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Hydrogen-Deuterium Exchange MS

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https://www.readbyqxmd.com/read/29645318/investigating-the-dynamics-and-polyanion-binding-sites-of-fibroblast-growth-factor-1-using-hydrogen-deuterium-exchange-mass-spectrometry
#1
Siva K Angalakurthi, Connie A Tenorio, Michael Blaber, C Russell Middaugh
In this study, we examined the local dynamics of acidic fibroblast growth factor (FGF-1) as well as the binding sites of various polyanions including poly-sulfates (heparin and low MW heparin) and poly-phosphates (phytic acid and ATP) using hydrogen-deuterium exchange mass spectrometry (HX-MS). For local dynamics, results are analyzed at the peptide level as well as in terms of buried amides employing crystallographic B-factors and compared with a residue level heat map generated from HX-MS results. Results show that strand 4 and 5 and the turn between them to be the most flexible regions as was previously seen by NMR...
April 12, 2018: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/29624844/a-vastly-increased-chemical-variety-of-rna-modifications-that-includes-a-thioacetal-structure
#2
Christina Dal Magro, Patrick Keller, Annika Kotter, Stephan Werner, Victor Duarte, Virginie Marchand, Michael Ignarski, Anja Freiwald, Roman-Ulrich Müller, Christoph Dieterich, Yuri Motorin, Falk Butter, Mohammed Atta, Mark Helm
Recently discovered new chemical entities in RNA modifications have provided surprises with respect to functional groups that enlarge the chemical space of RNA. Using LC-MS, we found over one hundred signals of RNA constituents that contained a ribose moiety in tRNAs from E. coli. Feeding experiments with variegated stable isotope labeled compounds identified 37 compounds, representing new structures of RNA modifications. One structure was elucidated by deuterium exchange and high resolution mass spectrometry...
April 6, 2018: Angewandte Chemie
https://www.readbyqxmd.com/read/29619829/native-state-organization-of-outer-membrane-porins-unraveled-by-hdx-ms
#3
Danilo Donnarumma, Claudio Maestri, Pietro Ivan Giammarinaro, Luigi Capriotti, Erika Bartolini, Daniele Veggi, Roberto Petracca, Maria Scarselli, Nathalie Norais
Hydrogen Deuterium exchange (HDx) associated with Mass Spectrometry (MS) is emerging as a powerful tool to provide conformational information on membrane proteins. Unfortunately, as for X-ray diffraction and NMR, HDx performed on reconstituted in vitro systems might not always reflect the in vivo environment. Outer Membrane Vesicles naturally released by E. coli were used to carry out analysis of native OmpF through HDx-MS. A new protocol compatible with HDx analysis and avoiding hindrance from the lipid contents was set-up...
April 5, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29605914/hydrogen-deuterium-exchange-mass-spectrometry-to-study-protein-complexes
#4
Brent A Kochert, Roxana E Iacob, Thomas E Wales, Alexandros Makriyannis, John R Engen
Hydrogen-deuterium exchange (HDX) mass spectrometry (MS) can provide valuable information about binding, allostery, and other conformational effects of interaction in protein complexes. For protein-ligand complexes, where the ligand may be a small molecule, peptide, nucleotide, or another protein(s), a typical experiment measures HDX in the protein alone and then compares that with HDX for the protein when part of the complex. Multiple factors are critical in the design and implementation of such experiments, including thoughtful consideration of the percent protein bound, the effects of the labeling protocol on the protein complex, and the dynamic range of the analysis method...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29601177/pulsed-hdx-illuminates-the-aggregation-kinetics-of-alpha-synuclein-the-causative-agent-for-parkinson-s-disease
#5
Eva Illes-Toth, Don L Rempel, Michael L Gross
Alpha-synuclein (aS) forms toxic intermediates ranging from small oligomers and protofibrils to large amyloid fibrils. Understanding the time course of aS fibril formation and the role played by its regions is critical for therapeutic intervention. Here, we used pulsed hydrogen-deuterium-exchange and mass spectrometry (HDX-MS) for the first time to probe kinetic intermediates of the full aS aggregation in vitro, achieving kinetic snapshots containing spatially resolved protein information about critical stages...
