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Hydrogen-Deuterium Exchange MS

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https://www.readbyqxmd.com/read/28515318/molecular-mechanism-of-activation-of-class-ia-phosphoinositide-3-kinases-pi3ks-by-membrane-localized-hras
#1
Braden D Siempelkamp, Manoj K Rathinaswamy, Meredith L Jenkins, John E Burke
Class IA PI3Ks are involved in the generation of the key lipid signaling molecule phosphatidylinositol 3,4,5-trisphosphate (PIP3), and inappropriate activation of this pathway is implicated in a multitude of human diseases, including cancer, inflammation, and primary immunodeficiencies. Class IA PI3Ks are activated downstream of the Ras superfamily of GTPases, and Ras-PI3K interaction plays a key role in promoting tumor formation and maintenance in Ras-driven tumors. Investigating the detailed molecular events in the Ras-PI3K interaction has been challenging because it occurs on a membrane surface...
May 17, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28505408/ion-mobility-hydrogen-deuterium-exchange-and-isotope-scrambling-tools-to-aid-compound-identification-in-omics-mixtures
#2
Hossein Maleki, Megan M Maurer, Nima Ronaghi, Stephen J Valentine
Liquid chromatography tandem mass spectrometry (LC-MS/MS), a widely used method for comparative 'omics analysis, experiences challenges with compound identification due to matrix effects, difficulty in separating isomer and isobaric ions, and long analysis times. Ion mobility spectrometry (IMS) has proven to be useful in separating isomer and isobar ions, however IMS-MS suffers from decreased peak capacity duet to the correlation in ion size and mass. In proof-of-principle experiments, the use of gas-phase hydrogen/deuterium exchange (HDX) combined with IMS-MS/MS techniques is demonstrated to offer advantages for compound identification...
May 15, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28504253/dynamic-diversity-of-synthetic-supramolecular-polymers-in-water-as-revealed-by-hydrogen-deuterium-exchange
#3
Xianwen Lou, René P M Lafleur, Christianus M A Leenders, Sandra M C Schoenmakers, Nicholas M Matsumoto, Matthew B Baker, Joost L J van Dongen, Anja R A Palmans, E W Meijer
Numerous self-assembling molecules have been synthesized aiming at mimicking both the structural and dynamic properties found in living systems. Here we show the application of hydrogen/deuterium exchange (HDX) mass spectrometry (MS) to unravel the nanoscale organization and the structural dynamics of synthetic supramolecular polymers in water. We select benzene-1,3,5-tricarboxamide (BTA) derivatives that self-assemble in H2O to illustrate the strength of this technique for supramolecular polymers. The BTA structure has six exchangeable hydrogen atoms and we follow their exchange as a function of time after diluting the H2O solution with a 100-fold excess of D2O...
May 15, 2017: Nature Communications
https://www.readbyqxmd.com/read/28497950/deamidation-slows-curli-amyloid-protein-aggregation
#4
Hanliu Wang, Qin Shu, Carl Frieden, Michael L Gross
Non-enzymatic deamidation of asparagine and glutamine in peptides and proteins is a frequent modification both in vivo and in vitro. The biological effect is not completely understood, but it is often associated with protein degradation and loss of biological function. Here we describe the deamidation of CsgA, the major protein subunit of curli, which are important proteinaceous components of biofilms. CsgA has a high content of Asn and Gln, a feature seen in other proteins that self-aggregate. We have implemented an approach to monitor deamidation rapidly by following the globally centroid mass shift, providing guidance for studies at the residue level...
May 12, 2017: Biochemistry
https://www.readbyqxmd.com/read/28488200/application-of-atmospheric-pressure-photoionization-h-d-exchange-mass-spectrometry-for-speciation-of-sulfur-containing-compounds
#5
Thamina Acter, Donghwi Kim, Arif Ahmed, Ji-Hyoung Ha, Sunghwan Kim
Herein we report the observation of atmospheric pressure in-source hydrogen-deuterium exchange (HDX) of thiol group for the first time. The HDX for thiol group was optimized for positive atmospheric pressure photoionization (APPI) mass spectrometry (MS). The optimized HDX-MS was applied for 31 model compounds (thiols, thiophenes, and sulfides) to demonstrate that exchanged peaks were observed only for thiols. The optimized method has been successfully applied to the isolated fractions of sulfur-rich oil samples...
