Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 20 of 32 for “"proteome-wide"”.
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Proteome-Wide Prediction of Acetylation Substrates
<p>Eukaryotic DNA is found packaged with proteins and RNA, which forms a substance called chromatin. This packaging is dynamic and regulates access to DNA for essential cellular processes such as transcription, replication, and repair. In recent years, studies have shown that regulated changes in …
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Deep learning and coevolution reveal proteome-wide protein-protein interactions
… interactions (PPI) within an organism's proteome guides a plethora of potential biological processes at an organism’s disposal. Understanding these PPIs is critical to our understanding of biological systems, however identifying interactions with high accuracy is challenging. Medium to …
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Proteome-wide Functional Profiling of Serine Hydrolases in the Human Malaria Parasite
The serine hydrolase (SH) enzyme superfamily is one of the largest and most diverse enzyme classes in eukaryotes and prokaryotes. The most virulent human malaria parasite Plasmodium falciparum has over 40 predicted serine hydrolases (SH). Prior investigation on a few of these have suggested their …
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Investigation of an energetic coupling between ligand binding and protein folding
… metabolites are being uncovered through proteome-wide screens. The homodimeric <em>Escherichia coli</em> cofactor-dependant phosphoglycerate mutase (dPGM) was identified as an ATP binding protein in a proteome-wide screen, but dPGM does not use ATP for catalysis. This dissertation …
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Proteomic analysis of protein complexes and cell cycle regulation in <i>Trypanosoma brucei</i>
… of protein interactions and the analysis of proteome changes across the cell-cycle.<br/>To enable these approaches, I developed protocols for proteome wide analysis of protein complexes in <i>Trypanosoma brucei</i>, combining multiple forms of chromatography on ‘native’ lysates of cells to …
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Targeting and Manipulating Endogenous Transcriptional Condensates
… spectrometry. Our approach opens the road to the proteome-wide investigation of the transcriptional condensates. In this thesis, we discuss the development and future outlook of the technique.
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Development and Application of a quantitative Mass spectrometry based Platform for Thermodynamic Analysis of Protein interaction Networks
… and application of a SPROX protocol for proteome-wide thermodynamic analyses that involves the use of Stable Isotope Labeling by Amino acid in cell Culture (SILAC) quantitation. A solution-based SILAC-SPROX protocol is described in Part III and a SILAC-SPROX protocol involving the use of …
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Asssessing the Liquid-Liquid Phase Separation Abilities of Eyes Absent Protein
… domain” (TAD) in the N-terminus. Despite wide sequence variation in human EYA1-4 TADs, with approximately 40% identity conserved vs. 77% identity conserved in the ED, all four EYA TADs were identified as potential drivers of liquid-liquid phase separation in a proteome-wide screen. The …
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Protein structure and interaction under environmental stress : from quality control recognition to evolution of collective behavior
… both acidifies its cytosol and exhibits widespread protein clustering. By employing a proteome-wide computational assay, I examine how this drop in pH could lead to the formation of higher order protein structures. This modeling framework also provides a rationale for why these two …
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Application and Evaluation of a Chemical Modification- and Mass Spectrometry-Based Thermodynamic Assay for the Study of Protein-Ligand Interactions in Complex Mixtures
… that could assay all the proteins in the proteome for both direct and indirect binding interactions of drugs would greatly facilitate studies of drug action. Recently, the SPROX (stability of proteins from rates of oxidation) technique was developed as a chemical modification- and mass …
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Characterization of the Ubiquitin N-end Rule Pathway in Arabidopsis
… tagging tool with the aim of conducting a proteome-wide screen for N-end rule substrates. Additionally, experiments were carried out to characterize a component of the Arabidopsis N-end rule pathway by expressing this enzyme in the yeast S. cerevisiae under different conditions. This study …
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Elucidating the role of SRSF1, a prototypical splicing factor, in liver physiology
… pathology was gained using transcriptome- and proteome-wide approaches such as RNA-Seq, eCLIP-Seq, and mass spectrometry. Extensive investigation to the molecular mechanism underlying the pathology revealed loss of SRSF1 activity leads to widespread DNA damage and defects in global translation. …
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Determining the Rates of Protein Synthesis in the Zebrafish Heart in Response to Chronic Unpredictable Stress
The proteome is in constant flux and therefore it is important to understand the contribution of protein dynamics to the function of an organism. The zebrafish (Danio rerio) is a recognised model organism that is widely used to investigate physiological processes. The focus of this thesis was to …
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Characterization of Protein Complexes and Protein Interaction Networks by Mass Spectrometry
… methods, such as yeast two hybrid screens or proteome-wide purification of protein complexes. We found that repetitive purification of protein complexes using different subunits as baits is crucially important for confident charting of proteomic environments. Accurate dissection of individual …
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Exploration of a liquid droplet state for α-synuclein in vitro and in vivo
A wide range of human disorders, including Parkinson’s disease (PD), are associated with protein misfolding and aggregation. Misfolded a-synuclein is a major constituent of intracellular inclusions called Lewy bodies, which are a key hallmark of PD. A large body of work shows that a-synuclein can …
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Systematic C-degron activity profiling implicates conditional regulation of the CTLH E3 ligase complex in ribosome maturation.
… by Cterminal degrons, providing the first proteome-wide genetic tool for exploring C-degron biology in the context of full-length substrates. This analysis identified that ZMYND19 harbours a C-degron targeted by the Muskelin substrate adapter of the CTLH E3 ligase complex. Characterisation …
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Proteomic Characterisation of the mdx-4cv mouse model of Duchenne Muscular Dystrophy
… the aged heart, and brain tissue to investigate proteome-wide changes in the skeletal musculature, the cardiorespiratory system and the central nervous system. In addition, proteomic profiling of serum and saliva samples from dystrophic mdx-4cv mice has been conducted to identify potential …
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Analysis of Human Protein Complexes by Quantitative Mass Spectrometry
… I present in this thesis enable the rapid, proteome-wide analysis of endogenous protein complexes, which will advance the future study of protein complexes in biology.<br/>
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Development and Application of Covalent-Labeling Strategies for the Large-Scale Thermodynamic Analysis of Protein Folding and Ligand Binding
… developed mass spectrometry-based approach for proteome-wide thermodynamic stability analysis. Since the proteomic coverage of SPROX is fundamentally limited by the detection of methionine-containing peptides, the use of tryptophan-containing peptides was investigated in this dissertation. A new …
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Web servers, databases, and algorithms for the analysis of protein interaction networks
… regression. Furthermore, we create a community-wide web-resource that predicts interactions between any protein sequence pair and provides proteome-wide pre-computed PPI predictions for Homo sapiens, Drosophila melanogaster, and Saccharomyces cerevisiae. 2. Comparative analysis of PPI networks …
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