Le but de ma thèse a été de réaliser de nouveaux composés hybrides constitués de nanotubes de carbone (ou fullerènes) et de nanotubes de peptide. L'approche choisie a consisté à greffer sur des nanotubes de carbone, ou dans un premier temps sur des fullerènes, via des bras espaceurs, des cyclopeptides « de type Ghadiri» conduisant aux nanotubes de peptide. Pour se faire, la synthèse de bras espaceurs a été nécessaire ainsi que leur fixation sur les nanotubes de carbones ou fullerènes. Les cyclopeptides sont constitués d'un nombre pair d'acides aminés (8) alternés D et L s'auto-assemblant en feuillets ß antiparallèles pour conduire à des nanotubes. Des essais de solubilisation du cyclopeptide diacide révèlent l'impossibilité d'utiliser ces composés en synthèse organique, dans la mesure ou ils ne sont pas solubles dans les solvants organiques classiques. Il a fallut ainsi revoir la synthèse en incluant soit le fullerène en cours de synthèse peptidique soit en modifiant les conditions pour permettre une solubilisation du peptide. Les composés synthétisés ont été caractérisés par différentes méthodes notamment en TEM, FT-IR, ATR, microscopie optique, diffusion de la lumière. De nouvelles applications aux peptides de Ghadiri ont été cherchées en imagerie (par encapsulation du Xénon hyperpolarisé dans les cavités). Il a été mis en évidence de nouvelles organisations cristallines des peptides possibles dans des conditions contrôlées à l'aide de contre ions tels que les éléments de la première colonne du tableau périodique (Li, Na, K, Rb, ou Cs). Ces organisations, différentes en fonction du contre ion choisi, ont un caractère fractal remarquable, une organisation cristalline régulière et on observe un réseau de liaisons hydrogène inattendu dans les conditions utilisés.

The plasma membrane functions as a barrier, restricting entry of hydrophilic pharmaceutical agents. Cell-penetrating peptides (CPPs) are capable of transporting bioactive cargos into the cell and have consequently been extensively investigated for their mechanism of entry and capability to deliver various cargos spanning from peptides to plasmids. The main aim of this thesis was to investigate the mechanism and capability of some of these CPPs to deliver mainly oligonucleotides and peptides into the cell. Oligonucleotides in the form of ds DNA decoy for sequestering of transcription factors or PNAs for redirection of splicing. In addition, peptides derived from the interaction interface of a tumor suppressor protein were investigated for their potential to combine a biological effect with internalization. Peptides with or without any cargo were predominantly dependent on some form of endocytic mechanism for internalization, substantiated by using a functional assay, where all tested CPPs were associated with endocytosis for delivery of splice correcting PNAs. A new CPP, M918 proved most efficient in promoting splice correction and internalized mainly via macropinocytosis. In addition, TP10 efficiently delivered dsDNA decoy oligonucleotides for sequestering of the transcription factor Myc with a concomitant biological response, i.e. reduced proliferation. Finally, for the first time, to our knowledge, a novel pro-apoptotic peptide with cell-penetrating properties was designed from the tumor suppressor p14ARF, which decreased proliferation and induced apoptosis in cancer cell-lines, potentially mimicking the full-length protein. Altogether, this thesis highlights the functionality of CPPs and the possibility to develop new CPPs with improved or new properties, having the potential to advance delivery of therapeutic compounds.

