conformations. The following studies will be continuously investigated

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Bettale, Jennifer Dawn. "Progress Toward Theonellamide F." BYU ScholarsArchive, 2011. https://scholarsarchive.byu.edu/etd/3022.

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Theonellamide is a bicyclic peptide isolated from a marine sponge, which shows interesting biological activity. It contains several unnatural amino acids, among which are (2S,3R)-3-hydroxyasparagine (L-erythro-β-hydroxyasparagine) (β-OHAsn) and τ-L-histindino-D-alanine (τ-HAL). Although there were previous synthetic efforts toward each of these unnatural amino acids, the efforts were not ideal due to expensive starting material, time-consuming steps, and poor regioselectivity. The presented work demonstrates an inexpensive, enantioselective synthesis of β-OHAsn, which can be completed in a matter of weeks, as well as several attempts at a novel regiospecific approach toward τ-HAL, including work on a model study.

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Lesma, Jacopo. "β-Hairpin peptidomimetics as inhibitors of hIAPP amyloid protein aggregation : design, synthesis and evaluation Introducing sequential aza-amino acids units induces repeated ß-turns and helical conformations in peptides β-Hairpin peptide mimics decrease human Islet Amyloid Polypeptide (hIAPP) Aggregation." Thesis, université Paris-Saclay, 2020. http://www.theses.fr/2020UPASQ018.

