Thèses : « Molecular recognitions »

1

Della, Sala Paolo. « Synthesis and properties of new macrocyclic derivates ». Doctoral thesis, Universita degli studi di Salerno, 2019. http://elea.unisa.it:8080/xmlui/handle/10556/4255.

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2017 - 2018
This PhD thesis is concerned with the design, synthesis and the characterization of new macrocyclic derivatives. Development of new macrocyclic compounds is a particularly interesting because they can involve like building block in Supramolecular chemistry and Nanochemistry. In the first place, I studied the supramolecular properties of different derivatives of the resorcin[6]arenes. Crystal of Resorcin[6]arene was obtained and it reveals that in the solid state the resorcin[6]arene assembles in a twin molecular capsule able to host toluene and ethyl acetate solvent molecules. Subsequently, I have reported the first example of resorcin[6]arene-based cavitand. Sulfate bridges play a double role, both, as structural element for the preorganization of the larger resorcin[6]arene macrocycle and as functional supramolecular interacting groups. Finally, I develop a new multivalent systems resorcin[n]arene based for inhibition of glycosidases and mannosidase that are involved in the malignant transformation of cells. These derivatives were synthetized starting to a pyrrolidine-based iminosugar and resorcinarenes compounds through CuAAS cycloaddition. Biological essays showed that all the resorcinarene derivatives have a good inhibitory activity towards mannosidase enzymes. In second instance, I synthetized new Cycloparaphenylenes (CPP) derivatives to molecular recognition and optoelectronic application. Particularly about molecular recognition field, I reported the synthesis of a [8]CPP derivative incorporating an electron-rich 1,4-dimethoxybenzene ring. This is the first example of substituted CPP derivative reported in literature able to recognize pyridinium guests. Owing to the presence of the 1,4-dimethoxybenzene ring a fine-tuning of the binding abilities toward pyridinium guests was obtained with respect to the native [8]CPP macrocycle. Hybrid Calixarene-CPP derivative that combine the supramolecular features of both the hosts was synthetized and studied in molecular recognition of Na+, Li+ and K+. This derivative shows a noncommon Li+ selectivity due to a more favorable interaction between the cation and the aromatic rings of the CPP bridge. Synthesis of incorporate the 9,10-diphenyl anthracene - [8]CPP derivative was performed and were studied optical and electronical features to obtain the first example of a CPP-based emitter in photon upconversion in the presence of the of octaethylporphyrin Pd(II) complex as a sensitizer, thus widening the application fields of this class of compounds. Finally, [8]CPP and [10]CPP was tested to produce Luminescent Solar Concentrators (LSCs). The high Stokes shift of the CPP macrocycles, enables the preparation of slabs in which a low reabsorption was observed. The results here obtained show clearly the photophysical performances of the CPPbased LSC closely matches with that of the lanthanide chelates based LSC, of interest for applications in colorless LSC. [edited by Author]
XXXI ciclo

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2

Kirsch, Nicole. « Molecular recognition of poorly functionalised molecules with imprinted polymers ». Thesis, University of Reading, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.325167.

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3

Eckel, Rainer. « Single molecules and nanocrystals : molecular recognition forces and optomechanical switching ». [S.l.] : [s.n.], 2006. http://deposit.ddb.de/cgi-bin/dokserv?idn=978888227.

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4

Kurahashi, Takuya. « Molecular Recognition and Regioselective Functionalization of Carbohydrates by Synthetic Host Molecules ». Kyoto University, 2000. http://hdl.handle.net/2433/157078.

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本文データは平成22年度国立国会図書館の学位論文(博士)のデジタル化実施により作成された画像ファイルを基にpdf変換したものである
Kyoto University (京都大学)
0048
新制・課程博士
博士(工学)
甲第8342号
工博第1907号
新制||工||1168(附属図書館)
UT51-2000-F246
京都大学大学院工学研究科合成・生物化学専攻
(主査)教授吉田潤一, 教授北川進, 教授森島績
学位規則第4条第1項該当

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5

Ourri, Benjamin. « Complex molecular architectures for the recognition of therapeutic bio(macro)molecules ». Thesis, Lyon, 2020. http://www.theses.fr/2020LYSE1001/document.

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La reconnaissance de biomolécules dans des milieux biologiques complexes est un réel défi pour les chimistes et les biologistes, associé à des enjeux médicaux majeurs. Face à cette problématique, le chimiste peut choisir d’utiliser des molécules désignées par ses soins, ou encore de sélectionner et d’utiliser directement des structures commerciales ou naturelles. Suivant cette dernière approche, les dendrigrafts de lysines (DGL) ont montré une neutralisation des héparines de différentes tailles supérieures à l’action de la protamine, le seul médicament autorisé en cas de surdosage de l’anticoagulant. Une étude par dynamique moléculaire a permis de mettre en avant le mécanisme d’interaction entre les héparines d’une part, et les DGLs et la protamine d’autre part. Par ailleurs, suivant la première approche de design et synthèse, nous avons utilisé la chimie combinatoire dynamique pour obtenir des nouveaux récepteurs synthétiques à partir de brique moléculaires diverses de type 1,4-dithiphénols. Des études à la fois théorique, en DFT et dynamique moléculaire, et expérimentale, ont été menés pour comprendre les phénomènes régissant l’auto-assemblage de ces briques en oligomères cycliques et la complexation de ces cavitands avec des biomolécules d’intérêt
The recognition of biomolecules in complex biological media is a challenge associated with various therapeutic applications. The chemist can address this issue following two approaches: either he designs him-self and synthesises its molecules or he selects a commercially available or natural molecule and directly uses it for its properties. Following the last strategy, dendrigraft of lysine (DGL) efficiently neutralised all classes of the anticoagulant heparin, with a superior effect compared to protamine, the only FDA-approved drug in case of heparin overdosage. A study by molecular dynamic revealed the mechanism of binding between heparins and DGL and protamine respectively. At the opposite of this approach, we used dynamic combinatorial chemistry in order to obtain disulfide bridged cyclophanes from the self-assembly of various 1,4-bisthiophenols by oxidation of thiols into disulfide bonds. By a combination of theoretical (DFT and molecular dynamic) and experimental studies, we investigated the driving forces and the influences of fundamental concepts such as solvation and steric effects for the self-assembly of these polythiols and the binding of the corresponding cavitands with therapeutic biomolecules

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6

Orro, Graña Adolfo. « Examination of the role of binding site water molecules in molecular recognition ». Thesis, SciLifeLab Stockholm, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-200164.

