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Hydrogen-Deuterium Exchange MS

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https://www.readbyqxmd.com/read/28077807/folding-of-apomyoglobin-analysis-of-transient-intermediate-structure-during-refolding-using-quick-hydrogen-deuterium-exchange-and-nmr
#1
Chiaki Nishimura
The structures of apomyoglobin folding intermediates have been widely analyzed using physical chemistry methods including fluorescence, circular dichroism, small angle X-ray scattering, NMR, mass spectrometry, and rapid mixing. So far, at least two intermediates (on sub-millisecond- and millisecond-scales) have been demonstrated for apomyoglobin folding. The combination of pH-pulse labeling and NMR is a useful tool for analyzing the kinetic intermediates at the atomic level. Its use has revealed that the latter-phase kinetic intermediate of apomyoglobin (6 ms) was composed of helices A, B, G and H, whereas the equilibrium intermediate, called the pH 4 molten-globule intermediate, was composed mainly of helices A, G and H...
2017: Proceedings of the Japan Academy. Series B, Physical and Biological Sciences
https://www.readbyqxmd.com/read/28069117/promotion-effect-of-sulfite-on-deoxyosones-and-4-methylimidazole-in-caramel-model-system
#2
Xian-Bing Xu, Pei Yu, Shu-Juan Yu
In this study, hydrogen-deuterium (H/D) exchange experiment was carried out to reveal the promotion effect of sulfite on the formation of deoxyosones and 4-methylimidazole (4-MeI) in the Maillard reaction. Glucose-ammonium (40mmol/L, pH 7.4 in PBS) model systems with different levels of sulfite were incubated at 110°C for 2h. Alpha-dicarbonyls were detected after derivatization by a high-performance liquid chromatography with a diode array detector (HPLC-DAD). 4-MeI in the Maillard reaction was tested using a high-performance anion exchange chromatography with an electrochemical detector (HPAEC-ED)...
May 15, 2017: Food Chemistry
https://www.readbyqxmd.com/read/28063489/using-hydrogen-deuterium-exchange-mass-spectrometry-to-examine-protein-membrane-interactions
#3
O Vadas, M L Jenkins, G L Dornan, J E Burke
Many fundamental cellular processes are controlled via assembly of a network of proteins at membrane surfaces. The proper recruitment of proteins to membranes can be controlled by a wide variety of mechanisms, including protein lipidation, protein-protein interactions, posttranslational modifications, and binding to specific lipid species present in membranes. There are, however, only a limited number of analytical techniques that can study the assembly of protein-membrane complexes at the molecular level. A relatively new addition to the set of techniques available to study these protein-membrane systems is the use of hydrogen-deuterium exchange mass spectrometry (HDX-MS)...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28024262/levothyroxine-sodium-revisited-a-wholistic-structural-elucidation-approach-of-new-impurities-via-hplc-hrms-ms-on-line-h-d-exchange-nmr-spectroscopy-and-chemical-synthesis
#4
M Ruggenthaler, J Grass, W Schuh, C G Huber, R J Reischl
The structural elucidation of unknown pharmaceutical impurities plays an important role in the quality control of newly developed and well-established active pharmaceutical ingredients (APIs). The United States Pharmacopeia (USP) monograph for the API Levothyroxine Sodium, a synthetic thyroid hormone, features two high pressure liquid chromatography (HPLC) methods using UV-VIS absorption detection to determine organic impurities in the drug substance. The impurity profile of the first USP method ("Procedure 1") has already been extensively studied, however for the second method ("Procedure 2"), which exhibits a significantly different impurity profile, no wholistic structural elucidation of impurities has been performed yet...
December 14, 2016: Journal of Pharmaceutical and Biomedical Analysis
https://www.readbyqxmd.com/read/28008853/ric-8a-a-g-protein-chaperone-with-nucleotide-exchange-activity-induces-long-range-secondary-structure-changes-in-g%C3%AE
#5
Ravi Kant, Baisen Zeng, Celestine J Thomas, Brian Bothner, Stephen R Sprang
Cytosolic Ric-8A has guanine nucleotide exchange factor (GEF) activity and is a chaperone for several classes of heterotrimeric G protein α subunits in vertebrates. Using Hydrogen-Deuterium Exchange-Mass Spectrometry (HDX-MS) we show that Ric-8A disrupts the secondary structure of the Gα Ras-like domain that girds the guanine nucleotide-binding site, and destabilizes the interface between the Gαi1 Ras and helical domains, allowing domain separation and nucleotide release. These changes are largely reversed upon binding GTP and dissociation of Ric-8A...