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Le diabète de type 2 (DT2), qui compte plus de 400 millions de cas dans le monde, représente 90 % du nombre total de cas de diabète. T2D est une maladie dégénérative associée à la résistance à l’insuline et à la mort des β-cellules pancréatiques liées aux dépôts de la protéine amyloïde hIAPP (également appelée amyline), qui sont observés dans le pancréas de plus de 95 % des patients atteints de DT2. Les traitements actuellement disponibles sont symptomatiques et caractérisés soit par des effets secondaires significatifs, soit par un faible impact sur l’incidence des pathologies associées et la réduction de la mortalité. Ainsi, pour trouver un traitement étiologique contre DT2, le ciblage de hIAPP est devenu une stratégie prometteuse à explorer. À ce jour, peu de classes de composés ont été proposées pour inhiber le processus d’agrégation de hIAPP. Cependant, à notre connaissance, seuls de très rares exemples de β-hairpin acycliques ont été décrits. Puisque l’agrégation hIAPP est un processus très complexe et dynamique, nous avons émis l’hypothèse que desβ-hairpins flexibles pourraient mieux s’adapter aux différentes conformations de hIAPP formées au cours du processus d’agrégation. Notre conception a été basée sur différents β-turn flexibles constitué d’un motif pipéridino-pyrrolidine lié à deux bras différents inspirés de la séquence primaire du peptide hIAPP, avec un élément d’auto-reconnaissance peptidique (SRE) dérivé de la séquence amyloïdogène de hIAPP, et faisant face à une séquence de blocage peptidique ou peptidomimétique. Afin de confirmer la conformation en β-hairpin de nos inhibiteurs, la conformation de nos composés a été étudiée par RMN et dans quelques cas par une dynamique moléculaire. Ensuite, leur capacité à interférer avec le processus d’agrégation de hIAPP a été principalement évaluée par la spectroscopie de fluorescence à la thioflavine-T. Les composés les plus prometteurs de la série ont ensuite été étudiés par d’autres essais biophysiques comme la microscopie électronique à transmission (TEM), l’électrophorèse capillaire (CE) et l’IMS-MS. Les meilleurs composés de la série ont ensuite été étudiés pour déterminer leur capacité à réduire la toxicité du hIAPP sur les cellules pancréatiques INS-1 du rat.Ayant prouvé la possibilité de moduler le processus d’agrégation de hIAPP par des petits mimes de β-hairpins acycliques portant à la fois des bras peptidiques et peptidomimétiques, nous avons ensuite concentré notre attention sur le développement de β-hairpins fluorés qui, jusqu’à présent, n’ont jamais été explorés ni comme inhibiteurs d’agrégation hIAPP, ni, à notre connaissance, plus largement en chimie médicinale. La préparation de ces analogues fluorés avait le double objectif d’étudier comment le fluor, avec ses caractéristiques uniques, pouvait influencer à la fois l’activité et la conformation de nos inhibiteurs. En conclusion, les travaux présentés dans cette thèse fournissent des informations précieuses pour le développement de nouveaux mimes de β-hairpins acycliques comme modulateurs de hIAPP et potentiellement comme nouveaux outils fluorés pour approfondir son processus d’agrégation
Type 2 Diabetes (T2D) with over 400 million cases worldwide represents 90% of total diabetes cases. T2D is a degenerative disease associated with insulin resistance and pancreatic β-cells death linked to deposits of the amyloid protein hIAPP (also called amylin), that are observed in the pancreas of over 95% of the T2D patients. The treatments currently available are symptomatic and characterized either by significant side effects or low impact on the incidence of related pathologies and mortality reduction. Thus, to find an etiological treatment for T2D, targeting hIAPP has become a promising strategy to explore. To date, few classes of compounds have been proposed to inhibit hIAPP aggregation process. However, to the best of our knowledge, only very scarce examples of acyclic β-hairpin have been described. Since hIAPP aggregation is a highly complex and dynamic process, we hypothesized that flexible β-hairpins could better adapt to different hIAPP conformations formed during the aggregation process. Our design was based on flexible piperidine pyrrolidine β-turn inducers linked to two different arms inspired by the primary sequence of hIAPP peptide, with a peptidic self-recognition element (SRE) derived from the hIAPP amyloidogenic sequence facing to a peptidic or peptidomimetic blocking sequence. In order to confirm β-hairpin conformation of our inhibitors, our compounds were conformationally studied by NMR and in few cases by molecular dynamics. Then, their ability to interfere with hIAPP aggregation process was primarily evaluated by thioflavin-T fluorescence spectroscopy. The most promising compounds of the series were then investigated by other biophysical assays such as transmission electron microscopy (TEM), capillary electrophoresis (CE) and IMS-MS. The best compounds of the series were then studied to determine their ability to reduce hIAPP toxicity on rat INS-1 pancreatic cells.Having proved the possibility to modulate hIAPP aggregation process employing small acyclic β-hairpin mimics bearing both peptidic and peptidomimetic arms, we then focused our attention on the development of fluorinated hairpin peptidomimetics that, until now, have never been explored either as hIAPP aggregation inhibitors, nor, to our knowledge, more broadly in medicinal chemistry. The preparation of these fluorinated analogues had the double scope to investigate how fluorine, with its unique characteristics, could influence both the activity and the conformations of our inhibitors. In conclusion, the work presented in this thesis provides valuable insight for the development of new acyclic β-hairpin mimics as modulators of hIAPP and potentially new fluorinated tools to further investigate its aggregation process

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39

Nicklagård, Erik. "Quantification of Alzheimer DiseaseAmyloid β Peptide 43 in Human BrainWith a Newly Developed Enzyme-LinkedImmunosorbent Assay (ELISA)." Thesis, Linköpings universitet, Biokemi, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-70490.