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A set of algorithms were designed, implemented and evaluated in order to, first, identifyclusters of conserved waters in binding pockets, i.e. hydration sites. Then, their contributionto the free energy of binding in a ligand-protein association was quantified by calculatingtheir enthalpy and entropy. The information obtained by using these algorithms couldcontribute to the development of new drugs by generating new ligands that target specifichigh-energy, unfavorable waters. Evaluation tests show that our algorithms can indeedprovide relevant data about how hydration sites influence ligand-protein binding.

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Dourado, Eduardo Manuel de Azevedo. « Computer simulations of adsorption and molecular recognition phenomena in molecularly imprinted polymers ». Thesis, University of Edinburgh, 2011. http://hdl.handle.net/1842/5680.

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Molecularly imprinted polymers (MIPs) are a novel, promising family of porous materials with potential applications ranging from separations, chemical sensing and catalysis to drug delivery and artificial immunoassays. The unique feature of these materials is their biomimetic molecular recognition functionality. Molecular recognition is the biological phenomenon of specific, selective and strong association between a substrate and a ligand. In man made MIPs this functionality is implemented via templated synthesis protocol. MIPs are synthesized in the presence of additional template molecules which form complexes with functional monomers in the pre‐polymerization mixture. After polymerization, the template is removed, leaving cavities in the structure which are complementary in shape and interaction patterns to the template molecules. These cavities act as mimics of biological receptors and are able to recognize and rebind template molecules. Although the imprinting concept is simple in principle, synthesis of MIPs with precisely controlled characteristics and performance remains a challenging task. Composition, polymerization conditions, template removal process and application conditions all affect the properties of MIPs. The material is affected at different scales, but crucially at the microscopic level, the number, fidelity and accessibility of binding sites are dependent on all the factors mentioned. The full potential of these materials can only be achieved if researchers can control and optimize the properties of MIPs through detailed understanding of adsorption and molecular recognition processes in these materials. The objective of this work is to, using computer simulations and statistical mechanics; develop a fundamental description of MIP formation and function, and to link morphological features of the model materials to their molecular recognition capabilities. In general, molecular simulations employed in this study should allow easier and more efficient exploration of a vast number of factors influencing the behaviour of MIPs. At the heart of the approach developed in this thesis is a computational strategy that imitates all the stages of MIP formation and function. First, the model simulates the pre‐polymerization mixture, allowing the formation of template‐functional monomer complexes. (This stage is implemented via canonical Monte Carlo simulation). Complexes can have different structures, depending on the chemical nature of template and functional monomer; therefore complexes can have a range of association constants. The distribution of template‐functional monomer complexes also translates into a distribution of binding sites of different specificity after template removal. In the second stage of the process, adsorption simulations (grand canonical Monte Carlo) are performed for a variety of model MIPs prepared to assess the role of various processing conditions such as composition, density and binding sites degeneration. This strategy was first applied to a simplified description of MIP species in order to identify the minimal model capable of molecular recognition and thus shed the light on the very nature of this phenomenon. In the developed model, the molecular species are constructed from hard spheres, featuring small interaction sites on their surfaces. The bond between two interaction sites has the strength and topological features of a typical hydrogen bond. The model exhibits molecular recognition, being able to preferentially adsorb template molecules. The associations between template and functional monomers were analyzed and classified to describe the distribution of binding sites and their heterogeneity. Using this model, several experimental trends typically observed in MIP studies could be explained, such as maximum in the selectivity as a function of monomer concentration. Using this model, we were also able to explore hypothetical, alternative protocols for MIP synthesis in order to improve their performance. These include the use of alternative templates and the post‐synthetic surface modifications of MIPs. The general strategy to modelling MIP, employed in this thesis, was then applied to a more detailed description of MIPs with realistic force field potentials for all the species involved. This more elaborate model is simulated with a combination of molecular dynamics (MD) and Monte Carlo techniques. This detailed model provided a wealth of information on various types of complexes observed in the pre‐polymerization mixture. Specifically, it revealed the relative weight of different interactions in the complex and their role in the binding energy of adsorbates. These simulations also provided the comparison of the relative contribution of different types of interactions (van der Waals, Coulombic) involved in a molecular recognition process. We believe the insights gained in this work will contribute to the development of rational MIP design strategies. In the discussion of the results of the thesis we speculate on how these models can be further developed in order to generate quantitative predictions and what type of systems it would be interesting and important to investigate in the future.

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8

Rajbanshi, Arbin. « Supramolecular interactions from small-molecule selectivity to molecular capsules ». Diss., Manhattan, Kan. : Kansas State University, 2010. http://hdl.handle.net/2097/3879.

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9

Brown, Susan Elizabeth. « Molecular recognition by cyclodextrins / ». Title page, contents and abstract only, 1994. http://web4.library.adelaide.edu.au/theses/09PH/09phb8798.pdf.

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10

Westwell, Martin Stuart. « Cooperativity in molecular recognition ». Thesis, University of Cambridge, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.388343.

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Grail, Barry Mark. « Molecular recognition of peptides ». Thesis, Bangor University, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.248898.

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12

Welsh, Fraser E. « Flavocytochrome b₂ : molecular recognition ». Thesis, University of Edinburgh, 1998. http://hdl.handle.net/1842/11539.

