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Self-assembly has emerged as a promising technique for fabrication of novel hybrid materials and nanostructures. The work presented in this thesis has been focused on developing nanoscale materials based on synthetic de novo designed polypeptides. The polypeptides have been utilized for the assembly of gold nanoparticles, fibrous nanostructures, and for sensing applications. The 42-residue polypeptides are designed to fold into helix-loop-helix motifs and dimerize to form four-helix bundles. Folding is primarily driven by the formation of a hydrophobic core made up by the hydrophobic faces of the amphiphilic helices. The peptides have either a negative or positive net charge at neutral pH, depending on the relative abundance of Glu and Lys. Charge repulsion thus prevents homodimerization at pH 7 while promoting hetero-dimerization through the formation of stabilising salt bridges. A Cys incorporated in position 22, located in the loop region, allowed for directed, thiol-dependent, immobilization on planar gold surfaces and gold nanoparticles. The negatively charged (Glu-rich) peptide formed homodimers and folded in solution at pH < 6 or in the presence of certain metal ions, such as Zn2+. The folding properties of this peptide were retained when immobilized directly on gold, which enabled reversible assembly of gold nanoparticles resulting in aggregates with well-defined interparticle separations. Particle aggregation was found to induce folding of the immobilized peptides but folding could also be utilized to induce aggregation of the particles by exploiting the highly specific interactions involved in both homodimerization and hetero-association. The possibility to control the assembly of polypeptide-functionalized gold nanoparticles was utilized in a colorimetric protein assay. Analyte binding to immobilized ligands prevented the formation of dense particle aggregates when subjecting the particles to conditions normally causing extensive aggregation. Analyte binding could hence easily be distinguished by the naked eye. Moreover, the peptides were utilized to assemble gold nanoparticles on planar gold and silica substrates. Fibrous nanostructures were realized by linking monomers through a disulphide-bridge. The disulphide-linked peptides were found to spontaneously assemble into long and extremely thin peptide fibres as a result of a propagating association mediated by folding into four-helix bundles. / Ingenjörer och vetenskapsmän har ofta inspirerats av naturen i sökandet efter lösningar på tekniska problem. Allt ifrån byggnadskonstruktioner, flygplansvingar, kompositmaterial till kardborrebandet har skapats med utgångspunkt från förebilder i naturen. Många av de material och konstruktioner som återfinns i naturen har åtråvärda egenskaper som är svåra att erhålla i syntetiska matrial med traditionell teknik. Även om vi i flera fall kan härma sammansättningen och formen blir resultatet inte nödvändigtvis det samma. Den största skillnaden mellan syntetiska material och material producerade av levande organismer är hur deras komponenter sinsemellan är organiserade och sammansatta. I syntetiska material är komponenterna ofta inbördes mer eller mindre slumpvis ordnade medan de i biologiska material är organiserade med en oerhörd precision som sträcker sig ända ned på molekyl- och atomnivå. Naturens byggstenar har genom evolutionens gång förfinats för att spontant kunna organisera sig och bilda komplexa material  och strukturer. Denna process, som styrs genom att många svaga krafter inom och mellan byggstenarna samverkar, kallas ofta för självorganisering och är en förutsättning för allt liv. Självorganisering har också blivit en allt viktigare metod inom nanotekniken för att konstruera material och strukturer med nanometerprecision. I den här avhandlingen beskrivs en typ av självorganiserande material där byggstenarna utgörs av nanometerstora guldpartiklar och syntetiska proteiner. De syntetiska proteinerna är designade för att efterlikna naturliga biomolekyler och antar en välbestämd tredimensionell struktur när två av dem interagerar med varandra. Denna interaktion är mycket specifik men kan styras genom att variera kemiska parametrar som surhet och jonstyrka vilket ger en möjlighet att påverka och kontrollera proteinernas struktur. Proteinerna har vidare modifierats för att spontant organisera sig till fibrer som är flera mikrometer långa men endast några nanometer tjocka. Proteinfibrer utgör en mycket viktig typ av strukturer i biologiska system och finns i alltifrån spindelväv till muskler. Syntetiska proteinfibrer är därför både ett intressant modellsystem och ett material med många potentiellt intressanta användningsområden. Genom att fästa de syntetiska proteinerna på ytan av guldnanopartiklar går interaktionerna mellan partiklarna att kontrollera på samma sätt som interaktionerna mellan proteinerna. Krafterna mellan proteinerna och interaktionerna involverade i proteinernas veckning har använts för att reversibelt aggregera och organisera nanopartiklarna. Ett antal olika byggstenar har studerats och utvecklats till något som liknar ett mycket enkelt nano-Lego, som på en given signal spontant bygger ihop sig eller trillar isär. Guldnanopartiklar är intressanta eftersom de är stabila och lätta att modifiera kemiskt men också på grund av deras optiska egenskaper som ger dem en ovanligt vacker vinröd färg. Färgen uppstår på grund av partiklarnas ringa storlek och varierar naturligt med egenskaperna hos den omgivande miljön. Detta gör det enkelt att studera hur partiklarna interagerar eftersom de byter färg när de närmar sig varandra, men gör dem också intressanta för sensortillämpningar. En enkel och robust sensor beskrivs i avhandlingen där syntetiska proteiner, speciellt utformade för att upptäcka och binda andra molekyler, har fästs på nanopartiklarna. Med partiklarnas hjälp går det att med blotta ögat detektera ett mänskligt protein i koncentrationer under ett tusendels gram per liter. En tidig diagnos av sjukdomstillstånd kan i de flesta fall avsevärt underlätta behandlingen och behovet av enkla sensorer för att bestämma närvaro och koncentration av medicinskt intressanta molekyler är därför mycket stort.

