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hydrogen deuterium exchange

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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
#1
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
#2
Juan Camilo Molano-Arevalo, Kevin Jeanne Dit Fouque, Khoa N 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)...
July 25, 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
#3
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/28731753/new-measurements-of-the-beam-normal-spin-asymmetries-at-large-backward-angles-with-hydrogen-and-deuterium-targets
#4
D Balaguer Ríos, K Aulenbacher, S Baunack, J Diefenbach, B Gläser, D von Harrach, Y Imai, E-M Kabuß, R Kothe, J H Lee, H Merkel, M C Mora Espí, U Müller, E Schilling, C Weinrich, L Capozza, F E Maas, J Arvieux, M A El-Yakoubi, R Frascaria, R Kunne, M Morlet, S Ong, J van de Wiele, S Kowalski, Y Prok
New measurements of the beam normal single spin asymmetry in the electron elastic and quasielastic scattering on the proton and deuteron, respectively, at large backward angles and at ⟨Q^{2}⟩=0.22  (GeV/c)^{2} and ⟨Q^{2}⟩=0.35  ( GeV/c)^{2} are reported. The experimentally observed asymmetries are compared with the theoretical calculation of Pasquini and Vanderhaeghen [Phys. Rev. C 70, 045206 (2004).PRVCAN0556-281310.1103/PhysRevC.70.045206]. The agreement of the measurements with the theoretical calculations shows a dominance of the inelastic intermediate excited states of the nucleon, πN and the Δ resonance...
July 7, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28727449/the-use-of-maldi-ms-combined-with-differential-hydrogen-deuterium-exchange-for-semi-automated-protein-global-conformational-screening
#5
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 may be challenging due to undesired back-exchange reactions during analysis. In this report, we survey an approach that utilizes MALDI coupled with automated sample preparation to compare global conformational changes of proteins under different solution conditions using differential HDX...
July 20, 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
#6
Bindu Y Srinivasu, Beena Bose, Gopa Mitra, Anura V Kurpad, Amit Kumar Mandal
In general, proteins in the biological system interact with nanoparticles (NPs) via adsorption on the particle surface. Understanding the adsorption at 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...
July 20, 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
#7
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/28702519/bottom-up-hydrogen-deuterium-exchange-mass-spectrometry-data-analysis-and-interpretation
#8
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...
July 13, 2017: Analyst
https://www.readbyqxmd.com/read/28700824/application-of-hdx-ms-to-biopharmaceutical-development-requirements-improved-sensitivity-to-detection-of-conformational-changes
#9
Lea Bonnington, Ingo Lindner, Ulrich Gilles, Tobias Kailich, Dietmar Reusch, Patrick Bulau
The usefulness of the higher-order structure information provided by hydrogen/deuterium exchange mass spectrometry (HDX-MS) in the protein therapeutic field is undisputed, however its applicability as a method for critical quality and comparability assessment has until now not been demonstrated. Here we present results demonstrating for the first time the applicability of the HDX-MS technique to monitor structural changes due to methionine oxidation at sensitivity levels realistic to the requirements of biopharmaceutical research and development...
July 12, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28696098/enhanced-binding-affinity-via-destabilization-of-the-unbound-state-a-millisecond-hydrogen-deuterium-exchange-study-of-the-interaction-between-p53-and-a-pleckstrin-homology-domain
#10
Shaolong Zhu, Rahima Khatun, Cristina Lento, Yi Sheng, Derek J Wilson
The incorporation of intrinsically disordered domains enables proteins to engage a wide variety of targets, with phosphorylation often modulating target specificity and affinity. Although phosphorylation can clearly act as a chemical driver of complexation in structured proteins, e.g., by abrogating or permitting new charge-charge interactions, the basis for enhancement of the hydrophobically driven interactions that are typical of disordered protein-target complexation is less clear. To determine how phosphorylation can positively impact target recruitment in disordered domains, we have examined the interaction between the disordered N-terminal transactivation domain (TAD) of p53 and the pleckstrin homology (PH) domain of p62...
