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hydrogen deuterium exchange

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https://www.readbyqxmd.com/read/28319116/quenched-hydrogen-deuterium-exchange-nmr-of-a-disease-relevant-a%C3%AE-1-42-amyloid-polymorph
#1
Marielle Aulikki Wälti, Julien Orts, Roland Riek
Alzheimer's disease is associated with the aggregation into amyloid fibrils of Aβ(1-42) and Aβ(1-40) peptides. Interestingly, these fibrils often do not obtain one single structure but rather show different morphologies, so-called polymorphs. Here, we compare quenched hydrogen-deuterium (H/D) exchange of a disease-relevant Aβ(1-42) fibril for which the 3D structure has been determined by solid-state NMR with H/D exchange previously determined on another structural polymorph. This comparison reveals secondary structural differences between the two polymorphs suggesting that the two polymorphisms can be classified as segmental polymorphs...
2017: PloS One
https://www.readbyqxmd.com/read/28318907/the-effects-of-mutating-tyr9-and-arg15-on-the-structure-stability-conformational-dynamics-and-mechanism-of-gsta3-3
#2
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/28315238/comprehensive-gas-phase-peptide-ion-structure-studies-using-ion-mobility-techniques-part-2-gas-phase-hydrogen-deuterium-exchange-for-ion-population-estimation
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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/28262794/capture-of-heavy-hydrogen-isotopes-in-a-metal-organic-framework-with-active-cu-i-sites
#12
I Weinrauch, I Savchenko, D Denysenko, S M Souliou, H-H Kim, M Le Tacon, L L Daemen, Y Cheng, A Mavrandonakis, A J Ramirez-Cuesta, D Volkmer, G Schütz, M Hirscher, T Heine
The production of pure deuterium and the removal of tritium from nuclear waste are the key challenges in separation of light isotopes. Presently, the technological methods are extremely energy- and cost-intensive. Here we report the capture of heavy hydrogen isotopes from hydrogen gas by selective adsorption at Cu(I) sites in a metal-organic framework. At the strongly binding Cu(I) sites (32 kJ mol(-1)) nuclear quantum effects result in higher adsorption enthalpies of heavier isotopes. The capture mechanism takes place most efficiently at temperatures above 80 K, when an isotope exchange allows the preferential adsorption of heavy isotopologues from the gas phase...
March 6, 2017: Nature Communications
https://www.readbyqxmd.com/read/28258193/structural-implications-for-the-formation-and-function-of-the-complement-effector-protein-ic3b
#13
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
#14
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
#15
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/28249778/dna-and-i%C3%AE%C2%BAb%C3%AE-both-induce-long-range-conformational-changes-in-nf%C3%AE%C2%BAb
#16
Kristen M Ramsey, Holly E Dembinski, Wei Chen, Clarisse G Ricci, Elizabeth A Komives
We recently discovered that IκBα enhances the rate of release of nuclear factor kappa B (NFκB) from DNA target sites in a process we have termed molecular stripping. Coarse-grained molecular dynamics simulations of the stripping pathway revealed two mechanisms for the enhanced release rate: the negatively charged PEST region of IκBα electrostatically repels the DNA, and the binding of IκBα appears to twist the NFκB heterodimer so that the DNA can no longer bind. Here, we report amide hydrogen/deuterium exchange data that reveal long-range allosteric changes in the NFκB (RelA-p50) heterodimer induced by DNA or IκBα binding...
February 27, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28242466/elucidation-of-trna-cytochrome-c-interactions-through-hydrogen-deuterium-exchange-mass-spectrometry
#17
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
#18
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/28235448/ir-spectroscopy-analysis-of-pancreatic-lipase-related-protein-2-interaction-with-phospholipids-1-discriminative-recognition-of-mixed-micelles-versus-liposomes
#19
Eduardo Mateos-Diaz, Jean-Claude Bakala N'Goma, Deborah Byrne, Sylvie Robert, Frédéric Carrière, Hélène Gaussier
Guinea pig pancreatic lipase-related protein 2 (GPLRP2) is an interesting model enzyme that can hydrolyze a large set of acylglycerols in vitro but displays however some selectivity depending on the supramolecular structure of substrate and the presence of surfactants like bile salts. We showed that GPLRP2 hydrolyzes 1,2-Dipalmitoyl phosphatidylcholine (DPPC) present in mixed micelles with sodium taurodeoxycholate (NaTDC) but not in multilamellar (MLV) and large unilamellar (LUV) vesicles of DPPC. After characterization of these lipid aggregates by dynamic light scattering (DLS), the discriminative recognition of DPPC in DPPC/NaTDC micelles versus MLV and LUV by an inactive variant (S152G) of GPLRP2 to avoid the effect of substrate hydrolysis was investigated using Fourier transform infrared spectroscopy (FTIR)...
February 21, 2017: Chemistry and Physics of Lipids
https://www.readbyqxmd.com/read/28223522/conformational-dynamics-of-a-neurotransmitter-sodium-symporter-in-a-lipid-bilayer
#20
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
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