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1
Romero, Durana Miguel Alfonso. "Improving the description of protein-protein association energy." Doctoral thesis, Universitat de Barcelona, 2018. http://hdl.handle.net/10803/665466.
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Proteins play a crucial role in virtually every biological process taking place within our cells. Most of the times, proteins do not participate in these processes alone but forming complexes of two or more proteins. Therefore, the study of protein-protein interactions (PPIs) and complex formation has become an important field of research in the last decades due to its scientific relevance and therapeutic interest. Protein docking is one of the several computational approaches that have been applied to study protein interactions over the last years. It aims to determine the three-dimensional structure of a protein complex based on the structure of its subunits. Although the field has experienced important advances in recent years, it faces significant challenges ahead. New strategies are necessary to overcome current sampling limitations and enhance the physico-chemical description of protein-protein association, understanding its intrinsic mechanisms and identifying the most relevant residues involved, i.e., hot-spot residues. This Ph.D. thesis has focused on developing new computational tools to address some of these challenges.
We have developed pyDockLite, a simplified scoring function derived from pyDock, the docking scoring function developed within our lab, which is up to 10 times faster at comparable performance. The key element in pyDockLite development is the new distance-based desolvation term, which drastically reduces the computation time required to calculate the desolvation contribution to pyDock docking energy.
Based on pyDockLite, we have developed a fast rigid-body minimization algorithm, which is very efficient when the complex subunits are in their bound conformation. To model backbone flexibility we have included normal modes in the minimization algorithm. This new feature improves the results, especially for the medium-flexible and flexible cases.
Most protein-protein docking protocols use scoring functions to evaluate docking poses and discriminate between good, i.e., near- native, and bad conformations. The implicit assumption is that the different energetic minima forming the docking energy landscape are represented by single docking poses which are scored individually. In this thesis, we have analyzed the concept that each energetic minima of the docking energy landscape can be formed by ensembles of docking orientations or conformations, and we have explored the consequences of scoring each minimum by such ensembles. We propose a novel ensemble-based description of the docking landscapes, integrating clustering, conformational sampling and consensus scoring, which improves docking performance.
In some circumstances, we might want to have a more detailed description, at the level of residue or atoms, of the docking energy of the different states conforming the docking landscapes. We have developed a method to partition pyDock docking energy at the residue level. Interestingly, we will show how we can use this partitioned energy to identify energetically relevant residues in the binding process (hot-spots) and to estimate changes in binding affinity upon mutation to alanine, i.e., as an in-silico alanine scanning mutagenesis predictor.
Regarding mutations to other residues, we have developed a new method to predict binding affinity changes upon mutation by combining MODELLER and pyDock. Results are in line with previous methods when tested on an external validation dataset.
Finally, we have explored how to apply the knowledge and tools we have developed to other protein interactions such as those between proteins and RNA molecules. We present a new scoring function that combines FTDock score and pyDock electrostatics and van der Waals energy terms. This scoring function can be used to evaluate docking models of protein-RNA complexes. Our work indicates that protein-protein and protein-RNA interactions may have distinctive features that prevent the direct application of protein-protein scoring functions to protein-RNA docking studies
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Samuel, Jarvie John. "Elicitation of Protein-Protein Interactions from Biomedical Literature Using Association Rule Discovery." Thesis, University of North Texas, 2010. https://digital.library.unt.edu/ark:/67531/metadc30508/.
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Extracting information from a stack of data is a tedious task and the scenario is no different in proteomics. Volumes of research papers are published about study of various proteins in several species, their interactions with other proteins and identification of protein(s) as possible biomarker in causing diseases. It is a challenging task for biologists to keep track of these developments manually by reading through the literatures. Several tools have been developed by computer linguists to assist identification, extraction and hypotheses generation of proteins and protein-protein interactions from biomedical publications and protein databases. However, they are confronted with the challenges of term variation, term ambiguity, access only to abstracts and inconsistencies in time-consuming manual curation of protein and protein-protein interaction repositories. This work attempts to attenuate the challenges by extracting protein-protein interactions in humans and elicit possible interactions using associative rule mining on full text, abstracts and captions from figures available from publicly available biomedical literature databases. Two such databases are used in our study: Directory of Open Access Journals (DOAJ) and PubMed Central (PMC). A corpus is built using articles based on search terms. A dataset of more than 38,000 protein-protein interactions from the Human Protein Reference Database (HPRD) is cross-referenced to validate discovered interactive pairs. A set of an optimal size of possible binary protein-protein interactions is generated to be made available for clinician or biological validation. A significant change in the number of new associations was found by altering the thresholds for support and confidence metrics. This study narrows down the limitations for biologists in keeping pace with discovery of protein-protein interactions via manually reading the literature and their needs to validate each and every possible interaction.
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Ahmad, Mazen [Verfasser], and Volkhard [Akademischer Betreuer] Helms. "Mechanisms of protein-protein association : atomistic molecular dynamics study of the association process / Mazen Ahmad. Betreuer: Volkhard Helms." Saarbrücken : Saarländische Universitäts- und Landesbibliothek, 2012. http://d-nb.info/1052551688/34.
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Donnini, S. (Serena). "Computing free energies of protein-ligand association." Doctoral thesis, University of Oulu, 2007. http://urn.fi/urn:isbn:9789514285745.
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Abstract
Spontaneous changes in protein systems, such as the binding of a ligand to an enzyme or receptor, are characterized by a decrease of free energy. Despite the recent developments in computing power and methodology, it remains challenging to accurately estimate free energy changes. Major issues are still concerned with the accuracy of the underlying model to describe the protein system and how well the calculation in fact emulates the behaviour of the system.
This thesis is largely concerned with the quality of current free energy calculation methods as applied to protein-ligand systems. Several methodologies were employed to calculate Gibbs standard free energies of binding for a collection of protein-ligand complexes, for which experimental affinities were available. Calculations were performed using system description with different levels of accuracy and included a continuum approach, which considers the protein and the ligand at the atomic level but includes solvent as a polarizable continuum, and an all-atom approach that relies on molecular dynamics simulations.
In most such applications, the effects of ionic strength are neglected. However, the severity of this approximation, in particular when calculating free energies of charged ligands, is not very clear. The issue of incorporating ionic strength in free energy calculations by means of explicit ions was investigated in greater detail and considerable attention was given to the affinities of charged peptides in the presence of explicit counter-ions. A second common approximation is concerned with the description of ligands that exhibit multiple protonation states. Because most of current methods do not model changes in the acid dissociation constants of titrating groups upon binding, protonation equilibria of such ligands are not taken into account in free energy calculations. The implications of this approximation when predicting affinities were analysed.
Finally, when calculating free energies of binding, a correct description of the interactions between the protein and the ligand is of fundamental importance. However, active sites of enzymes, where strained conformations may hold a functional role, are not always accurately modelled by molecular mechanics force fields. The case of a strained planar proline in the active site of triosephosphate isomerase was investigated using an hybrid quantum mechanics/molecular mechanics method, which implies a higher level of accuracy.
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Doig, Andrew James. "Thermodynamics of peptide association and protein folding." Thesis, University of Cambridge, 1991. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.386389.
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Irudayam, Sheeba Jem. "Thermodynamics of Protein-Ligand Association and Hydration." Thesis, University of Manchester, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.506575.
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Morrow, Robert Peter. "A study into human erythrocyte membrane protein association." Thesis, University of Bristol, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.288406.
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Li, X. F. "Investigation of protein-protein interactions : multibody docking, association/dissociation kinetics and macromolecular crowding." Thesis, University College London (University of London), 2011. http://discovery.ucl.ac.uk/1302277/.
