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Hydrogen exchange mass spectrometry

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https://www.readbyqxmd.com/read/29210567/correction-to-empirical-correction-for-differences-in-chemical-exchange-rates-in-hydrogen-exchange-mass-spectrometry-measurements
#1
Ronald T Toth, Brittney J Mills, Sangeeta B Joshi, Reza Esfandiary, Steven M Bishop, C Russell Middaugh, David B Volkin, David D Weis
No abstract text is available yet for this article.
December 6, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29196701/the-repeat-region-of-cortactin-is-intrinsically-disordered-in-solution
#2
Xiaofeng Li, Yeqing Tao, James W Murphy, Alexander N Scherer, TuKiet T Lam, Alan G Marshall, Anthony J Koleske, Titus J Boggon
The multi-domain protein, cortactin, contains a 37-residue repeating motif that binds to actin filaments. This cortactin repeat region comprises 6½ similar copies of the motif and binds actin filaments. To better understand this region of cortactin, and its fold, we conducted extensive biophysical analysis. Size exclusion chromatography with multi-angle light scattering (SEC-MALS) reveals that neither constructs of the cortactin repeats alone or together with the adjacent helical region homo-oligomerize. Using circular dichroism (CD) we find that in solution the cortactin repeats resemble a coil-like intrinsically disordered protein...
December 1, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29185984/conserved-rna-binding-specificity-of-polycomb-repressive-complex-2-is-achieved-by-dispersed-amino-acid-patches-in-ezh2
#3
Yicheng Long, Ben Bolanos, Lihu Gong, Wei Liu, Karen J Goodrich, Xin Yang, Siming Chen, Anne R Gooding, Karen A Maegley, Ketan S Gajiwala, Alexei Brooun, Thomas R Cech, Xin Liu
Polycomb repressive complex 2 (PRC2) is a key chromatin modifier responsible for methylation of lysine 27 in histone H3. PRC2 has been shown to interact with thousands of RNA species in vivo, but understanding the physiological function of RNA binding has been hampered by the lack of separation-of-function mutants. Here, we use comprehensive mutagenesis and hydrogen deuterium exchange mass spectrometry (HDX-MS) to identify critical residues for RNA interaction in PRC2 core complexes from Homo sapiens and Chaetomium thermophilum, for which crystal structures are known...
November 29, 2017: ELife
https://www.readbyqxmd.com/read/29182876/solid-state-hydrogen-deuterium-exchange-mass-spectrometry-correlation-of-deuterium-uptake-and-long-term-stability-of-lyophilized-monoclonal-antibody-formulations
#4
Balakrishnan S Moorthy, Isidro E Zarraga, Lokesh Kumar, Benjamin T Walters, Pierre Goldbach, Elizabeth M Topp, Andrea Allmendinger
Solid state hydrogen-deuterium exchange with mass spectrometric analysis (ssHDX-MS) has been used to assess protein conformation and matrix interactions in lyophilized solids. ssHDX-MS metrics have been previously correlated to the formation of aggregates of lyophilized myoglobin on storage. Here, ssHDX-MS was applied to lyophilized monoclonal antibody (mAb) formulations and correlated to their long-term stability. After exposing lyophilized samples to D2O(g), the amount of deuterium incorporated at various time points was determined by mass spectrometry for four different lyophilized mAb formulations...
November 28, 2017: Molecular Pharmaceutics
https://www.readbyqxmd.com/read/29171882/characterization-of-epitope-specificities-of-reference-antibodies-used-for-the-quantification-of-the-birch-pollen-allergen-bet-v-1
#5
Sébastien Brier, Maxime Le Mignon, Karine Jain, Constance Lebrun, François Peurois, Christine Kellenberger, Véronique Bordas-Le Floch, Laurent Mascarell, Emmanuel Nony, Philippe Moingeon
BACKGROUND: Accurate allergen quantification is needed to document the consistency of allergen extracts used for immunotherapy. Herein, we characterize the epitope specificities of two monoclonal antibodies used in an ELISA for the quantification of the major birch pollen allergen Bet v 1, established as a reference by the BSP090 European project. METHODS: The ability of mAbs 5B4 and 6H4 to recognize Bet v 1 isoforms was addressed by immunochromatography. The capacity of each mAb to compete with patients' IgE for binding to Bet v 1 was measured by ELISA inhibition...