March 30, 2018: ACS Chemical Neuroscience
https://www.readbyqxmd.com/read/29587225/hydrogen-deuterium-exchange-reveals-changes-to-protein-dynamics-of-recombinant-human-erythropoietin-upon-n-and-o-desialylation
#6
Andrea L Wang, Ying Zhou, Michael J Palmieri, Gang G Hao
Recombinant human erythropoietin (EPO) is a therapeutic glycoprotein widely used for treating anemia. EPO glycans carry extensive sialylation and the level of the modification is known to affect receptor binding, protein stability and pharmacokinetics. Nonetheless, a detailed understanding of the effects of sialylation on EPO conformation and dynamics is still lacking. Here we investigate the changes to EPO dynamics following enzymatic trimming of terminal sialic acid by amide hydrogen deuterium exchange mass spectrometry (HDX-MS)...
March 16, 2018: Journal of Pharmaceutical and Biomedical Analysis
https://www.readbyqxmd.com/read/29555555/the-xenobiotic-extrusion-mechanism-of-the-mate-transporter-norm_ps-from-pseudomonas-stutzeri
#7
Martin Lorenz Eisinger, Laiyin Nie, Aline Ricarda Dörrbaum, Julian David Langer, Hartmut Michel
Multidrug resistance (MDR) in bacterial pathogens has become a severe threat to public health. Membrane transporters of the multidrug and toxic compound extrusion (MATE) family contribute critically to MDR, making them promising drug targets. Despite recent advances, structures in different conformations and the mechanistic details of their antiport cycle are still elusive. Here we studied NorM_PS, a representative MATE transporter from Pseudomonas stutzeri, using biochemical assays in combination with hydrogen/deuterium exchange-mass spectrometry (HDX-MS)...
March 16, 2018: Journal of Molecular Biology
https://www.readbyqxmd.com/read/29531348/structural-model-of-human-dutpase-in-complex-with-a-novel-proteinaceous-inhibitor
#8
Kinga Nyíri, Haydyn D T Mertens, Borbála Tihanyi, Gergely N Nagy, Bianka Kőhegyi, Judit Matejka, Matthew J Harris, Judit E Szabó, Veronika Papp-Kádár, Veronika Németh-Pongrácz, Olivér Ozohanics, Károly Vékey, Dmitri I Svergun, Antoni J Borysik, Beáta G Vértessy
Human deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase), essential for DNA integrity, acts as a survival factor for tumor cells and is a target for cancer chemotherapy. Here we report that the Staphylococcal repressor protein StlSaPIBov1 (Stl) forms strong complex with human dUTPase. Functional analysis reveals that this interaction results in significant reduction of both dUTPase enzymatic activity and DNA binding capability of Stl. We conducted structural studies to understand the mechanism of this mutual inhibition...
March 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29520892/deconvolution-in-mass-spectrometry-based-proteomics
#9
Guang Xu, Jacek Stupak, Li Yang, Luokai Hu, Bo Guo, Jianjun Li
Mass spectrometry (MS) has played a vital role across a broad range of fields and applications in proteomics. The development of high-resolution MS for the past decades has significantly advanced biology, such as protein structure, function, post translational modification and global protein dynamics. In MS, two ionization techniques are often used-electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI). ESI mass spectra are generally crowded by signals of multiple charge values for each molecular mass and an isotopic cluster for each nominal mass-to-charge (m/z) value...
March 8, 2018: Rapid Communications in Mass Spectrometry: RCM
https://www.readbyqxmd.com/read/29500740/determination-of-backbone-amide-hydrogen-exchange-rates-of-cytochrome-c-using-partially-scrambled-electron-transfer-dissociation-data
#10
Yoshitomo Hamuro, Sook Yen E
The technological goal of hydrogen/deuterium exchange-mass spectrometry (HDX-MS) is to determine backbone amide hydrogen exchange rates. The most critical challenge to achieve this goal is obtaining the deuterium incorporation in single-amide resolution, and gas-phase fragmentation may provide a universal solution. The gas-phase fragmentation may generate the daughter ions which differ by a single amino acid and the difference in deuterium incorporations in the two analogous ions can yield the deuterium incorporation at the sub-localized site...