The next generation of toxic chemicals and hazardous wastes from sophisticated chemical industries will demand the environmental agencies to employ biological methods over the conventional physical and chemical remediation methods. Over the past decade, natural metallo-enzymes have been identified to degrade some of the major chemical contaminants through electron transfer pathways. However, these natural enzymes are less stable in organic solvents and they are not effective for the degradation of toxic compounds such as polychlorinated biphenyls or dioxins. This thesis explores the use of protein design approaches to produce chemically and molecularly modified enzymes, which are highly stable, possess little substrate specificity, and have higher activity than the natural enzymes. The experiments presented in this thesis make use of solid phase synthesis and site-directed mutagenesis for the synthesis and production of these enzymes and popular chromatographic techniques for their purification. The partial characterization of these proteins revealed the essential structural features of these proteins, and their catalytic activity was demonstrated by the use of peroxidase assays. / Master of Science

<p>This thesis describes the design and synthesis of molecules with potential roles in biomedicine, with an emphasis on molecular recognition in complex biological environments. The first chapter describes the synthesis and evaluation of compounds for use in nuclide therapy. Carboranes are frequently used in the development of drugs for Boron Neutron Capture Therapy. New routes for monohydroxylation at the B and C atoms of <i>p</i>-carborane have been developed. The Suzuki-Miyaura reaction has been applied to the cross-coupling of <i>bis</i>(neopentyl glycolato)diboron or <i>bis</i>(pinacolato)diboron and 2-I-<i>p</i>-carborane. The synthesized derivatives are important intermediates in the synthesis of a number of potentially biologically active carborane-containing molecules.</p><p>The DNA intercalator doxorubicin has been functionalized to enable ¹²⁵I labelling. The aim of combining the DNA intercalator with ¹²⁵I was to achieve high delivery of cytotoxic radiation to the nucleus. The DNA-binding ability and cellular uptake of the synthesized compounds have been evaluated. One of the compounds bound strongly to DNA and had similar cellular uptake as daunorubicin, which makes the compound very interesting for further biological evaluation.</p><p>The second chapter describes the use of polypeptide conjugates to broaden our knowledge of molecular recognition. The polypeptides consist of 42 amino acids each and are designed to fold into helix-loop-helix motifs that dimerize due to their amphiphilic character. The polypeptides are combined with a variety of small organic molecules. The incorporation of small aromatic molecules to influence the structure and dynamics of a polypeptide has been investigated. By attaching a dansyl group to the side chain of a lysine residue, the dynamics of the protein’s hydrophobic core where affected to such a degree that a native-like fold was formed. The polypeptide conjugates have also been used to study the binding and recognition of native proteins. High-affinity binders for chitinases and acetylcholine esterase have been developed and evaluated.</p>

This thesis describes the design and synthesis of molecules with potential roles in biomedicine, with an emphasis on molecular recognition in complex biological environments. The first chapter describes the synthesis and evaluation of compounds for use in nuclide therapy. Carboranes are frequently used in the development of drugs for Boron Neutron Capture Therapy. New routes for monohydroxylation at the B and C atoms of p-carborane have been developed. The Suzuki-Miyaura reaction has been applied to the cross-coupling of bis(neopentyl glycolato)diboron or bis(pinacolato)diboron and 2-I-p-carborane. The synthesized derivatives are important intermediates in the synthesis of a number of potentially biologically active carborane-containing molecules. The DNA intercalator doxorubicin has been functionalized to enable 125I labelling. The aim of combining the DNA intercalator with 125I was to achieve high delivery of cytotoxic radiation to the nucleus. The DNA-binding ability and cellular uptake of the synthesized compounds have been evaluated. One of the compounds bound strongly to DNA and had similar cellular uptake as daunorubicin, which makes the compound very interesting for further biological evaluation. The second chapter describes the use of polypeptide conjugates to broaden our knowledge of molecular recognition. The polypeptides consist of 42 amino acids each and are designed to fold into helix-loop-helix motifs that dimerize due to their amphiphilic character. The polypeptides are combined with a variety of small organic molecules. The incorporation of small aromatic molecules to influence the structure and dynamics of a polypeptide has been investigated. By attaching a dansyl group to the side chain of a lysine residue, the dynamics of the protein’s hydrophobic core where affected to such a degree that a native-like fold was formed. The polypeptide conjugates have also been used to study the binding and recognition of native proteins. High-affinity binders for chitinases and acetylcholine esterase have been developed and evaluated.