December 23, 2016: ELife
https://www.readbyqxmd.com/read/28000716/%C3%AE-subunit-myristoylation-functions-as-an-energy-sensor-by-modulating-the-dynamics-of-amp-activated-protein-kinase
#6
Nada Ali, Naomi Ling, Srinath Krishnamurthy, Jonathan S Oakhill, John W Scott, David I Stapleton, Bruce E Kemp, Ganesh Srinivasan Anand, Paul R Gooley
The heterotrimeric AMP-activated protein kinase (AMPK), consisting of α, β and γ subunits, is a stress-sensing enzyme that is activated by phosphorylation of its activation loop in response to increases in cellular AMP. N-terminal myristoylation of the β-subunit has been shown to suppress Thr172 phosphorylation, keeping AMPK in an inactive state. Here we use amide hydrogen-deuterium exchange mass spectrometry (HDX-MS) to investigate the structural and dynamic properties of the mammalian myristoylated and non-myristoylated inactivated AMPK (D139A) in the presence and absence of nucleotides...
December 21, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27998708/conformations-of-jnk3%C3%AE-splice-variants-analyzed-by-hydrogen-deuterium-exchange-mass-spectrometry
#7
Ji Young Park, Youngjoo Yun, Ka Young Chung
c-Jun N-terminal kinases (JNKs) are members of the mitogen-activated protein kinase (MAPK) family that regulate apoptosis, inflammation, cytokine production, and metabolism. MAPKs undergo various splicing within their kinase domains. Unlike other MAPKs, JNKs have alternative splicing at the C-terminus, resulting in long and short variants. Functional or conformational effects due to the elongated C-terminal tail in the long splice variants have not been investigated nor has the conformation of the C-terminal tail been analyzed...
December 18, 2016: Journal of Structural Biology
https://www.readbyqxmd.com/read/27992649/kinetic-isotope-effects-and-hydrogen-deuterium-exchange-reveal-large-conformational-changes-during-the-catalysis-of-the-clostridium-acetobutylicum-spore-photoproduct-lyase
#8
Linlin Yang, Jagat Adhikari, Michael L Gross, Lei Li
Spore photoproduct lyase (SPL) catalyzes the direct reversal of a thymine dimer 5-thyminyl-5,6-dihydrothymine (i.e., the spore photoproduct (SP)) to two thymine residues in germinating endospores. Previous studies suggest that SPL from the bacterium Bacillus subtilis (Bs) harbors an unprecedented radical transfer pathway starting with cysteine 141 proceeding through tyrosine 99. However, in SPL from the bacterium C. acetobutylicum (Ca), the cysteine (at position 74) and tyrosine are located on the opposite sides of a substrate binding pocket that has to collapse to bring the two residues into proximity, enabling the C→Y radical passage as implied in SPL(Bs) ...
December 19, 2016: Photochemistry and Photobiology
https://www.readbyqxmd.com/read/27989622/the-molecular-basis-of-aichi-virus-3a-protein-activation-of-phosphatidylinositol-4-kinase-iii%C3%AE-pi4kb-through-acbd3
#9
Jacob A McPhail, Erik H Ottosen, Meredith L Jenkins, John E Burke
Phosphatidylinositol 4-kinase III beta (PI4KIIIβ) is an essential enzyme in mediating membrane transport, and plays key roles in facilitating viral infection. Many pathogenic positive-sense single-stranded RNA viruses activate PI4KIIIβ to generate phosphatidylinositol 4-phosphate (PI4P)-enriched organelles for viral replication. The molecular basis for PI4KIIIβ activation during viral infection has remained largely unclear. We describe the biochemical reconstitution and characterization of the complex of PI4KIIIβ with the Golgi protein Acyl-coenzyme A binding domain containing protein 3 (ACBD3) and Aichi virus 3A protein on membranes...
December 7, 2016: Structure
https://www.readbyqxmd.com/read/27975228/protein-structural-analysis-via-mass-spectrometry-based-proteomics
#10
Antonio Artigues, Owen W Nadeau, Mary Ashley Rimmer, Maria T Villar, Xiuxia Du, Aron W Fenton, Gerald M Carlson
Modern mass spectrometry (MS) technologies have provided a versatile platform that can be combined with a large number of techniques to analyze protein structure and dynamics. These techniques include the three detailed in this chapter: (1) hydrogen/deuterium exchange (HDX), (2) limited proteolysis, and (3) chemical crosslinking (CX). HDX relies on the change in mass of a protein upon its dilution into deuterated buffer, which results in varied deuterium content within its backbone amides. Structural information on surface exposed, flexible or disordered linker regions of proteins can be achieved through limited proteolysis, using a variety of proteases and only small extents of digestion...