November 24, 2017: Allergy
https://www.readbyqxmd.com/read/29166011/a-cooperative-folding-unit-as-the-structural-link-for-energetic-coupling-within-a-protein
#6
Nathan W Gardner, Sarah M McGinness, Jainik Panchal, Elizabeth M Topp, Chiwook Park
Previously, we demonstrated that ligand binding to Escherichia coli cofactor-dependent phosphoglycerate mutase (dPGM), a homodimeric protein, is energetically coupled with dimerization. The equilibrium unfolding of dPGM occurs with a stable, monomeric intermediate. Binding of several non-substrate metabolites stabilizes the dimeric native form over the monomeric intermediate, reducing the population of the intermediate. Both the active site and the dimer interface appear to be unfolded in the intermediate. We hypothesized that a loop containing residues 118-152 was responsible for the energetic coupling between the dimer interface and the distal active site and was unfolded in the intermediate...
November 22, 2017: Biochemistry
https://www.readbyqxmd.com/read/29151349/changes-in-enzyme-structural-dynamics-studied-by-hydrogen-exchange-mass-spectrometry-ligand-binding-effects-or-catalytically-relevant-motions
#7
Courtney S Fast, Siavash Vahidi, Lars Konermann
It is believed that enzyme catalysis is facilitated by conformational dynamics of the protein scaffold that surrounds the active site. Yet, the exact nature of catalytically relevant protein motions remains largely unknown. Hydrogen/deuterium exchange (HDX) mass spectrometry (MS) reports on backbone H-bond fluctuations. HDX/MS therefore represents a promising avenue for probing the relationship between enzyme dynamics and catalysis. A seemingly straightforward strategy for such measurements involves comparative measurements during substrate turnover and in the resting state...
November 18, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29138428/structural-disorder-and-induced-folding-within-two-cereal-aba-stress-and-ripening-asr-proteins
#8
Karama Hamdi, Edoardo Salladini, Darragh P O'Brien, Sébastien Brier, Alexandre Chenal, Ines Yacoubi, Sonia Longhi
Abscisic acid (ABA), stress and ripening (ASR) proteins are plant-specific proteins involved in plant response to multiple abiotic stresses. We previously isolated the ASR genes and cDNAs from durum wheat (TtASR1) and barley (HvASR1). Here, we show that HvASR1 and TtASR1 are consistently predicted to be disordered and further confirm this experimentally. Addition of glycerol, which mimics dehydration, triggers a gain of structure in both proteins. Limited proteolysis showed that they are highly sensitive to protease degradation...
November 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29135326/hydrogen-deuterium-exchange-mass-spectrometry-and-computational-modeling-reveal-a-discontinuous-epitope-of-an-antibody-tl1a-interaction
#9
Richard Y-C Huang, Stanley R Krystek, Nathan Felix, Robert F Graziano, Mohan Srinivasan, Achal Pashine, Guodong Chen
TL1A, a tumor necrosis factor-like cytokine, is a ligand for the death domain receptor DR3. TL1A, upon binding to DR3, can stimulate lymphocytes and trigger secretion of proinflammatory cytokines. Therefore, blockade of TL1A/DR3 interaction may be a potential therapeutic strategy for autoimmune and inflammatory diseases. Recently, the anti-TL1A monoclonal antibody 1 (mAb1) with a strong potency in blocking the TL1A/DR3 interaction was identified. Here, we report on the use of hydrogen/deuterium exchange mass spectrometry (HDX-MS) to obtain molecular-level details of mAb1's binding epitope on TL1A...
November 14, 2017: MAbs
https://www.readbyqxmd.com/read/29129068/structural-and-functional-characterization-of-a-hole-hole-homodimer-variant-in-a-knob-into-hole-bispecific-antibody
#10
Hui-Min Zhang, Charlene Li, Ming Lei, Victor Lundin, Ho Young Lee, Milady Ninonuevo, Kevin Lin, Guanghui Han, Wendy Sandoval, Dongsheng Lei, Gang Ren, Jennifer Zhang, Hongbin Liu
Bispecific antibodies have great potential to be the next-generation biotherapeutics due to their ability to simultaneously recognize two different targets. Compared to conventional monoclonal antibodies, knob-into-hole bispecific antibodies face unique challenges in production and characterization due to the increase in variant possibilities, such as homodimerization in covalent and non-covalent forms. In this study, a storage- and pH-sensitive hydrophobic interaction chromatography (HIC) profile change was observed for the hole-hole homodimer, and the multiple HIC peaks were explored and shown to be conformational isomers...