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Protein-protein interactions are central to understanding how cells carry out their wide array of functions and metabolic procedures. Conventional studies on specific protein interactions focus either on details of one-to-one binding interfaces, or on large networks that require a priori knowledge of binding strengths. Moreover, specific protein interactions, occurring within a crowded macromolecular environment, which is precisely the case for interactions in a real cell, are often under-investigated. A macromolecular simulation package, called BioSimz, has been developed to perform Langevin dynamics simulations on multiple protein-protein interactions at atomic resolution, aimed at bridging the gaps between structural, kinetic and crowding studies on protein-protein interactions. Simulations on twenty-seven experimentally determined protein-protein interactions, indicated that the use of contact frequency information of proteins forming specific encounters can guide docking algorithms towards the most likely binding regions. Further evidence from eleven benchmarked protein interactions showed that the association rate constant of a complex, kon, can be estimated, with good agreement to experimental values, based on the retention time of its specific encounter. Performing these simulations with ten types of environmental protein crowders, it suggests, from the change of kon, that macromolecular crowding improves the association kinetics of slower-binding proteins, while it damps the association kinetics of fast, electrostatics-driven protein-protein interactions. It is hypothesised, based on evidence from docking, kinetics and crowding, that the dynamics of specific protein-protein encounters is vitally important in determining their association affinity. There are multiple factors by which encounter dynamics, and subsequently the kon, can be influenced, such as anchor residues, long-range forces, and environmental steering via crowders’ electrostatics and/or volume exclusion. The capacity of emulating these conditions on a common platform not only provides a holistic view of interacting dynamics, but also offers the possibility of evaluating and engineering protein-protein interactions from aspects that have never been opened before.
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Huang, Wenhui. "Towards constructing disease relationship networks using genome-wide association studies." Thesis, Virginia Tech, 2009. http://hdl.handle.net/10919/46326.
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Background: Genome-wide association studies (GWAS) prove to be a powerful
approach to identify the genetic basis of various human[1] diseases. Here we take
advantage of existing GWAS data and attempt to build a framework to understand the
complex relationships among diseases. Specifically, we examined 49 diseases from all
available GWAS with a cascade approach by exploiting network analysis to study the
single nucleotide polymorphisms (SNP) effect on the similarity between different
diseases. Proteins within perturbation subnetwork are considered to be connection
points between the disease similarity networks.
Results: shared disease subnetwork proteins are consistent, accurate and sensitive to
measure genetic similarity between diseases. Clustering result shows the evidence of
phenome similarity.
Conclusion: our results prove the usefulness of genetic profiles for evaluating disease
similarity and constructing disease relationship networks.Master of Science
10
Jaeger, Samira. "Network-based inference of protein function and disease-gene association." Doctoral thesis, Humboldt-Universität zu Berlin, Mathematisch-Naturwissenschaftliche Fakultät II, 2012. http://dx.doi.org/10.18452/16623.
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Proteininteraktionen sind entscheidend für zelluläre Funktion. Interaktionen reflektieren direkte funktionale Beziehungen zwischen Proteinen. Veränderungen in spezifischen Interaktionsmustern tragen zur Entstehung von Krankheiten bei. In dieser Arbeit werden funktionale und pathologische Aspekte von Proteininteraktionen analysiert, um Funktionen für bisher nicht charakterisierte Proteine vorherzusagen und Proteine mit Krankheitsphänotypen zu assoziieren. Verschiedene Methoden wurden in den letzten Jahren entwickelt, die die funktionalen Eigenschaften von Proteinen untersuchen. Dennoch bleibt ein wesentlicher Teil der Proteine, insbesondere menschliche, uncharakterisiert. Wir haben eine Methode zur Vorhersage von Proteinfunktionen entwickelt, die auf Proteininteraktionsnetzwerken verschiedener Spezies beruht. Dieser Ansatz analysiert funktionale Module, die über evolutionär konservierte Prozesse definiert werden. In diesen Modulen werden Proteinfunktionen gemeinsam über Orthologiebeziehungen und Interaktionspartner vorhergesagt. Die Integration verschiedener funktionaler Ähnlichkeiten ermöglicht die Vorhersage neuer Proteinfunktionen mit hoher Genauigkeit und Abdeckung. Die Aufklärung von Krankheitsmechanismen ist wichtig, um ihre Entstehung zu verstehen und diagnostische und therapeutische Ansätze zu entwickeln. Wir stellen einen Ansatz für die Identifizierung krankheitsrelevanter Genprodukte vor, der auf der Kombination von Proteininteraktionen, Proteinfunktionen und Netzwerkzentralitätsanalyse basiert. Gegeben einer Krankheit, werden krankheitsspezifische Netzwerke durch die Integration von direkt und indirekt interagierender Genprodukte und funktionalen Informationen generiert. Proteine in diesen Netzwerken werden anhand ihrer Zentralität sortiert. Das Einbeziehen indirekter Interaktionen verbessert die Identifizierung von Krankheitsgenen deutlich. Die Verwendung von vorhergesagten Proteinfunktionen verbessert das Ranking von krankheitsrelevanten Proteinen.Protein interactions are essential to many aspects of cellular function. On the one hand, they reflect direct functional relationships. On the other hand, alterations in protein interactions perturb natural cellular processes and contribute to diseases. In this thesis we analyze both the functional and the pathological aspect of protein interactions to infer novel protein function for uncharacterized proteins and to associate yet uncharacterized proteins with disease phenotypes, respectively. Different experimental and computational approaches have been developed in the past to investigate the basic characteristics of proteins systematically. Yet, a substantial fraction of proteins remains uncharacterized, particularly in human. We present a novel approach to predict protein function from protein interaction networks of multiple species. The key to our method is to study proteins within modules defined by evolutionary conserved processes, combining comparative cross-species genomics with functional linkage in interaction networks. We show that integrating different evidence of functional similarity allows to infer novel functions with high precision and a very good coverage. Elucidating the pathological mechanisms is important for understanding the onset of diseases and for developing diagnostic and therapeutic approaches. We introduce a network-based framework for identifying disease-related gene products by combining protein interaction data and protein function with network centrality analysis. Given a disease, we compile a disease-specific network by integrating directly and indirectly linked gene products using protein interaction and functional information. Proteins in this network are ranked based on their network centrality. We demonstrate that using indirect interactions significantly improves disease gene identification. Predicted functions, in turn, enhance the ranking of disease-relevant proteins.
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Wang, Zhaoshuai. "ILLUMINATE THE PATHWAY OF MEMBRANE PROTEIN ASSOCIATION AND DEGRADATION." UKnowledge, 2017. http://uknowledge.uky.edu/chemistry_etds/87.
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Escherichia coli transporter protein AcrB and its homologues are the inner membrane components of the Resistance-Nodulation-Division (RND) family efflux pumps in Gram-negative bacteria. It is well accepted that soluble proteins are only marginally stable, but such insight is missing for membrane proteins. The lack of stability data, including thermodynamic stability and oligomer association affinity is a result of intrinsic difficulties in working with membrane proteins. In addition, the degradation of soluble proteins in E. coli has been extensively studied whereas the degradation process of membrane proteins remains unclear. A focus of my thesis is the validation and development of methods used to measure the thermo- and oligomeric- stability of membrane proteins. I investigated the mechanism of a popular thermal-stability assay developed specifically for the study of membrane proteins uses a thiol-specific probe, 7-diethylamino-3-(4-maleimidophenyl)-4-methylcoumarin (CPM). I found that, contrary to current understanding, the presence of a sulfhydryl group was not a prerequisite for the CPM thermal stability assay. The observed fluorescence increase is likely caused by binding of the fluorophore to hydrophobic patches exposed upon protein unfolding. I then applied these methods in the study of three projects. In the first project, I investigated how suppressor mutations restore the function of AcrBP223G, in which the Pro223 to Gly mutation compromised the function of AcrB via disrupting AcrB trimerization. The results suggested that the function loss resulted from compromised AcrB trimerization could be restored through various mechanisms involving the compensation of trimer stability and substrate binding. In the second project, I created two AcrB fusion proteins, with C-terminal yellow fluorescence protein (YFP) and cyan fluorescence protein (CFP), respectively. YFP and CFP form a fluorescence resonance energy transfer (FRET) pair. Using this pair of fusion proteins, I studied AcrB assembly both in detergent micelles and in lipid bilayers. A positive cooperativity was observed in kinetic studies of association of AcrB trimer. Reconstitution experiment revealed that the association showed a higher FRET efficiency and faster association rate in liposome than in DDM. In the last project, I developed a fluorescence method to study the degradation of AcrB-ssrA by the ClpXP system. Comparing to the degradation of GFP-ssrA, degradation of AcrB-CFP-ssrA showed a lower maximum velocity and tighter binding to the enzymes with a positive cooperativity.