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Flavocytochrome b₂ from Saccharomyces cerevisiae is a L-lactate:cytochrome c oxidoreductase found in the mitochondrial intermembrane space. The crystal structure has been solved to 2.4Å resolution showing the enzyme to be a homotetramer (M_r 230 000). Each subunit (511 amino acids) is composed of two domains: A cytochrome domain containing protohaem IX (residues 1-100); and a flavodehydrogenase domain, FDH, which contains FMN (residues 101-511). The two domains are tethered by a "hinge" region (residues 92-103). In the crystal structure residues 295-311 are highly disordered and so not visible. This region is a proteolytically sensitive loop for which a function has not yet been determined. Flavocytochrome b₂ has been fully characterised and shown to be a "biological transformer" accepting electrons from a strictly 2-electron donor, L-lactate, and passing them individually to a 1-electron acceptor, cytochrome c. FDH has been independently expressed in E.coli allowing accurate characterisation of its properties without interference from the intense absorbance of the cytochrome domain. This has shown that although FDH remains an efficient L-lactate dehydrogenase, it has negligible cytochrome c reductase activity. This is intriguing as the thermodynamic driving force for electron transfer from FDH to cytochrome c, as determined from reduction potentials, is greater than 1/3V. We believe a lack of inter-protein recognition between the two proteins prevents them forming an effective electron transfer complex. The aim of this work was to alter the electron acceptor specificity of FDH to favour interactions with positively charged molecules.

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Petti, Michael A. Dougherty Dennis A. « Studies in molecular recognition / ». Diss., Pasadena, Calif. : California Institute of Technology, 1988. http://resolver.caltech.edu/CaltechETD:etd-04272006-160954.

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14

CATTANEO, VITTORIO. « OLIGOSACCHARIDES AND MOLECULAR RECOGNITION ». Doctoral thesis, Università degli Studi di Milano, 2014. http://hdl.handle.net/2434/229556.

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Carbohydrates have been established as the most abundant – and arguably the most structural diverse – organic molecules found in nature. They are chiral molecules readily available in nature in a variety of diastereomeric forms. Their conformational rigidity provides a well defined three-dimensional spatial arrangement of substituents with various multi-configured hydroxyl groups for chemical modification. Carbohydrates play a fundamental role in signal transduction and vital molecular recognition phenomena, they dominate the landscape of the cell and are responsible for cell-cell interaction, the recognition of virus and bacteria, binding of toxins and are involved in cell growth. For these reasons they are an attractive material for the development of new therapeutic agents, such as their application as antigenic material in vaccines formulation. In this framework we focused our attention in a troublesome nosocomial pathogen: Acinetobacter baumannii, a Gram-negative coccobacillus, in particular on the strain ATCC 17961. We synthesized three different fragments of the O-chain LPS of this bacterium, containing the unusual sugar residue 2,3-diacetamido-2,3- dideoxy-D-glucuronic acid. The binding affinity of these fragments will be evaluated by competitive ELISA assay against the anti-LPS serum of Acinetobacter baumannii ATCC 17961. Furthermore, thanks to chemical flexibility of carbohydrates, they are attractive chiral molecular scaffolds in asymmetric catalysis. They could be employed as metal ligands for enantioselective catalysis or themselves as metal-free organocatalysts. Sugars are an attractive material in this field for their low cost, potential polyfunctionalization, and the possibility to modify the chemical structure of the molecule in order to tune the chemical and physical properties for example the steric hindrance, the electronic and solubility properties of the catalyst. We synthesized two different carbohydrate-based organocatalyst, and we tested their activity in reaction between acetylacetone or diethylmalonate with β-nitrostyrene. e5

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15

Alaparthi, Madhubabu. « Molecular Recognition Involving Anthraquinone Derivatives and Molecular Clips ». Thesis, University of South Dakota, 2017. http://pqdtopen.proquest.com/#viewpdf?dispub=10285748.

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In the past, we have demonstrated that 1,8-anthraquinone-18-crown-5 (1) and its heterocyclic derivatives act as luminescent hosts for a variety of cations of environmental and clinical concern. We report here a series of heteroatom-substituted macrocycles containing an anthraquinone moiety as a fluorescent signaling unit and a cyclic polyheteroether chain as the receptor. Sulfur, selenium, and tellurium derivatives of 1,8-anthraquinone-18-crown-5 (1) were synthesized by reacting sodium sulfide (Na₂S), sodium selenide (Na₂Se) and sodium telluride (Na₂Te) with 1,8-bis(2-bromoethylethyleneoxy)anthracene - 9,10-dione in a 1:1 ratio (2,3, and 6). These sensors bind metal ions in a 1:1 ratio (7 and 8), and the optical properties of the new complexes were examined and the sulfur and selenium analogues show that selectivity for Pb(II) is markedly improved as compared to the oxygen analogue 1 which was competitive for Ca(II) ion.

Selective reduction of 1 yields secondary alcohols where either one or both of the anthraquinone carbonyl groups has been reduced ( 15 and 9). A new mechanism for the fluorescence detection of metal cations in solution is introduced involving a unique keto-enol tautomerization. Reduction of 1 yields the doubly reduced secondary alcohol, 9. 9 acts as a chemodosimeter for Al(III) ion producing a strong blue emission due to the formation of the anthracene fluorophore, 10, via dehydration of the internal secondary alcohol in DMSO/aqueous solution. The enol form is not the most thermodynamically stable form under these conditions however, and slowly converts to the keto form 11.