November 12, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29109150/role-of-salt-bridges-in-the-dimer-interface-of-14-3-3%C3%AE-in-dimer-dynamics-n-terminal-%C3%AE-helical-order-and-molecular-chaperone-activity
#11
Joanna M Woodcock, Katy L Goodwin, Jarrod J Sandow, Carl Coolen, Matthew A Perugini, Andrew I Webb, Stuart M Pitson, Angel F Lopez, John A Carver
The 14-3-3 family of intracellular proteins are dimeric, multi-functional adaptor proteins that bind to and regulate the activities of many important signaling proteins. The subunits within 14-3-3 dimers are predicted to be stabilized by salt bridges that are largely conserved across the 14-3-3 protein family and allow the different isoforms to form heterodimers. Here, we have examined the contributions of conserved salt-bridging residues in stabilizing the dimeric state of 14-3-3ζ. Using analytical ultracentrifugation, our results revealed that Asp-21 and Glu-89 both play key roles in dimer dynamics and contribute to dimer stability...
November 6, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29099587/combining-h-d-exchange-mass-spectrometry-and-computational-docking-to-derive-the-structure-of-protein-protein-complexes
#12
Victoria A Roberts, Michael E Pique, Simon Hsu, Sheng Li
Protein-protein interactions are essential for biological function, but structures of protein-protein complexes are difficult to obtain experimentally. To derive the protein complex of the DNA-repair enzyme human uracil-DNA-glycosylase (hUNG) with its protein inhibitor (UGI), we combined rigid-body computational docking with hydrogen/deuterium exchange mass spectrometry (DXMS). Computational docking of the unbound protein structures provides a list of possible three-dimensional models of the complex; DXMS identifies solvent-protected protein residues...
November 16, 2017: Biochemistry
https://www.readbyqxmd.com/read/29092908/coordination-and-redox-state-dependent-structural-changes-of-the-heme-based-oxygen-sensor-afgchk-associated-with-intraprotein-signal-transduction
#13
Martin Stranava, Petr Man, Tereza Skalova, Petr Kolenko, Jan Blaha, Veronika Fojtikova, Vaclav Martinek, Jan Dohnalek, Alzbeta Lengalova, Michal Rosulek, Toru Shimizu, Marketa Martinkova
The heme-based oxygen sensor histidine kinase AfGcHK is part of a two-component signal transduction system in bacteria. O2 binding to the Fe(II) heme complex of its N-terminal globin domain strongly stimulates autophosphorylation at His-183 in its C-terminal kinase domain. The 6-coordinate heme Fe(III)-OH- and -CN- complexes of AfGcHK are also active, but the 5-coordinate heme Fe(II) complex and the heme-free apo-form are inactive. Here, we determined the crystal structures of the isolated dimeric globin domains of the active Fe(III)-CN- and inactive 5-coordinate Fe(II) forms, revealing striking structural differences on the heme-proximal side of the globin domain...
November 1, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29082630/separation-of-selenium-species-and-their-sensitive-determination-in-rice-samples-by-ion-pairing-reversed-phase-liquid-chromatography-with-inductively-coupled-plasma-tandem-mass-spectrometry
#14
Huan-Huan Gao, Ming-Xue Chen, Xian-Qiao Hu, Shuang-Shuang Chai, Mei-Ling Qin, Zhao-Yun Cao
A highly sensitive method was developed for the simultaneous separation and determination of organic and inorganic selenium species in rice by ion-pairing reversed-phase chromatography combined with inductively coupled plasma tandem mass spectrometry. To achieve a good separation of these species, a comparison between anion-exchange chromatography and ion-pairing reversed-phase chromatography was performed. The results indicated that ion-pairing reversed-phase chromatography was more suitable due to better separation and higher sensitivity for all analytes...
October 30, 2017: Journal of Separation Science
https://www.readbyqxmd.com/read/29080206/structural-dynamics-of-the-gw182-silencing-domain-including-its-rna-recognition-motif-rrm-revealed-by-hydrogen-deuterium-exchange-mass-spectrometry
#15
Maja K Cieplak-Rotowska, Krzysztof Tarnowski, Marcin Rubin, Marc R Fabian, Nahum Sonenberg, Michal Dadlez, Anna Niedzwiecka
The human GW182 protein plays an essential role in micro(mi)RNA-dependent gene silencing. miRNA silencing is mediated, in part, by a GW182 C-terminal region called the silencing domain, which interacts with the poly(A) binding protein and the CCR4-NOT deadenylase complex to repress protein synthesis. Structural studies of this GW182 fragment are challenging due to its predicted intrinsically disordered character, except for its RRM domain. However, detailed insights into the properties of proteins containing disordered regions can be provided by hydrogen-deuterium exchange mass spectrometry (HDX/MS)...
