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Hydrogen exchange mass spectrometry

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https://www.readbyqxmd.com/read/29049865/interrogating-membrane-protein-conformational-dynamics-within-native-lipid-compositions
#1
Eamonn Reading, Zoe Hall, Chloe Martens, Tabasom Haghighi, Heather Findlay, Zainab Ahdash, Argyris Politis, Paula J Booth
Membrane protein-lipid interplay is important for cellular function, however, tools enabling the interrogation of protein dynamics within native lipid environments are scarce and often invasive. We establish that the styrene-maleic acid anhydride lipid particle (SMALP) technology can be coupled with hydrogen-deuterium exchange mass spectrometry (HDX-MS) to investigate membrane protein conformational dynamics within native lipid bilayers. We demonstrate changes in accessibility and dynamics of the rhomboid protease, GlpG, captured within three different native lipid compositions, and identify protein regions sensitive to changes in the native lipid environment...
October 19, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/29046335/molecular-basis-for-inner-kinetochore-configuration-through-rwd-domain-peptide-interactions
#2
Florian Schmitzberger, Magdalena M Richter, Yuliya Gordiyenko, Carol V Robinson, Michał Dadlez, Stefan Westermann
Kinetochores are dynamic cellular structures that connect chromosomes to microtubules. They form from multi-protein assemblies that are evolutionarily conserved between yeasts and humans. One of these assemblies-COMA-consists of subunits Ame1(CENP-U), Ctf19(CENP-P), Mcm21(CENP-O) and Okp1(CENP-Q) A description of COMA molecular organization has so far been missing. We defined the subunit topology of COMA, bound with inner kinetochore proteins Nkp1 and Nkp2, from the yeast Kluyveromyces lactis, with nanoflow electrospray ionization mass spectrometry, and mapped intermolecular contacts with hydrogen-deuterium exchange coupled to mass spectrometry...
October 18, 2017: EMBO Journal
https://www.readbyqxmd.com/read/29046307/high-definition-mapping-of-four-spatially-distinct-neutralizing-epitope-clusters-on-rivax-a-candidate-ricin-toxin-subunit-vaccine
#3
Ronald Toth, Siva Krishna Angalakurthi, Greta Van Slyke, David J Vance, John M Hickey, Sangeeta B Joshi, C Russell Middaugh, David B Volkin, David D Weis, Nicholas J Mantis
RiVax is a promising recombinant ricin toxin A subunit (RTA) vaccine antigen that has been shown to be safe and immunogenic in humans and effective at protecting Rhesus macaques against lethal dose aerosolized toxin exposure. We previously used a panel of RTA-specific monoclonal antibodies (mAbs) to demonstrate, by competition ELISA, that RiVax elicits similar serum antibody profiles in both humans and macaques. However, the actual mAb binding sites on RiVax have yet to be defined. In this study, we employed hydrogen exchange-mass spectrometry (HX-MS) to localize the epitopes on RiVax recognized by nine toxin-neutralizing mAbs and one non-neutralizing mAb...
October 18, 2017: Clinical and Vaccine Immunology: CVI
https://www.readbyqxmd.com/read/29035497/conformational-dynamics-of-dna-binding-and-cas3-recruitment-by-the-crispr-rna-guide-cascade-complex
#4
Paul B G van Erp, Angela Patterson, Ravi Kant, Luke Berry, Sarah M Golden, Brittney L Forsman, Joshua Carter, Ryan N Jackson, Brian Bothner, Blake Wiedenheft
Bacteria and archaea rely on CRISPR (clustered regularly interspaced short palindromic repeats) RNA-guided adaptive immune systems for sequence specific elimination of foreign nucleic acids. In Escherichia coli, short CRISPR-derived RNAs (crRNAs) assemble with Cas (CRISPR-associated) proteins into a 405-kilodalton multi-subunit surveillance complex called Cascade (CRISPR-associated complex for antiviral defense). Cascade binds foreign DNA complementary to the crRNA guide and recruits Cas3, a trans-acting nuclease-helicase required for target degradation...
October 16, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/29030554/hdx-reveals-the-conformational-dynamics-of-dna-sequence-specific-vdr-co-activator-interactions
#5
Jie Zheng, Mi Ra Chang, Ryan E Stites, Yong Wang, John B Bruning, Bruce D Pascal, Scott J Novick, Ruben D Garcia-Ordonez, Keith R Stayrook, Michael J Chalmers, Jeffrey A Dodge, Patrick R Griffin
The vitamin D receptor/retinoid X receptor-α heterodimer (VDRRXRα) regulates bone mineralization via transcriptional control of osteocalcin (BGLAP) gene and is the receptor for 1α,25-dihydroxyvitamin D3 (1,25D3). However, supra-physiological levels of 1,25D3 activates the calcium-regulating gene TRPV6 leading to hypercalcemia. An approach to attenuate this adverse effect is to develop selective VDR modulators (VDRMs) that differentially activate BGLAP but not TRPV6. Here we present structural insight for the action of a VDRM compared with agonists by employing hydrogen/deuterium exchange...