March 2, 2018: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/29470989/redox-exchange-of-the-disulfides-of-human-two-domain-cd4-regulates-the-conformational-dynamics-of-each-domain-providing-insight-into-its-mechanisms-of-control
#11
Gavin R Owen, Doris Le, Stoyan Stoychev, Nichole M Cerutti, Maria Papathanasopoulos
CD4, a membrane glycoprotein expressed by specific leukocytes, plays a vital role in the human immune response and acts as a primary receptor for HIV entry. Of its four ecto-domains (D1-D4), D1, D2, and D4 each contain a distinctive disulfide bond. Whereas the disulfides of D1 and D4 are more traditional in nature, providing structural functions, that of D2 is referred to as an "allosteric" disulfide due to its high dihedral strain energy and relative ease of reduction that is thought to regulate CD4 structure and function by shuffling its redox state...
February 19, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29457883/mapping-the-h-nox-hk-binding-interface-in-vibrio-cholerae-by-hydrogen-deuterium-exchange-mass-spectrometry
#12
Yirui Guo, Anthony T Iavarone, Matthew M Cooper, Michael A Marletta
Heme-nitric oxide/oxygen binding (H-NOX) proteins are a group of hemoproteins that bind diatomic gas ligands such as nitric oxide (NO) and oxygen (O2 ). H-NOX proteins typically regulate histidine kinases (HK) located within the same operon. It has been reported that NO-bound H-NOXs inhibit cognate histidine kinase autophosphorylation in bacterial H-NOX/HK complexes, however, a detailed mechanism of NO-mediated regulation of the H-NOX/HK activity remains unknown. In this study, the binding interface of Vibrio cholerae (Vc) H-NOX/HK complex was characterized by hydrogen/deuterium exchange mass spectrometry (HDX-MS) and further validated by mutagenesis, leading to a new model for NO-dependent kinase inhibition...
February 19, 2018: Biochemistry
https://www.readbyqxmd.com/read/29450991/mass-spectrometry-based-fast-photochemical-oxidation-of-proteins-fpop-for-higher-order-structure-characterization
#13
Ke Sherry Li, Liuqing Shi, Michael L Gross
Assessment of protein structure and interaction is crucial for understanding protein structure/function relationships. Compared to high-resolution structural tools, including X-ray crystallography, nuclear magnetic resonance (NMR), and cryo-EM, and traditional low-resolution methods, such as circular dichroism, UV-vis, and florescence spectroscopy, mass spectrometry (MS)-based protein footprinting affords medium-to-high resolution (i.e., regional and residue-specific insights) by taking advantage of proteomics methods focused on the primary structure...
February 16, 2018: Accounts of Chemical Research
https://www.readbyqxmd.com/read/29436927/quantitative-analysis-of-glycation-and-its-impact-on-antigen-binding
#14
Jingjie Mo, Renzhe Jin, Qingrong Yan, Izabela Sokolowska, Michael J Lewis, Ping Hu
Glycation has been observed in antibody therapeutics manufactured by the fed-batch fermentation process. It not only increases the heterogeneity of antibodies, but also potentially affects product safety and efficacy. In this study, non-glycated and glycated fractions enriched from a monoclonal antibody (mAb1) as well as glucose-stressed mAb1 were characterized using a variety of biochemical, biophysical and biological assays to determine the effects of glycation on the structure and function of mAb1. Glycation was detected at multiple lysine residues and reduced the antigen binding activity of mAb1...
February 13, 2018: MAbs
https://www.readbyqxmd.com/read/29369433/comparing-the-fragmentation-reactions-of-protonated-cyclic-indolyl-%C3%AE-amino-esters-in-q-orbitrap-and-qtof-mass-spectrometers
#15
Xiaoji Cao, Xue Cai, Weimin Mo
RATIONALE: The comparative study of higher-energy collisional dissociation(HCD) and collision-induced dissociation(CID) mechanisms for protonated cyclic indolyl α-amino esters in quadrupole/orbitrap(Q/Orbitrap) and quadrupole time-of-flight(QTOF) mass spectrometers, respectively, is helpful to study the structures and properties of biologically active indole derivatives using tandem mass spectrometry(MS/MS) technology. METHODS: HCD and CID experiments were carried out using electrospray ionization Q/Orbitrap MS and QTOFMS in positive ion mode, respectively...