Currently we are focusing on cucurbituril derivatives, also described as molecular clips due to their folded geometry used as molecular recognition hosts. We first investigated the synthesis and characterization of aromatic methoxy/catechol terminated cucurbituril units that act as hosts for small solvent molecules, such as CH₂Cl₂, CH₃CN, DMF, and MeOH, through dual pi…H-C T-shaped interactions. We have calculated the single-point interaction energies of these non-covalent interactions and compared them to the dihedral angle formed from the molecular clip. We have also synthesized a molecular clip that contains terminal chelating phenanthroline ligands. This tetradentate ligand shows 2:3 metal:ligand binding with Fe(II) and 1:2 metal:ligand binding with Co(II) and Ni(II) cations.

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Martínez, Rodríguez Luis. « Molecule and catalyst design for recognition and activation of small molecules ». Doctoral thesis, Universitat Rovira i Virgili, 2016. http://hdl.handle.net/10803/398693.

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17

Jiang, Yu-Lin. « Molecular recognition of biotin derivatives / ». Title page, contents and abstract only, 1999. http://web4.library.adelaide.edu.au/theses/09PH/09phj5998.pdf.

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Mackay, Joel Peter. « Probing molecular recognition in nature ». Thesis, University of Cambridge, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.318437.

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Tovilla, Cao-Romero Jorge Alberto Francisco. « Molecular recognition with metal complexes ». Thesis, Imperial College London, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.436343.

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Moral, Natalia Perez. « Molecular recognition in polymeric microparticles ». Thesis, University of Reading, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.343068.

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Shimizu, Ken. « New scaffolds for molecular recognition ». Thesis, Massachusetts Institute of Technology, 1995. http://hdl.handle.net/1721.1/32677.

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Conn, Michael Morgan. « Molecular recognition of adenosine derivatives ». Thesis, Massachusetts Institute of Technology, 1994. http://hdl.handle.net/1721.1/17346.

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Hollfelder, Florian. « Molecular recognition of transition states ». Thesis, University of Cambridge, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.624786.

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Mountford, Christopher Paul. « Molecular recognition with DNA nanoswitches ». Thesis, University of Edinburgh, 2008. http://hdl.handle.net/1842/12121.

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This thesis describes an investigation of the use of DNA junctions as functional nanoswitches, capable of molecular recognition tasks in nucleic acids. The topological branch point allows a conformational change from a planar, open structure to a closed conformation which allows the junction arms to stack. A stable nanoswitch was designed which formed a complete cruciform structure only when hybridised to a complementary target. Introduction of single base mismatches in the target at the nanoswitch branch point caused changes in FRET efficiency, depending upon the mismatch in question. This methodology was shown to be applicable to both DNA and RNA target sequences. The structural origins of these changes in FRET efficiency were then investigated using time-resolved fluorescence spectroscopy. Donor florescence decays were fitted using an assumption of a Gaussian distribution form for the fluorophore separation. The results showed a maximal change in peak position of 10 Angstroms, illustrating the sensitivity of these devices. The fluorescent analogue of adenine, 2-amino purine (2AP), was used as s direct probe of the branch point structure. Finally, a high throughput analysis mechanism was demonstrated. This used a fluorescence lifetime plate reader to obtain donor fluorescence decays for numerous samples in a short exposure time, which were used to determine the nanoswitch conformation. This method was initially shown to be applicable to DNA nanoswitches, with the use of FLIM also demonstrated, before the method was shown to be useful for distinguishing single base mismatches. Using a time-resolved approach has the benefit of being independent of local sample concentration, ideal for nanotechnology applications. These nanoswitches have been shown to be promising prototype molecular recognition devices.

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Gong, Yun. « Molecular Recognition at the Membrane ». The Ohio State University, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=osu1261499732.

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Steele, John. « Molecular recognition in plant immunity ». Thesis, University of East Anglia, 2016. https://ueaeprints.uea.ac.uk/58564/.

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Plant pathogens constitute a major threat to global food security. The use of naturally resistant crop varieties can limit crop losses, however new races of pathogen can arise that are able to overcome these defences. Plant breeding for race-specific resistance typically relies on disease-resistance genes, which generally encode proteins with nucleotide-binding and leucine-rich repeat domains (NB-LRRs). NB-LRRs are a large of proteins found in both plants and animals, with plant NB-LRRs further classified by the presence of N-terminal coiled-coil or toll-interleukin receptor domains. Although qualitative models exist to describe R-protein regulation and activation, these are predominantly based on genetic and molecular studies. Biochemical investigations into R-protein function have been hampered by difficulties obtaining sufficient yields of material. When suitable material has been identified, biochemical studies have been used to complement well-established in planta assays to validate numerous hypotheses. This work describes the screening processes undertaken to obtain R-protein domains suitable for downstream experiments. Using E. coli for high-throughput screening of constructs from a single R-protein, traditional construct design to investigate multiple R-protein domains and expanding our expression hosts to eukaryotic systems we successfully purified four coiled-coil domains and a single NBARC domain for use in downstream experiments. Characterisation of this NBARC domain by circular dichroism and small-angle X-ray scattering indicates that the protein is well-folded and stable in solution, allowing in vitro investigations. In testing models for R-protein regulation we were able to confirm previous findings, such as low levels of ATPase activity, however we were unable to find evidence for a commonly cited method of signal repression. A preliminary crystal structure of the NBARC domain shows significant similarity to Apaf-1, and highlights the importance of conserved motifs in NBARC architecture. The tools presented here should prove a valuable resource to complement existing models to better understand the structure, biochemistry, and ultimately regulation of plant R-proteins.

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Grotzfeld, Robert M. (Robert Martin). « Studies in molecular recognition : self-assembling molecular host-guest sytems ». Thesis, Massachusetts Institute of Technology, 1996. http://hdl.handle.net/1721.1/10865.

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Schauenburg, Andrea J. A. « Molecular mechanisms underlying pMHC-II recognition ». Thesis, Cardiff University, 2016. http://orca.cf.ac.uk/96291/.

