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Hydrogen exchange mass spectrometry

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https://www.readbyqxmd.com/read/28318907/the-effects-of-mutating-tyr9-and-arg15-on-the-structure-stability-conformational-dynamics-and-mechanism-of-gsta3-3
#1
Gary J Robertson, Stoyan H Stoychev, Yasien Sayed, Ikechukwu Achilonu, Heini W Dirr
Glutathione S-transferase A3-3 is the most catalytically efficient steroid isomerase enzyme known in humans, transforming Δ(5)-androstene-3-17-dione into Δ(4)-androstene-3-17-dione. GSTA3-3 catalyzes this reaction with ten-fold greater efficiency than GSTA1-1, its closest competitor in the Alpha class of GSTs. In order to examine the differences between Alpha class GSTs and to better elucidate the mechanism of GSTA3-3 the roles of Tyr9 and Arg15 were examined. Tyr9 is the major catalytic residue of Alpha class GSTs and Arg15 is proposed to be catalytically important to GSTA3-3 but never before experimentally examined...
March 1, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28304155/gas-phase-hydrogen-deuterium-exchange-for-distinguishing-isomeric-carbohydrate-ions
#2
Sanjit S Uppal, Sarah E Beasley, Michele Scian, Miklos Guttman
The structural diversity of carbohydrates presents a major challenge for glycobiology and the analysis of glycoconjugates. Mass spectrometry has become a primary tool for glycan analysis thanks to its speed and sensitivity, but the information content regarding the glycan structure of protonated glycoconjugates is hindered by the inability to differentiate linkage and stereoisomers. Here we examine a variety of protonated carbohydrate structures by gas-phase hydrogen/deuterium exchange (HDX) to discover that the exchange rates are distinct for isomeric carbohydrates with even subtle structural differences...
March 17, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28288347/exploration-of-the-metal-coordination-region-of-concanavalin-a-for-its-interaction-with-human-norovirus
#3
Duwoon Kim, Hee-Min Lee, Kyung-Seo Oh, Ah Young Ki, Rachael A Protzman, Dongkyun Kim, Jong-Soon Choi, Min Ji Kim, Sung Hyun Kim, Bipin Vaidya, Seung Jae Lee, Joseph Kwon
Rapid methods for the detection and clinical treatment of human norovirus (HuNoV) are needed to control foodborne disease outbreaks, but reliable techniques that are fast and sensitive enough to detect small amounts of HuNoV in food and aquatic environments are not yet available. We explore the interactions between HuNoV and concanavalin A (Con A), which could facilitate the development of a sensitive detection tool for HuNoV. Biophysical studies including hydrogen/deuterium exchange (HDX) mass spectrometry and surface plasmon resonance (SPR) revealed that when the metal coordinated region of Con A, which spans Asp16 to His24, is converted to nine alanine residues (mCon A(MCR)), the affinity for HuNoV (GII...
March 6, 2017: Biomaterials
https://www.readbyqxmd.com/read/28275051/protein-footprinting-comes-of-age-mass-spectrometry-for-biophysical-structure-assessment
#4
Liwen Wang, Mark R Chance
Protein footprinting mediated by mass spectrometry has evolved over the last 30 years from proof of concept to commonplace biophysics tool, with unique capabilities for assessing structure and dynamics of purified proteins in physiological states in solution. This review outlines the history and current capabilities of two major methods of protein footprinting: reversible hydrogen-deuterium exchange (HDX) and hydroxyl radical footprinting (HRF), an irreversible covalent labeling approach. Technological advances in both approaches now permit high-resolution assessments of protein structure including secondary and tertiary structure stability mediated by backbone interactions (measured via HDX) and solvent accessibility of side chains (measured via HRF)...