January 25, 2018: Rapid Communications in Mass Spectrometry: RCM
https://www.readbyqxmd.com/read/29355022/probing-the-conformation-of-an-igg1-monoclonal-antibody-in-lyophilized-solids-using-solid-state-hydrogen-deuterium-exchange-with-mass-spectrometric-analysis-sshdx-ms
#16
Ehab M Moussa, Satish K Singh, Michael Kimmel, Sandeep Nema, Elizabeth M Topp
Therapeutic proteins are often formulated as lyophilized products to improve their stability and prolong shelf life. The stability of proteins in the solid-state has been correlated with preservation of native higher order structure and/or molecular mobility in the solid matrix, with varying success. In the studies reported here, we used solid-state hydrogen-deuterium exchange with mass spectrometric analysis (ssHDX-MS) to study the conformation of an IgG1 monoclonal antibody (mAb) in lyophilized solids and related the extent of ssHDX to aggregation during storage in the solid phase...
February 5, 2018: Molecular Pharmaceutics
https://www.readbyqxmd.com/read/29334167/cross-linking-mass-spectrometry-for-studying-protein-structures-and-protein-protein-interactions-where-are-we-now-and-where-should-we-go-from-here
#17
Andrea Sinz
Structural mass spectrometry (MS) is gaining increasing importance in deriving valuable three-dimensional structural information on proteins and protein complexes and complements existing techniques, such as NMR spectroscopy and X-ray crystallography. Structural MS unites different MS-based techniques, i.e, hydrogen-deuterium exchange, native MS, ion-mobility MS, protein footprinting, and chemical cross-linking/MS, and allows fundamental questions in structural biology to be addressed. In this article, I will focus on the cross-linking/MS strategy...
January 15, 2018: Angewandte Chemie
https://www.readbyqxmd.com/read/29330778/isotopic-exchange-hplc-hrms-ms-applied-to-cyclic-proanthocyanidins-in-wine-and-cranberries
#18
Edoardo Longo, Fabrizio Rossetti, Matteo Scampicchio, Emanuele Boselli
Cyclic B-type proanthocyanidins in red wines and grapes have been discovered recently. However, proanthocyanidins of a different chemical structure (non-cyclic A-type proanthocyanidins) already known to be present in cranberries and wine possess an identical theoretical mass. As a matter of fact, the retention times and the MS/MS fragmentations found for the proposed novel cyclic B-type tetrameric proanthocyanidin in red wine and the known tetrameric proanthocyanidin in a cranberry extract are herein shown to be identical...
April 2018: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/29299838/optimization-of-feasibility-stage-for-hydrogen-deuterium-exchange-mass-spectrometry
#19
Yoshitomo Hamuro, Stephen J Coales
The practice of HDX-MS remains somewhat difficult, not only for newcomers but also for veterans, despite its increasing popularity. While a typical HDX-MS project starts with a feasibility stage where the experimental conditions are optimized and the peptide map is generated prior to the HDX study stage, the literature usually reports only the HDX study stage. In this protocol, we describe a few considerations for the initial feasibility stage, more specifically, how to optimize quench conditions, how to tackle the carryover issue, and how to apply the pepsin specificity rule...
March 2018: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/29299701/effects-of-drying-process-on-an-igg1-monoclonal-antibody-using-solid-state-hydrogen-deuterium-exchange-with-mass-spectrometric-analysis-sshdx-ms
#20
Ehab M Moussa, Nathan E Wilson, Qi Tony Zhou, Satish K Singh, Sandeep Nema, Elizabeth M Topp
PURPOSE: Lyophilization and spray drying are widely used to manufacture solid forms of therapeutic proteins. Lyophilization is used to stabilize proteins vulnerable to degradation in solution, whereas spray drying is mainly used to prepare inhalation powders or as an alternative to freezing for storing bulk drug substance. Both processes impose stresses that may adversely affect protein structure, stability and bioactivity. Here, we compared lyophilization with and without controlled ice nucleation, and spray drying for their effects on the solid-state conformation and matrix interactions of a model IgG1 monoclonal antibody (mAb)...
January 3, 2018: Pharmaceutical Research
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