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Yalamanchili, Hari Krishna. "Computational approaches for protein functions and gene association networks." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2014. http://hdl.handle.net/10722/206477.
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Entire molecular biology revolves primarily around proteins and genes (DNA and RNA). They collaborate with each other facilitating various biomolecular systems. Thus, to comprehend any biological phenomenon from very basic cell division to most complex cancer, it is fundamental to decode the functional dynamics of proteins and genes. Recently, computational approaches are being widely used to supplement traditional experimental approaches. However, each automated approach has its own advantages and limitations. In this thesis, major shortcomings of existing computational approaches are identified and alternative fast yet precise methods are proposed.
First, a strong need for reliable automated protein function prediction is identified. Almost half of protein functional interpretations are enigmatic. Lack of universal functional vocabulary further elevates the problem. NRProF, a novel neural response based method is proposed for protein functional annotation. Neural response algorithm simulates human brain in classifying images; the same is applied here for classifying proteins. Considering Gene Ontology (GO) hierarchical structure as background, NRProF classifies a protein of interest to a specific GO category and thus assigns the corresponding function.
Having established reliable protein functional annotations, protein and gene collaborations are studied next. Interactions amongst transcription factors (TFs) and transcription factor binding sites (TFBSs) are fundamental for gene regulation and are highly specific, even in evolution background. To explain this binding specificity a Co-Evo (co-evolutionary) relationship is hypothesized. Pearson correlation and Mutual Information (MI) metrics are used to validate the hypothesis. Residue level MI is used to infer specific binding residues of TFs and corresponding TFBSs, assisting a thorough understanding of gene regulatory mechanism and aid targeted gene therapies.
After comprehending TF and TFBS associations, interplay between genes is abstracted as Gene Regulatory Networks. Several methods using expression correlations are proposed to infer gene networks. However, most of them ignore the embedded dynamic delay induced by complex molecular interactions and other riotous cellular mechanisms, involved in gene regulation. The delay is rather obvious in high frequency time series expression data. DDGni, a novel network inference strategy is proposed by adopting gapped smith-waterman algorithm. Gaps attune expression delays and local alignment unveils short regulatory windows, which traditional methods overlook.
In addition to gene level expression data, recent studies demonstrated the merits of exon-level RNA-Seq data in profiling splice variants and constructing gene networks. However, the large number of exons versus small sample size limits their practical application. SpliceNet, a novel method based on Large Dimensional Trace is proposed to infer isoform specific co-expression networks from exon-level RNA-Seq data. It provides a more comprehensive picture to our understanding of complex diseases by inferring network rewiring between normal and diseased samples at isoform resolution. It can be applied to any exon level RNA-Seq data and exon array data.
In summary, this thesis first identifies major shortcomings of existing computational approaches to functional association of proteins and genes, and develops several tools viz. NRProF, Co-Evo, DDGni and SpliceNet. Collectively, they offer a comprehensive picture of the biomolecular system under study.published_or_final_version
Biochemistry
Doctoral
Doctor of Philosophy
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Vagedes, Peter. "Simulation of enzyme reactions the influence of protonation on catalysis and on protein protein association /." [S.l. : s.n.], 2001. http://www.diss.fu-berlin.de/2001/49/index.html.
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Taniguchi, Yoshihito. "LIM protein KyoT2 negatively regulates transcription by association with the RBP-J DNA-binding protein." Kyoto University, 1998. http://hdl.handle.net/2433/182239.
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Strout, Stephen Lewis. "Association between systemic lupus erythematosus and periodontitis." [Gainesville, Fla.] : University of Florida, 2004. http://purl.fcla.edu/fcla/etd/UFE0004857.
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Thesis (M.S.)--University of Florida, 2004.Typescript. Title from title page of source document. Document formatted into pages; contains 43 pages. Includes Vita. Includes bibliographical references.
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Huffman, Jennifer Elizabeth. "Genetic analysis of protein N-glycosylation." Thesis, University of Edinburgh, 2014. http://hdl.handle.net/1842/10038.
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The majority of human proteins are post-translationally modified by covalent addition of one or more complex oligosaccharides (glycans). Alterations in glycosylation processing are associated with numerous diseases and glycans are attracting increasing attention both as disease biomarkers and as targets for novel therapeutic approaches. Using a recently developed high performance liquid chromatography (HPLC) method for high-throughput glycan analysis, genome-wide association studies (GWAS) of 33 directly measured and 13 derived N-glycan features were performed in 3533 individuals from four European isolated populations. Polymorphisms at six loci were found to show genome-wide significant association with plasma concentrations of N-glycans. Several of these gene products have well characterised roles in glycosylation, however, SLC9A9 and HNF1A were two of the novel findings. Subsequent work performed by collaborators found HNF1A to be a “master regulator” of genes involved in the fucosylation of plasma N-glycans. Additionally, this work led to the discovery that N-glycans could act as biomarkers to discriminate HNF1A-MODY from type 1 and type 2 diabetes mellitus (T1D, T2D) patients. After the success of the total plasma N-glycan GWAS, it was thought that stronger and more biologically interpretable associations may be found from the investigation of N-glycans isolated from a single protein. Glycosylation of immunoglobulin G (IgG) influences IgG effector function by modulating binding to Fc receptors. To identify genetic networks that govern IgG glycosylation, N-linked IgG glycans were quantitated using ultra performance liquid chromatography (UPLC) in 2247 individuals from the same four European populations from the previous study. GWAS of the 77 N-glycan measures identified 15 loci with a p-value < 5x10-08. Four loci contained genes encoding glycosyltransferases, while the remaining loci contained genes that have not previously been implicated in protein glycosylation. However, most have been associated with autoimmune and inflammatory conditions and/or hematological cancers. Several high-throughput methods for the analysis of N-glycans have been developed in the past few years but thorough validation and standardization of these methods is required before significant resources are invested in large-scale studies. To this end, four of these methods were compared, UPLC, multiplexed capillary gel electrophoresis (xCGE), and two mass spectrometric (MS) methods, for quantitative profiling of N-glycosylation of plasma IgG in a subset of 1201 individuals recruited from two of the cohorts used in the previous GWAS studies. A “minimal” dataset was compiled of N-glycan structures able to be measured by all four methods. To evaluate their accuracy, correlations were calculated for each structure in the minimal dataset. Additionally, GWAS was performed to test if the same associations would be observed across methodologies. Chromatographic methods with either fluorescent or MS-detection yielded slightly stronger associations than MS-only and xCGE, but at the expense of lower levels of throughput. Advantages and disadvantages of each method were identified, which should aid in the selection of the most appropriate method for future studies. This work shows that it is possible to identify new loci that control glycosylation of plasma proteins using GWAS and the potential of N-glycans for biomarker development. It also provides some guidelines for methodology selection for future studies of N-glycans.
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Jacobs, Michael Graham. "Membrane association of dengue 2 virus non-structural protein 1." Thesis, Imperial College London, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.325917.
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Deng, Yu. "Regulation of mammalian STE20-like kinase (MST2) by phosphorylation/dephosphorylation, proteolysis and association with HSP90 during apoptosis /." View Abstract or Full-Text, 2003. http://library.ust.hk/cgi/db/thesis.pl?BICH%202003%20DENG.
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Thesis (Ph. D.)--Hong Kong University of Science and Technology, 2003.Includes bibliographical references (leaves 148-164). Also available in electronic version. Access restricted to campus users.
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Kemper, Courtney Paige. "Association Among Physical Activity, Protein, Intake and Clinical Indicators of Sarcopenia." Miami University / OhioLINK, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=miami1605816952601922.
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Kidd, Kameha Rae. "Angiogenesis and neovascularization in association with extracellular matrix protein modified biomaterials." Diss., The University of Arizona, 2002. http://hdl.handle.net/10150/279992.