<p>Functional genomic analyses provide information that allows hypotheses to be formulated on protein function. These hypotheses, however, need to be validated using reverse genetic approaches, which are difficult to perform on a large scale and in diploid organisms. To address this problem, we developed a genetic screen to rapidly isolate lariat peptides that function as trans dominant inhibitors of protein function.</p> <p>We engineered intein proteins to genetically produce lariats. A lariat consists of a lactone peptide covalently attached to a linear peptide. Cyclizing peptides with a lactone bond imposes a constraint even within the reducing environment found inside of cells. The covalently attached linear peptide provides a site for fusing protein moieties. We fused a transcriptional activation domain to a combinatorial lactone peptide, which allowed combinatorial lariat libraries to be screened for protein interactions using the yeast two-hybrid assay.</p> <p>We confirmed that the intein processed in yeast using Western blot analysis. A chemoselective ring opening of the lactone bond with heavy water, followed by mass spectrometry analysis showed that ~ 44% of purified lariat contained an intact lactone bond. To improve the stability of the lactone bond, we introduced mutations into the engineered intein and analyzed their processing and stability by mass spectrometery. Several mutations were identified that increased the amount of intact lariat.</p> <p>Combinatorial libraries of lactone peptides were generated and screened using the yeast-two-hybrid interaction trap. Lactone cyclic peptides that bound to a number of different targets including LexA, Jak2, and Riz1 were isolated. A lactone cyclic peptide isolated against the bacterial repressor protein LexA was characterized. LexA regulates bacterial SOS response and LexA mutants that cannot undergo autoproteolyis make bacteria more sensitive to, and inhibit resistance against cytotoxic reagents. The anti-LexA lariat interacted with LexA with a dissociation constant of 37 µM by surface plasmon resonance. The lactone constraint was determined to be required for the interaction of the anti-LexA L2 lariat with LexA in the yeast-two-hybrid assay. Alanine scanning showed that only two amino acids (G8 and E9) in the anti-LexA L2 sequence (1-SRSWDLPGEY-10) were not required for the interaction with LexA. The interaction of the anti-LexA lariat with LexA in vivo was confirmed by chromatin precipitation of the lactone peptide-LexA-DNA complex. The anti-microbial properties of the anti-LexA lariat were also characterized. The anti-LexA lariat potentiated the activity of a DNA damaging agent mitomycin C and inhibited the cleavage of LexA, preventing the SOS response pathway from being activated.</p> <p>In summary, lariats possess desired traits for characterizing the function and therapeutic potential of proteins. The ability to genetically and chemically synthesize lariats allows the lariat transcription activation domain to be replaced by other peptide and chemical moieties such as affinity tags, fluorescent molecules, localization sequences, et cetera, which give them advantages over head to tail cyclized peptides, which have no free end to attach moieties.</p>

A new paradigm for the treatment of infectious disease is through the modulation of innate immune responses. In this capacity, host defense peptides (HDPs) and synthetic Toll-like receptor 9 (TLR9) ligands have the greatest demonstrated potentials. The work presented here considers mechanisms for the improvement of these treatments through optimization, or in the case of HDPs the minimization, of the interactions of these ligands with sensory receptors.<p>Toll-like Receptor 9 activates the innate immune system in response to microbial DNA or immune-modulating oligodeoxynucleotides. While cell stimulation experiments demonstrate the preferential activating ability of CpG-containing nucleic acids, direct binding investigations have reached contradictory conclusions regarding the sequence-specificity of TLR9 ligand binding. To address this discrepancy the characterization of human TLR9 ligand binding properties is reported. TLR9 has a high degree of ligand specificity in being able to discriminate not only CpG dinucleotides, but also higher order six nucleotide motifs that mediate species-specific activation. However, TLR9 ligand binding is also functionally influenced by nucleic acids in a sequence-independent manner both in vitro and in cell proliferation experiments. A model is proposed in which TLR9 activation is mediated specifically by CpG-containing ligands while sensitivity of the receptor is modulated by the absolute concentration of nucleic acids in a sequence-independent fashion. <p>Host defense peptides are among the leading candidates to combat antibiotic resistant bacterial strains. Recently, HDPs have been demonstrated to function as ligands for the bacterial sensory kinase PhoQ resulting in the induction of virulence and adaptive responses. Thus, concerns have been raised regarding therapeutic applications of HDPs. Here a methodology is described that permits discrimination and quantification of the distinct, but related, peptide behaviors of direct antimicrobial activity and PhoQ ligand potential. Utilizing peptide derivatives of the model HDP Bac2A it is demonstrated that antimicrobial efficiency is significantly, and inversely, related to PhoQ ligand efficacy. This provides a rational basis for HDP selection with greater therapeutic potential and minimized potential for initiation of bacterial resistance.

