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Hydrogen exchange mass spectrometry

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https://www.readbyqxmd.com/read/28816444/mapping-the-intricate-reactivity-of-nanojars-toward-molecules-of-varying-acidity-and-their-conjugate-bases-leading-to-exchange-of-pyrazolate-ligands
#1
Christian K Hartman, Gellert Mezei
A comprehensive reactivity study of nanojars toward 18 different acidic compounds with varying pKa, including 12 different carboxylic acids (both aliphatic and aromatic mono- and dicarboxylic acids), p-toluenesulfonic acid, hydrogen sulfate, hydrogen carbonate, carbonic acid, 1-decanethiol, and methanol, as well as four different conjugate bases (formate, acetate, benzoate, 2-bromoethanesulfonate) is carried out with the aid of electrospray-ionization mass spectrometry. Thus, the effect on nanojar substitution and breakdown pattern of a number of variables, such as concentration of reagent (acid or conjugate base), acidity of reagent (pKa), effect of acid vs conjugate base, steric effects, aromaticity, incarcerated anion and size of the nanojar, is evaluated...
August 17, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28810123/electrochemical-dissolution-of-iridium-and-iridium-oxide-par-ticles-in-acidic-media-transmission-electron-microscopy-electrochemical-flow-cell-coupled-to-inductively-coupled-plasma-mass-spectrometry-and-x-ray-absorption-spectros-copy-study
#2
Primož Jovanovič, Nejc Hodnik, Francisco Ruiz-Zepeda, Iztok Arcon, Barbara Jozinović, Milena Zorko, Marjan Bele, Martin Šala, Vid Simon Šelih, Samo B Hocevar, Miran Gaberscek
Iridium based particles as the most promising proton exchange membrane electrolyser electrocatalysts were investigated by transmission electron microscopy (TEM), and by coupling of electrochemical flow cell (EFC) with online inductively coupled plasma mass spectrometer (ICP-MS). Additionally, a thin-film rotating disc electrode (RDE), an identical location trans-mission and scanning electron microscopy (IL-TEM and IL-SEM) as well as an X-ray absorption spectroscopy (XAS) studies have been performed. Extremely sensitive online time-and potential-resolved electrochemical dissolution profiles revealed that iridium particles dissolved already well below oxygen evolution reaction (OER) potentials, presumably induced by iridium surface oxidation and reduction processes, also referred to as transient dissolution...
August 15, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28809482/structural-dynamics-of-15-lipoxygenase-2-via-hydrogen-deuterium-exchange
#3
Kristin Diane Droege, Mary E Keithly, Charles R Sanders, Richard N Armstrong, Matthew K Thompson
Eicosanoids are inflammatory signaling lipids that are biosynthesized in response to cellular injury or threat. They were originally thought to be pro-inflammatory molecules, but at least one sub-class, the lipoxins, are able to resolve inflammation. The first step in lipoxin synthesis is the oxygenation of arachidonic acid by 15-Lipoxygenase (15-LOX). 15-LOX contains two domains: a Ca2+ binding PLAT domain and a catalytic domain. 15-LOX is a soluble cytosolic protein until Ca2+ binding to the PLAT domain promotes translocation to the membrane surface...
August 15, 2017: Biochemistry
https://www.readbyqxmd.com/read/28797100/mapping-the-contact-surfaces-in-the-lamin-a-aimp3-complex-by-hydrogen-deuterium-exchange-ft-icr-mass-spectrometry
#4
Yeqing Tao, Pengfei Fang, Sunghoon Kim, Min Guo, Nicolas L Young, Alan G Marshall
Aminoacyl-tRNA synthetases-interacting multifunctional protein3 (AIMP3/p18) is involved in the macromolecular tRNA synthetase complex via its interaction with several aminoacyl-tRNA synthetases. Recent reports reveal a novel function of AIMP3 as a tumor suppressor by accelerating cellular senescence and causing defects in nuclear morphology. AIMP3 specifically mediates degradation of mature Lamin A (LmnA), a major component of the nuclear envelope matrix; however, the mechanism of how AIMP3 interacts with LmnA is unclear...
2017: PloS One
https://www.readbyqxmd.com/read/28781083/kras-g12c-drug-development-discrimination-between-switch-ii-pocket-configurations-using-hydrogen-deuterium-exchange-mass-spectrometry
#5
Jia Lu, Rane A Harrison, Lianbo Li, Mei Zeng, Sudershan Gondi, David Scott, Nathanael S Gray, John R Engen, Kenneth D Westover
KRAS G12C, the most common RAS mutation found in non-small-cell lung cancer, has been the subject of multiple recent covalent small-molecule inhibitor campaigns including efforts directed at the guanine nucleotide pocket and separate work focused on an inducible pocket adjacent to the switch motifs. Multiple conformations of switch II have been observed, suggesting that switch II pocket (SIIP) binders may be capable of engaging a range of KRAS conformations. Here we report the use of hydrogen/deuterium-exchange mass spectrometry (HDX MS) to discriminate between conformations of switch II induced by two chemical classes of SIIP binders...