2016: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/27929190/mechanism-and-kinetics-of-tyrosinase-inhibition-by-glycolic-acid-a-study-using-conventional-spectroscopy-methods-and-hydrogen-deuterium-exchange-coupling-with-mass-spectrometry
#11
Da Ma, Zong-Cai Tu, Hui Wang, Lu Zhang, Na He, David Julian McClements
Tyrosinase is an enzyme that promotes enzymatic browning of fruits and vegetables, thereby reducing product quality. A variety of analytical tools were used to characterize the interactions between tyrosinase and a natural tyrosinase inhibitor (glycolic acid). Hydrogen/deuterium exchange coupling with mass spectrometry (HDX-MS) was used to elucidate the interaction mechanism between glycolic acid and tyrosinase. UV-visible, fluorescence and circular dichroism spectroscopy analysis indicated that glycolic acid inhibited tyrosinase activity in a mixed-type manner with an IC50 of 83 ± 14 μM...
December 8, 2016: Food & Function
https://www.readbyqxmd.com/read/27924262/mass-spectrometric-analysis-of-protein-ligand-interactions
#12
Kentaro Ishii, Masanori Noda, Susumu Uchiyama
The interactions of small molecules with proteins (protein-ligand interactions) mediate various biological phenomena including signal transduction and protein transcription and translation. Synthetic compounds such as drugs can also bind to target proteins, leading to the inhibition of protein-ligand interactions. These interactions typically accompany association-dissociation equilibrium according to the free energy difference between free and bound states; therefore, the quantitative biophysical analysis of the interactions, which uncovers the stoichiometry and dissociation constant, is important for understanding biological reactions as well as for rational drug development...
2016: Biophysics and Physicobiology
https://www.readbyqxmd.com/read/27916388/application-of-dual-protease-column-for-hdx-ms-analysis-of-monoclonal-antibodies
#13
Sasidhar N Nirudodhi, Justin B Sperry, Jason C Rouse, James A Carroll
A co-immobilized, dual protease column was developed and implemented to more efficiently digest IgG molecules for hydrogen/deuterium exchange mass spectrometry (HDX-MS). The low-pH proteolytic enzymes pepsin and type XIII protease from Aspergillus were packed into a single column to most effectively combine the complementary specificities. The method was optimized using an IgG2 monoclonal antibody as a substrate because they are known to be more difficult to efficiently digest. The general applicability of the method was then demonstrated using IgG1 and IgG4 mAbs...
February 2017: Journal of Pharmaceutical Sciences
https://www.readbyqxmd.com/read/27915195/hydrogen-deuterium-exchange-a-unique-and-effective-method-for-ms-fragmentation-behavior-elucidation-of-ginkgolides-and-its-application-to-systematic-research-in-ginkgo-biloba
#14
Xingliang Niu, Jun Luo, Deran Xu, Hongyan Zou, Lingyi Kong
Ginkgolides, the main active constituents of Ginkgo biloba, possess significant selectively inhibition on platelet-activating factor and pancreatic lipase and attract wide attention in pharmacological research area. In our study, an effective hydrogen/deuterium (H/D) exchange method was developed by exchanging the α-Hs of lactone groups in ginkgolides with Ds, which was very useful for the elucidation of the fragmentation patterns of ginkgolides in Quadrupole Time-of-flight Mass Spectrometry (Q-TOF-MS), especially in accurately distinguishing the type and position of substituent in framework of ginkgolides...
February 5, 2017: Journal of Pharmaceutical and Biomedical Analysis
https://www.readbyqxmd.com/read/27879668/structure-functional-basis-of-ion-transport-in-sodium-calcium-exchanger-ncx-proteins
#15
REVIEW
Moshe Giladi, Reut Shor, Michal Lisnyansky, Daniel Khananshvili
The membrane-bound sodium-calcium exchanger (NCX) proteins shape Ca(2+) homeostasis in many cell types, thus participating in a wide range of physiological and pathological processes. Determination of the crystal structure of an archaeal NCX (NCX_Mj) paved the way for a thorough and systematic investigation of ion transport mechanisms in NCX proteins. Here, we review the data gathered from the X-ray crystallography, molecular dynamics simulations, hydrogen-deuterium exchange mass-spectrometry (HDX-MS), and ion-flux analyses of mutants...