July 19, 2017: Biochemistry
https://www.readbyqxmd.com/read/28695211/solving-protein-structures-using-short-distance-cross-linking-constraints-as-a-guide-for-discrete-molecular-dynamics-simulations
#11
Nicholas I Brodie, Konstantin I Popov, Evgeniy V Petrotchenko, Nikolay V Dokholyan, Christoph H Borchers
We present an integrated experimental and computational approach for de novo protein structure determination in which short-distance cross-linking data are incorporated into rapid discrete molecular dynamics (DMD) simulations as constraints, reducing the conformational space and achieving the correct protein folding on practical time scales. We tested our approach on myoglobin and FK506 binding protein-models for α helix-rich and β sheet-rich proteins, respectively-and found that the lowest-energy structures obtained were in agreement with the crystal structure, hydrogen-deuterium exchange, surface modification, and long-distance cross-linking validation data...
July 2017: Science Advances
https://www.readbyqxmd.com/read/28692141/a-discontinuous-autoinhibitory-module-masks-the-a1-domain-of-von-willebrand-factor
#12
Wei Deng, Yingchun Wang, Samuel A Druzak, John F Healey, Anum K Syed, Pete Lollar, Renhao Li
BACKGROUND: How von Willebrand factor (VWF) senses and responds to shear flow remains unclear. In the absence of shear VWF or its fragments can be induced to bind spontaneously to platelet GPIbα. Objectives To elucidate the auto-inhibition mechanism of VWF. METHODS: Hydrogen-deuterium exchange (HDX) of two recombinant VWF fragments expressed from baby hamster kidney cells were measured and compared. RESULTS: The shortA1 protein contains VWF residues 1261-1472 and binds GPIbα with a significantly higher affinity than the longA1 protein that contains VWF residues 1238-1472...
July 10, 2017: Journal of Thrombosis and Haemostasis: JTH
https://www.readbyqxmd.com/read/28691068/hydrogen-deuterium-exchange-of-lipoxygenase-uncovers-a-relationship-between-distal-solvent-exposed-protein-motions-and-the-thermal-activation-barrier-for-catalytic-proton-coupled-electron-tunneling
#13
Adam R Offenbacher, Shenshen Hu, Erin M Poss, Cody A M Carr, Alexander D Scouras, Daniil M Prigozhin, Anthony T Iavarone, Ali Palla, Tom Alber, James S Fraser, Judith P Klinman
Defining specific pathways for efficient heat transfer from protein-solvent interfaces to their active sites represents one of the compelling and timely challenges in our quest for a physical description of the origins of enzyme catalysis. Enzymatic hydrogen tunneling reactions constitute excellent systems in which to validate experimental approaches to this important question, given the inherent temperature independence of quantum mechanical wave function overlap. Herein, we present the application of hydrogen-deuterium exchange coupled to mass spectrometry toward the spatial resolution of protein motions that can be related to an enzyme's catalytic parameters...
June 28, 2017: ACS Central Science
https://www.readbyqxmd.com/read/28683921/biology-mechanism-and-structure-of-enzymes-in-the-%C3%AE-d-phosphohexomutase-superfamily
#14
Kyle M Stiers, Andrew G Muenks, Lesa J Beamer
Enzymes in the α-d-phosphohexomutases superfamily catalyze the reversible conversion of phosphosugars, such as glucose 1-phosphate and glucose 6-phosphate. These reactions are fundamental to primary metabolism across the kingdoms of life and are required for a myriad of cellular processes, ranging from exopolysaccharide production to protein glycosylation. The subject of extensive mechanistic characterization during the latter half of the 20th century, these enzymes have recently benefitted from biophysical characterization, including X-ray crystallography, NMR, and hydrogen-deuterium exchange studies...
2017: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/28671821/the-t-cell-receptor-can-bind-to-the-peptide-bound-major-histocompatibility-complex-and-uncomplexed-beta-2-microglobulin-through-distinct-binding-sites
#15
Patrick Sascha Merkle, Melita Irving, Song Hongjian, Mathias Ferber, Thomas J D Jørgensen, Kirsten Scholten, Immanuel Florian Luescher, George Coukos, Vincent Zoete, Michel A Cuendet, Olivier Michielin, Kasper D Rand
T-cell receptor (TCR)-mediated recognition of peptide-bound major histocompatibility complex (pMHC) initiates an adaptive immune response against antigen-presenting target cells. The recognition events take place at the TCR-pMHC interface and their implications on TCR conformation and dynamics are controversial. Here, we have measured the time-resolved hydrogen/deuterium exchange (HDX) of a soluble TCR in the presence and absence of its cognate pMHC by mass spectrometry to delineate the impact of pMHC binding on solution-phase structural dynamics in the TCR...