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Synthetic biomedical implants are used to replace diseased tissues and organs. Unfortunately, these implants often fail due to a lack of biocompatibility and poor integration by the recipient. This implant failure is associated with the formation of an avascular fibrous capsule and chronic inflammatory response. Additionally, small diameter vascular grafts have complications associated with surface thrombogenenicity and intimal hyperplasia. Porous polymers are often incorporated in the construction of biomedical devices because they permit tissue integration and improved biocompatibility. While the inclusion of porosity has enhanced device performance, these devices still do not perform optimally. The incorporation of a vascular network in association with and within the pores of these materials is believed to improve tissue integration and long-term device function. Several approaches are actively being studied for their ability to stimulate new vessel growth, angiogenesis, as well as to improve the direct interaction of cells with material surfaces. The process of angiogenesis involves the coordinated involvement of both soluble and insoluble factors such as growth factors and cytokines, and extracellular matrix proteins respectively. Often, growth factors and cytokines are expressed by the inflammatory cells associated with the biomedical implants, but the microenvironment within the polymer remains unstable with respect to the presence of the appropriate extracellular matrix proteins. The overall hypothesis of this dissertation is that the reestablishment of an extracellular microenvironment on and within a porous polymer will provide the appropriate substrates for promoting angiogenesis and neovascularization of porous polymers. The results of the studies within this dissertation demonstrate that extracellular matrix modifications of commercially available expanded polytetrafluoroethylene (ePTFE) successfully promote new vessel growth in the tissue surrounding the implant, termed angiogenesis, and new vessel growth within the pores of the polymer, termed neovascularization. Furthermore, the extracellular matrix protein laminin 5 was determined to promote human microvessel endothelial cell adhesion to ePTFE as well as support angiogenesis and neovascularization when used as a surface modification of ePTFE. Based on these studies, the extracellular matrix protein, laminin 5, could be utilized in the tissue engineering of biomedical implant devices to promote increased new vessel integration and improve the long-term viability of these devices.
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Foster, Andrew. "Development of a novel two-hybrid system for the identification of cyclic peptide induced protein-protein association." Thesis, University of Southampton, 2017. https://eprints.soton.ac.uk/418010/.
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Chemically-induced protein association is involved in key regulatory pathways throughout the body. Many natural products exert their downstream effect by the stabilisation of naturally occurring interactions, either by an allosteric effect or by the direct binding of two distinct protein partners. The targeting of these interactions by small-molecules is a relatively under developed field, with the inhibition of existing protein-protein interactions (PPIs) a more investigated target. One such method to investigate PPI inhibition is a bacterial reverse two-hybrid system (RTHS), which has been successfully coupled to a split-intein based library of cyclic peptides to identify novel inhibitors (split-intein circular ligation of peptides and proteins, SICLOPPS). Here, the existing RTHS technology was rebuilt to enable the screening of cyclic peptides for their ability to induce dimerisation of two target proteins. The well-studied mTOR-FKBP12 interaction, with heterodimerisation induced by the natural product rapamycin, was used to build and validate a novel two-hybrid system. This utilises the tetracycline repressor to reverse the transcriptional control from the RTHS, leading to a selectable phenotype upon dimerisation. Rapamycin addition successfully results in the association of these target proteins, leading to the downstream expression of two essential reporter genes and a fluorescent protein. This rapamycin-dependent interaction can be identified both by an agarbased growth assay, and a liquid media-based fluorescent assay. A large number of SICLOPPS libraries were screened with little success at replicating the action of brapamycin. The SICLOPPS technology was optimised and expanded, enabling an improved screening platform for the future.
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Panova, Stanislava. "NMR approaches to understanding intramolecular and intermolecular interactions in proteins." Thesis, University of Manchester, 2017. https://www.research.manchester.ac.uk/portal/en/theses/nmr-approaches-to-understanding-intramolecular-and-intermolecular-interactions-in-proteins(95a44c16-fd44-4909-8ee2-435f574d2970).html.
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Inhibition of the intrinsically disordered proteins (IDP) is a recognized issue in drug research. Standard approaches, based on key-lock model, cannot be used in the absence of rigid structure and defined active site. Here a basic helix-loop-helix leucine zipper (bHLHZip) domain of c-Myc was studied, which is intrinsically disordered and prone to aggregation. Chemical denaturation of proteins is a widely accepted technique to study protein folding, but here this methodology was applied to IDP, observing its effect on the structural ensemble of c-Myc by NMR spectroscopy. Nonlinear chemical shift changes indicated cooperative unfolding of the helical structure of the part of the leucine zipper domain in parallel with the melting of the N-terminal helix. Paramagnetic relaxation enhancement (PRE) was used to probe long-range structure and revealed presence of long-range contacts. The following search for inhibitors can be directed to the search for ligands, locking c-Myc in its more compact conformation. Protein self-association is a problem typical for IDPs and intrinsic process for all proteins at high concentrations. It leads to increased viscosity, gelation and possible precipitation, which cause problems in protein manufacturing, stability and delivery. If protein drugs require high dosing, special approaches are needed. At high concentrations proteins experience conditions close to the crystal state, therefore interactions in solution could potentially coincide with crystal lattice contacts. A range of diverse methods is used to study this process, but the complexity of the mechanism makes it hard to build a reliable model. Here, the self-association of streptococcal Protein G (PrtG) was studied using Nuclear Magnetic Resonance (NMR) spectroscopy in solution. The properties of protein-protein interactions at high concentration, up to ~ 160 mg/ml, were studied at residue-level resolution. Residue specific information on protein dynamics was obtained using 15N relaxation measurements. The experiments were carried out at multiple concentrations. Variation in the rotational correlation time over these concentrations showed changes in the protein dynamics, which indicated weak protein-protein interactions occurring in solution. Pulsed-field gradient NMR spectroscopy was used to monitor translational diffusion coefficients in order to estimate the degree of protein self-association. Oligomer formation was also monitored by looking at variations in 1H and 15N amide chemical shifts. Better understanding of protein self-association mechanisms under different conditions could assist in developing methods to reduce the level of reversible protein self-association in solution at high protein concentrations.
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Ozer, Hatice Gulcin. "Residue Associations In Protein Family Alignments." The Ohio State University, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=osu1211570026.
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Cai, Jingfei. "Probing the Membrane Association Mechanisms for Pulmonary Collectins and Mammalian Phospholipase C." Thesis, Boston College, 2013. http://hdl.handle.net/2345/3872.
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Thesis advisor: Mary F. RobertsThesis advisor: Eranthie Weerapana
Peripheral proteins from mammals often exhibit multi-domain structures and require metal ions such as calcium as co-factors. This dissertation investigates two types of such proteins -- pulmonary collectins (surfactant proteins A and D) and phosphatidylinositol-specific phospholipase C (PLC) delta1 -- and their interactions with model membranes. One approach to work around the complexity brought upon by such multi-domain protein structure is to use a truncated construct or an isolated single domain. For pulmonary collectins, homotrimers consisting of the neck domain and the carbohydrate recognition domain were used in a novel NMR assay for better understanding of their lipid-specific interactions with the membranes. For PLC delta1, we were particularly interested in the role of the EF-hand domain. The isolated EF-hand domain of PLC delta1 was first used to characterize its interactions with membranes and identify key residues responsible for such interactions. These key residues in the N terminal lobe of the EF-hand domain, either cationic or hydrophobic, were then found to affect the hydrolysis activity of the full-length enzyme. A common role for this region of the PLC in facilitating proper membrane association was thus proposed
Thesis (PhD) — Boston College, 2013
Submitted to: Boston College. Graduate School of Arts and Sciences
Discipline: Chemistry
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Hill, Stephanie. "Folding and association of spectrin tetramer domains : a study of intrinsically disordered proteins from a protein folding perspective." Thesis, University of Cambridge, 2014. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.648579.
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Martínez, Barrio Álvaro. "Novel Bioinformatics Applications for Protein Allergology, Genome-Wide Association and Retrovirology Studies." Uppsala : Acta Universitatis Upsaliensis, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-111932.
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Martínez, Barrio Álvaro. "Novel Bioinformatics Applications for Protein Allergology, Genome-Wide Association and Retrovirology Studies." Doctoral thesis, Uppsala universitet, Centrum för bioinformatik, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-111932.
