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Dissertations / Theses on the topic 'Study of protein-ligand interactions'

Author: Grafiati

Published: 4 June 2021

Last updated: 8 February 2022

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1

Abboud, Martine. "Using NMR to study protein-ligand interactions." Thesis, University of Oxford, 2016. https://ora.ox.ac.uk/objects/uuid:a4aa5995-625a-4814-8c91-e0114c1e2004.

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The work described in this thesis focused on the use of nuclear magnetic resonance spectroscopy (NMR) to study two classes of metallo enzymes - the Fe(II)- and 2oxoglutarate (2OG)-dependent dioxygenases and the metallo β-lactamases (MBLs). These enzymes are involved in clinically important biological processes, i.e. the hypoxic response and antimicrobial resistance, respectively. Both protein systems are interesting from an NMR perspective because they have dynamic regions involved in catalysis and ligand interactions. The work included mechanistic studies, protein-ligand interaction studies,

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2

Pearson, Joshua Thomas. "A biophysical study of protein dynamics and protein-ligand interactions /." Thesis, Connect to this title online; UW restricted, 2006. http://hdl.handle.net/1773/8173.

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3

Choy, Desmond Chun Yu. "Haemoproteins and the study of protein-ligand interactions." Thesis, University of Cambridge, 2015. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.709179.

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4

Martínez-Jiménez, Francisco 1988. "Structural study of the therapeutic potential of protein-ligand interactions." Doctoral thesis, Universitat Pompeu Fabra, 2016. http://hdl.handle.net/10803/565402.

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Most of the cellular functions are driven by small-molecules that selectively bind to their protein targets. Is such their importance, that the pharmacological intervention of proteins by small molecule drugs is frequently used to treat multiple conditions. Herein I present a thesis that leverages a threedimensional study of small molecule protein interactions to improve their therapeutic relevance. More specifically, it introduces nAnnolyze, a method for predicting structurally detailed protein-ligand interactions at proteome scale. The method exemplified its applicability by predictin

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5

Morris, Daniel L. "NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY IN THE STUDY OF PROTEIN-LIGAND INTERACTIONS." University of Akron / OhioLINK, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=akron1524681449524557.

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6

Green, Roderic charles Edward. "A computational study of protein-protein and protein-ligand interactions : A focus on HNF4a and ATP synthase." Thesis, University of Surrey, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.533173.

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7

Brown, Marc B. "The use of long wavelength fluorescence in the study of ligand-protein interactions." Thesis, Loughborough University, 1993. https://dspace.lboro.ac.uk/2134/12677.

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The binding of a drug or other ligand to plasma proteins can effect their absorption, metabolism and excretion which can lead to a change in its toxicity and therapeutic action. Fluorescence is a technique that has been used to study such interactions and has the advantages of extreme sensitivity and specificity. Previously fluorescence has been monitored in the UV /vis range of the spectrum. However, a new development is long wavelength fluorescence (600-1000nm), which has the added benefits of a lower background, decreased scattering, decreased photodecomposition and the availability of inex

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8

Williamson, Philip Thomas Franklin. "The application of solid state nuclear magnetic resonance to the study of ligand protein interactions." Thesis, University of Oxford, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.302109.

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9

Lampinen, Milla. "AMPA receptor ligand-binding domain : site-directed mutagenesis study of ligand-receptor interactions." Helsinki : University of Helsinki, 2003. http://ethesis.helsinki.fi/julkaisut/mat/bioti/vk/lampinen/.

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10

Zenonos, Zenon. "Applying recombinant protein technology to study Plasmodium falciparum erythrocyte receptor-ligand interactions and their potential as therapeutic targets." Thesis, University of Cambridge, 2014. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.648790.

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11

Lapenna, Silvia. "A study of the ligand-receptor interactions of ecdysteroids." Thesis, University of Exeter, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.441813.

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12

Dyachenko, Andrey. "Molecular recognition in gas phase: theoretical and experimental study of non-covalent protein-ligand complexes by mass-spectrometry." Doctoral thesis, Universitat de Barcelona, 2013. http://hdl.handle.net/10803/113301.

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In the present thesis we have explored different factors that impede accurate quantitative description of non-covalent protein-protein and protein-ligand interactions and design of new potent and specific binders from the scratch. Firstly, we addressed the role of solvent in the mechanism of non-covalent interactions. Secondly, we tackled the question about the intrinsic conformational flexibility of the protein molecules and the part it plays in weak interactions between proteins. In the first part of the thesis we studied the interactions of vascular endothelial growth factor (VEGF) prot

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13

García-García, Javier 1982. "Protein-protein interaction network : management of databases and its applications on the computational study of protein-protein interactions." Doctoral thesis, Universitat Pompeu Fabra, 2015. http://hdl.handle.net/10803/286512.