July 3, 2017: Biochemistry
https://www.readbyqxmd.com/read/28665589/visualization-and-quantification-of-igg-antibody-adsorbed-at-the-cellulose-liquid-interface
#16
Vikram Singh Raghuwanshi, Jielong Su, Christopher J Garvey, Stephen A Holt, Peter J Holden, Warren J Batchelor, Gil Garnier
Quantification of adsorbed biomolecules (enzymes, proteins) at the cellulose interface is a major challenge in developing eco-friendly biodiagnostics. Here, a novel methodology is developed to visualize and quantify the adsorption of antibody from solution to the cellulose-liquid interface. The concept is to deuterate cellulose by replacing all nonexchangeable hydrogens from the glucose rings with deuterium in order to enhance the scattering contrast between the cellulose film surface and adsorbed antibody molecules...
July 12, 2017: Biomacromolecules
https://www.readbyqxmd.com/read/28657415/the-investigation-of-the-bio-oil-produced-by-hydrothermal-liquefaction-of-spirulina-platensis-using-ultrahigh-resolution-fourier-transform-ion-cyclotron-resonance-mass-spectrometry
#17
Yury Kostyukevich, Mikhail Vlaskin, Gleb Vladimirov, Alexander Zherebker, Alexey Kononikhin, Igor Popov, Eugene Nikolaev
We report the investigation of the hydrothermal liquefaction products of the Spirulina platensis microalgae by using the Fourier transform ion cyclotron resonance mass spectrometry. The hydrothermal liquefaction produced two fractions: one with boiling temperature below 300℃ and the dense residue that remained in the reactor. It was observed that N2 and N classes of compounds that dominate in the positive ESI Fourier transform ion cyclotron resonance spectra for both fractions, and that the light fraction is considerably more saturated then the heavy one...
April 2017: European Journal of Mass Spectrometry
https://www.readbyqxmd.com/read/28657298/the-aspergillus-niger-prolyl-endoprotease-an-pep-for-hydrogen-deuterium-exchange-mass-spectrometry-and-protein-structural-studies
#18
Liana Tsiatsiani, Michiel Akeroyd, Maurien Olsthoorn, Albert J R Heck
To monitor the structural integrity of therapeutic proteins, hydrogen-deuterium exchange mass spectrometry (HDX-MS) is increasingly utilized in the pharmaceutical industry. The successful outcome of HDX-MS analyses depends on the sample preparation conditions, which involve the rapid digestion of proteins at 0°C and pH 2.5. Very few proteases are able to withstand such harsh conditions, with pepsin being the best-known exception, even though its activity is also strongly reduced at 0°C. Here, we evaluate the usage of a Prolyl-endopeptidase from Aspergillus niger (An-PEP) for HDX-MS...
June 28, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28652337/mine-conformational-dynamics-regulate-membrane-binding-mind-interaction-and-min-oscillation
#19
Kyung-Tae Park, Maria T Villar, Antonio Artigues, Joe Lutkenhaus
In Escherichia coli MinE induces MinC/MinD to oscillate between the ends of the cell, contributing to the precise placement of the Z ring at midcell. To do this, MinE undergoes a remarkable conformational change from a latent 6β-stranded form that diffuses in the cytoplasm to an active 4β-stranded form bound to the membrane and MinD. How this conformational switch occurs is not known. Here, using hydrogen-deuterium exchange coupled to mass spectrometry (HDX-MS) we rule out a model in which the two forms are in rapid equilibrium...
June 26, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28638775/host-guest-complexes-of-c-ethyl-2-methylresorcinarene-and-aromatic-n-n-dioxides
#20
Rakesh Puttreddy, Ngong Kodiah Beyeh, Robin H A Ras, Kari Rissanen
The C-ethyl-2-methylresorcinarene (1) forms 1:1 in-cavity complexes with aromatic N,N'-dioxides, only if each of the aromatic rings has an N-O group. The structurally different C-shaped 2,2'-bipyridine N,N'-dioxide (2,2'-BiPyNO) and the linear rod-shaped 4,4'-bipyridine N,N'-dioxide (4,4'-BiPyNO) both form 1:1 in-cavity complexes with the host resorcinarene in C4v crown and C2v conformations, respectively. In the solid state, the host-guest interactions between the 1,3-bis(4-pyridyl)propane N,N'-dioxide (BiPyPNO) and the host 1 stabilize the unfavorable anti-gauche conformation...
June 2017: ChemistryOpen
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