A new paradigm for the treatment of infectious disease is through the modulation of innate immune responses. In this capacity, host defense peptides (HDPs) and synthetic Toll-like receptor 9 (TLR9) ligands have the greatest demonstrated potentials. The work presented here considers mechanisms for the improvement of these treatments through optimization, or in the case of HDPs the minimization, of the interactions of these ligands with sensory receptors.<p>Toll-like Receptor 9 activates the innate immune system in response to microbial DNA or immune-modulating oligodeoxynucleotides. While cell stimulation experiments demonstrate the preferential activating ability of CpG-containing nucleic acids, direct binding investigations have reached contradictory conclusions regarding the sequence-specificity of TLR9 ligand binding. To address this discrepancy the characterization of human TLR9 ligand binding properties is reported. TLR9 has a high degree of ligand specificity in being able to discriminate not only CpG dinucleotides, but also higher order six nucleotide motifs that mediate species-specific activation. However, TLR9 ligand binding is also functionally influenced by nucleic acids in a sequence-independent manner both in vitro and in cell proliferation experiments. A model is proposed in which TLR9 activation is mediated specifically by CpG-containing ligands while sensitivity of the receptor is modulated by the absolute concentration of nucleic acids in a sequence-independent fashion. <p>Host defense peptides are among the leading candidates to combat antibiotic resistant bacterial strains. Recently, HDPs have been demonstrated to function as ligands for the bacterial sensory kinase PhoQ resulting in the induction of virulence and adaptive responses. Thus, concerns have been raised regarding therapeutic applications of HDPs. Here a methodology is described that permits discrimination and quantification of the distinct, but related, peptide behaviors of direct antimicrobial activity and PhoQ ligand potential. Utilizing peptide derivatives of the model HDP Bac2A it is demonstrated that antimicrobial efficiency is significantly, and inversely, related to PhoQ ligand efficacy. This provides a rational basis for HDP selection with greater therapeutic potential and minimized potential for initiation of bacterial resistance.

<p>Functional genomic analyses provide information that allows hypotheses to be formulated on protein function. These hypotheses, however, need to be validated using reverse genetic approaches, which are difficult to perform on a large scale and in diploid organisms. To address this problem, we developed a genetic screen to rapidly isolate lariat peptides that function as trans dominant inhibitors of protein function.</p> <p>We engineered intein proteins to genetically produce lariats. A lariat consists of a lactone peptide covalently attached to a linear peptide. Cyclizing peptides with a lactone bond imposes a constraint even within the reducing environment found inside of cells. The covalently attached linear peptide provides a site for fusing protein moieties. We fused a transcriptional activation domain to a combinatorial lactone peptide, which allowed combinatorial lariat libraries to be screened for protein interactions using the yeast two-hybrid assay.</p> <p>We confirmed that the intein processed in yeast using Western blot analysis. A chemoselective ring opening of the lactone bond with heavy water, followed by mass spectrometry analysis showed that ~ 44% of purified lariat contained an intact lactone bond. To improve the stability of the lactone bond, we introduced mutations into the engineered intein and analyzed their processing and stability by mass spectrometery. Several mutations were identified that increased the amount of intact lariat.</p> <p>Combinatorial libraries of lactone peptides were generated and screened using the yeast-two-hybrid interaction trap. Lactone cyclic peptides that bound to a number of different targets including LexA, Jak2, and Riz1 were isolated. A lactone cyclic peptide isolated against the bacterial repressor protein LexA was characterized. LexA regulates bacterial SOS response and LexA mutants that cannot undergo autoproteolyis make bacteria more sensitive to, and inhibit resistance against cytotoxic reagents. The anti-LexA lariat interacted with LexA with a dissociation constant of 37 µM by surface plasmon resonance. The lactone constraint was determined to be required for the interaction of the anti-LexA L2 lariat with LexA in the yeast-two-hybrid assay. Alanine scanning showed that only two amino acids (G8 and E9) in the anti-LexA L2 sequence (1-SRSWDLPGEY-10) were not required for the interaction with LexA. The interaction of the anti-LexA lariat with LexA in vivo was confirmed by chromatin precipitation of the lactone peptide-LexA-DNA complex. The anti-microbial properties of the anti-LexA lariat were also characterized. The anti-LexA lariat potentiated the activity of a DNA damaging agent mitomycin C and inhibited the cleavage of LexA, preventing the SOS response pathway from being activated.</p> <p>In summary, lariats possess desired traits for characterizing the function and therapeutic potential of proteins. The ability to genetically and chemically synthesize lariats allows the lariat transcription activation domain to be replaced by other peptide and chemical moieties such as affinity tags, fluorescent molecules, localization sequences, et cetera, which give them advantages over head to tail cyclized peptides, which have no free end to attach moieties.</p>