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A 20 weeks project at Karolinska Institutet (KI), Huddinge, Sweden is in this master thesis summarized. Alzheimer’s disease is the most common form of dementia in the world. One of the pathological hallmarks seen in AD patients consists of amyloid plaques assembled of beta amyloid (Aβ) peptide aggregates. A lot of research has been done on Aβ40 and Aβ42 but not on the longer variant with 43 residues. An earlier study by Welander et al, quantified the Aβ43 peptide from amyloid plaque cores with high-performance liquid chromatography coupled to mass-spectrometry (HPLC-MS/MS)1. Here, I present the initial development of an enzyme-linked immunosorbent assay (ELISA) with the goal to quantify Aβ43 peptides in soluble fractions of human brain tissue. An ELISA method with the possibility to quantify Aβ43 peptides from cerebral spinal fluid might have the prospect to serve as a diagnostic tool for AD in the future. Commercial ELISA kits coated with antibodies against all Aβ species was not suitable for detecting Aβ43 in soluble brain tissue from human AD patients. This is due to the high amount of Aβ40 (and in some extent Aβ42) in the samples, which will bind to the same epitope as Aβ43 on the capturing antibody. These shorter Aβ species will be in excess and bind to the capturing antibody thereby ousting Aβ43 from binding in. A better way for quantifying Aβ43 with ELISA might instead be to coat a polystyrene plate with α-Aβ43 antibodies, which are c-terminal specific to Aβ43. This will abolish the competition between the different Aβ species and function as an immunoprecipitation of unwanted species. This yielded adequate quantification of Aβ43 (2.64 pM) from tris-buffer saline (TBS) fractions from a human brain sample from AD.

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Santini, Sébastien. "Flexibilité et changements topologiques de la protéine prion et du peptide β-amyloi͏̈de d'Alzheimer par simulations numériques." Aix-Marseille 1, 2004. http://www.theses.fr/2004AIX11029.

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Les amyloi͏̈doses sont des maladies neuro-dégénératives caractérisées par l'accumulation de fibres protéiques dans le système nerveux. Nous avons choisi d'étudier les mécanismes d'agrégation en fibre pour deux des protéines amyloi͏̈des les plus connues : la protéine prion (fragment PrP90-231) et le peptide Aß d'Alzheimer (fragment 16-22). Les études de la protéine prion ont été menées par dynamique moléculaire pour appréhender les changements topologiques impliqués lors de la conversion de PrP[C] en PrP[Sc]. Ainsi, nous avons mis en évidence que la dynamique du coeur structuré (124-226) de PrP est indépendante de la longueur de la queue amino-terminale (Nt). A pH neutre, les mutations G131V et M129V propagent un feuillet ß à trois brins successifs antiparallèles impliquant les résidus 112-130 et 115-130 respectivement. Ce feuillet pourrait constituer un point de départ pour le changement de conformation décrit expérimentalement. Les simulations de délétions des brins S1 et S2 de PrP confirment l'existence d'un intermédiaire de type globule fondu. L'hélice H1 est très stable sur l'ensemble des simulations et ne semble pas se déplier dans les étapes précoces du mécanisme de conversion de PrP. Pour comprendre le phénomène d'agrégation des fibres amyloi͏̈des, nous avons choisi d'utiliser la technique d'activation relaxation combinée au potentiel OPEP sur des dimères et trimères de Aß[16-22]. En accord avec la RMN du solide, nous montrons que le dimère et le trimère Aß[16-22] adoptent préférentiellement un arrangement antiparallèle et que l'agrégation se fait par de multiples chemins n'impliquant pas forcément un intermédiaire en hélice α. Nos simulations montrent que la conformation obtenue dans la fibre Aß[16-22] nécessite un plus grand nombre de chaînes et mettent en évidence, lors du repliement, des pièges cinétiques qui peuvent être surmontés par le mouvement de reptation des chaînes.

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41

Laporte, Vincent. "Elimination du peptide β-amyloi͏̈de par les cellules microgliales dans la maladie d'Alzheimer : implication du récepteur LRP." Université Louis Pasteur (Strasbourg) (1971-2008), 2002. http://www.theses.fr/2002STR13087.