October 13, 2017: Nature Communications
https://www.readbyqxmd.com/read/29030428/a-retractable-lid-in-lecithin-cholesterol-acyltransferase-provides-a-structural-mechanism-for-activation-by-apolipoprotein-a-i
#6
Kelly A Manthei, Joomi Ahn, Alisa Glukhova, Wenmin Yuan, Christopher Larkin, Taylor D Manett, Louise Chang, James A Shayman, Milton J Axley, Anna Schwendeman, John J G Tesmer
Lecithin:cholesterol acyltransferase (LCAT) plays a key role in reverse cholesterol transport by transferring an acyl group from phosphatidylcholine to cholesterol, promoting the maturation of high density lipoproteins (HDL) from discoidal to spherical particles. LCAT is activated through an unknown mechanism by apolipoprotein A-I (ApoA-I) and other mimetic peptides that form a belt around HDL. Here we report the crystal structure of LCAT with an extended lid that blocks access to the active site, consistent with an inactive conformation...
October 13, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29021580/the-quaternary-architecture-of-rar%C3%AE-rxr%C3%AE-heterodimer-facilitates-domain-domain-signal-transmission
#7
Vikas Chandra, Dalei Wu, Sheng Li, Nalini Potluri, Youngchang Kim, Fraydoon Rastinejad
Assessing the physical connections and allosteric communications in multi-domain nuclear receptor (NR) polypeptides has remained challenging, with few crystal structures available to show their overall structural organizations. Here we report the quaternary architecture of multi-domain retinoic acid receptor β-retinoic X receptor α (RARβ-RXRα) heterodimer bound to DNA, ligands and coactivator peptides, examined through crystallographic, hydrogen-deuterium exchange mass spectrometry, mutagenesis and functional studies...
October 11, 2017: Nature Communications
https://www.readbyqxmd.com/read/29021300/high-resolution-epitope-positioning-of-a-large-collection-of-neutralizing-and-non-neutralizing-single-domain-antibodies-on-ricin-toxin-s-enzymatic-and-binding-subunits
#8
David J Vance, Jacqueline M Tremblay, Yinghui Rong, Siva Krishna Angalakurthi, David B Volkin, C Russell Middaugh, David D Weis, Charles B Shoemaker, Nicholas J Mantis
We previously produced a heavy chain-only antibody VH domain (VHH)-displayed phage library from two alpacas that had been immunized with ricin toxoid and non-toxic mixtures of ricin's enzymatic (RTA) and binding (RTB) subunits (Vance et al J. Biol. Chem. 288:36538-47. doi: 10.1074/jbc.M113.519207). Initial and subsequent screens of that library by direct ELISA yielded more than two dozen unique RTA- and RTB-specific VHHs, including 10 whose structures were subsequently solved in complex with RTA. To generate a more complete antigenic map of ricin toxin and define the epitopes associated with toxin-neutralizing activity, we subjected the VHH-displayed phage library to additional pannings on both receptor bound and antibody-captured ricin...
October 11, 2017: Clinical and Vaccine Immunology: CVI
https://www.readbyqxmd.com/read/28993252/h-d-exchange-mass-spectrometry-and-statistical-coupling-analysis-reveal-a-role-for-allostery-in-a-ferredoxin-dependent-bifurcating-transhydrogenase-catalytic-cycle
#9
Luke Berry, Saroj Poudel, Monika Tokmina-Lukaszewska, Daniel R Colman, Diep M N Nguyen, Gerrit J Schut, Michael W W Adams, John W Peters, Eric S Boyd, Brian Bothner
Recent investigations into ferredoxin-dependent transhydrogenases, a class of enzymes responsible for electron transport, have highlighted the biological importance of flavin-based electron bifurcation (FBEB). FBEB generates biomolecules with very low reduction potential by coupling the oxidation of an electron donor with intermediate potential to the reduction of high and low potential molecules. Bifurcating systems can generate biomolecules with very low reduction potentials, such as reduced ferredoxin (Fd), from species such as NADPH...