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The use of protein-protein interaction networks has become crucial due to the emergence of systems biology. The completeness and quality of networks, crucial to understand the biochemical mechanisms underlying a system such as a cell, are still challenging the scientific community. This thesis focuses on the data completeness challenge by the development of flexible tools for biological data management. It presents a database framework, BIANA, in which the integrated access to several information sources tackles this problem by unraveling hidden biological associations. BIANA is used to develo

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14

Bastidas, Oscar. "Computational Study of Protein-Protein Interactions in Misfolded States." VCU Scholars Compass, 2014. http://scholarscompass.vcu.edu/etd/3521.

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Protein-protein interactions (PPI’s) play important roles in biological systems. In particular, intra-protein interactions help create and maintain correctly folded protein states and mutations that result in misfolded states may be associated with significant changes in PPI behavior. Six unrelated protein systems with known structure files, each consisting of a wild-type and mutant strain, were studied using the computational algorithm OpenContact©. OpenContact© is a simple tool that can be used to rapidly identify or map interactions “hot-spots” in a protein and was, consequently, used in th

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15

Callaghan, J. M. "The study of chromodomain protein interactions." Thesis, University of Cambridge, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.597229.

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The packaging of DNA into chromatin is not merely a means by which DNA is confined within the cell, moreover, it also provides a mechanism by which gene expression is regulated. How eukaryotic genomes are manipulated within the chromatin environment is a fundamental biological issue in which the histone proteins and the proteins that interact with them, play a key role. This thesis describes the biochemical and biophysical characterisation of four chromodomain proteins, the chromodomain and the shadow chromodomain of Heterochromatin Protein 1 (HP1) and the chromodomains of the Polycomb protein

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16

Morell, Fernández Montserrat. "Protein reporters to study in vivo protein interactions and aggregation." Doctoral thesis, Universitat Autònoma de Barcelona, 2008. http://hdl.handle.net/10803/3593.

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L'objectiu dels dos primers capítols va ser l'aplicació de la tècnica "Bimolecular fluorescent protein complementation" (BIFC) per a detectar interaccions intracel·lulars proteiques de caràcter dèbil in vivo. Durant l'estudi s'ha demostrat que es pot acoblar a la citometria de flux creant una eina d'anàlisi proteòmica. D'altra banda, també es demostra que l'emissió de fluorescència depèn de la força de la interacció. A més a més, el mètode BIFC pot ser aplicat per a obtenir informació sobre la superfície d'interacció. D'altra banda, es descriu l'ús de BIFC com a mètode per a detectar composto

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17

Dhayalan, Arunkumar [Verfasser]. "Study of protein-protein interactions in molecular epigenetics / Arunkumar Dhayalan." Bremen : IRC-Library, Information Resource Center der Jacobs University Bremen, 2009. http://d-nb.info/103472231X/34.

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18

Beard, Matthew Brian. "A study of protein-protein interactions involving Type 4 phosphodiesterase." Thesis, University of Glasgow, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.301782.

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19

McDonnell, S. J. "Study of novel protein-protein interactions modulating PERP-mediated apoptosis." Thesis, University of Liverpool, 2018. http://livrepository.liverpool.ac.uk/3023828/.

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20

Nguyen, Huynh Nha Thi. "Développements en spectrométrie de masse pour l’étude des complexes biologiques." Thesis, Strasbourg, 2015. http://www.theses.fr/2015STRAF045/document.

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L’élucidation des interactions non-covalentes des complexes biologiques revêt d’une importance majeure dans la compréhension du fonctionnement cellulaire. L’objectif de ce travail de thèse est d’approfondir les développements de la spectrométrie de masse (MS) pour l’étude de ces complexes, que ce soit par MALDI-MS (la désorption-ionisation laser assistée par matrice) ou par ESI-MS (l’ionisation électrospray). Ce travail s’est articulé autour de trois axes : i) étude de la stœchiométrie et de la topologie du complexe SAGA HAT (Spt-Ada-Gcn5 Acétyltransferase, module Histone Acétyl Transferase) p

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21

Watt, Stephen J. "Use of electrospray ionization mass spectrometry to study protein conformation and protein-protein interactions." Access electronically, 2005. http://www.library.uow.edu.au/adt-NWU/public/adt-NWU20060516.114814/index.html.