May 9, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28481113/hydrogen-deuterium-exchange-mass-spectrometry-reveals-mechanistic-details-of-activation-of-nucleoside-diphosphate-kinases-by-oligomerization
#6
Alain Dautant, Philippe Meyer, Florian Georgescauld
Most oligomeric proteins become active only after assembly, but why oligomerization is required to support function is not well understood. Here, we address this question using the wild type (WT) and a destabilized mutant (D93N) of the hexameric nucleoside diphosphate kinase from the pathogen Mycobacterium tuberculosis (Mt-NDPK). The conformational dynamics and oligomeric states of each were analyzed during unfolding and/or folding by hydrogen/deuterium exchange mass spectrometry (HDX-MS) at peptide resolution and by additional biochemical techniques...
May 17, 2017: Biochemistry
https://www.readbyqxmd.com/read/28474266/gas-phase-intercluster-thiyl-radical-induced-c-h-bond-homolysis-selectively-forms-sugar-c2-radical-cations-of-methyl-d-glucopyranoside-isotopic-labeling-studies-and-cleavage-reactions
#7
Sandra Osburn, Gaetano Speciale, Spencer J Williams, Richard A J O'Hair
A suite of isotopologues of methyl D-glucopyranosides is used in conjunction with multistage mass spectrometry experiments to determine the radical site and cleavage reactions of sugar radical cations formed via a recently developed 'bio-inspired' method. In the first stage of CID (MS(2)), collision-induced dissociation (CID) of a protonated noncovalent complex between the sugar and S-nitrosocysteamine, [H3NCH2CH2SNO + M](+), unleashes a thiyl radical via bond homolysis to give the noncovalent radical cation, [H3NCH2CH2S(•) + M](+)...
May 4, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28448048/time-resolved-electrospray-ionization-hydrogen-deuterium-exchange-mass-spectrometry-for-studying-protein-structure-and-dynamics
#8
Cristina Lento, Shaolong Zhu, Kerene A Brown, Ruth Knox, Peter Liuni, Derek J Wilson
Intrinsically disordered proteins (IDPs) have long been a challenge to structural biologists due to their lack of stable secondary structure elements. Hydrogen-Deuterium Exchange (HDX) measured at rapid time scales is uniquely suited to detect structures and hydrogen bonding networks that are briefly populated, allowing for the characterization of transient conformers in native ensembles. Coupling of HDX to mass spectrometry offers several key advantages, including high sensitivity, low sample consumption and no restriction on protein size...
April 17, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28442430/design-and-purification-of-active-truncated-phosphoinositide-3-kinase-gamma-protein-constructs-for-structural-studies
#9
A Vujičić Žagar, L Scapozza, O Vadas
Phosphoinositide 3-kinase gamma (PI3Kγ) is a lipid kinase that plays a crucial role in cell migration, chemotaxis, oxidative burst and myocardial contractility. It is activated downstream of G protein-coupled receptors (GPCRs) and small GTPases of Ras superfamily. PI3Kγ is a heterodimer composed of a catalytic and a regulatory subunit that is expressed mostly in hematopoietic cells and in the heart. Although it has attracted a lot of attention because of its link with tumor inflammation and heart diseases, its regulation is still not fully understood...
April 22, 2017: Protein Expression and Purification
https://www.readbyqxmd.com/read/28441028/application-of-gc-ms-soft-ionization-for-isomeric-biological-compound-analysis
#10
Takeshi Furuhashi, Koji Okuda
Isomers are compounds with the same molecular formula. Many different types of isomers are ubiquitous and play important roles in living organisms. Despite their early discovery, the actual analysis of isomers has been tricky and has confounded researchers. Using mass spectrometry (MS) to distinguish or identify isomers is an emergent topic and challenge for analytical chemists. We review some techniques for analyzing isomers with emphasis on MS, e.g., the roles of ion reaction, hydrogen-deuterium exchange, ion mobility mass spectrometry, ion spectroscopy and energy change in producing isomer-specific fragments...
April 25, 2017: Critical Reviews in Analytical Chemistry
https://www.readbyqxmd.com/read/28431242/structural-and-functional-analysis-of-a-%C3%AE-2-adrenergic-receptor-complex-with-grk5
#11
Konstantin E Komolov, Yang Du, Nguyen Minh Duc, Robin M Betz, João P G L M Rodrigues, Ryan D Leib, Dhabaleswar Patra, Georgios Skiniotis, Christopher M Adams, Ron O Dror, Ka Young Chung, Brian K Kobilka, Jeffrey L Benovic
The phosphorylation of agonist-occupied G-protein-coupled receptors (GPCRs) by GPCR kinases (GRKs) functions to turn off G-protein signaling and turn on arrestin-mediated signaling. While a structural understanding of GPCR/G-protein and GPCR/arrestin complexes has emerged in recent years, the molecular architecture of a GPCR/GRK complex remains poorly defined. We used a comprehensive integrated approach of cross-linking, hydrogen-deuterium exchange mass spectrometry (MS), electron microscopy, mutagenesis, molecular dynamics simulations, and computational docking to analyze GRK5 interaction with the β2-adrenergic receptor (β2AR)...