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The immune system is a complex network of cells and molecules working together with the purpose of fending off potentially harmful pathogens. CD4+ T cells take key roles within this network by orchestrating a multitude of its players. They recognise pathogen or self-derived peptides (p) bound to molecules of the major histocompatibility class II (MHC-II) through their T cell receptor (TCR). Cytokines secreted in response to recognition aid antibody production and cytotoxic T cell activity, both critical for anti-viral immunity. In this thesis, TCR/pMHC-II interactions were investigated using a range of functional and molecular approaches in order to gain valuable insight into the mechanisms underlying successful antigen recognition. To aid these investigations, a versatile, insect cell based expression system for HLA-DR1 was successfully implemented to generate soluble protein for use in multimer stainings and biophysical assays. Two HLA-DR1 restricted peptides encoded within influenza heamagglutinin (HA) were confirmed as being highly conserved making them ideal targets for vaccine development and allowing identification of influenza specific CD4+ T cells. Furthermore, the various roles of peptide flanking residues (PFR) were investigated using two experimental models. In a HA derived peptide, C-terminal PFR proved essential for peptide binding stability to HLA-DR1 and in consequence, CD4+ T cell activation. Clonotyping of CD4+ T cells grown against peptides of varying PFR lengths showed that TCR gene selection was heavily influenced by PFR. A HIV gag24 derived peptide displaying an unusual secondary structure within its N-terminal PFR gave further insight into how seemingly small modifications to PFR can have wide reaching impact on CD4+ T cell activation. Both studies highlighted the need for more in depths investigations into this emerging field and the wide reaching impacts of this inherent feature of MHC-II restricted peptides. Overall, the results in this thesis added novel insight into the mechanisms underlying TCR/pMHC-II interactions.

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Beck, Elizabeth Rose. « Molecular recognition by novel macrocyclic compounds ». Thesis, University of Hull, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.337244.

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Dondi, Ruggero. « Directed metallisation using molecular recognition tools ». Thesis, University of Leicester, 2012. http://hdl.handle.net/2381/11030.

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During this thesis a new infrastructure of methods to template functional materials at specific sites in a DNA architecture using molecular recognition of specific DNA duplexes has been developed. The project focused on the use of naturally occurring duplex DNA and the Tollens’ reaction as a mild source of metal amenable to reduction in the presence of aldehyde functional groups. The advantages of this choice are: 1) The use of naturally-occurring DNA increases modularity; 2) The Tollens’ reagent acts as a mild selective metallising reagent that enables the reduction of metal ions at specific sites along DNA. Molecules such as Pyrrole-Imidazole polyamides were prepared and were tested to determine whether selective metallisation of DNA nano-architectures can be achieved by confining the nucleation and growth of silver nanostructures to defined regions along a DNA duplex.

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31

Huxley, Allen John McAllister. « Switches based on molecular recognition processes ». Thesis, Queen's University Belfast, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.322948.

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Stanley, Simon Mark. « Molecular imprinting for sensor recognition elements ». Thesis, Nottingham Trent University, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.271781.

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Hubbard, Simon Jeremy. « Analysis of protein-protein molecular recognition ». Thesis, University College London (University of London), 1991. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.360151.

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34

Wang, Changnan. « Gel phase transition and molecular recognition ». Thesis, Massachusetts Institute of Technology, 1997. http://hdl.handle.net/1721.1/43921.

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Miller, Kiley Preston-Halfmann. « Molecular recognition of chlorine-doped polypyrrole ». Thesis, Massachusetts Institute of Technology, 2005. http://hdl.handle.net/1721.1/33864.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Biological Engineering Division, 2005.
Vita.
Includes bibliographical references (p. 108-111).
The objective of this work is to functionalize an existing polymer such that it better mimics natural tissue for tissue growth and regeneration. Numerous other processes have tried and accomplished this by non-specific protein adsorption, covalent attachment, biomolecule entanglement, and synthesis of new polymers with the desired functionality. The focus of this work is to modify the polymer's binding capability to cells while not altering the bulk properties. Through the use of both phage display of peptide libraries and yeast surface display of scFv libraries the surface of chlorine-doped polypyrrole (PPyCl) has been modified to facilitate binding of neuronal phenotype cells. The selection of peptides using phage display found a surface specific recognition peptide (T59) that was made bivalent by altering the C-terminus with an integrin binding epitope. The bivalency of the modified T59 peptide was exploited to tether phenochromocytoma (PC12) cells to the surface of PPyCl. Furthermore the tethering of the cells to PPyCl through the peptide does not decrease the cells neuronal function and maintains the bulk conductive polymers characteristics. Using the peptide as a bivalent linker, the addition of other types of cells, drugs, growth factors, and enzymes could be incorporated for various biomedical applications.
(cont.) An antibody (Y2) specific to PPyC1 was found using yeast surface display. This antibody was utilized to mediate cellular binding to PPyCl by expression of the antibody on the surface of PC12 cells. Complimenting the peptide studies of having an exterior bivalent linker the antibody recognition provides the means for any cell type to adhere to PPyCl, through expression of the antibody on the surface of the cell. This type of system could be used for various types of tissue growth supports.
by Kiley Preston-Halfmann Miller.
Ph.D.

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Park, Tae Kyo. « Molecular recognition of nucleic acid components ». Thesis, Massachusetts Institute of Technology, 1992. http://hdl.handle.net/1721.1/13113.

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Beauregard, Daniel Aaron. « Molecular recognition by vancomycin-group antibiotics ». Thesis, University of Cambridge, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.627484.

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Epa, Kanishka Navodh. « Understanding and fine tuning molecular recognition ». Diss., Kansas State University, 2013. http://hdl.handle.net/2097/16239.