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Recently, the pace of growth in the amount of data sources within Life Sciences has increased exponentially until pose a difficult problem to efficiently manage their integration. The data avalanche we are experiencing may be significant for a turning point in science, with a change of orientation from proprietary to publicly available data and a concomitant acceptance of studies based on the latter. To investigate these issues, a Network of Excellence (EMBRACE) was launched with the aim to integrate the major databases and the most popular bioinformatics software tools. The focus of this thesis is therefore to approach the problem of seamlessly integrating varied data sources and/or distributed research tools. In paper I, we have developed a web service to facilitate allergenicity risk assessment, based on allergen descriptors, in order to characterize proteins with the potential for sensitization and cross-reactivity. In paper II, a web service was developed which uses a lightweight protocol to integrate human endogenous retrovirus (ERV) data within a public genome browser. This new data catalogue and many other publicly available sources were integrated and tested in a bioinformatics-rich client application. In paper III, GeneFinder, a distributed tool for genome-wide association studies, was developed and tested. Useful information based on a particular genomic region can be easily retrieved and assessed. Finally, in paper IV, we developed a prototype pipeline to mine the dog genome for endogenous retroviruses and displaying the transcriptional landscape of these retroviral integrations. Moreover, we further characterized a group that until this point was believed to be primate-specific. Our results also revealed that the dog has been very effective in protecting itself from such integrations. This work integrates different applications in the fields of protein allergology, biotechnology, genome association studies and endogenous retroviruses.EMBRACE NoE EU FP6
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di, Bard Barbara Lelj Garolla. "Self-association and chaperon activity of the small heat shock protein 27." Thesis, University of British Columbia, 2007. http://hdl.handle.net/2429/31382.
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Human Hsp27 is a member of the small heat shock protein family that is over-expressed during cellular stress and that is involved in biological functions ranging from inhibition of apoptosis to regulation of cellular glutathione levels. In addition, Hsp27 is an ATP-independent molecular chaperon that binds to unfolding peptides and inhibits their precipitation. Roles for Hsp27 in several human diseases have also been proposed. For example, the expression of Hsp27 by several human tumors has been noted as a potential diagnostic feature or a therapeutic target. Increasing evidence indicates that the biological functions of Hsp27 are linked to the reversible self-association of the protein to form large oligomers in a process that is at least in part regulated by reversible phosphorylation of three Ser residues. The three-dimensional structure of Hsp27 is not available, and relatively few rigorous physical studies of the protein have been reported. In the present study, analytical ultracentrifugation has been used to define self-association of Hsp27 and selected variants as a function of protein concentration, pH, temperature, and ionic strength to evaluate the role of structural domains believed to be functionally significant. These results are correlated with the chaperon activity, as determined by monitoring the inhibition of insulin unfolding, and with the kinetics of subunit exchange, monitored by fluorescence resonance energy transfer. The results establish that wild-type Hsp27 forms a distribution of oligomers that ranges from dimers to at least 32-mers and that oligomerization is highly regulated by temperature but not ionic strength or pH. Moreover, the oligomeric size of Hsp27 increases with increased temperature in a manner that correlates well with increased chaperon activity and rate of subunit exchange. Comparison of results from all three types of experiments obtained for the wild-type protein to those obtained with Hsp27 variants has led to the development of a model for Hsp27 self-association and chaperon activity.Medicine, Faculty of
Biochemistry and Molecular Biology, Department of
Graduate
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Naji, Hassan Salim. "Association of Bisphenol A and C-Reactive Protein Concentrations with Cardiovascular Diseases." ScholarWorks, 2015. http://scholarworks.waldenu.edu/dissertations/1707.
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Bisphenol A (BPA), a widely used chemical in plastic, has drawn wide attention due to its presence in many consumer products and the environment. The purpose of this study was to examine the association between urinary BPA and the reporting of cardiovascular diseases (CVD), and then to examine the effect of C-reactive protein (CRP) as a moderating variable. The data used in this research were extracted from the National Health and Nutrition Examination Survey collected in 2009-2010. Guided by the advanced epidemiological triangle, analysis involved 2 stepwise binary logistic regressions. The first step suggested that the controls were significant in predicting CVD (Ï?2 (5) = 83.72, p < .001, R2 = .15). The Nagelkerke R2 coefficient of determination indicated that the controls explained approximately 15% of the variance in instances of CVD. The second step of the binary logistic regression included the controls and BPA level in the model together. The regression analysis suggested that the Nagelkerke coefficient of determination (Ï?2 (6) = 83.76, p < .001, R2 = .15) did not increase from the 15% explained by the controls, and BPA level was found to be a nonsignificant predictor of CVD (p = .853). Due to lack of association between BPA and CVD, the analysis was shifted to examine the association between urinary BPA and serum CRP. The association between urinary BPA and serum CRP was also statistically nonsignificant (Spearman correlation coefficient, rs= .06, p = .015). The results may have positive social change by contributing to the body of knowledge on BPA and by increasing scientific scrutiny for substances used in people's daily lives.
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Lawton, Edward. "Self association and transcription activation determinants in a bacterial enhancer binding protein." Thesis, Imperial College London, 2013. http://hdl.handle.net/10044/1/29205.
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Bacterial transcription initiation relies on the binding of a dissociable sigma factor to the catalytic RNA polymerase (RNAP) 'core' enzyme to enable promoter specific DNA recognition. While the initial σ70 RNAP-promoter DNA bound complex (termed the closed complex) can spontaneously isomerise to form open promoter complexes, RNAP containing the major variant, the σ54 factor requires activation by bacterial enhancer binding proteins (bEBPs) which reorganize the initial closed promoter complex to an open complex in an ATP consuming reaction. These bEBPs belong to the AAA+ (ATPases associated with various cellular activities) superfamily of proteins that form oligomeric rings (often hexamers) on upstream activation sequences (UAS) ~150bp upstream of the promoter. A DNA looping event, often mediated by integration host factor (IHF), brings the bEBP in close proximity to the σ54-RNAP closed complex (RPc). The interaction between σ54 (within the context of the RPc) and the bEBP is strictly dependent on a sequence insertion (that is common to all bEBPs) termed the L1 loop, which is thought to be the major structural determinant in energy transfer between the bEBP and σ54. The σ54 subunit is split up into three distinct regions (termed Regions I, II and III), where the L1 loop interacts with the mobile Region I and Region III forms the DNA contacts necessary for engaging with -12 and -24 consensus sequences on promoter DNA. A basic understanding of the global interactions that mediate σ54-dependent transcription has already been obtained, yet many specific mechanistic details remain unknown. In this study we elucidate three features of σ54 transcription activation: i) The interactions required within the bEBP complex for functional oligomerisation, ii) the mechanism that transcription activation determinants act and iii) the role of Region III in binding to the -12 element.
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Hallén, Elin. "Coagulation properties of milk : association with milk protein composition and genetic polymorphism /." Uppsala : Department of Food Science, Swedish University of Agricultural Sciences, 2008. http://epsilon.slu.se/200875.pdf.
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Cromwell, Mary Ellen Miley. "Self-association, crystallization, and phase separation : understanding intermolecular interactions for a monoclonal antibody /." Connect to full text via ProQuest. Limited to UCD Anschutz Medical Campus, 2008.
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Thesis (Ph.D. in Pharmaceutical Sciences) -- University of Colorado Denver, 2008.Typescript. Includes bibliographical references (leaves 209-236). Free to UCD affiliates. Online version available via ProQuest Digital Dissertations;
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Atway, Nader G. "The Association of Cell Cycle and Growth Related Protein Kinases with the Fibroblast Cytoskeleton." Connect to online version at Digital.Maag Connect to online version at OhioLINK ETD, 1999. http://hdl.handle.net/1989/4814.
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Meng, Hai Yun. "Determinants of cis-trans isomerism of the aromatic-prolyl amide bond and design of lathanide-binding peptides." Access to citation, abstract and download form provided by ProQuest Information and Learning Company; downloadable PDF file 2.04 Mb., 133 p, 2006. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&res_dat=xri:pqdiss&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&rft_dat=xri:pqdiss:1432291.
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Costanzi, Elisa. "Structural analysis of molecular recognition and ligand association processes." Doctoral thesis, Università degli studi di Padova, 2018. http://hdl.handle.net/11577/3421838.