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La plaque sénile, un des marqueurs fondamentaux de la maladie d'Alzheimer, est une lésion extracellulaire et se présente sous la forme d'un dépôt sphérique constitué majoritairement de fibres de peptide beta-amyloi͏̈de [A?]. L'amoncellement de la substance amyloi͏̈de induirait l'activation locale des cellules microgliales et il en résulterait une libération chronique de protéines inflammatoires. Ce processus immunologique pourrait être la cause de l'atrophie cérébrale observée dans le cerveau des patients. Pour traiter la maladie, il est donc nécessaire de limiter la formation des dépôts amyloi͏̈des en agissant sur la synthèse du peptide A? ou sur sa dégradation. Les cellules microgliales qui bordent le dépôt amyloi͏̈de présentent des fonctions de phagocytose. Ainsi, elles pourraient être capables d'ingérer les fibres amyloi͏̈des et de maîtriser l'apparition des dépôts amyloi͏̈des pathologiques chez les personnes agées. De telles observations ont été réalisées in vitro. Cependant les études portant sur les interactions entre les cellules microgliales et le peptide A? utilisent des systèmes dans lesquels la modélisation du dépôt amyloi͏̈de est imparfaite. C'est pourquoi nous avons développé un nouveau modèle d'étude dans lequel sont utilisé (a) une lignée cellulaire de cellules microgliales murines établie au laboratoire et (b) un nouveau modèle du dépôt amyloi͏̈de. Dans ce travail, nous avons caractérisé les différents types cellulaires présents dans la culture de cellules microgliales et nous avons validé le modèle de dépôt amyloi͏̈de, dans lequel des fibres de peptide A? sont immobilisées à la surface de levures préalablement autoclavées. Enfin, nous avons étudié le devenir de ces dépôts amyloi͏̈des artificiels au contact des cellules microgliales : ils sont ingérés par phagocytose. L'identification des récepteurs membranaires impliqués dans ce processus a été également amorcée
The senile plaque is one of the fundamental markers of Alzheimer's disease. It is an extracellular lesion made up mainly of a deposit of ?eta-amyloid [A?] peptide fibrils. Accumulation of A? fibrils would induce activation of microglial cells which would result in a chronic release of inflammatory proteins. This immunological process could be the cause of the cerebral atrophy observed in patients' brain. It is thus necessary to limit the formation of the amyloid deposits by inhibiting the synthesis of A? peptide or improve its degradation. Microglia which border the amyloid deposit present functions of phagocytosis. Thus, they could be able to ingest amyloid fibres and to control the appearance of the pathological amyloid deposits in elderly. Such observations were carried out in vitro. However, studies relating interactions between microglia and A? peptide use systems in which the modeling of amyloid deposit is not perfect. This is why we developed a new model of study in which (a) murine microglial cell line established at the laboratory and (b) a new model of amyloid deposit are used. In this work, we characterized the different cell types present in the culture of microglia and we presented the model of amyloid deposit, in which A? peptide fibrils are immobilized onto heat-killed yeast surface. Lastly, we studied the fate of these artificial amyloid deposits when they are placed in contact with microglial cells: they are ingested by phagocytosis. The identification of the microglial cell receptors implied in this process was also started

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Erdélyi, Máté. "Towards the Development of Photoswitchable β-Hairpin Mimetics." Doctoral thesis, Uppsala universitet, Avdelningen för organisk kemi, 2004. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-4057.

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Peptide secondary structure mimetics are important tools in medicinal chemistry, as they provide analogues of endogeneous peptides with new physicochemical and pharmacological properties. The β-hairpin motif has been shown to be involved in numerous physiological processes, among others in regulation of eucariotic gene transcription. This thesis addresses the design, synthesis and conformational analysis of photoswitchable β-hairpin mimetics. The developmental work included the establishment of an improved procedure for cross coupling of aryl halides with terminal alkynes. Microwave mediated Sonogashira couplings in closed vessels were optimized under homogeneous and solid-phase conditions furnishing excellent yields for a large variety of substrates within 5 – 25 minutes. In addition, microwave heating was shown not to have any non-conventional effect on the reaction rate. Furthermore, the most important factors affecting β-hairpin stability were evaluated. Studies of tetrapeptide and decapeptide analogues revealed the essential role of the β-turn in initiation of hairpin folding. Moreover, hydrogen bonding was shown to be the main interchain stabilizing force, whereas hydrophobic interactions were found to be relatively weak. Nevertheless, hydrophobic packing appears to provide an important contribution to the thermodynamic stability of β-hairpins. Photoswitchable peptidomimetics were prepared by incorporation of various stilbene moieties into tetra- and decapeptides. Synthesis, photochemical isomerisation and spectroscopic conformational analysis of the compounds were performed.