The rotavirus NSP4 protein is the first described viral enterotoxin. Abundant data from our laboratory reveals that NSP4 binds both the N- and C-termini of caveolin- 1 (aa2-31 and 161-178, respectively). Yeast two-hybrid and peptide binding analysis mapped the caveolin-1 binding site to three hydrophobic residues within the amphipathic a-helix, enterotoxic peptide domain (aa114-135). The research studies herein utilized peptides to investigate the interaction between NSP4 and caveolin-1. Peptides were synthesized corresponding to the amphipathic a-helix and caveolin-1 binding domain of NSP4 (aa112-140) and to the N- (aa2-20 and 19-40) and C- (161-178) termini of caveolin-1, and were utilized in structural and functional studies. Fluorescence binding assays revealed that NSP4 (aa112-140) binds to the N-terminus (aa19-40) of caveolin-1 with a stronger affinity than the C-terminus (aa161-178). In addition, this assay further delineated the NSP4 binding domain on caveolin-1 to aa19-40. Secondary structural changes following NSP4-caveolin-1 peptide-peptide interactions were investigated by circular dichroism analysis. Changes in a-helix formation were observed only upon interaction of the NSP4112-140 peptide with the C-terminal caveolin-1 peptide (C-Cav161- 178). The NSP4112-140 peptide contains a potential cholesterol recognition amino acid consensus (CRAC) sequence. Therefore this peptide was examined for cholesterol binding. Results of the binding assay revealed NSP4 binds cholesterol with a Kd of 7.67 +/- 1.49nM and this interaction occurs via aa112-140. Mutation of amino acid residues within the CRAC motif resulted in weaker binding affinities between each of the corresponding mutant peptides and cholesterol. NSP4 peptides containing mutations within the hydrophobic and charged faces of the amphipathic a-helix, enterotoxic peptide and caveolin-1 binding domain of NSP4 were examined for changes in secondary structure as well as diarrhea induction in mouse pups. Circular dichroism analysis revealed that mutation of hydrophobic residues resulted in a decrease in a-helix formation, whereas mutation of acidic and basic charged residues caused little to no change in a-helical content. When tested for diarrhea induction in mouse pups, the peptides containing mutations of either the hydrophobic or basic charged residues did not cause diarrhea. Taken together, the results of this research suggest a complex interplay between NSP4 secondary structure, caveolin-1 and cholesterol binding and diarrheagenic function.

Diss. (sammanfattning) Stockholm : Karolinska institutet, 2006. / Härtill 6 uppsatser.

Master of Science / Department of Grain Science and Industry / Yonghui Li / Antioxidants are widely used in food industries to delay lipid oxidation and prevent oxidative deterioration. In recent years, growing interests in developing safe and efficient antioxidants from natural sources due to the health-related risks associated with synthetic antioxidants. Recently, peptide antioxidants have drawn growing interests as since proteins are a macronutrient with various functionalities and high consumer acceptability. A lot of dietary proteins have been validated for their antioxidant potentials especially those obtained from animal proteins, nuts and pulses. Relatively less information is available on characterizing the antioxidant profile of cereal protein, and even less for sorghum protein. Sorghum is the fifth largest crop worldwide and is the third in United States. U.S. is leading in global sorghum production and distribution, and the state of Kansas is producing nearly half of U.S. sorghum. Currently, about one third of the U.S. sorghum is being used for ethanol production, resulting in more than 450 kilotons of by-products (e.g., DDGS) annually, which were often discarded or underutilized. DDGS is a premium protein source (~ 30% protein) that could be potentially modified into value-added products such as peptide antioxidants. In this study, relevant literatures detailing the extraction of cereal proteins, enzymatic hydrolysis of proteins, purification and characterization of hydrolysates, and evaluation of antioxidant profiles were extensively reviewed in Chapter 1. As preliminary experiments, sorghum kafirin protein was extracted from defatted sorghum white flour and hydrolyzed by 10 different types of enzymes from microbial, plant and animal sources. Hydrolysates prepared with Neutrase, Alcalase, and Papain displayed the most promising antioxidant activities as well as total protein recovery were primarily selected and investigated in depth described in Chapter 2, Chapter 3, and Chapter 4. The reaction conditions including substrate content, enzyme-to-substrate ratio, and hydrolysis time are critical parameters in producing peptides with desired activity and consistency, were therefore examined and optimized for each case of kafirin hydrolysates. The antioxidant capacity of the resulting hydrolysates was measured for antioxidant capacity through in vitro assays (DPPH, ABTS, ORAC, reducing power, and metal chelating) and then demonstrated in model systems (oil-in-water emulsion and ground meat). The fractions of hydrolysates possessing strongest activities were further fractionated by gel filtration and HPLC. Peaks representing the largest areas from HPLC were identified for major sequences by MALDI-TOF-MS. The experiment results indicated that all the three selected fractions of kafirin hydrolysates revealed excellent inhibition effects against oil and fat oxidations, which could be employed as tools to predict their performances in real food products. In addition, the structure studies showed that medium-sized hydrolysates of Neutrase (3 – 10 kDa) and Alcalase (5 – 10 kDa), and small-sized hydrolysates of Papain (1 – 3 kDa) exhibited relatively stronger activities. This study provided a workable processing method and critical reaction parameters for the production of peptide antioxidants from sorghum protein. The experiment results revealed that the sorghum peptide antioxidant could act through multiple mechanisms including free radical scavenging, metal ion chelation, hydrogen donating, and forming physical barriers to minimize the contact of oxidative agents to targets. These antioxidative peptides are a promising ingredient that can be potentially incorporated to food and feed products as alternatives to synthetic antioxidants or synergetic elements to nonpeptic antioxidants for protection of susceptible food ingredients. This study also made a positive impact to sorghum ethanol industry by guiding the conversion of sorghum protein-rich by-products into value-added antioxidant products as an additional revenue stream.

