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https://www.readbyqxmd.com/read/28318507/usefulness-of-diffusion-tensor-mri-in-the-diagnosis-of-parkinson-variant-of-multiple-system-atrophy-and-parkinson-s-disease-a-valuable-tool-to-differentiate-between-them
#1
B Chen, G Fan, W Sun, X Shang, S Shi, S Wang, G Lv, C Wu
AIM: To evaluate the differences between patients with Parkinson's disease (PD) and Parkinson variant of multiple system atrophy (MSAp) at fractional anisotropy (FA) in the white matter when using the tract-based spatial statistics (TBSS) algorithm to provide objective markers for a differential diagnosis. MATERIALS AND METHODS: Diffusion-tensor imaging (DTI) data were acquired from 18 PD patients, 20 MSAp patients, and 24 healthy controls using a GE 3 T Signa HDx magnetic resonance imaging (MRI) system...
March 16, 2017: Clinical Radiology
https://www.readbyqxmd.com/read/28315238/comprehensive-gas-phase-peptide-ion-structure-studies-using-ion-mobility-techniques-part-2-gas-phase-hydrogen-deuterium-exchange-for-ion-population-estimation
#2
Mahdiar Khakinejad, Samaneh Ghassabi Kondalaji, Amirmahdi Tafreshian, Stephen J Valentine
Gas-phase hydrogen/deuterium exchange (HDX) using D2O reagent and collision cross-section (CCS) measurements are utilized to monitor the ion conformers of the model peptide acetyl-PAAAAKAAAAKAAAAKAAAAK. The measurements are carried out on a home-built ion mobility instrument coupled to a linear ion trap mass spectrometer containing electron transfer dissociation (ETD) capabilities. ETD is utilized to obtain per-residue deuterium uptake data for select ion conformers, and a new algorithm is presented for interpreting the HDX data...
March 17, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28304155/gas-phase-hydrogen-deuterium-exchange-for-distinguishing-isomeric-carbohydrate-ions
#3
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/28289188/ligand-induced-allostery-in-the-interaction-of-the-pseudomonas-aeruginosa-heme-binding-protein-with-heme-oxygenase
#4
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/28288347/exploration-of-the-metal-coordination-region-of-concanavalin-a-for-its-interaction-with-human-norovirus
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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/28194741/deciphering-the-biophysical-effects-of-oxidizing-sulfur-containing-amino-acids-in-interferon-beta-1a-using-ms-and-hdx-ms
#11
Damian J Houde, George M Bou-Assaf, Steven A Berkowitz
Introduction of a chemical change to one or more amino acids in a protein's polypeptide chain can result in various effects on its higher-order structure (HOS) and biophysical behavior (or properties). These effects range from no detectable change to significant structural or conformational alteration that can greatly affect the protein's biophysical properties and its resulting biological function. The ability to reliably detect the absence or presence of such changes is essential to understanding the structure-function relationship in a protein and in the successful commercial development of protein-based drugs (biopharmaceuticals)...
February 13, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28194737/regio-selective-intramolecular-hydrogen-deuterium-exchange-in-gas-phase-electron-transfer-dissociation
#12
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
#13
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
#14
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/28168880/increased-%C3%AE-sheet-dynamics-and-d-e-loop-repositioning-are-necessary-for-cu-ii-induced-amyloid-formation-by-%C3%AE-2-microglobulin
#15
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/28137577/analysis-of-translocation-competent-secretory-proteins-by-hdx-ms
#16
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/28134246/discovery-of-a-junctional-epitope-antibody-that-stabilizes-il-6-and-gp80-protein-protein-interaction-and-modulates-its-downstream-signaling
#17
Ralph Adams, Rebecca J Burnley, Chiara R Valenzano, Omar Qureshi, Carl Doyle, Simon Lumb, Maria Del Carmen Lopez, Robert Griffin, David McMillan, Richard D Taylor, Chris Meier, Prashant Mori, Laura M Griffin, Ulrich Wernery, Jörg Kinne, Stephen Rapecki, Terry S Baker, Alastair D G Lawson, Michael Wright, Anna Ettorre
Protein:protein interactions are fundamental in living organism homeostasis. Here we introduce VHH6, a junctional epitope antibody capable of specifically recognizing a neo-epitope when two proteins interact, albeit transiently, to form a complex. Orthogonal biophysical techniques have been used to prove the "junctional epitope" nature of VHH6, a camelid single domain antibody recognizing the IL-6-gp80 complex but not the individual components alone. X-ray crystallography, HDX-MS and SPR analysis confirmed that the CDR regions of VHH6 interact simultaneously with IL-6 and gp80, locking the two proteins together...
January 30, 2017: Scientific Reports
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
#18
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/28105936/pathways-of-aging-comparative-analysis-of-gene-signatures-in-replicative-senescence-and-stress-induced-premature-senescence
#19
Kamil C Kural, Neetu Tandon, Mikhail Skoblov, Olga V Kel-Margoulis, Ancha V Baranova
BACKGROUND: In culturing normal diploid cells, senescence may either happen naturally, in the form of replicative senescence, or it may be a consequence of external challenges such as oxidative stress. Here we present a comparative analysis aimed at reconstruction of molecular cascades specific for replicative (RS) and stressinduced senescence (SIPS) in human fibroblasts. RESULTS: An involvement of caspase-3/keratin-18 pathway and serine/threonine kinase Aurora A/ MDM2 pathway was shared between RS and SIPS...
December 28, 2016: BMC Genomics
https://www.readbyqxmd.com/read/28063489/using-hydrogen-deuterium-exchange-mass-spectrometry-to-examine-protein-membrane-interactions
#20
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
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