November 22, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27879053/n-arylsulfonyl-indolines-as-retinoic-acid-receptor-related-orphan-receptor%C3%A2-%C3%AE-ror%C3%AE-agonists
#16
Christelle Doebelin, Rémi Patouret, Ruben D Garcia-Ordonez, Mi Ra Chang, Venkatasubramanian Dharmarajan, Dana S Kuruvilla, Scott J Novick, Li Lin, Michael D Cameron, Patrick R Griffin, Theodore M Kamenecka
The nuclear retinoic acid receptor-related orphan receptor γ (RORγ; NR1F3) is a key regulator of inflammatory gene programs involved in T helper 17 (TH 17) cell proliferation. As such, synthetic small-molecule repressors (inverse agonists) targeting RORγ have been extensively studied for their potential as therapeutic agents for various autoimmune diseases. Alternatively, enhancing TH 17 cell proliferation through activation (agonism) of RORγ may boost an immune response, thereby offering a potentially new approach in cancer immunotherapy...
December 6, 2016: ChemMedChem
https://www.readbyqxmd.com/read/27870250/new-insights-into-interactions-between-the-nucleotide-binding-domain-of-cftr-and-keratin-8
#17
Aiswarya Premchandar, Anna Kupniewska, Arkadiusz Bonna, Grazyna Faure, Tomasz Fraczyk, Ariel Roldan, Brice Hoffmann, Mélanie Faria da Cunha, Harald Herrmann, Gergely L Lukacs, Aleksander Edelman, Michał Dadlez
The intermediate filament protein keratin 8 (K8) interacts with the nucleotide-binding domain 1 (NBD1) of the cystic fibrosis transmembrane regulator (CFTR) with phenylalanine 508 deletion (ΔF508), and this interaction hampers the biogenesis of functional ΔF508-CFTR and its insertion into the plasma membrane. Interruption of this interaction may constitute a new therapeutic target for cystic fibrosis patients bearing the ΔF508 mutation. Here we aimed to determine the binding surface between these two proteins, to facilitate the design of the interaction inhibitors...
November 21, 2016: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/27851982/interdomain-electron-transfer-in-cellobiose-dehydrogenase-is-governed-by-surface-electrostatics
#18
Alan Kadek, Daniel Kavan, Julien Marcoux, Johann Stojko, Alfons K G Felice, Sarah Cianférani, Roland Ludwig, Petr Halada, Petr Man
BACKGROUND: Cellobiose dehydrogenase (CDH) is a fungal extracellular oxidoreductase which fuels lytic polysaccharide monooxygenase with electrons during cellulose degradation. Interdomain electron transfer between the flavin and cytochrome domain in CDH, preceding the electron flow to lytic polysaccharide monooxygenase, is known to be pH dependent, but the exact mechanism of this regulation has not been experimentally proven so far. METHODS: To investigate the structural aspects underlying the domain interaction in CDH, hydrogen/deuterium exchange (HDX-MS) with improved proteolytic setup (combination of nepenthesin-1 with rhizopuspepsin), native mass spectrometry with ion mobility and electrostatics calculations were used...
February 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27807976/a-residue-resolved-bayesian-approach-to-quantitative-interpretation-of-hydrogen-deuterium-exchange-from-mass-spectrometry-application-to-characterizing-protein-ligand-interactions
#19
Daniel John Saltzberg, Howard B Broughton, Riccardo Pellarin, Michael J Chalmers, Alfonso Espada, Jeffrey A Dodge, Bruce D Pascal, Patrick R Griffin, Christine Humblet, Andrej Sali
Characterization of interactions between proteins and other molecules is crucial for understanding the mechanisms of action of biological systems and, thus, drug discovery. An increasingly useful approach to mapping these interactions is measurement of hydrogen/deuterium exchange (HDX) using mass spectrometry (HDX-MS), which measures the time-resolved deuterium incorporation of peptides obtained by enzymatic digestion of the protein. Comparison of exchange rates between apo- and ligand-bound conditions results in a mapping of the differential HDX (ΔHDX) of the ligand...
November 3, 2016: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/27797822/the-diverse-and-expanding-role-of-mass-spectrometry-in-structural-and-molecular-biology
#20
REVIEW
Philip Lössl, Michiel van de Waterbeemd, Albert Jr Heck
The emergence of proteomics has led to major technological advances in mass spectrometry (MS). These advancements not only benefitted MS-based high-throughput proteomics but also increased the impact of mass spectrometry on the field of structural and molecular biology. Here, we review how state-of-the-art MS methods, including native MS, top-down protein sequencing, cross-linking-MS, and hydrogen-deuterium exchange-MS, nowadays enable the characterization of biomolecular structures, functions, and interactions...
December 15, 2016: EMBO Journal
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