March 8, 2017: Molecular & Cellular Proteomics: MCP
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
#5
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/28272426/post-translational-modifications-in-prp-expand-the-conformational-diversity-of-prions-in-vivo
#6
Patricia Aguilar-Calvo, Xiangzhu Xiao, Cyrus Bett, Hasier Eraña, Katrin Soldau, Joaquin Castilla, K Peter R Nilsson, Witold K Surewicz, Christina J Sigurdson
Misfolded prion protein aggregates (PrP(Sc)) show remarkable structural diversity and are associated with highly variable disease phenotypes. Similarly, other proteins, including amyloid-β, tau, α-synuclein, and serum amyloid A, misfold into distinct conformers linked to different clinical diseases through poorly understood mechanisms. Here we use mice expressing glycophosphatidylinositol (GPI)-anchorless prion protein, PrP(C), together with hydrogen-deuterium exchange coupled with mass spectrometry (HXMS) and a battery of biochemical and biophysical tools to investigate how post-translational modifications impact the aggregated prion protein properties and disease phenotype...
March 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28265093/common-coding-variant-in-serpina1-increases-the-risk-for-large-artery-stroke
#7
Rainer Malik, Therese Dau, Maria Gonik, Anirudh Sivakumar, Daniel J Deredge, Evgeniia V Edeleva, Jessica Götzfried, Sander W van der Laan, Gerard Pasterkamp, Nathalie Beaufort, Susana Seixas, Steve Bevan, Lisa F Lincz, Elizabeth G Holliday, Annette I Burgess, Kristiina Rannikmäe, Jens Minnerup, Jennifer Kriebel, Melanie Waldenberger, Martina Müller-Nurasyid, Peter Lichtner, Danish Saleheen, Peter M Rothwell, Christopher Levi, John Attia, Cathie L M Sudlow, Dieter Braun, Hugh S Markus, Patrick L Wintrode, Klaus Berger, Dieter E Jenne, Martin Dichgans
Large artery atherosclerotic stroke (LAS) shows substantial heritability not explained by previous genome-wide association studies. Here, we explore the role of coding variation in LAS by analyzing variants on the HumanExome BeadChip in a total of 3,127 cases and 9,778 controls from Europe, Australia, and South Asia. We report on a nonsynonymous single-nucleotide variant in serpin family A member 1 (SERPINA1) encoding alpha-1 antitrypsin [AAT; p.V213A; P = 5.99E-9, odds ratio (OR) = 1.22] and confirm histone deacetylase 9 (HDAC9) as a major risk gene for LAS with an association in the 3'-UTR (rs2023938; P = 7...
March 6, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28263714/r468a-mutation-in-perfringolysin-o-destabilizes-toxin-structure-and-induces-membrane-fusion
#8
Magdalena Kulma, Aleksandra Kacprzyk-Stokowiec, Katarzyna Kwiatkowska, Gabriela Traczyk, Andrzej Sobota, Michał Dadlez
Perfringolysin O (PFO) belongs to the family of cholesterol-dependent cytolysins. Upon binding to a cholesterol-containing membrane, PFO undergoes a series of structural changes that result in the formation of a β-barrel pore and cell lysis. Recognition and binding to cholesterol are mediated by the D4 domain, one of four domains of PFO. The D4 domain contains a conserved tryptophan-rich loop named undecapeptide (E458CTGLAWEWWR468) in which arginine 468 is essential for retaining allosteric coupling between D4 and other domains during interaction of PFO with the membrane...
March 2, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28258193/structural-implications-for-the-formation-and-function-of-the-complement-effector-protein-ic3b
#9
Malvina Papanastasiou, Sophia Koutsogiannaki, Yiannis Sarigiannis, Brian V Geisbrecht, Daniel Ricklin, John D Lambris
Complement-mediated opsonization, phagocytosis, and immune stimulation are critical processes in host defense and homeostasis, with the complement activation fragment iC3b playing a key effector role. To date, however, there is no high-resolution structure of iC3b, and some aspects of its structure-activity profile remain controversial. Here, we employed hydrogen-deuterium exchange mass spectrometry to describe the structure and dynamics of iC3b at a peptide resolution level in direct comparison with its parent protein C3b...