July 25, 2017: Structure
https://www.readbyqxmd.com/read/28771359/modulation-of-the-extent-of-cooperative-structural-change-during-protein-folding-by-chemical-denaturant
#6
Prashant N Jethva, Jayant B Udgaonkar
Protein folding and unfolding reactions invariably appear to be highly cooperative reactions, but the structural and sequence determinants of cooperativity are poorly understood. Importantly, it is not known whether cooperative structural change occurs throughout the protein, or whether some parts change cooperatively and other parts change non-cooperatively. In the current study, hydrogen exchange mass spectrometry has been used to show that the mechanism of unfolding of the PI3K SH3 domain is similar in the absence and presence of 5 M urea...
August 3, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28770632/an-overview-of-hydrogen-deuterium-exchange-mass-spectrometry-hdx-ms-in-drug-discovery
#7
Glenn R Masson, Meredith L Jenkins, John E Burke
Introduction- Hydrogen deuterium exchange mass spectrometry (HDX-MS) is a powerful methodology to study protein dynamics, protein folding, protein-protein interactions, and protein small molecule interactions. The development of novel methodologies and technical advancements in mass spectrometers has greatly expanded the accessibility and acceptance of this technique within both academia and industry. Areas covered- This review examines the theoretical basis of how amide exchange occurs, how different mass spectrometer approaches can be used for HDX-MS experiments, as well as the use of HDX-MS in drug development, specifically focusing on how HDX-MS is used to characterize bio-therapeutics, and its use in examining protein-protein and protein small molecule interactions...
August 3, 2017: Expert Opinion on Drug Discovery
https://www.readbyqxmd.com/read/28770577/sec-saxs-and-hdx-ms-a-powerful-combination-the-case-of-the-calcium-binding-domain-of-a-bacterial-toxin
#8
REVIEW
Darragh P O'Brien, Sébastien Brier, Daniel Ladant, Dominique Durand, Alexandre Chenal, Patrice Vachette
Small-angle X-ray Scattering (SAXS) is a relatively simple experimental technique that provides information on the global conformation of macromolecules in solution, be they fully structured, partially, or extensively unfolded. Size Exclusion chromatography in line with a SAXS measuring cell considerably improves the mono-dispersity and ideality of solutions, the two main requirements of a "good" SAXS sample. Hydrogen/Deuterium eXchange monitored by Mass Spectrometry (HDX-MS) offers a wealth of information regarding the solvent accessibility at the local (peptide) level...
August 2, 2017: Biotechnology and Applied Biochemistry
https://www.readbyqxmd.com/read/28765527/calcium-ion-induced-structural-changes-promote-dimerization-of-secretagogin-which-is-required-for-its-insulin-secretory-function
#9
Jae-Jin Lee, Seo-Yun Yang, Jimin Park, James E Ferrell, Dong-Hae Shin, Kong-Joo Lee
Secretagogin (SCGN), a hexa EF-hand calcium binding protein, plays key roles in insulin secretion in pancreatic β-cells. It is not yet understood how the binding of Ca(2+) to human SCGN (hSCGN) promotes secretion. Here we have addressed this question, using mass spectrometry combined with a disulfide searching algorithm DBond. We found that the binding of Ca(2+) to hSCGN promotes the dimerization of hSCGN via the formation of a Cys193-Cys193 disulfide bond. Hydrogen/deuterium exchange mass spectrometry (HDX-MS) and molecular dynamics studies revealed that Ca(2+) binding to the EF-hands of hSCGN induces significant structural changes that affect the solvent exposure of N-terminal region, and hence the redox sensitivity of the Cys193 residue...
August 1, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28763166/comparison-of-three-methods-for-the-methylation-of-aliphatic-and-aromatic-compounds
#10
Hyejung Lee, Sarah J Feakins, Zhiyao Lu, Arndt Schimmelmann, Alex L Sessions, Jessica E Tierney, Travis J Williams
RATIONALE: Methylation protocols commonly call for acidic, hot conditions that are known to promote organic (1) H/(2) H exchange in aromatic and aliphatic C-H bonds. Here we tested two such commonly-used methods and compared a third that avoids these acidic conditions, to quantify isotope effects with each method and to directly determine acidic-exchange rates relevant to experimental conditions. METHODS: We compared acidic and non-acidic methylation approaches catalyzed by hydrochloric acid, acetyl chloride and EDCI (1-ethyl-3-(3-dimethylaminopropyl)carbodiimide) / DMAP (4-dimethylaminopyridine) respectively...