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Thesis (Ph.D.)--University of Wollongong, 2005.<br>Typescript. EMBARGOED-this thesis is subject to a six months embargo (07/09/06) and may only be viewed and copied with the permission of the author. For further information please Contact the Archivist. Includes bibliographical references: leaf 159-194.

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22

Ivanova, Vesselka Petrova. "Theoretical and experimental study of protein lipid interactions." Doctoral thesis, [S.l. : s.n.], 2000. http://deposit.ddb.de/cgi-bin/dokserv?idn=961248726.

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23

Formiggini, Fabio. "In vivo study of nuclear-localized protein-protein interactions in plant cells." Thesis, Open University, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.397908.

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24

Si, Chao. "Theoretical Study of Intermolecular Interactions in Protein-Drug Binding and Protein Folding." University of Toledo / OhioLINK, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=toledo1341632548.

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25

Dogra, Navneet. "INVESTIGATING PROTEIN - BILAYER COMPLEXES: A STUDY OF LIGAND - RECEPTOR INTERACTIONS AT MODEL MEMBRANE SURFACE BY USING ELECTRONIC ABSORPTION SPECTROSCOPY AND FLUORESCENCE RESONANCE ENERGY TRANSFER." OpenSIUC, 2014. https://opensiuc.lib.siu.edu/dissertations/812.

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The main aim of work presented here is to design, develop and characterize a colorimetric model membrane (liposome) systems, which can bind with proteins, enzymes, bacteria, virus and other biomolecules. PDA molecules are utilized as a scaffold for the bilayer membrane, and a colorimetric assay is carried out. The holy grail of present work contributes towards the better understanding of protein interactions with the cell bilayer surface. Chapter 1 introduces a brief history on the advent of bilayer systems for cellular research exploration. We presented a literature survey about how liposom

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26

Marín, López Manuel Alejandro 1987. "On the development of computational tools for the study of protein-protein interactions and protein-protein binding." Doctoral thesis, Universitat Pompeu Fabra, 2017. http://hdl.handle.net/10803/565599.

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Proteins are involved in almost all cell processes, with physical interaction between them being key to their function and dictated by its 3D structure. Hence, the study of protein-protein interactions and protein-protein binding is crucial to fully understand biological systems. In this thesis, we present V-D2OCK, a fast and accurate data-driven docking tool for high throughput prediction of the structure of protein complexes. We have also studied the conformational space of potential encounter complexes by means of non-specific decoys obtained by docking in order to develop BADock, an accura

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27

Sarkar, Mohosin M. "Engineering Proteins with GFP: Study of Protein-Protein Interactions In vivo, Protein Expression and Solubility." The Ohio State University, 2009. http://rave.ohiolink.edu/etdc/view?acc_num=osu1261418776.

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28

Douglas, Chanel Catherine. "A study into the protein/protein interactions involved in HIV-1 capsid assembly." Thesis, Birmingham, Ala. : University of Alabama at Birmingham, 2007. https://www.mhsl.uab.edu/dt/2008r/douglas.pdf.

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29

Bodmer, Nicholas. "Molecular Investigations into the Titin-Telethonin Complex: A study in Protein-Protein Interactions." University of Cincinnati / OhioLINK, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1439307071.

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30

Phillips, Gareth W. "A study on the interactions of the beta-spectrins." Thesis, University of Kent, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.263696.

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31

LoÌpez, DiÌez E. Consuelo. "A study on protein sugar interactions : implications for bioprotection." Thesis, Bangor University, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.247770.

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32

Huster, Daniel. "Solid-state NMR spectroscopy to study protein-lipid interactions." Universitätsbibliothek Leipzig, 2015. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-190961.

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The appropriate lipid environment is crucial for the proper function of membrane proteins. There is a tremendous variety of lipid molecules in the membrane and so far it is often unclear which component of the lipid matrix is essential for the function of a respective protein. Lipid molecules and proteins mutually influence each other; parameters such as acyl chain order, membrane thickness, membrane elasticity, permeability, lipid-domain and annulus formation are strongly modulated by proteins. More recent data also indicates that the influence of proteins goes beyond a single annulus of next

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33

Huster, Daniel. "Solid-state NMR spectroscopy to study protein-lipid interactions." Universität Leipzig, 2014. https://ul.qucosa.de/id/qucosa%3A14047.