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Fujita, Naotaka. "Noninvasive longitudinal quantification of β-cell mass with [111In]-labeled exendin-4." Doctoral thesis, Kyoto University, 2020. http://hdl.handle.net/2433/245834.

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京都大学
0048
新制・課程博士
博士(医学)
甲第22149号
医博第4540号
新制||医||1039(附属図書館)
京都大学大学院医学研究科医学専攻
(主査)教授川口義弥, 教授上本伸二, 教授富樫かおり
学位規則第4条第1項該当
Doctor of Medical Science
Kyoto University
DFAM

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Megy, Simon. "Etude de la structure de la protéine β [Bêta]-Caténine et de son interaction avec la protéine β [Bêta]-TrCP par RMN et modélisation moléculaire." Paris 6, 2005. http://www.theses.fr/2005PA066331.

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Ganga, Ramu Vasanthakumar [Verfasser]. "Studies on Chemical Synthesis of Peptides: Efficient Synthetic Methods for β-Amino Acids, Azides, Amino Acid Hydroxamates and Esters : Methodologies in peptide synthesis / Vasanthakumar Ganga Ramu." München : GRIN Verlag, 2011. http://d-nb.info/119000478X/34.

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Dietrich, Laura [Verfasser], Susanne [Akademischer Betreuer] Brakmann, and Tom N. [Gutachter] Grossmann. "Zellgängige Peptide zur Inhibition des Wnt/β-Catenin Signalweges / Laura Dietrich ; Gutachter: Tom N. Grossmann ; Betreuer: Susanne Brakmann." Dortmund : Universitätsbibliothek Dortmund, 2017. http://d-nb.info/1137702125/34.

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MOORE, COURTNEY MARIE. "EFFECT OF A HETEROBIVALENT GLUCAGON LIKE PEPTIDE-1 LINKED TO CHOLECYSTOKININ ON INSULIN SECRETION IN PANCREATIC β-CELLS." Thesis, The University of Arizona, 2016. http://hdl.handle.net/10150/613295.

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A goal of diabetes therapeutics is to deliver agents that target insulin secreting pancreaticβ-cells with high specificity while leaving other cells unaffected.Linking two ligands for two different receptors promotes binding to cells expressing the complementary receptors, thereby increasing the specificity for the target cells. Both Glucagon LikePeptide 1 (GLP-1) and Cholecystokinin (CCK) receptors are expressed on the surface of pancreatic β-cells. A ligand composed of GLP-1 linked to CCK-6 was produced and evaluated for its effect on β-cell insulin secretion. A combination of unlinked monomers activates insulin secretion at 100 nM in the absence of stimulatory glucose, an effect similar to CCK alone. However, the GLP-1/CCK-6 dimer potentiated glucose stimulated insulin secretin (GSIS) at low concentrations with higher sensitivity than the combined monomers.These findings suggest that the GLP-1 effect on GSIS(potentiation) is retained in the bivalent ligand, but the CCK effect may be attenuated or shifted in efficacy. The observed enhanced sensitivity to potentiate GSIS indicates that the binding affinity of the GLP-1/CCK-6 is increased via bivalent interactions as expected. Since bivalent binding requires the expression of both complementary receptors, this also suggests that the GLP-1/CCK-6 may have enhanced specificity for β-cells.

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48

Mari, Meropi. "Investigating the aggregation of β-amyloid peptide (Aβ₄₂) and its interactions with lipid bilayers using advanced microscopy techniques." Thesis, University of Edinburgh, 2014. http://hdl.handle.net/1842/8889.