April 20, 2017: Cell
https://www.readbyqxmd.com/read/28428550/structure-based-dynamic-arrays-in-regulatory-domains-of-sodium-calcium-exchanger-ncx-isoforms
#12
Moshe Giladi, Su Youn Lee, Yarden Ariely, Yotam Teldan, Rotem Granit, Roi Strulovich, Yoni Haitin, Ka Young Chung, Daniel Khananshvili
Mammalian Na(+)/Ca(2+) exchangers, NCX1 and NCX3, generate splice variants, whereas NCX2 does not. The CBD1 and CBD2 domains form a regulatory tandem (CBD12), where Ca(2+) binding to CBD1 activates and Ca(2+) binding to CBD2 (bearing the splicing segment) alleviates the Na(+)-induced inactivation. Here, the NCX2-CBD12, NCX3-CBD12-B, and NCX3-CBD12-AC proteins were analyzed by small-angle X-ray scattering (SAXS) and hydrogen-deuterium exchange mass-spectrometry (HDX-MS) to resolve regulatory variances in the NCX2 and NCX3 variants...
April 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28426082/deciphering-of-interactions-between-platinated-dna-and-hmgb1-by-hydrogen-deuterium-exchange-mass-spectrometry
#13
Yuanyuan Wang, Zhifeng Du, Wei Zheng, Kui Wu, Decheng Xu, Qun Luo, Yao Zhao, Juanjuan Han, Yangzhong Liu, Fuyi Wang
A high mobility group box 1 (HMGB1) protein has been reported to recognize both 1,2-intrastrand crosslinked DNA by cisplatin (1,2-cis-Pt-DNA) and monofunctional platinated DNA using trans-[PtCl2(NH3)(thiazole)] (1-trans-PtTz-DNA). However, the molecular basis of recognition between the trans-PtTz-DNA and HMGB1 remains unclear. In the present work, we described a hydrogen/deuterium exchange mass spectrometry (HDX-MS) method in combination with docking simulation to decipher the interactions of platinated DNA with domain A of HMGB1...
May 16, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28402104/hydrogen-deuterium-exchange-mass-spectrometry-of-human-green-opsin-reveals-a-conserved-pro-pro-motif-in-extracellular-loop-2-of-monostable-visual-g-protein-coupled-receptors
#14
Lukas Hofmann, Nathan S Alexander, Wenyu Sun, Jianye Zhang, Tivadar Orban, Krzysztof Palczewski
Opsins comprise the protein component of light sensitive G protein-coupled receptors (GPCRs) in the retina of the eye that are responsible for the transduction of light into a biochemical signal. Here, we used hydrogen/deuterium (H/D) exchange coupled with mass spectrometry to map conformational changes in green cone opsin upon light activation. We then compared these findings with those reported for rhodopsin. The extent of H/D exchange in green cone opsin was greater than in rhodopsin in the dark and bleached states, suggesting a higher structural heterogeneity for green cone opsin...
May 2, 2017: Biochemistry
https://www.readbyqxmd.com/read/28397397/the-structural-basis-for-the-functional-comparability-of-factor-viii-and-the-long-acting-variant-recombinant-factor-viii-fc-fusion-protein
#15
N C Leksa, P-L Chiu, G M Bou-Assaf, C Quan, Z Liu, A B Goodman, M G Chambers, S E Tsutakawa, M Hammel, R T Peters, T Walz, J D Kulman
Essentials Recombinant factor VIII (rFVIII) Fc fusion protein has a 1.5-fold longer half-life than rFVIII. Five orthogonal methods were used to characterize the structure of rFVIIIFc compared to rFVIII. The C-terminal Fc fusion does not perturb the structure of FVIII in rFVIIIFc. The FVIII and Fc components of rFVIIIFc are flexibly tethered and functionally independent. SUMMARY: Background Fusion of the human IgG1 Fc domain to the C-terminal C2 domain of B-domain-deleted (BDD) factor VIII (FVIII) results in the recombinant FVIII Fc (rFVIIIFc) fusion protein, which has a 1...