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The appropriate lipid environment is crucial for the proper function of membrane proteins. There is a tremendous variety of lipid molecules in the membrane and so far it is often unclear which component of the lipid matrix is essential for the function of a respective protein. Lipid molecules and proteins mutually influence each other; parameters such as acyl chain order, membrane thickness, membrane elasticity, permeability, lipid-domain and annulus formation are strongly modulated by proteins. More recent data also indicates that the influence of proteins goes beyond a single annulus of next

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34

Yagnik, Asutosh Trilochan. "Molecular modelling applications in rational drug design and the study of enzyme-ligand interactions." Thesis, University of Exeter, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.245931.

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35

Patton, Randy Alexander. "Utilizing DNA Nanostructures for the study of the Force Dependency of Receptor – Ligand Interactions." The Ohio State University, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=osu1503071673023257.

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36

Bush, Derek B. "A Molecular Simulation Study of Antibody-Antigen Interactions on Surfaces for the Rational Design of Next-Generation Antibody Microarrays." BYU ScholarsArchive, 2017. https://scholarsarchive.byu.edu/etd/6631.

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Antibody microarrays constitute a next-generation sensing platform that has the potential to revolutionize the way that molecular detection is conducted in many scientific fields. Unfortunately, current technologies have not found mainstream use because of reliability problems that undermine trust in their results. Although several factors are involved, it is believed that undesirable protein interactions with the array surface are a fundamental source of problems where little detail about the molecular-level biophysics are known. A better understanding of antibody stability and antibody-antig

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37

Hinerman, Jennifer M. "The Study of Protein-Protein Interactions Involved in Lagging Strand DNA Replication and Repair." Connect to full text in OhioLINK ETD Center, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=toledo1216824884.

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Thesis (Ph. D.)--University of Toledo, 2008.<br>Typescript. "Submitted as partial fulfillment of the requirements for the Doctor of Philosophy in Chemistry." Includes bibliographical references (leaves 245-252).

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38

Zhang, Weiling. "A study of protein interactions by electrospray ionization mass spectrometry." Morgantown, W. Va. : [West Virginia University Libraries], 1999. http://etd.wvu.edu/templates/showETD.cfm?recnum=388.

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Thesis (M.S.)--West Virginia University, 1999.<br>Title from document title page. Document formatted into pages; contains viii, 72 p. : ill. (some col.). Includes abstract. Includes bibliographical references (p. 68-72).

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39

Oher, Hanna. "A combined ab initio and time-resolved laser-induced fluorescence study of uranium-ligand interactions." Thesis, Lille 1, 2020. http://www.theses.fr/2020LIL1R032.

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Les complexes d'uranyle ont fait l'objet de nombreux travaux de recherche pour la chimie fondamentale des actinides, les enjeux environnementaux ou les procédés du cycle du combustible nucléaire. La formation de divers complexes d'uranium(VI), avec des ligands en solution doit être caractérisée pour une meilleure compréhension de la spéciation de U(VI). Les interactions uranyl-ligand et la symétrie des complexes modifient la structure électronique de U(VI) et donc ses propriétés de luminescence. La spectrofluorimétrie laser résolue en temps (SLRT) est l'une des techniques largement utilisées p

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40

Beard, Hester Annie. "Affinity-guided chemical probes for the study of protein interactions." Thesis, University of Leeds, 2018. http://etheses.whiterose.ac.uk/20637/.

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Chemical methods that allow for the targeted labelling of a specific protein within a complex biological environment can enable valuable information regarding the structure and function of proteins to be gained. This thesis explores two different projects where affinity-guided chemical probes were used to study the interactions of proteins, both with small molecules (Chapter 2) and interacting protein partners (Chapter 3). Firstly, chemical labelling methods based on a recognition unit for the protein of interest are reviewed in Chapter 1. Then, Chapter 2 describes how a combination of chemica

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41

Meyer, Andrew James. "A calorimetric study of host-guest and protein-substrate interactions." Thesis, University of Leicester, 1997. http://hdl.handle.net/2381/30009.

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This thesis describes a study of molecular recognition processes involving - and - cyclodextrins, and the enzymes chloramphenicol acetyltransferase and DNA gyrase.;An isothermal titration calorimeter of high sensitivity was used to investigate the binding of a number of relatively small guest molecules with much larger host molecules. The calorimetric technique allows the direct determination of the apparent binding enthalpy bindH0', the evaluation of the apparent association constant Ka' and hence evaluation of the apparent Gibbs energy and entropy of binding, bindG0' and TbindS0'.;The energe

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42

Yin, Ming. "NMR study of interaction between cytochrome P450cam and putidaredoxin and structural study of cytochrome P450 3A4." Waltham, Mass. : Brandeis University, 2009. http://dcoll.brandeis.edu/handle/10192/23190.