August 1, 2017: Rapid Communications in Mass Spectrometry: RCM
https://www.readbyqxmd.com/read/28758397/calcium-mediated-control-of-s100-proteins-allosteric-communication-via-an-agitator-signal-blocking-mechanism
#11
Yiming Xiao, Gary Stephen Shaw, Lars Konermann
Allosteric proteins possess dynamically coupled residues for the propagation of input signals to distant target binding sites. The input signals usually correspond to "effector is present" or "effector is not present". Many aspects of allosteric regulation remain incompletely understood. This work focused on S100A11, a dimeric EF-hand protein with two hydrophobic target binding sites. An annexin peptide (Ax) served as target. Target binding is allosterically controlled by Ca2+ over a distance of ~26 Å. Ca2+ promotes formation of a [Ca4 S100 Ax2] complex, where the Ax peptides are accommodated between helices III/IV and III'/IV'...
July 31, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28753295/empirical-correction-for-differences-in-chemical-exchange-rates-in-hydrogen-exchange-mass-spectrometry-measurements
#12
Ronald T Toth, Brittney J Mills, Sangeeta B Joshi, Reza Esfandiary, Steven M Bishop, C Russell Middaugh, David B Volkin, David D Weis
A barrier to the use of hydrogen exchange-mass spectrometry (HX-MS) in many contexts, especially analytical characterization of various protein therapeutic candidates, is that differences in temperature, pH, ionic strength, buffering agent, or other additives can alter chemical exchange rates, making HX data gathered under differing solution conditions difficult to compare. Here, we present data demonstrating that HX chemical exchange rates can be substantially altered not only by the well-established variables of temperature and pH but also by additives including arginine, guanidine, methionine, and thiocyanate...
August 11, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28747729/conformational-preludes-to-the-latency-transition-in-pai-1-as-determined-by-atomistic-computer-simulations-and-hydrogen-deuterium-exchange-mass-spectrometry
#13
Michael Petersen, Jeppe B Madsen, Thomas J D Jørgensen, Morten B Trelle
Both function and dysfunction of serine protease inhibitors (serpins) involve massive conformational change in their tertiary structure but the dynamics facilitating these events remain poorly understood. We have studied the dynamic preludes to conformational change in the serpin plasminogen activator inhibitor 1 (PAI-1). We report the first multi-microsecond atomistic molecular dynamics simulations of PAI-1 and compare the data with experimental hydrogen/deuterium-exchange data (HDXMS). The simulations reveal notable conformational flexibility of helices D, E and F and major fluctuations are observed in the W86-loop which occasionally leads to progressive detachment of β-strand 2 A from β-strand 3 A...
July 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28742962/characterization-of-intramolecular-interactions-of-cytochrome-c-using-hydrogen-deuterium-exchange-trapped-ion-mobility-spectrometry-mass-spectrometry-and-molecular-dynamics
#14
Juan Camilo Molano-Arevalo, Kevin Jeanne Dit Fouque, Khoa Pham, Jaroslava Miksovska, Mark E Ridgeway, Melvin A Park, Francisco Fernandez-Lima
Globular proteins, such as cytochrome c (cyt c), display an organized native conformation, maintained by a hydrogen bond interaction network. In the present work, the structural interrogation of kinetically trapped intermediates of cyt c was performed by correlating the ion-neutral collision cross section (CCS) and charge state with the starting solution conditions and time after desolvation using collision induced activation (CIA), time-resolved hydrogen/deuterium back exchange (HDX) and trapped ion mobility spectrometry-mass spectrometry (TIMS-MS)...
August 11, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28737905/metabolism-of-t-2-toxin-in-farm-animals-and-human-in-vitro-and-in-chickens-in-vivo-using-ultra-high-performance-liquid-chromatography-quadrupole-time-of-flight-hybrid-mass-spectrometry-along-with-online-hydrogen-deuterium-exchange-technique
#15
Shupeng Yang, Marthe De Boevre, Huiyan Zhang, Karl De Ruyck, Feifei Sun, Jinzhen Zhang, Yue Jin, Yanshen Li, Zhanhui Wang, Suxia Zhang, Jinhui Zhou, Yi Li, Sarah De Saeger
After incubated with animals' and human liver microsomes, metabolites of phase I and II were investigated. A comparison was performed by ultrahigh performance liquid chromatography-quadrupole/time-of-flight coupled to mass spectrometry (UHPLC-Q/TOF). Consequently, a total of four phase I metabolites and three glucuronide binding metabolites of T-2 toxin were discovered. Although a significant metabolic difference was observed among six species, HT-2 toxin was the major product in all species. In addition, the in vivo metabolism of T-2 toxin after oral administration was also investigated in chickens, In total, 18 metabolites were detected, of which 13 were novel, to our knowledge, and reported for the first time...