March 3, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28256224/lipid-mediated-regulation-of-embedded-receptor-kinases-via-parallel-allosteric-relays
#10
Madhubrata Ghosh, Loo Chien Wang, Ranita Ramesh, Leslie K Morgan, Linda J Kenney, Ganesh S Anand
Membrane-anchored receptors are essential cellular signaling elements for stimulus sensing, propagation, and transmission inside cells. However, the contributions of lipid interactions to the function and dynamics of embedded receptor kinases have not been described in detail. In this study, we used amide hydrogen/deuterium exchange mass spectrometry, a sensitive biophysical approach, to probe the dynamics of a membrane-embedded receptor kinase, EnvZ, together with functional assays to describe the role of lipids in receptor kinase function...
February 28, 2017: Biophysical Journal
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
#11
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/28242466/elucidation-of-trna-cytochrome-c-interactions-through-hydrogen-deuterium-exchange-mass-spectrometry
#12
Yi-Ting Lo, Hung-Wei Huang, Yi-Chuan Huang, Jui-Fen Chan, Yuan-Hao Howard Hsu
Cytochrome c (cyt c) is a mitochondrial protein responsible for transferring electrons between electron transport chain complexes III and IV. The release of cyt c from the mitochondria has been considered as a commitment step in intrinsic apoptosis. Transfer RNA (tRNA) has recently been found to interact with the released cyt c to prevent the formation of the apoptosome complex, thus preventing cell apoptosis. To understand the molecular basis of tRNA-cyt c interactions, we applied hydrogen/deuterium exchange mass spectrometry (HDXMS) to analyze the interactions between tRNA and cyt c...
February 27, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28236290/the-area-between-exchange-curves-as-a-measure-of-conformational-differences-in-hydrogen-deuterium-exchange-mass-spectrometry-studies
#13
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
#14
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
#15
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
#16
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
#17
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/28186093/conformational-changes-in-intact-dengue-virus-reveal-serotype-specific-expansion
#18
Xin-Xiang Lim, Arun Chandramohan, Xin Ying Elisa Lim, Nirmalya Bag, Kamal Kant Sharma, Melissa Wirawan, Thorsten Wohland, Shee-Mei Lok, Ganesh S Anand
Dengue virus serotype 2 (DENV2) alone undergoes structural expansion at 37 °C (associated with host entry), despite high sequence and structural homology among the four known serotypes. The basis for this differential expansion across strains and serotypes is unknown and necessitates mapping of the dynamics of dengue whole viral particles to describe their coordinated motions and conformational changes when exposed to host-like environments. Here we capture the dynamics of intact viral particles of two serotypes, DENV1 and DENV2, by amide hydrogen/deuterium exchange mass spectrometry (HDXMS) and time resolved Förster Resonance Energy Transfer...
February 10, 2017: Nature Communications
https://www.readbyqxmd.com/read/28185882/s-transnitrosation-reactions-of-hydrogen-sulfide-h2s-hs-s-2-with-s-nitrosated-cysteinyl-thiols-in-phosphate-buffer-of-ph-7-4-results-and%C3%A2-review-of-the-literature
#19
Dimitrios Tsikas, Anke Böhmer
Cysteine (CysSH) and its derivatives including N-acetylcysteine (NAC) and glutathione (GSH), and cysteine residues in proteins and enzymes are nitrosated with nitric oxide (NO) reaction products such as N2O3 to form S-nitrosated cysteine thiols (RCysSNO). RCysSNO undergo with cysteine thiols (RCysSH) S-transnitrosation reactions, thereby transferring reversibly their nitrosyl ((+)NO) group to RCysSH to form RCysSNO. (•)NO release from RCysSNO and S-transnitrosation are considered the most important features and signalling pathways of RCysSNO...
February 6, 2017: Nitric Oxide: Biology and 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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