October 27, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/29080204/design-and-validation-of-in-source-atmospheric-pressure-photoionization-hydrogen-deuterium-exchange-mass-spectrometry-with-continuous-feeding-of-d2o
#16
Thamina Acter, Seulgidaun Lee, Eunji Cho, Maeng-Joon Jung, Sunghwan Kim
In this study, continuous in-source hydrogen/deuterium exchange (HDX) atmospheric pressure photoionization (APPI) mass spectrometry (MS) with continuous feeding of D2O was developed and validated. D2O was continuously fed using a capillary line placed on the center of a metal plate positioned between the UV lamp and nebulizer. The proposed system overcomes the limitations of previously reported APPI HDX-MS approaches where deuterated solvents were premixed with sample solutions before ionization. This is particularly important for APPI because solvent composition can greatly influence ionization efficiency as well as the solubility of analytes...
October 27, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/29078272/ligand-induced-conformational-dynamics-of-the-escherichia-coli-na-h-antiporter-nhaa-revealed-by-hydrogen-deuterium-exchange-mass-spectrometry
#17
Martin Lorenz Eisinger, Aline Ricarda Dörrbaum, Hartmut Michel, Etana Padan, Julian David Langer
Na(+)/H(+) antiporters comprise a family of membrane proteins evolutionarily conserved in all kingdoms of life and play an essential role in cellular ion homeostasis. The NhaA crystal structure of Escherichia coli has become the paradigm for this class of secondary active transporters. However, structural data are only available at low pH, where NhaA is inactive. Here, we adapted hydrogen/deuterium-exchange mass spectrometry (HDX-MS) to analyze conformational changes in NhaA upon Li(+) binding at physiological pH...
October 31, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29058415/online-simultaneous-hydrogen-deuterium-exchange-of-multitarget-gas-phase-molecules-by-electrospray-ionization-mass-spectrometry-coupled-with-gas-chromatography
#18
Eun Sook Jeong, Eunju Cha, Sangwon Cha, Sunghwan Kim, Han Bin Oh, Oh-Seung Kwon, Jaeick Lee
In this study, a hydrogen/deuterium (H/D) exchange method using gas chromatography-electrospray ionization/mass spectrometry (GC-ESI/MS) was first investigated as a novel tool for online H/D exchange of multitarget analytes. The GC and ESI source were combined with a homemade heated column transfer line. GC-ESI/MS-based H/D exchange occurs in an atmospheric pressure ion source as a result of reacting the gas-phase analyte eluted from GC with charged droplets of deuterium oxide infused as the ESI spray solvent...
October 31, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29056864/understanding-curli-amyloid-protein-aggregation-by-hydrogen-deuterium-exchange-and-mass-spectrometry
#19
Hanliu Wang, Qin Shu, Don L Rempel, Carl Frieden, Michael L Gross
Bacteria within Curli biofilms are protected from environmental pressures (e.g., disinfectants, antibiotics), and this is responsible for intractable infections. Understanding aggregation of the major protein component of Curli, CsgA, may uncover disease-associated amyloidogenesis mechanisms. Here, we report the application of pulsed hydrogen-deuterium exchange and mass spectrometry (HDX-MS) to study CsgA aggregation, thereby obtaining region-specific information. By following time-dependent peptide signal depletion, presumably a result of insoluble fibril formation, we acquired sigmoidal profiles that are specific for regions (region-specific) of the protein...
September 2017: International Journal of Mass Spectrometry
https://www.readbyqxmd.com/read/29049865/interrogating-membrane-protein-conformational-dynamics-within-native-lipid-compositions
#20
Eamonn Reading, Zoe Hall, Chloe Martens, Tabasom Haghighi, Heather Findlay, Zainab Ahdash, Argyris Politis, Paula J Booth
Membrane protein-lipid interplay is important for cellular function, however, tools enabling the interrogation of protein dynamics within native lipid environments are scarce and often invasive. We establish that the styrene-maleic acid anhydride lipid particle (SMALP) technology can be coupled with hydrogen-deuterium exchange mass spectrometry (HDX-MS) to investigate membrane protein conformational dynamics within native lipid bilayers. We demonstrate changes in accessibility and dynamics of the rhomboid protease, GlpG, captured within three different native lipid compositions, and identify protein regions sensitive to changes in the native lipid environment...
October 19, 2017: Angewandte Chemie
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