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Molecular recognition is a fundamental step in essentially any biochemical process. Detailed structural knowledge is crucial to have a better understanding of the processes in which the two interacting molecular partners are involved and can be exploited in several applied fields such as supramolecular design of new molecular assemblies, rational drug design, and enzyme engineering. In the context of molecular recognition, I have investigated (mainly by single crystal x-ray crystallography) some relevant protein-protein and protein-ligand systems in order to gain detailed structural insights on the interactions involved, at atomic level.
First, the STAS domain of prestin, an anion-dependent motor protein, and its interaction with monovalent anions and with calmodulin.
Second, the interaction between protein kinases (CDK2 and CK2) and BCLXL, and inhibitors, for the rational design of specific drugs targeting these proteins involved in different types of cancer.Il riconoscimento molecolare è uno step fondamentale nei processi biochimici. Una conoscenza strutturale dettagliata è cruciale per capire meglio i processi in cui sono coinvolti due partner molecolari interagenti e può essere sfruttata in vari campi come il disegno di nuovi assemblamenti sopramolecolari, il disegno razionale di farmaci e l’ingegnerizzazione di enzimi. In questo contesto, ho investigato (prevalentemente tramite cristallografia a raggi x su cristallo singolo) alcuni sistemi proteina-proteina e proteina-ligando per ottenere dettagli strutturali delle interazioni coinvolte, a livello atomico. In primis, il dominio STAS di prestina, una proteina motrice anionidipendente, e la sua interazione con anioni monovalenti e con calmodulina. Poi, l’interazione tra protein chinasi (CDK2 e CK2) e BCL-XL, e inibitori, per il disegno razionale di farmaci specifici nel colpire queste proteine coinvolte in vari tipi di cancro.
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Perschbacher, Katherine. "Regulator of G Protein Signaling 2 (RGS2) in preeclampsia: association, consequence, and cause." Diss., University of Iowa, 2018. https://ir.uiowa.edu/etd/6621.
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Increased signaling of various hormones through their cognate G Protein-Coupled Receptors (GPCRs), including the angiotensin, endothelin, and vasopressin systems, are implicated in human preeclampsia (PreE) and animal models of the disorder. Cascade-specific termination of GPCR signaling following receptor activation is catalyzed by the Regulator of G protein Signaling (RGS) family members. Within the RGS B/R4 family, RGS5 and RGS2 are implicated in human PreE and gestational hypertensive disorders. Mutations within the RGS2 gene, a B/R4 RGS member, are associated with human hypertensive populations and increased risk of developing PreE and its sequelae. Given the role for the placenta in the pathogenesis of PreE, we hypothesized a role for RGS2 in the placenta during PreE.
My studies showed RGS2 mRNA expression is reduced in placentas from pregnancies affected by PreE. Reduced fetal-placental Rgs2 induces gestational hypertension, proteinuria, and increased plasma ALT activity in wildtype dams. Placentas with reduced Rgs2 expression exhibit reduced vascularization, increased thickness of the labyrinth and spongiotrophoblast layers, and enrichment for pathways associated with human PreE. Analysis of human PreE placenta samples reveals an increase in the cAMP/CREB signaling pathway, yet we demonstrate loss of CREB occupancy at the RGS2 promoter. HTR8 cell cultures indicate HDAC activity may be required CREB transcription of specific gene sets. In silico analysis supports this concept and further implies it may be impaired in human PreE placentas.
These findings demonstrate heterozygous loss of fetal-placental Rgs2 is sufficient to induce PreE phenotypes in wildtype dams during pregnancy. Additionally, they highlight the role of the placenta in maternal pathogenesis of PreE and support the concept that paternal genetics influence the risk of developing PreE.
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Köster, Liza Sally. "C-reactive protein in canine babesiosis caused by Babesia rossi and its association with outcome." Pretoria : [s.n.], 2010. http://upetd.up.ac.za/thesis/available/etd-02262010-140236/.
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Chen, Bernard. "Discovery and Extraction of Protein Sequence Motif Information that Transcends Protein Family Boundaries." Digital Archive @ GSU, 2009. http://digitalarchive.gsu.edu/cs_diss/42.
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Protein sequence motifs are gathering more and more attention in the field of sequence analysis. The recurring patterns have the potential to determine the conformation, function and activities of the proteins. In our work, we obtained protein sequence motifs which are universally conserved across protein family boundaries. Therefore, unlike most popular motif discovering algorithms, our input dataset is extremely large. As a result, an efficient technique is essential. We use two granular computing models, Fuzzy Improved K-means (FIK) and Fuzzy Greedy K-means (FGK), in order to efficiently generate protein motif information. After that, we develop an efficient Super Granular SVM Feature Elimination model to further extract the motif information. During the motifs searching process, setting up a fixed window size in advance may simplify the computational complexity and increase the efficiency. However, due to the fixed size, our model may deliver a number of similar motifs simply shifted by some bases or including mismatches. We develop a new strategy named Positional Association Super-Rule to confront the problem of motifs generated from a fixed window size. It is a combination approach of the super-rule analysis and a novel Positional Association Rule algorithm. We use the super-rule concept to construct a Super-Rule-Tree (SRT) by a modified HHK clustering, which requires no parameter setup to identify the similarities and dissimilarities between the motifs. The positional association rule is created and applied to search similar motifs that are shifted some residues. By analyzing the motifs results generated by our approaches, we realize that these motifs are not only significant in sequence area, but also in secondary structure similarity and biochemical properties.
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Ahmadi-Abhari, Sara. "Epidemiology of C-reactive protein in the older adult population : distribution, determinants, and association with health outcomes." Thesis, University of Cambridge, 2015. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.709155.
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Ragheb, Amro M. Brook Michael A. "Controlling protein-silicone interactions by the modification of silicone elastomers with poly(ethylene oxide) /." *McMaster only, 2005.
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Ostermeir, Katja [Verfasser], Martin [Akademischer Betreuer] Zacharias, Iris [Akademischer Betreuer] Antes, and Ulrich [Akademischer Betreuer] Gerland. "Advanced sampling to study protein plasticity and protein association / Katja Ostermeir. Gutachter: Martin Zacharias ; Iris Antes ; Ulrich Gerland. Betreuer: Martin Zacharias." München : Universitätsbibliothek der TU München, 2014. http://d-nb.info/1061126188/34.
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Vilaprinyó, Pascual Sílvia. "The dynamic nature of amyloid-beta protein aggregation and its association to Alzheimer’s disease." Doctoral thesis, Universitat de Barcelona, 2015. http://hdl.handle.net/10803/305364.
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Amyloid-beta protein (Aß) is strongly linked to the aetiology of Alzheimer’s disease (AD). Even though Aß has a central role in AD, this protein is normally produced in healthy humans. It is the aberrant processing of Aß that determines its accumulation and aggregation into large oligomer species that evolve into the fibrillar structures deposited in amyloid plaques in the brain of AD patients. The neurotoxicity observed in AD has been attributed to the oligomeric intermediates, although their stoichiometry and structure still remain unknown. This is the reason why no AD therapeutic approaches tackling Aß aggregation have arrived to the market yet.
In the present thesis, we have determined the stoichiometry and the structure of the oligomers formed in the early stages of Aß aggregation. Due to their highly dynamic nature, we have first obtained their covalent counterparts through the use of a photo-induced crosslinking methodology. Successful isolation of cross-linked Aß dimers and trimers has been achieved by means of a disaggregating treatment coupled to size exclusion chromatography. The combined study of these isolated cross-linked species through ion mobility coupled to electrospray ionization mass spectrometry, circular dichroism and molecular dynamics simulations, has shown that Aß dimers and trimers possess a globular shape without defined secondary structure. Moreover, we have proved that these cross-linked oligomers induce calcium influx, an intracellular marker for neurotoxicity, in primary neuroglial cultures, and that these cross-linked species effectively modulate Aß aggregation. Additionally, we have demonstrated that classical SDS-PAGE analysis provides misleading results when determining oligomer stoichiometry.