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43

Aveiro, Susana Seabra. "The p22HBP heme binding protein: an NMR study of the dynamics and heme-protein interactions." Doctoral thesis, Universidade de Aveiro, 2015. http://hdl.handle.net/10773/14278.

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Doutoramento em Bioquímica<br>The work presented in this Thesis investigates the dynamics and molecular interactions of p22HBP and the p22HBP-tetrapyrrole complex. Specifically, the key residues involved when a tetrapyrrole binds to p22HBP were sought. Previous molecular modelling studies identified three possible charged residues R56, K64 and K177 as possibly being important in tetrapyrrole binding via electrostatic interactions with the propionate groups of the tetrapyrrole. A number of variants of murine p22HBP were therefore prepared and fluorescence quenching and NMR used to verify the in

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44

Seco, Martins Marques Neves João Filipe. "NMR study of 14-3-3 protein-protein interactions and modulation thereof by small molecules." Thesis, Lille, 2019. http://www.theses.fr/2019LIL1S108.

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Les protéines 14-3-3 sont des protéines adaptatrices qui exercent leurs fonctions biologiques en modulant l’activité de centaines d’autres protéines. De part leur impressionnant interactome, les protéines 14-3-3 sont des acteurs qui influencent de nombreux événements cellulaires et, par conséquent, de maladies associées. La stabilisation ou l’inhibition sélective d’interactions protéine-protéine (IPP) de 14-3-3 sont considérées comme des approches prometteuses pour trouver des thérapies innovantes contre des maladies comme la maladie d’Alzheimer, certains cancers ou la maladie de Parkinson.Not

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45

Bird, Antony Colin. "A study of the use of fractionation diagrams for the study of bioprocess interactions." Thesis, University College London (University of London), 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.312989.

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46

Dorward, Andrew John. "A study of process engineering interactions for protein recovery using crystallisation." Thesis, University College London (University of London), 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.407257.

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47

Bender, Shana Lynn. "A study of protein dynamics and cofactor interactions in Photosystem I." Diss., Atlanta, Ga. : Georgia Institute of Technology, 2008. http://hdl.handle.net/1853/26463.

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Thesis (Ph. D.)--Chemistry and Biochemistry, Georgia Institute of Technology, 2009.<br>Committee Chair: Barry, Bridette; Committee Member: Doyle, Donald; Committee Member: Kelly, Wendy; Committee Member: McCarty, Nael; Committee Member: Schimdt-Krey, Ingaborg. Part of the SMARTech Electronic Thesis and Dissertation Collection.

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48

Zhang, Xirui. "Dual-spectral interferometric sensor for quantitative study of protein-DNA interactions." Thesis, Boston University, 2014. https://hdl.handle.net/2144/19699.

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Thesis (Ph.D.)--Boston University<br>The maintenance and functions of the genome are facilitated by DNA-binding proteins, whose specific binding mechanisms are not yet fully understood. Recently, it was discovered that the recognition and capture ofDNA conformational flexibility and deformation by DNA-binding proteins serve as an indirect readout mechanism for specific recognition and facilitate important cellular functions. Various biophysical techniques have been employed to elucidate this conformational specificity of protein-DNA interactions. These techniques are not sufficiently high-thro

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49

Malmgren, Lisa M. "Using in situ click chemistry to modulate protein-protein interactions : Bcl-XL as a case study." [Tampa, Fla.] : University of South Florida, 2007. http://purl.fcla.edu/usf/dc/et/SFE0002233.

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50

Heseltine, Sophie Jane. "Developing a toolbox of Affimer reagents targeting SH2 domains to study protein-protein interactions in disease." Thesis, University of Leeds, 2019. http://etheses.whiterose.ac.uk/22642/.

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Src Homology 2 (SH2) domains are phosphotyrosine-binding modules that mediate a range of protein-protein interactions. These domains are found in over 120 human proteins and are involved in several signalling pathways that can become deregulated in diseases such as cancer. Research into the role of individual SH2s in disease has been hampered by a lack of protein-specific reagents available for intracellular functional assays. Specificity of reagents is difficult to achieve, due to the high sequence and structural homology of the domains. Research presented in this thesis investigates the use

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