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Doctor of Philosophy
Department of Chemistry
Christer B. Aakeröy
Co-crystallization allows the manipulation of physical properties of a given compound without affecting its chemical behavior. The ability to predict hydrogen bonding interactions, provides means to the rational design of supramolecular architectures. It also makes it possible to select with a degree of accuracy, a few co-formers that have a high probability of forming co-crystals with a compound of interest, instead of blindly screening against a large number of candidates. To study the effects of changing electronic environment on the ability to form co-crystals, five symmetric dioximes of different hydrogen bond donating ability were synthesized with different functional groups on the carbon α to the oxime moiety. It was shown that the supramolecular yield increase with the positive MEP value on the donor site. In order to further explore this relationship between calculated MEP values and supramolecular selectivity three asymmetric ditopic donors containing phenol carboxylic acid and aldoxime groups were screened against a series of asymmetric ditopic acceptors. Nine crystal structures show that the supramolecular outcome can be predicted according to Etter’s rules by ranking donors and acceptors according to calculated MEP values. To explore the possibility of using the same approach with other hydrogen bond donors, three asymmetric ditopic donor ligands containing cyanooxime groups were synthesized and screened against a series of asymmetric ditopic acceptors. Nine out of ten times the supramolecular outcome could be predicted by MEP calculations 1-deazapurine exists in two tautomeric forms (1H and 3H) in aqueous solution, which have very different hydrogen bonding environments. The 3H tautomer forms a self-complementary dimer involving a donor and an acceptor site leaving a second acceptor site vacant. In order to stabilize this tautomer the molecule was screened against a of series hydrogen and halogen bond donors. Four out of five structures obtained showed 3H tautomer. The 1H tautomer is the geometric complement of urea. Therefore the molecule was screened against a series of N,N-diphenylureas and all five structures showed the 1H tautomer.

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Daldrop, Peter. « Structure and molecular recognition in riboswitches ». Thesis, University of Dundee, 2011. https://discovery.dundee.ac.uk/en/studentTheses/db338d42-75c1-43a6-be6a-11399f04989e.

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Riboswitches are cis-acting gene regulatory RNAs, which function without involvement of proteins. They have been implicated as drug targets and are attractive systems for the study of RNA-ligand binding and RNA folding. The purine riboswitch was used as a model system for RNA-ligand docking. Published binding data was successfully reproduced in silico and compounds predicted to bind the riboswitch in a virtual screening were tested experimentally. Structural data confirming the predicted binding mode for several cases was obtained. The problems encountered were not specific to RNA-ligand docking but known from the far more explored field of protein-ligand docking.The SAM-I riboswitch was also subjected to virtual ligand screening. This receptor is a system of greater complexity than the purine riboswitch and consequently posed a harder challenge to the docking protocol. After initial validation of the docking setup based on previously published data, a set of compounds selected from the in-house database of commercially available compounds was screened. One compound identfied in silico was cofirmed to bind experimentally.The k-turn motif found in the SAM-I riboswitch was investigated with respect to its folding. The k-turn motif was found to be foldable in context of the SAMI riboswitch as well as in isolation as was expected. Furthermore, mutations disrupting key interactions within the k-turn motif were found to be prohibitive of k-turn folding in isolation as well as in context of the riboswitch, leading to a loss of ligand binding. Interestingly, two sequences were identfied which fold in context of the riboswitch but do not fold in isolation. This confirms the contribution of tertiary interactions to k-turn folding. This conclusion was backed up with structural data is a system of greater complexity than the purine riboswitch and consequently posed a harder challenge to the docking protocol. After initial validation of the to its folding. The k-turn motif was found to be foldable in context of the SAMI riboswitch as well as in isolation as was expected. Furthermore, mutations disrupting key interactions within the k-turn motif were found to be prohibitive of k-turn folding in isolation as well as in context of the riboswitch, leading to a loss of ligand binding. Interestingly, two sequences were identi ed which fold in context of the riboswitch but do not fold in isolation. This con rms the contribution of tertiary interactions to k-turn folding. This conclusion was backed

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40

Fortugno, Cecilia <1986&gt. « Multimethodological study of molecular recognition phenomena ». Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2014. http://amsdottorato.unibo.it/6376/1/fortugno_cecilia_tesi.pdf.

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The study of the bio-recognition phenomena behind a biological process is nowadays considered a useful tool to deeply understand physiological mechanisms allowing the discovery of novel biological target and the development of new lead candidates. Moreover, understanding this kind of phenomena can be helpful in characterizing absorption, distribution, metabolism, elimination and toxicity properties of a new drug (ADMET parameters). Recent estimations show that about half of all drugs in development fail to make it to the market because of ADMET deficiencies; thus a rapid determination of ADMET parameters in early stages of drug discovery would save money and time, allowing to choose the better compound and to eliminate any losers. The monitoring of drug binding to plasma proteins is becoming essential in the field of drug discovery to characterize the drug distribution in human body. Human serum albumin (HSA) is the most abundant protein in plasma playing a fundamental role in the transport of drugs, metabolites and endogenous factors; so the study of the binding mechanism to HSA has become crucial to the early characterization of the pharmacokinetic profile of new potential leads. Furthermore, most of the distribution experiments carried out in vivo are performed on animals. Hence it is interesting to determine the binding of new compounds to albumins from different species to evaluate the reliability of extrapolating the distribution data obtained in animals to humans. It is clear how the characterization of interactions between proteins and drugs determines a growing need of methodologies to study any specific molecular event. A wide variety of biochemical techniques have been applied to this purpose. High-performance liquid affinity chromatography, circular dichroism and optical biosensor represent three techniques that can be able to elucidate the interaction of a new drug with its target and with others proteins that could interfere with ADMET parameters.

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41

Fortugno, Cecilia <1986&gt. « Multimethodological study of molecular recognition phenomena ». Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2014. http://amsdottorato.unibo.it/6376/.