July 24, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/28727449/use-of-maldi-ms-combined-with-differential-hydrogen-deuterium-exchange-for-semiautomated-protein-global-conformational-screening
#16
Gregory F Pirrone, Heather Wang, Nicole Canfield, Alexander S Chin, Timothy A Rhodes, Alexey A Makarov
Matrix-assisted laser desorption/ionization (MALDI) coupled with a time-of-flight (TOF) mass-spectrometry (MS) detector is acknowledged to be very useful for analysis of biological molecules. At the same time, hydrogen-deuterium exchange (HDX) is a well-known technique for studying protein higher-order structure. However, coupling MALDI with HDX has been challenging because of undesired back-exchange reactions during analysis. In this report, we survey an approach that utilizes MALDI coupled with an automated sample preparation to compare global conformational changes of proteins under different solution conditions using differential HDX...
August 4, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28727441/adsorption-induced-changes-of-human-hemoglobin-on-ferric-pyrophosphate-nanoparticle-surface-probed-by-isotope-exchange-mass-spectrometry-an-implication-on-structure-function-correlation
#17
Bindu Y Srinivasu, Beena Bose, Gopa Mitra, Anura V Kurpad, Amit K Mandal
In general, proteins in the biological system interact with nanoparticles (NPs) via adsorption on the particle surface. Understanding the adsorption at the molecular level is crucial to explore NP-protein interactions. The increasing concerns about the risk to human health on NP exposure have been explored through the discovery of a handful protein biomarkers and biochemical analysis. However, detailed information on structural perturbation and associated functional changes of proteins on interaction with NPs is limited...
August 2, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28724631/the-axl-kinase-domain-in-complex-with-a-macrocyclic-inhibitor-offers-first-structural-insights-into-an-active-tam-receptor-kinase
#18
Ketan S Gajiwala, Neil Grodsky, Ben Bolaños, Junli Feng, RoseAnn Ferre, Sergei Timofeevski, Meirong Xu, Brion W Murray, Ted W Johnson, Al Stewart
The receptor tyrosine kinase (RTK) family consisting of Tyro3, Axl and Mer (TAM) is one of the most recently identified RTK families. TAM receptors are upregulated postnatally and maintained at high levels in adults. They all play an important role in immunity, but Axl has also been implicated in cancer and therefore is a target in the discovery and development of novel therapeutics. However, of the three members of the TAM family, the Axl kinase domain is the only one that has so far eluded structure determination...
July 19, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28714672/chemical-denaturants-smoothen-ruggedness-on-the-free-energy-landscape-of-protein-folding
#19
Pooja Malhotra, Prashant N Jethva, Jayant B Udgaonkar
To characterize experimentally the ruggedness of the free energy landscape of protein folding is challenging, because the distributed small free energy barriers are usually dominated by one, or a few, large activation free energy barriers. This study delineates changes in the roughness of the free energy landscape by making use of the observation that a decrease in ruggedness is accompanied invariably by an increase in folding cooperativity. Hydrogen exchange (HX) coupled to mass spectrometry was used to detect transient sampling of local energy minima and the global unfolded state on the free energy landscape of the small protein single-chain monellin...
August 8, 2017: Biochemistry
https://www.readbyqxmd.com/read/28702519/bottom-up-hydrogen-deuterium-exchange-mass-spectrometry-data-analysis-and-interpretation
#20
Kerene A Brown, Derek J Wilson
Hydrogen Deuterium Exchange (HDX) Mass Spectrometry (MS) is a sensitive analytical technique that provides information on protein conformation and dynamics in solution. It is commonly used in the study of protein-ligand and protein-protein interactions and more recently in the pharmaceutical industry for epitope mapping, screening drug candidates and in the comparison of biopharmaceuticals to biosimilars. HDX-MS monitors the exchange of protein backbone hydrogen atoms with deuterium in solution. Recent advancements in HDX automation and data analysis, have taken the emphasis off developing a fundamental understanding of HDX, which is still lacking...
August 7, 2017: Analyst
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