The present thesis was also aimed at providing insights into the role of Aß amyloid fibrils in AD. Aß fibrils had been previously shown to be in dynamic equilibrium with soluble Aß species. The objective was to find evidences on the nature of these soluble species in equilibrium with Aß fibrils. Determination of their stoichiometry has been achieved by incubating Aß fibrils with insulin degrading enzyme, an enzyme which we have demonstrated to specifically proteolyze monomeric Aß. Subsequent analysis of Aß fibrils by hydrogen/deuterium exchange monitored by mass spectrometry has revealed that Aß fibrils are in equilibrium with monomers and low molecular weight oligomers. This equilibrium has been proved to be highly dependent on the physicochemical properties of Aß fibrils.La proteïna beta amiloide (Aß) es troba estretament lligada a la malaltia d’Alzheimer (MA). Tot i el seu rol central en la malaltia, Aß es produeix de forma regular en humans sans. És el processament aberrant de la proteïna que en determina la seva acumulació i agregació, primer en intermedis oligomèrics transitoris que evolucionen cap a les estructures fibril·lars que composen les plaques amiloides dipositades al cervell dels malalts de la MA. La neurotoxicitat associada a la malaltia s’atribueix a les espècies intermèdies, per bé que se’n desconeix l’estequiometria i l’estructura. En la present tesi doctoral, hem determinat l’estequiometria i l’estructura dels oligòmers d’Aß formats en els estadiatges inicials de l’agregació. Hem provat que aquests oligòmers mostren neurotoxicitat en cultius neuronals primaris. Addicionalment, hem demostrat que el clàssic anàlisi per electroforesi en gel proporciona resultats confusos a l’hora de determinar l’estequiometria dels oligòmers. Els resultats presentats en la tesi doctoral també mostren evidències de que les fibres amiloides d’Aß es troben en equilibri amb monòmers i oligòmers de baix pes molecular. Aquest equilibri ha demostrat ser dependent de les propietats fisicoquímiques de les pròpies fibres d’Aß.
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Barnett, Catherine Margaret Eleanor. "Association of Single Nucleotide Polymorphisms in Surfactant Protein A and D with Otitis Media." The University of Waikato, 2007. http://hdl.handle.net/10289/2338.
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Otitis Media is one of the most common childhood diseases. Recurrent acute otitis media RAOM is characterized by repeated episodes of inflammation of the middle ear in conjunction with middle ear fluid, and often with an inflamed or bulging eardrum. Defective clearance by the Eustachian tube results in mucus build-up and is characteristic of otitis media with effusion (OME). Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, respiratory syncytial virus, and rhinovirus are the most common contributors to otitis media pathogenesis. In New Zealand, OME has been implicated with conductive hearing loss in childhood and has been shown to significantly impact on speech and language development. New Zealand Māori and Polynesian children have displayed significantly higher hearing test failure rates than European-Caucasian children. The collectins, Surfactant Protein (SP)-A and -D are encoded by three genes (SP-A1, SP-A2, and SP-D) and are host defense proteins present in the middle ear and Eustachian tube. Single nucleotide polymorphisms (SNPs) in SP-A1 and SP-A2 have been associated with increased or decreased susceptibility to otitis media, meningococcal disease, and range of respiratory diseases. Using allele-specific primers and real-time PCR with SYBR Green I melting curve analysis, four groups of individuals were genotyped for eleven SP-A1, SP-A2, and SP-D SNPs: European-Caucasian individuals with RAOM/OME; New Zealand Māori/Polynesian individuals with RAOM/OME; individuals with meningococcal disease; and a control group. The computer program, Haploview, was employed to perform χ2 analyses and identify statistically significant associations of alleles/haplotypes with RAOM/OME or meningococcal disease. In the European-Caucasian population, two SP-A1 alleles, one SP-A2 allele, and four haplotypes (CGAGC, 1A3, 1A9, and 1A10) were found to be associated with increased risk of RAOM/OME (P lt; 0.05). Conversely, haplotypes 6A2 and 1A2 were found to be protective against susceptibility to RAOM/OME (P lt; 0.05). In New Zealand Māori and Polynesian individuals, two SP-A1 alleles, three SP-A2 alleles, one SP-D allele, and four haplotypes (6A8, 6A10, 1A3, and 1A10) were found to be associated with increased risk of RAOM/OME (P lt; 0.05). An additional four haplotypes (6A2, 1A0, 1A2, and TA) were determined to be protective against susceptibility to RAOM/OME (P lt; 0.05). However, protective SPA1/SPA2/SPD haplotype 6A2-1A0-TA was significantly under-represented in the New Zealand Māori and Polynesian population (P lt; 0.05). A single allele and haplotype were associated with increased risk of meningococcal disease (P lt; 0.05). The findings of this study confirm that specific genetic variants of SP-A and SP-D are associated with either increased or decreased risk of developing RAOM and/or OME. Furthermore, it was demonstrated that New Zealand Māori and Polynesian individuals appear to exhibit more haplotypes susceptible to RAOM/OME. This may provide a partial explanation for the higher RAOM/OME-related failure rates of hearing tests in New Zealand Māori and Polynesian children. However, there are numerous socio-economic and environmental factors that also contribute to otitis media pathogenesis which were not considered in this study. The effects of the SP-A1, SP-A2, and SP-D alleles and haplotypes on the bacterial/viral binding efficiencies of SP-A and SP-D need to be investigated by further research, using a large population, to confirm the association with susceptibility or resistance with RAOM/OME.
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Dunne, P. D. "Association and segregation : fluorescence studies of protein organisation in the membranes of living cells." Thesis, University of Cambridge, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.598700.
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This thesis details efforts to develop and adapt fluorescence microscopy techniques for the study of membrane protein association and segregation in live cells, both within membranes and between different membranes. After an initial introduction to the cell membrane and fluorescence microscopy, the experimental section of this thesis is split into two parts. Part A concerns the development of techniques to explore the unresolved triggering mechanism through which T-cells, a cell of the adaptive immune system, first recognise threats. After a brief introduction to T-cell biology, association of key proteins are examined at the single molecule level through two new techniques- Two Colour Coincidence Detection (TCCD) and Dynamic Single Molecule Colocalisation (DySCo). Association of proteins between different membranes also provides important clues relating to the triggering mechanism. To this end, an artificial bilayer system is created where the re-distribution of bilayer-bound fluorophore-tagged receptors upon encounter of a ligand-bearing cell provides kinetic and thermodynamic data about binding. Part B details aspects of TCCD and DySCo that have been adapted to examine protein association in other biological systems. An experimental protocol and data analysis software are developed to allow examination of the colocalisation of stationary, surface-adsorbed molecules; specifically those related to neurodegenerative conditions such as amyloid diseases. Following this, results are shown demonstrating segregation of membrane components in spermatozoa- a compartmentalised polarised cell type. Early results suggesting the passive size-dependent segregation of T-cell proteins attached to artificial bilayers upon interaction with B-cells are presented.
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Van, Niekerk Michelle. "Association of nonstructural protein NS3 of African horsesickness virus with cytotoxicity and virus virulence." Thesis, University of Pretoria, 2002. http://hdl.handle.net/2263/29951.