April 11, 2017: Journal of Thrombosis and Haemostasis: JTH
https://www.readbyqxmd.com/read/28392260/hybrid-mass-spectrometry-approaches-to-determine-how-l-histidine-feedback-regulates-the-enzyzme-mtatp-phosphoribosyltransferase
#16
Kamila J Pacholarz, Rebecca J Burnley, Thomas A Jowitt, Victoria Ordsmith, João Pedro Pisco, Massimiliano Porrini, Gérald Larrouy-Maumus, Rachel A Garlish, Richard J Taylor, Luiz Pedro Sório de Carvalho, Perdita E Barran
MtATP-phosphoribosyltransferase (MtATP-PRT) is an enzyme catalyzing the first step of the biosynthesis of L-histidine in Mycobacterium tuberculosis, and proposed to be regulated via an allosteric mechanism. Native mass spectrometry (MS) reveals MtATP-PRT to exist as a hexamer. Conformational changes induced by L-histidine binding and the influence of buffer pH are determined with ion mobility MS, hydrogen deuterium exchange (HDX) MS, and analytical ultracentrifugation. The experimental collision cross-section ((DT)CCSHe) decreases from 76...
May 2, 2017: Structure
https://www.readbyqxmd.com/read/28381646/analysis-of-phosphoinositide-3-kinase-inhibitors-by-bottom-up-electron-transfer-dissociation-hydrogen-deuterium-exchange-mass-spectrometry
#17
Glenn Robert Masson, Sarah L Maslen, Roger L Williams
Until recently, one of the major limitations of Hydrogen/Deuterium Exchange Mass Spectrometry (HDX-MS) was the peptide-level resolution afforded by proteolytic digestion. This limitation can be selectively overcome through the use of Electron Transfer Dissociation (ETD) to fragment peptides in a manner that allows the retention of the deuterium signal to produce Hydrogen Deuterium Exchange Tandem Mass Spectrometry (HDX-MS/MS). Here we describe the application of HDX-MS/MS to structurally screen inhibitors of the oncogene phosphoinositide 3-kinase (PI3K) catalytic p110α subunit...
April 5, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28374315/online-hydrogen-deuterium-exchange-traveling-wave-ion-mobility-mass-spectrometry-hdx-im-ms-a-systematic-evaluation
#18
Adam Cryar, Kate Groves, Milena Quaglia
Hydrogen-deuterium exchange mass spectrometry (HDX-MS) is an important tool for measuring and monitoring protein structure. A bottom-up approach to HDX-MS provides peptide level deuterium uptake values and a more refined localization of deuterium incorporation compared with global HDX-MS measurements. The degree of localization provided by HDX-MS is proportional to the number of peptides that can be identified and monitored across an exchange experiment. Ion mobility spectrometry (IMS) has been shown to improve MS-based peptide analysis of biological samples through increased separation capacity...
April 3, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28355543/structural-analysis-of-a-temperature-induced-transition-in-a-viral-capsid-probed-by-hdx-ms
#19
Michiel van de Waterbeemd, Aida Llauró, Joost Snijder, Alejandro Valbuena, Alicia Rodríguez-Huete, Miguel Angel Fuertes, Pedro J de Pablo, Mauricio G Mateu, Albert J R Heck
Icosahedral viral capsids are made of a large number of symmetrically organized protein subunits whose local movements can be essential for infection. In the capsid of the minute virus of mice, events required for infection that involve translocation of peptides through capsid pores are associated with a subtle conformational change. In vitro, this change can be reversibly induced by overcoming the energy barrier through mild heating of the capsid, but little is known about the capsid regions involved in the process...
March 28, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28347518/semi-automated-screen-for-global-protein-conformational-changes-in-solution-by-ion-mobility-spectrometry-massspectrometry-combined-with-size-exclusion-chromatography-and-differential-hydrogen-deuterium-exchange
#20
Nicholas A Pierson, Alexey A Makarov, Christopher A Strulson, Yun Mao, Bing Mao
Development of methodologies for studying protein higher-order structure in solution helps to establish a better understanding of the intrinsic link between protein conformational structure and biological function and activity. The goal of this study was to demonstrate a simultaneous screening approach for global protein conformational changes in solution through the combination of ion mobility spectrometry-mass spectrometry (IMS-MS) with differential hydrogen-deuterium exchange (ΔHDX) on the size-exclusion chromatography (SEC) platform in a single on-line workflow...
May 5, 2017: Journal of Chromatography. A
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