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Hydrogen-Deuterium Exchange MS

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https://www.readbyqxmd.com/read/28431242/structural-and-functional-analysis-of-a-%C3%AE-2-adrenergic-receptor-complex-with-grk5
#1
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
#2
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
#3
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...
April 20, 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
#4
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...
April 21, 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
#5
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
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 rFVIIIFc fusion protein that has a 1.5-fold longer half-life in humans. OBJECTIVE: To assess the structural properties of rFVIIIFc by comparing its constituent FVIII and Fc elements with their respective isolated components and evaluating their structural independence within rFVIIIFc. METHODS: rFVIIIFc and its isolated FVIII and Fc components were compared by hydrogen-deuterium exchange mass spectrometry (HDX-MS)...
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
#6
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...
March 30, 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
#7
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
#8
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
#9
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-ims-ms-combined-with-size-exclusion-chromatography-and-differential-hydrogen-deuterium-exchange
#10
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...
March 16, 2017: Journal of Chromatography. A
https://www.readbyqxmd.com/read/28346764/mapping-the-interactions-of-selective-biochemical-probes-of-antibody-conformation-by-hydrogen-deuterium-exchange-mass-spectrometry
#11
Ulrike Leurs, Hermann Beck, Lea Bonnington, Ingo Lindner, Ewa Pol, Kasper Dyrberg Rand
Protein-based pharmaceuticals represent the fastest growing group of drugs in development in the pharmaceutical industry. One of the major challenges in the discovery, development and distribution of biopharmaceuticals is the assessment of changes in their higher-order structure due to chemical modifications. Here, we investigate the interactions of three different biochemical probes (Fabs) generated to detect conformational changes in a therapeutic IgG1 antibody (mAbX) by local hydrogen-deuterium exchange mass spectrometry (HDX-MS)...
March 27, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28289188/ligand-induced-allostery-in-the-interaction-of-the-pseudomonas-aeruginosa-heme-binding-protein-with-heme-oxygenase
#12
Daniel J Deredge, Weiliang Huang, Colleen Hui, Hirotoshi Matsumura, Zhi Yue, Pierre Moënne-Loccoz, Jana Shen, Patrick L Wintrode, Angela Wilks
A heme-dependent conformational rearrangement of the C-terminal domain of heme binding protein (PhuS) is required for interaction with the iron-regulated heme oxygenase (HemO). Herein, we further investigate the underlying mechanism of this conformational rearrangement and its implications for heme transfer via site-directed mutagenesis, resonance Raman (RR), hydrogen-deuterium exchange MS (HDX-MS) methods, and molecular dynamics (MD). HDX-MS revealed that the apo-PhuS C-terminal α6/α7/α8-helices are largely unstructured, whereas the apo-PhuS H212R variant showed an increase in structure within these regions...
March 28, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28274452/monitoring-of-the-functional-properties-and-unfolding-change-of-ovalbumin-after-dhpm-treatment-by-hdx-and-fticr-ms-functionality-and-unfolding-of-oval-after-dhpm-by-hdx-and-fticr-ms
#13
Guang-Xian Liu, Zong-Cai Tu, Hui Wang, Lu Zhang, Tao Huang, Da Ma
Dynamic high-pressure microfluidizaiton (DHPM) induced unfolding of proteins and enzymes could enhance the functional properties and hydrolytic ability of the molecules. In this study, the effect of DHPM on the surface activities of Ovalbumin (Oval), namely foaming and emulsifying properties, was investigated at 0, 40, 80, 120 and 160MPa. Improvement in the foaming and emulsifying properties was observed at 120 and 80MPa, respectively. Hydrogen/deuterium exchange (HDX) coupled with Fourier transform infrared spectroscopy-mass spectrometry (FTICR MS) was performed to investigate the exact unfolded region of Oval and analyze the mechanism promoting the foaming and emulsifying properties after 120 and 80MPa, respectively, compared with those at 0MPa...
July 15, 2017: Food Chemistry
https://www.readbyqxmd.com/read/28252287/characterizing-the-structure-and-oligomerization-of-major-royal-jelly-protein-1-mrjp1-by-mass-spectrometry-and-complementary-biophysical-tools
#14
Samuel C Mandacaru, Luis H F do Vale, Siavash Vahidi, Yiming Xiao, Owen S Skinner, Carlos A O Ricart, Neil L Kelleher, Marcelo Valle de Sousa, Lars Konermann
Royal jelly (RJ) triggers the development of female honeybee larvae into queens. This effect has been attributed to the presence of major royal jelly protein 1 (MRJP1) in RJ. MRJP1 isolated from royal jelly is tightly associated with apisimin, a 54-residue α-helical peptide that promotes the noncovalent assembly of MRJP1 into multimers. No high-resolution structural data are available for these complexes, and their binding stoichiometry remains uncertain. We examined MRJP1/apisimin using a range of biophysical techniques...
March 21, 2017: Biochemistry
https://www.readbyqxmd.com/read/28236290/the-area-between-exchange-curves-as-a-measure-of-conformational-differences-in-hydrogen-deuterium-exchange-mass-spectrometry-studies
#15
Sharlyn J Mazur, Daniel P Weber
Hydrogen-deuterium exchange mass spectrometry (HDX-MS) provides information about protein conformational mobility under native conditions. The area between exchange curves, A bec , a functional data analysis concept, was adapted to the interpretation of HDX-MS data and provides a useful measure of exchange curve dissimilarity for tests of significance. Importantly, for most globular proteins under native conditions, A bec values provide an estimate of the log ratio of exchange-competent fractions in the two states, and thus are related to differences in the free energy of microdomain unfolding...