La chimie des foldamères est un domaine de recherche en pleine expansion où les chimistes explorent la construction d’architectures artificielles variées mimant les structures repliées des biopolymères naturels. Les foldamères d’oligoamides quinoline, constituent une branche importante des foldamères montrant de nombreuses caractéristiques attractives, incluant la stabilité et la prédictibilité de leurs conformations repliées, qui en font de bons candidats pour des applications biologiques. Jusqu’à présent, la plupart des études sur les foldamères d’oligoamides quinolines ont été menées dans des solvants organiques. Cette thèse a pour objectif d’étendre leur portée au milieu aqueux et présente plusieurs méthodologies pour parvenir à leur solubilité, leur repliement, la variation de leurs chaines latérales, leur agrégation et leur capacité à former des cristaux dans l’eau.Tout d’abord, une méthode de synthèse en phase solide a été développée permettant l’accès rapide aux foldamères hybrides α-amino acide/quinoline (X/Q). Leur étude dans l’eau montre que contrairement aux foldamères hybrides de type (XQ)n, ceux de type (XQ2)n sont capables d’adopter une conformation hélicoïdale présentant un alignement des chaines α-amino acides dans l’espace. Ensuite, plusieurs chaines latérales courtes ont été identifiées pour doter les foldamères aromatiques d’une solubilité et d’une capacité à cristalliser dans l’eau. Six oligoamides quinoline ont ainsi été synthétisés pour une étude modèle. Des cristaux ont été obtenus pour toutes les séquences sauf une, présentant une excessive solubilité dans l’eau. Enfin, des efforts ont été faits pour construire des faisceaux d’hélices auto-assemblés dans l’eau à base d’effets hydrophobes et d’interactions électrostatiques. Les études RMN et cristallographiques ont indiqué que les effets hydrophobes étaient plus faibles qu’attendu et ne provoquaient pas d’agrégation forte. / Foldamer chemistry is a rapidly expanding research field where chemists explore the construction of various artificial architectures that mimic the folded structures of biopolymers found in nature. Quinoline oligoamide foldamers, as an important branch of foldamers, have been shown to possess many desirable features, including stability and predictability of their folded conformations, and are promising candidates to achieve biological applications. Up to now, most investigations of quinoline oligoamide foldamers have been carried out in organic solvents. This thesis is aimed to expand their scope in aqueous medium and presents several methodologies to achieve solubility, folding, side-chain variation, aggregation and crystal growth ability in water.First, a solid phase synthesis method was developed to enable the fast access to α-amino acid/quinoline (X/Q) hybrid oligoamide foldamers. The study of these hybrid foldamers in water showed that contrary to (XQ)n-type foldamers the (XQ2)n-type foldamers could adopt aromatic helical conformations with α-amino acid side chains aligned in space. Then, several short side chains were identified to endow aromatic foldamers with both solubility in, and crystal growth ability from water. Six quinoline oligoamides displaying these side chains were synthesized as a case study. Crystals were obtained from aqueous medium in all cases but one, exceedingly soluble in water. At last, efforts were made to construct self-assembled aromatic helix bundles in water based on hydrophobic effects and electrostatic interactions. NMR and crystallographic studies indicated that hydrophobic effects are weaker than expected and not strongly conducive of aggregation.