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 22 for “"HDX"”.
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Advancing the characterization of glycan dynamics with in-electrospray ionization hydrogen/deuterium exchange-mass spectrometry.
… information. Hydrogen/deuterium exchange (HDX-MS) is a labeling technique that monitors the exchanging labile hydrogen atoms for molecules across different timepoints. Traditionally, HDX-MS has been used to study protein structure and dynamics; however, this deuterium labeling method has …
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Application of hydrogen deuterium exchange mass spectrometry in protein-ligand and protein-protein interactions
… Hydrogen-deuterium exchange mass spectrometry (HDX-MS), a combination of HPLC and MS, has become a common and sensitive tool to probe protein structural flexibility and solution dynamics. In this dissertation, HDX-MS was applied to study dynamic changes of proteins due to substrate binding and …
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From Solution Into the Gas Phase: Studying Protein Hydrogen Exchange and Electrospray Ionization Using Molecular Dynamics Simulation
… underlying Hydrogen/Deuterium exchange (HDX). HDX interrogates structural dynamics of proteins by measuring the rate of Deuterium uptake into backbone amides. We perform microsecond MD simulations on ubiquitin to investigate this process. We find that HDX protection often cannot be …
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Hydrogen-deuterium exchange studies by mass spectrometry: A method for obtaining conformational structures of proteins in solution
Hydrogen-deuterium exchange (HDX) coupled with electrospray ionization (ESI) in mass spectrometry (MS) has become an important method in the study of protein structure and dynamics. It provides an opportunity for obtaining conformational structures of protein motions in physiological conditions and …
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Investigating the Rotary Mechanism of ATP Synthase Using Molecular Dynamics Simulations
… opening events coincided with experimental HDX patterns obtained in our laboratory. HDX-MS data suggests that in vitro operation of F1-ATPase is associated with significant rotational resistance in the apical bearing. These conditions cause the γ C-terminal helix to get “stuck” while the …
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Biophysical Investigation into the Protein Dynamics Governing the Allosteric Regulation of Plant and Animal 15-Lipoxygenases
… hydrogen-deuterium exchange mass spectrometry (HDX-MS), revealing that the addition of the allosteric effector, oleyl sulfate (OS), alters a specific region of the enzyme. Herein, we used a combination of thermodynamic and biophysical techniques such as isothermal titration calorimetry and …
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Mass Spectrometry-Based Strategies for Biomolecular Structure Analysis: Steroid Metabolites Structures and Protein-Protein Interactions
… strategies, namely, hydrogen-deuterium exchange (HDX) and fast photochemical oxidation of proteins (FPOP), are applied in two studies of protein-protein interactions, including: (1) dimerization of SecA, which is a motor protein in bacteria translocation pathway; and (2) interface mapping of EGFR …
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Investigating the Structure and Physical Stability of Glp1-Like Peptides Using Mass Spectrometry
… MS (TWIMS) and hydrogen-deuterium exchange MS (HDX-MS), and the two peptide systems in this work provided different case studies with which structural mass spectrometry could be used to investigate the origins of batch variation in physical stability. TWIMS was used to investigate the five …
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Endothelial progenitor cells, uraemic toxins, and the development of endothelial dysfunction in chronic kidney disease.
… At a clinical level, in groups of haemodialysis (HDx), KTx patients and controls, low peripheral blood (PB) EPC numbers were correlated with surrogate markers of CVD and ED. No clear relationship of IS and PC/S with ED was seen (although study power was limited). For in vitro studies, techniques …
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Structural Basis of Signal Transduction within Environmental Sensing PAS Regulated Ser/Thr Kinases
… biochemical and biophysical tools, including HDX-MS, cryo-EM, NMR, and X-ray crystallography to elucidate the structural dynamics of these proteins both at the domain and multi-domain levels.</p> <p>In hPASK, our high-pressure NMR and HDX-MS data with artificial ligands identified ligand …
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Efficient sampling of protein conformational dynamics and prediction of mutation effects.
… ensembles with Hydrogen/Deuterium exchange (HDX) protection measurements, by constructing multi-ensemble Markov State Models (MEMMs) from biased MD simulations, and reconciling these predictions against the experimental data using the BICePs (Bayesian Inference of Conformational Populations) …
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Structural Polymorphism of Alpha-Synuclein in Conditions Resembling the Cellular Environment
… via Hydrogen-Deuterium Mass Spectrometry (HDX-MS) and the fibril products formed at the end of the kinetic assays were analysed structurally by Atomic Force Microscopy (AFM). The environmental parameters interrogated were high calcium concentrations, (which are particularly relevant in the …
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Characterizing Conformational Dynamics and Catalytic Activity of Enzymes by Hydrogen-Deuterium Exchange Mass Spectrometry
… and an adjustable reaction volume, time resolved HDX experimentation was used to monitor deuteration events concurrently with catalytic activity on the millisecond to second timescale. Native mass spectrometry enabled studies into binding affinity and monitoring of substrate inactivation on a …
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Study of the Dynamics of Retaining GT-B Fold Glycosyltransferases Using Hydrogen Deuterium Exchange Mass Spectrometry
… hydrogen-deuterium exchange mass spectrometry(HDX-MS) is used to analyze CgMshA from Corynebacterium glutamicum, a model enzymefrom GT-B fold. In the presence of acceptor substrate inositol-1-phosphate (I1P), decreaseddynamics occur in CgMshA's N-terminal domain (NTD) and linker regions. …
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Actin-like filament A (AlfA) and AlfA-driven plasmid segregation
… hydrogen-deuterium exchange mass spectrometry (HDX-MS). A comparison of AlfA structure with other actins revealed a unique nucleotide binding conformation, which causes AlfA to remain stable after nucleotide hydrolysis. In addition to the filament structure, we reconstituted the segresome …
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Structural and Functional Characterisation of the Nutrient Sensing Kinase GCN2
… use of biochemical methods in combination with HDX-MS to characterise the interactions between Hsp90’s co-chaperone Cdc37 and client kinases. These analyses enabled the identification of a correlation between protein stability and dependence on Hsp90/Cdc37, and revealed that Cdc37 binding causes …
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Characterisation of Prodomains in the GDNF Family
… hydrogen deuterium exchange mass spectrometry (HDX-MS) no interaction between the NRTN prodomain and mature domain could be identified, again unlike other TGF-β proteins. This work highlights the diversity of prodomain structure and function in the TGF-β superfamily and suggests a common theme …
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Data Standardization and Machine Learning Models for Histopathology
… used when recording histopathological diagnoses (HDX, one or more HF from one or more tissues). Next, our aim was to identify free-text HF not currently expressed in the WSAVA format that may provide evidence for distinguishing between IBD and ALA in cats. As part of this work, we hypothesized …
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Discovery and Identification of New DNA Photoproducts and Investigation of the Redox Mechanism of Human Apurinic/Apyrimidinic Endonuclease 1 (hApe1) Protein
… We used amide hydrogen/deuterium exchange: HDX) and N-ethylmaleimide: NEM) labeling coupled MS analysis to probe the interaction of hApe1 and E3330. Our study suggests there is a minor amount of a locally unfolded form existing in equilibrium with the major folded form of hAp1. This locally …
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FROM ANTIBODY-DRUG CONJUGATES TO MASKED ANTIBODIES: BIOPHYSICAL INSIGHT FOR THE RATIONAL DESIGN OF FUTURE THERAPIES
… undertaken under the quench conditions used in HDX-MS experiments. Results provide confirmation that the rate of unfolding of an antibody domain limits resolution in these experiments.
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