February 24, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28223522/conformational-dynamics-of-a-neurotransmitter-sodium-symporter-in-a-lipid-bilayer
#16
Suraj Adhikary, Daniel J Deredge, Anu Nagarajan, Lucy R Forrest, Patrick L Wintrode, Satinder K Singh
Neurotransmitter:sodium symporters (NSSs) are integral membrane proteins responsible for the sodium-dependent reuptake of small-molecule neurotransmitters from the synaptic cleft. The symporters for the biogenic amines serotonin (SERT), dopamine (DAT), and norepinephrine (NET) are targets of multiple psychoactive agents, and their dysfunction has been implicated in numerous neuropsychiatric ailments. LeuT, a thermostable eubacterial NSS homolog, has been exploited as a model protein for NSS members to canvass the conformational mechanism of transport with a combination of X-ray crystallography, cysteine accessibility, and solution spectroscopy...
March 7, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28194737/regio-selective-intramolecular-hydrogen-deuterium-exchange-in-gas-phase-electron-transfer-dissociation
#17
Yoshitomo Hamuro
Protein backbone amide hydrogen/deuterium exchange mass spectrometry (HDX-MS) typically utilizes enzymatic digestion after the exchange reaction and before MS analysis to improve data resolution. Gas-phase fragmentation of a peptic fragment prior to MS analysis is a promising technique to further increase the resolution. The biggest technical challenge for this method is elimination of intramolecular hydrogen/deuterium exchange (scrambling) in the gas phase. The scrambling obscures the location of deuterium...
February 13, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28193043/removal-of-n-linked-glycosylations-at-acidic-ph-by-pngase-a-facilitates-hydrogen-deuterium-exchange-mass-spectrometry-analysis-of-n-linked-glycoproteins
#18
Pernille Foged Jensen, Gerard Comamala, Morten Beck Trelle, Jeppe Buur Madsen, Thomas J D Jørgensen, Kasper D Rand
Protein glycosylation is the most frequent post-translational modification and is present on more than 50% of eukaryotic proteins. Glycosylation covers a wide subset of modifications involving many types of complex oligosaccharide structures, making structural analysis of glycoproteins and their glycans challenging for most analytical techniques. Hydrogen/deuterium exchange monitored by mass spectrometry is a sensitive technique for investigation of protein conformational dynamics of complex heterogeneous proteins in solution...
December 20, 2016: Analytical Chemistry
https://www.readbyqxmd.com/read/28193005/mapping-the-energetic-epitope-of-an-antibody-interleukin-23-interaction-with-hydrogen-deuterium-exchange-fast-photochemical-oxidation-of-proteins-mass-spectrometry-and-alanine-shave-mutagenesis
#19
Jing Li, Hui Wei, Stanley R Krystek, Derek Bond, Ty M Brender, Daniel Cohen, Jena Feiner, Nels Hamacher, Johanna Harshman, Richard Y-C Huang, Susan H Julien, Zheng Lin, Kristina Moore, Luciano Mueller, Claire Noriega, Preeti Sejwal, Paul Sheppard, Brenda Stevens, Guodong Chen, Adrienne A Tymiak, Michael L Gross, Lumelle A Schneeweis
Epitope mapping the specific residues of an antibody/antigen interaction can be used to support mechanistic interpretation, antibody optimization, and epitope novelty assessment. Thus, there is a strong need for mapping methods, particularly integrative ones. Here, we report the identification of an energetic epitope by determining the interfacial hot-spot that dominates the binding affinity for an anti-interleukin-23 (anti-IL-23) antibody by using the complementary approaches of hydrogen/deuterium exchange mass spectrometry (HDX-MS), fast photochemical oxidation of proteins (FPOP), alanine shave mutagenesis, and binding analytics...
February 21, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28171682/unusual-electrospray-ionization-induced-fragmentation-structural-elucidation-of-an-in-process-synthetic-intermediate-of-doravirine-mk-1439-using-liquid-chromatography-high-resolution-tandem-mass-spectrometry-and-two-dimensional-nuclear-magnetic-resonance
#20
Huaming Sheng, Katrina W Lexa, Li-Kang Zhang, Rong-Sheng Yang, Timothy J Wright, Benjamin D Sherry, Roy Helmy, Gary E Martin
RATIONALE: During the development of a novel synthetic route to doravirine (1), a human immunodeficiency type 1 virus (HIV-1) nonnucleoside reverse transcriptase inhibitor (NNRTI), an unanticipated reaction intermediate, methyl (Z)-2-(3-chloro-5-cyanophenoxy)-5-(3-(3-chloro-5-cyanophenoxy)-2-oxo-4-(trifluoromethyl)pyridin-1(2H)-yl)-5-ethoxy-3-(trifluoromethyl)pent-2-enoate (2), was isolated. Moreover, an unusual electrospray ionization (ESI)-induced fragmentation was observed for 2. Hence, efforts were made towards the understanding of the structure of 2, which was crucial for the understanding of the reaction mechanism...
April 30, 2017: Rapid Communications in Mass Spectrometry: RCM
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