Les microalgues présentes à la fois dans les eaux douces et salées compteraient plus de 200 000 espèces. Cette diversité en fait une source potentielle de métabolites spécialisés originaux. Parmi les principales familles de substances naturelles valorisées actuellement, on peut citer les pigments, lipides, protéines, polysaccharides, caroténoïdes. Une vision plus globale du métabolome de chacune des espèces apparaît aujourd’hui nécessaire pour mieux mettre en valeur le potentiel commercial que représente cette « microbiodiversité ». Pour cela, nous avons tout d’abord choisi d’approcher le métabolome de différentes souches de microalgues cultivées au sein de la Société Greensea en s’appuyant sur les techniques d’HPTLC, de RMN et d’UHPLC-QTOF pour une visualisation large. Cette étude nous a permis de regrouper les espèces par analogie métabolique après traitement statistique des données. Une seconde partie a consisté en une étude phytochimique approfondie de certaines souches et a conduit à l’isolement et la caractérisation de plusieurs molécules. Ainsi, en plus de métabolites connus, un peptide original portant un motif isoprényl, le cumbriamide a été caractérisé au sein de Lyngbya sp. et une première évaluation de son potentiel thérapeutique a été entreprise. Une large diversité en glycolipides s’est montrée prépondérante dans de nombreuses souches et une méthode de caractérisation a pu être mise au point pour leur identification par UHPLC-QTOF. Enfin, différentes applications des approches métabolomiques ont été envisagées. Ainsi, des études chimiotaxonomiques ont été menées sur les différentes souches de microalgues et l’influence de changements de conditions de culture sur la production de métabolites chez Nannochloropsis oculata a été observée. / Microalgae are present both in Oceans and freshwaters and could include more than 200 000 species. This diversity is a source of original specialized metabolites that can find a large array of applications. Pigments, lipids, proteins, polysaccharides and carotenoids are usual compounds produced by microalgae that have found commercial applications. A global vision of the metabolome of each species has showed promises to highlight the commercial value of this “microdiversity”. We then decided to assess the metabolome of several microalgae species grown at the Greensea company by using HPTLC, NMR and UHPLC-QTOF techniques for a rapid and global overview. A classification of the species according to their metabolomics similarities was obtained after statistics treatment of the data. A second part was dedicated to a phytochemical study of the extracts of selected strains and led to the isolation and characterization of several metabolites. Thus, in addition to known molecules, an original peptide substituted by an isoprenyl moiety and named cumbriamide has been characterized in Lyngbya sp and a first assessment of its therapeutical potential has been undertaken. Glycolipids have been identified as the major metabolites in the extracts of numerous strains and a UHPLC-QTOF method was developed for their identification. Finally, several applications of the metabolomics approaches were considered. Chemotaxonomic studies were first carried out and the influence of growth conditions on the metabolome of Nannochloropsis oculata was observed.