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Factors that determine the molecular basis of African horsesickness virus (AHSV) virulence are unclear. Several proteins and different events in the viral replication cycle together with different environmental factors are likely to contribute to the virulence phenotype. The aim of this investigation was to study the possible contribution of AHSV nonstructural protein NS3 to virus virulence. NS3 is a cytotoxic protein that localizes in areas of plasma membrane disruption and is assumed to be associated with the release of virus particles from infected cells. A conserved feature in all AHSV NS3 proteins is the presence of two hydrophobic domains. To investigate whether these hydrophobic domains interact with membranes, cell surface localization and membrane association studies were conducted on NS3 and the two hydrophobic domain mutant forms of NS3. Results indicated that mutations in either hydrophobic domain did not prevent membrane targeting but abolished membrane anchoring. This prevented cell surface localization and obviated the cytotoxic effect of NS3. AHSV NS3 is a highly variable protein. This level of variation may influence virulence properties. To compare the NS3 sequence variation level of South African AHSVs and bluetongue viruses (BTV/s) with those previously described, the NS3 protein sequences of field isolates, reference and vaccine strains were determined and analysed. The variation level of AHSV NS3 was found to be higher than previously reported. Comparison of the AHSV vaccine and field strain NS3 sequences revealed no obvious NS3 virulence marker. The level of AHSV NS3 sequence variation could distinguish between field isolates and vaccine strains and differentiate between sub-populations within a serotype. The inferred phylogeny of AHSV NS3 corresponded well with the described NS3 phylogenetic clusters with exception of AHSV-8 and one AHSV-6 encoded NS3. BTV NS3 inferred phylogeny indicated that the three BTV NS3 clusters that occur as geographically defined entities are all simultaneously present in S.A. This would suggest that BTV originated in southern Africa. To investigate the impact of minor NS3 variation on AHSV virulence, the membrane permeabilization properties of AHSV-2 vaccine and virulent NS3 proteins were compared. The AHSV-2 S10 genes were cloned and NS3 was expressed using the BAC-TO-BAC system. The membrane permeabilization effect of NS3 expression was monitored by calcium influx into insect cells. Expression of either the vaccine or virulent associated AHSV-2 NS3 protein equally increased membrane permeability. The NS3 sequence variation therefore had a limited influence on membrane permeabilization properties and the virulence status of the vaccine and virulent AHSV-2 strains in this study. The possible effect of larger NS3 sequence variation levels on AHSV virulence was investigated by NS3 associated properties such as virus release and membrane permeabilization. AHSV infections increased the permeability of cell membranes and the different strains had different virus release properties. Virus release was not exclusively related to increased membrane permeability of infected cells or to the yield of the virus in the infected cells. The level of NS3 variation may influence AHSV release mechanisms and membrane permeabilization properties thereby contributing to AHSV virulence properties.Thesis (PhD (Genetics))--University of Pretoria, 2005.
Genetics
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Martinez, Jessica A., Betsy C. Wertheim, Cynthia A. Thomson, Jennifer W. Bea, Robert Wallace, Matthew Allison, Linda Snetselaar, Zhao Chen, Rami Nassir, and Patricia A. Thompson. "Physical Activity Modifies the Association between Dietary Protein and Lean Mass of Postmenopausal Women." ELSEVIER SCIENCE INC, 2017. http://hdl.handle.net/10150/623078.
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Background Maintenance of lean muscle mass and related strength is associated with lower risk for numerous chronic diseases of aging in women. Objective Our aim was to evaluate whether the association between dietary protein and lean mass differs by physical activity level, amino acid composition, and body mass index categories. Design We performed a cross-sectional analysis of a prospective cohort. Participants/setting Participants were postmenopausal women from the Womens Health Initiative with body composition measurements by dual-energy x-ray absorptiometry (n=8,298). Main outcome measures Our study measured percent lean mass, percent fat mass, and lean body mass index. Statistical analyses performed Linear regression models adjusted for scanner serial number, age, calibrated energy intake, race/ethnicity, neighborhood socioeconomic status, and recreational physical activity were used to determine the relationship between protein intake and body composition measures. Likelihood ratio tests and stratified analysis were used to investigate physical activity and body mass index as potential effect modifiers. Results Biomarker-calibrated protein intake was positively associated with percent lean mass; women in the highest protein quintile had 6.3 percentage points higher lean mass than the lowest quintile (P<0.001). This difference rose to 8.5 percentage points for physically active women in the highest protein quintile (P-interaction=0.023). Percent fat mass and lean body mass index were both inversely related to protein intake (both P<0.001). Physical activity further reduced percent fat mass (P-interaction=0.022) and lean body mass index (P-interaction=0.011). Leucine intake was associated with lean mass, as were branched chain amino acids combined (both P<0.001), but not independent of total protein. All associations were observed for normal-weight, overweight, and obese women. Conclusions Protein consumption up to 2.02 g/kg body weight daily is positively associated with lean mass in postmenopausal women. Importantly, those that also engage in physical activity have the highest lean mass across body mass index categories.
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Carnio, Leanne Katherine. "Direct association of integrin-linked kinase with a novel calponin homology domain-containing protein, CLINT." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 2000. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape2/PQDD_0022/MQ50412.pdf.
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Lilja, Sandra. "The association of the genes HvNAM1 and HvNAM2 with grain protein content in Nordic barley." Thesis, Linköpings universitet, Institutionen för fysik, kemi och biologi, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-119194.
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In barley, the GPC (Grain Protein Content) has proved to be of great importance for both feed, food and beer production. When it comes to feed and food, a high GPC is desirable since it indicates good nutritional values, while in beer production a low and stable GPC is needed to avoid beer chill haze. In previous studies a decrease in the GPC has been seen in different accessions of barley developed at different time periods during the last 100 years. The gene family HvNAM, including the genes HvNAM1 and HvNAM2, has in previous studies been shown to be important for the remobilization of nutrients towards the grains during the senescence and thus also for the GPC. In this study, 40 Nordic accessions from different improvement groups from the end of the 19th century until today have been analyzed for polymorphism in those genes. Statistical analyses has been conducted to investigate if there are any associations between the polymorph nucleotide positions and the nutritional values of grain protein, iron and zinc contents. However, no such associations were found. Instead some correlations could be seen between the nutrient content and thousand grain weight, a relative measurement of the grain size. In conclusion, since no polymorphisms were found to be associated to the nutritional value there might instead be a correlation between the gene expression and the nutritional value. Future work should thus focus on the gene expression of HvNAM1 and HvNAM2 in Nordic accessions of barley.
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Koster, Liza Sally. "C-reactive protein in canine babesiosis caused by Babesia rossi and its association with outcome." Diss., University of Pretoria, 2009. http://hdl.handle.net/2263/22860.
Full textAbstract:
Acute phase proteins (APP) are ideal biomarkers for inflammation due to their stability, relative ease of assay and apparent relation between their concentration and the extent of the insult to tissue. C-reactive protein (CRP) is a positive major APP in dogs and can be used as a predictive marker for risk of disease and to monitor the response to treatment. Increased concentrations in certain diseases are associated with poor outcome. This cross-sectional, observational study of 75 dogs naturally infected with Babesia rossi, a cause of virulent canine babesiosis, was designed to examine the association of CRP concentration at admission and the magnitude of CRP change 24 hours after admission with outcome. Dogs were excluded if there was evidence of concurrent inflammatory diseases at the time of admission, infection with subtypes other than B. rossi, concurrent Ehrlichia canis infections or euthanasia for reasons other than poor prognosis. Diagnosis was confirmed by polymerase chain reaction and reverse line blot. CRP concentrations were determined by an automated human CRP Turbidometric Immunoassay (TIA), previously validated for use in dogs (Bayer CRP TIA, Newbury, UK), on serum samples collected by jugular venipuncture on admission, prior to any therapy, and thereafter daily until discharge or death. There was no significant difference in admission CRP concentration between survivors (n = 57; median = 97.4 mg/l; mean ± SD = 107.5 ± 49.5), and non-survivors (n = 11; median = 101.4 mg/l; mean ± SD = 122.1 ± 64.6) (p = 0.39). After elimination of non-significant predictors, a multiple exact logistic regression model for predicting mortality contained glucose and CRP. Mortality was associated with decreased glucose levels (p = 0.0002) and increased CRP levels (p = 0.045) on admission. Multiple regression analysis failed to show a significant relationship between admission CRP concentration and number of days of hospitalization in the survivors, adjusting for age and sex (p = 0.65). No significance was found in the relationship between the magnitude of change in CRP concentration 24 hours after admission, and the number of days of hospitalization in survivors, (p = 0.34). Using an admission CRP concentration cut-off of 60 mg/l, survival proportions between the two groups were no different (p = 0.34) and when applied to the group of dogs that survived, it was not associated with length of hospitalization (p = 0.25). In corroboration with previous reports glucose was identified as a major prognostic marker for mortality, but additionally the pro-inflammatory marker CRP was identified as a significant co-prognosticator. CopyrightDissertation (MMedVet)--University of Pretoria, 2009.
Companion Animal Clinical Studies
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Zhang, Yifeng. "Association of Protein Disulfide Isomerase and ATP Synthase β Subunit with Membrane-Bound P-Glycoprotein." Thesis, The University of Arizona, 2014. http://hdl.handle.net/10150/322110.
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