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Hydrogen-Deuterium Exchange MS

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https://www.readbyqxmd.com/read/28289188/ligand-induced-allostery-in-the-interaction-of-the-pseudomonas-aeruginosa-heme-binding-protein-with-heme-oxygenase
#1
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 13, 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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
https://www.readbyqxmd.com/read/28168880/increased-%C3%AE-sheet-dynamics-and-d-e-loop-repositioning-are-necessary-for-cu-ii-induced-amyloid-formation-by-%C3%AE-2-microglobulin
#10
Nicholas B Borotto, Zhe Zhang, Jia Dong, Brittney Burant, Richard W Vachet
β-2-Microglobulin (β2m) forms amyloid fibrils in the joints of patients undergoing dialysis treatment as a result of kidney failure. One of the ways in which β2m can be induced to form amyloid fibrils in vitro is via incubation with stoichiometric amounts of Cu(II). To better understand the structural changes caused by Cu(II) binding that allow β2m to form amyloid fibrils, we compared the effect of Ni(II) and Zn(II) binding, which are two similarly sized divalent metal ions that do not induce β2m amyloid formation...
February 28, 2017: Biochemistry
https://www.readbyqxmd.com/read/28154854/nanospray-hx-ms-configuration-for-structural-interrogation-of-large-protein-systems
#11
Joey G Sheff, Morgan Hepburn, Yaping Yu, Susan P Lees-Miller, David C Schriemer
Hydrogen-deuterium exchange mass spectrometry (HX-MS) has made important contributions to the study of protein structure and function. Unfortunately, it is not known for low limits of detection, when compared with other forms of peptide-based or bottom-up protein MS methods. Systems perform poorly on sub-pmol quantities of protein states with greater than 300 kDa of unique sequences. The HX-MS analysis of complex protein states would be possible if proteomics-grade configurations could be used reliably, but temperature and temporal constraints have proven to be significant design challenges...
March 13, 2017: Analyst
https://www.readbyqxmd.com/read/28137577/analysis-of-translocation-competent-secretory-proteins-by-hdx-ms
#12
A Tsirigotaki, M Papanastasiou, M B Trelle, T J D Jørgensen, A Economou
Protein folding is an intricate and precise process in living cells. Most exported proteins evade cytoplasmic folding, become targeted to the membrane, and then trafficked into/across membranes. Their targeting and translocation-competent states are nonnatively folded. However, once they reach the appropriate cellular compartment, they can fold to their native states. The nonnative states of preproteins remain structurally poorly characterized since increased disorder, protein sizes, aggregation propensity, and the observation timescale are often limiting factors for typical structural approaches such as X-ray crystallography and NMR...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28108962/determination-of-equine-cytochrome-c-backbone-amide-hydrogen-deuterium-exchange-rates-by-mass-spectrometry-using-a-wider-time-window-and-isotope-envelope
#13
Yoshitomo Hamuro
A new strategy to analyze amide hydrogen/deuterium exchange mass spectrometry (HDX-MS) data is proposed, utilizing a wider time window and isotope envelope analysis of each peptide. While most current scientific reports present HDX-MS data as a set of time-dependent deuteration levels of peptides, the ideal HDX-MS data presentation is a complete set of backbone amide hydrogen exchange rates. The ideal data set can provide single amide resolution, coverage of all exchange events, and the open/close ratio of each amide hydrogen in EX2 mechanism...
January 20, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28077807/folding-of-apomyoglobin-analysis-of-transient-intermediate-structure-during-refolding-using-quick-hydrogen-deuterium-exchange-and-nmr
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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...
March 2017: Journal of Structural Biology
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