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The cell membrane is a highly complex structure consisting of a large diversity of phospholipids and macromolecules. There exist a variety of diseases that compromise the integrity of this key component of the cell. This thesis considers the investigation of interactions between β-amyloid peptide (Aβ₄₂) and lipid bilayers. To facilitate understanding of this complex system, it is advantageous to employ a model sample; supported lipid bilayers (SLB) and giant multilamellar vesicles (MLVs) are used as proxy cell membranes. These nanostructures are widely used as models of cellular membranes in many areas of scientific research. Phospholipid molecules self-organise into bilayer structures containing phase-separated microdomains, which are believed to be important in many biological processes. This study aims to develop model systems and experimental tools to explore hypothetical mechanisms through which the β-amyloid interacts with the lipid membranes. A lack of mechanistic understanding is the major challenge to our efforts to elucidate not only the interactions of the Aβ42 with the lipid membranes, but also the behaviour of these systems towards the changes of the environmental conditions (pH, concentration, temperature). Our results suggest that there are various different methods, such as AFM, CARS microscopy and Raman spectroscopy as well as neutron scattering that are capable of fast imaging. Overall, all these techniques contributed in a complementary study of Aβ₄₂ aggregation states under extreme and physiological conditions as well as to image Aβ₄₂ interactions with lipid bilayers consisted of specific lipids.

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Leeb, Elena [Verfasser]. "Ways for a targeted enzymatic hydrolysis of β-lactoglobulin - Control of reaction kinetics and peptide fractionation / Elena Leeb." München : Verlag Dr. Hut, 2021. http://d-nb.info/1235279324/34.

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50

Mahalakshmi, R. "Aromatic Interactions In Peptides : Designed Helices And β-Hairpins." Thesis, 2006. http://hdl.handle.net/2005/458.

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Design of complex protein folds requires complete understanding of the stereochemical principles that govern polypeptide chain folding. Extensive studies on design and synthesis of specific secondary structures like β-helices, β -sheets and hairpins have taught us that the unnatural amino acid aminoisobutyric acid (Aib) can be successfully employed for helix nucleation and tight turns of appropriate stereochemistry are facilitated by the use of DPro-Xxx sequences. Availability of such rigid secondary structure scaffolds therefore permits the design of synthetic peptides that can be used as models for investigation of tertiary interactions, primarily that of aromatic residues. Chapter 1 summarizes the present knowledge of peptide design using non-protein amino acids. The chapter also details the unique features of aromatic amino acids, especially tryptophan, and their employment as secondary structure stabilizing elements. Chapters 2-7 contain detailed descriptions of the work carried out on design, synthesis, and structural characterization of designed peptides containing aromatic amino acids. In Chapter 2, the use of aromatic pairs in strand segments of peptide hairpins has been discussed with the results clearly indicating that aromatic interactions at the non-hydrogen bonding position of peptide hairpins contribute to structure stability. In Chapter 3, accommodation of the Leu-Trp-Val segment in helical scaffolds the role of Trp residues in crystallization has been discussed. Chapter 4 outlines the influence of a large number of Trp residues on the preferred backbone conformation, with the studies clearly indicating a preference for helical scaffolds in small peptides. The role of Trp residues at turn regions of peptide hairpins has been discussed in Chapter 5, using examples from both synthetic peptides and from natural peptides containing Pro-Trp segments. The studies suggest that the Pro-Trp segments serve as helix nucleators and disrupt formation of peptide hairpins. The results of this study have been further extended to Conus monile peptides, discussed in Chapter 6. The studies also suggest the role of an aromatic-Pro segment on the cis-trans isomerization of the Xxx-Pro tertiary amide unit. Chapter 7 discusses the contribution of a Cys-His vs Tyr-His pair on strand segment stability in diproline nucleated peptide hairpins. Chapter 8 summarizes the key findings of the work. Chapter 9 lists the references cited in the thesis and the Appendix chapter provides details of experimental techniques used in the study.β

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Dissertations / Theses on the topic 'Β Peptide'

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