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The study of the bio-recognition phenomena behind a biological process is nowadays considered a useful tool to deeply understand physiological mechanisms allowing the discovery of novel biological target and the development of new lead candidates. Moreover, understanding this kind of phenomena can be helpful in characterizing absorption, distribution, metabolism, elimination and toxicity properties of a new drug (ADMET parameters). Recent estimations show that about half of all drugs in development fail to make it to the market because of ADMET deficiencies; thus a rapid determination of ADMET parameters in early stages of drug discovery would save money and time, allowing to choose the better compound and to eliminate any losers. The monitoring of drug binding to plasma proteins is becoming essential in the field of drug discovery to characterize the drug distribution in human body. Human serum albumin (HSA) is the most abundant protein in plasma playing a fundamental role in the transport of drugs, metabolites and endogenous factors; so the study of the binding mechanism to HSA has become crucial to the early characterization of the pharmacokinetic profile of new potential leads. Furthermore, most of the distribution experiments carried out in vivo are performed on animals. Hence it is interesting to determine the binding of new compounds to albumins from different species to evaluate the reliability of extrapolating the distribution data obtained in animals to humans. It is clear how the characterization of interactions between proteins and drugs determines a growing need of methodologies to study any specific molecular event. A wide variety of biochemical techniques have been applied to this purpose. High-performance liquid affinity chromatography, circular dichroism and optical biosensor represent three techniques that can be able to elucidate the interaction of a new drug with its target and with others proteins that could interfere with ADMET parameters.

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Triulzi, Robert C. « Nanotechnology for Molecular Recognition of Biological Analytes ». Scholarly Repository, 2009. http://scholarlyrepository.miami.edu/oa_dissertations/195.

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Nanotechnology is a term used to describe nanometer scaled systems. This thesis presents various nanomaterials and systems for the investigation of biologically relevant analytes in general, and in particular for their detection, decontamination, or destruction. The validation of short peptide fragments as models for protein aggregation is initially discussed through applying spectroscopic and microscopic techniques to Langmuir monolayer surface chemistry. Following this validation, the use of nanogold as a photoablative material for the destruction of aggregated protein is investigated. Subsequently, the versatility of nanotechnology is shown by investigating a different form of nanogold; namely, gold quantum dots and the interesting phenomenon that arise when dealing with materials on a nanoscale. Experiments involving a complex between these gold quantum dots and an antibody are performed for the detection of an immunoglobulin in solution. The power of this analytical technique is highlighted by the capability of detecting the analyte at nanomolar concentrations. Finally, a limitation-the multiple synthetic steps necessary for imparting biological activity-- of quantum dots is addressed: a single step reaction is studied that allows for direct stabilization and conjugation of quantum dots with proteins and enzymes. As a representative application of the above mentioned procedure, the detection and decontamination of an organophosphorus compound is explored. In general, methods for overcoming limitations of nanoparticles and nanocrystals are discussed.

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Zanardelli, Sara. « ADAMTS13 : molecular recognition of Von Willebrand factor ». Thesis, Imperial College London, 2006. http://hdl.handle.net/10044/1/8241.

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44

Mortishire-Smith, Russell Julian. « Structural and molecular recognition studies on peptides ». Thesis, University of Cambridge, 1990. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.359832.

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45

Gerhard, Ute. « Molecular recognition studies on vancomycin group antibiotics ». Thesis, University of Cambridge, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.259725.

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46

Jiranusornkul, Supat. « Molecular modelling studies of DNA damage recognition ». Thesis, University of Nottingham, 2008. http://eprints.nottingham.ac.uk/11303/.

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How DNA repair proteins search and recognise the rare sites of damage from the massive numbers of normal DNA remains poorly understood. FapydG (2,6-diamino-4-hydroxy-5-formamidopyrimidine) is one of the most prevalent guanine derived lesions involving opening of the imidazole ring. It is typically repaired by formamidopyrimidine-DNA glycosylase (Fpg) as an initial step in base excision repair; if not repaired, the lesion generates a G: C -+ T: A transversion. Unfortunately, studies on the recognition of FapydG have been hindered by difficulties to synthesise and incorporate the FapydG residue into a DNA duplex. Crystal structures of Fpg-DNA complexes have demonstrated three common recognition events: the protein specifically binding to the extrahelical lesion, bending DNA centred on the damaged base, and flipping the damage into the pocket. Thus, molecular modelling and dynamics simulation have been used to gather dynamical information of those recognition events for damaged and undamaged DNA. The simulations were initially performed when FapydG or G occurs in several dodecamer B-DNA sequences in aqueous solution, then inside the lesion-recognition pocket of Fpg, and during the flipping pathway from the helical stack to an extrahelical position. The influence of the damage on DNA stability and flexibility was first investigated. Energetic analysis revealed that damage to DNA does appear to destabilise the duplex. DNA curvature analysis and a novel combined method of the principal component analysis (PCA) and the Mahalanobis distance (DM) indicated that damaged DNA can adopt the observed protein-bound conformation with lower energetic penalties than its normal counterpart. Results of these studies have provided the validation of DNA bending enhancement by the FapydG lesion. It also suggested that intrinsic DNA bending could be a principal element of how the repair protein locates the lesion from vast expanse of normal bases. Considering the specific recognition of FapydG by Fpg, the aF-/39 loop of the Fpg enzyme may function as a gatekeeping to accommodate the lesion while denying the normal base. Remarkably fluctuating movement of the flipped G residue and the aF-ß9 loop is due to the formation of the non-specific Fpg/G complex with a lower binding energy by 8.4 kcal/mol compared to the specific Fpg/FapydG complex. Free-energy profiles for both damaged and undamaged base flipping were generated from the umbrella sampling simulations and the Weight Histogram Analysis Method (WHAM). An energy barrier for flipping the damage out from the helix is 2.7 kcal/mol higher than its equivalent G and the lesion is highly stabilised inside the pocket. In contrast, G flipping seems to be rapidly rotated out and into the duplex without the formation of a specific complex. These studies could unravel a potentially comprehensive process of the repair protein to find and recognise the lesion through the slow kinetic pathway in which the more deformable damaged DNA is initially located by the protein; the protein subsequently compresses the duplex into an appropriate angle and direction to form a specific protein-DNA complex prior to being flipped and repaired.

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Madigan, Evelyn. « Synthesis of novel calixarenes for molecular recognition ». Thesis, Queen's University Belfast, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.238988.

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48

Hamann, Blake. « Ureas in molecular recognition : complexation and encapsulation ». Thesis, Massachusetts Institute of Technology, 1996. http://hdl.handle.net/1721.1/38781.

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Zhang, Jingqing Ph D. Massachusetts Institute of Technology. « Molecular recognition using nanotube-adsorbed polymer complexes ». Thesis, Massachusetts Institute of Technology, 2012. http://hdl.handle.net/1721.1/79193.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, February 2013.
Cataloged from PDF version of thesis. "December 2012."
Includes bibliographical references (p. 234-249).
We first reported the selective detection of single nitric oxide (NO) molecules using a specific DNA sequence of d(AT) 15 oligonucleotides, adsorbed to an array of near infrared fluorescent semiconducting single-walled carbon nanotubes (AT₁₅-SWCNT). While SWNT suspended with eight other variant DNA sequences show fluorescence quenching or enhancement from analytes such as dopamine, NADH, L-ascorbic acid, and riboflavin, d(AT)₁₅ imparts SWNT with a distinct selectivity toward NO. In contrast, the electrostatically neutral polyvinyl alcohol, enables no response to nitric oxide, but exhibits fluorescent enhancement to other molecules in the tested library. For AT₁₅ - SWCNT, a stepwise fluorescence decrease is observed when the nanotubes are exposed to NO, reporting the dynamics of single-molecule NO adsorption via SWCNT exciton quenching. We describe these quenching traces using a birth-and-death Markov model, and the maximum likelihood estimator of adsorption and desorption rates of NO is derived. Applying the method to simulated traces indicates that the resulting error in estimation is less than 5% under our experimental conditions, allowing for calibration using a series of NO concentrations. As expected, the adsorption rate is found to be linearly proportional to NO concentration, and the intrinsic single-SWCNT-site NO adsorption rate constant is 0.001 s-¹ [mu]M NO-¹. The ability to detect nitric oxide quantitatively at the single-molecule level may find applications in new cellular assays for the study of nitric oxide carcinogenesis and chemical signaling, as well as medical diagnostics for inflammation. Further, we also explored the concept of creating molecular recognition sites using polymer-SWCNT complexes. Molecular recognition is central to the design of therapeutics, chemical catalysis and sensor platforms, with the most common mechanisms involving biological structures such as antibodies[l] and aptamers[2, 3]. The key to this molecular recognition is a folded and constrained heteropolymer pinned, via intra-molecular forces, into a unique three-dimensional orientation that creates a binding pocket or interface to recognize a specific molecule. An alternate approach to constraining a polymer in three-dimensional space involves adsorbing it onto a cylindrical nanotube surface[4-7]. To date, however, the molecular recognition potential of these structured, nanotube-associated complexes has been unexplored. In this work, we demonstrate three distinct examples in which synthetic polymers create unique and highly selective molecular recognition sites once adsorbed onto a single-walled carbon nanotube (SWCNT) surface. The phenomenon is shown to be generic, with new recognition complexes demonstrated for riboflavin, L-thyroxine, and estradiol, predicted using a 2D thermodynamic model of surface interactions. The dissociation constants are continuously tunable by perturbing the chemical structure of the heteropolymer. The complexes can be used as new types of sensors based on modulation of SWCNT photoemission, as demonstrated using a complex for real time spatio-temporal detection of riboflavin in murine macrophages. Cardiac biomarkers troponin I and T are recognized as standard indicators for acute myocardial infarction (AMI, or heart attack), a condition that comprises 10% of U.S. emergency room visits [8]. There is significant interest in a rapid, point-of-cae (POC) device for troponin detection[9]. In this work we demonstrate a rapid, quantitative, and label-free assay specific for cardiac troponin T detection, using fluorescent single-walled carbon nanotubes (SWCNTs). Chitosan-wrapped carbon nanotubes are crosslinked to form a thin gel that is further functionalized with nitrilotriacetic acid (NTA) moieties. Upon chelation of Ni²+, the Ni²+ -NTA group binds to a hexa-histidine-modified troponin antibody, which specifically recognizes the target protein, troponin T. As the troponin T binds to the antibody, the local environment of the sensor changes, allowing for the detection through changes in SWCNT bandgap fluorescence intensity. In this work, we have developed the first near-infrared SWCNT sensor array for specific cTnT detection. Detection can be completed within 3 minutes, and the sensor responds linearly to the cTnT concentrations, with the experimental detection limit of 100 ng/ml (2.5 nM). This platform may provide a promising new tool for POC AMI detection in the future. Moreover, the work presented two useful methods of characterizing two commonly used functional groups, amines and carboxylic acids in soft gels, and this will be useful for other researchers studying hydrogel chemistry. In addition, we synthesized and characterized chitosan-gels both with and without NTA groups, and we compared fluorescence responses upon the addition of four different divalent cations, including Ni²+ , CO², Mg²+, and Mn²+. We proposed a model based Flory-Huggins theory, without any fitted parameters, that is able to describe the fluorescence increase as the Ni²+ concentration increases. The model suggests that the strong binding of Ni²+ onto NTA groups decreases the number of mobile ions in the gel, resulting in a reduction in the ionic chemical potential inside the gel. As a result, the gel de-swells, leading to a local SWCNT concentration increase and an increase in the SWCNT fluorescence signal.
by Jingqing Zhang.
Ph.D.

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Wintner, Edward Aurel. « Molecular recognition through rational and combinatorial synthesis ». Thesis, Massachusetts Institute of Technology, 1996. http://hdl.handle.net/1721.1/40168.

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