October 6, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28992596/deciphering-the-electric-code-of-geobacter-sulfurreducens-in-cocultures-with-pseudomonas-aeruginosa-via-swath-ms-proteomics
#10
Lucie Semenec, Andrew E Laloo, Benjamin L Schulz, Ismael A Vergara, Philip L Bond, Ashley E Franks
Interspecies electron transfer (IET) occurs in many microbial communities, enabling extracellular electron exchange for syntrophic utilization of mixed resources. Various mechanisms of IET have been characterized including direct IET (DIET) and hydrogen IET (HIT) but their evolution throughout syntrophic adaptation has not been investigated through an omics approach. A syntrophic coculture of Geobacter sulfurreducens and Pseudomonas aeruginosa was established and evolved in restricted medium. The medium required cooperative metabolism due to preferential utilization of formate and fumarate by P...
October 3, 2017: Bioelectrochemistry
https://www.readbyqxmd.com/read/28985017/characterization-of-stress-degradation-products-of-amodiaquine-dihydrochloride-by-liquid-chromatography-with-high-resolution-mass-spectrometry-and-prediction-of-their-properties-by-using-admet-predictor%C3%BB
#11
Vivek Dhiman, Dilip Kumar Singh, Mayurbhai Kathadbhai Ladumor, Saranjit Singh
The degradation behavior of amodiaquine dihydrochloride, an antimalarial drug, was investigated in solution as well as solid states. The drug was subjected to hydrolytic, photolytic, oxidative and thermal stress conditions, according to International Conference on Harmonization guideline Q1A(R2). It showed extensive hydrolysis in acidic, alkaline and neutral solutions both with and without light, while it proved to be stable to thermal and oxidative conditions. In total, six degradation products were formed, which were separated on a C8 column, employing a gradient reversed-phase high-performance liquid chromatography method in which acetonitrile and 10 mM ammonium formate (pH 3...
October 6, 2017: Journal of Separation Science
https://www.readbyqxmd.com/read/28972141/dissecting-the-molecular-assembly-of-the-toxoplasma-gondii-myoa-motility-complex
#12
Cameron J Powell, Meredith L Jenkins, Michelle L Parker, Raghavendran Ramaswamy, Anne Kelsen, David M Warshaw, Gary E Ward, John E Burke, Martin J Boulanger
Apicomplexan parasites such as Toxoplasma gondii rely on a unique form of locomotion known as gliding motility. Generating the mechanical forces to support motility are divergent class XIV myosins (MyoA) coordinated by accessory proteins known as light chains. While the importance of the MyoA-light chain complex is well established, the detailed mechanisms governing its assembly and regulation are relatively unknown. To establish a molecular blueprint of this dynamic complex, we first mapped the adjacent binding sites of light chains MLC1 and ELC1 on the MyoA neck (residues 775-818) using a combination of hydrogen-deuterium exchange mass spectrometry (HDX-MS) and isothermal titration calorimetry (ITC)...
September 25, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28971440/probing-conformational-dynamics-of-tau-protein-by-hydrogen-deuterium-exchange-mass-spectrometry
#13
Richard Y-C Huang, Roxana E Iacob, Sethu Sankaranarayanan, Ling Yang, Michael Ahlijanian, Li Tao, Adrienne A Tymiak, Guodong Chen
Fibrillization of the microtubule-associated protein tau has been recognized as one of the signature pathologies of the nervous system in Alzheimer's disease, progressive supranuclear palsy, and other tauopathies. The conformational transition of tau in the fibrillization process, tau monomer to soluble aggregates to fibrils in particular, remains unclear. Here we report on the use of hydrogen/deuterium exchange mass spectrometry (HDX-MS) in combination with other biochemical approaches, including Thioflavin S fluorescence measurements, enzyme-linked immunosorbent assay (ELISA), and Western blotting to understand the heparin-induced tau's fibrillization...
October 2, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28970104/nucleotide-binding-to-arl2-in-the-tbcd%C3%A2-arl2%C3%A2-%C3%AE-tubulin-complex-drives-conformational-changes-in-%C3%AE-tubulin
#14
Joshua W Francis, Devrishi Goswami, Scott J Novick, Bruce D Pascal, Emily R Weikum, Eric A Ortlund, Patrick R Griffin, Richard A Kahn
Microtubules are highly dynamic tubulin polymers that are required for a variety of cellular functions. Despite the importance of a cellular population of tubulin dimers, we have incomplete information about the mechanisms involved in the biogenesis of αβ-tubulin heterodimers. In addition to prefoldin and the TCP-1 Ring Complex, five tubulin-specific chaperones, termed cofactors A-E (TBCA-E), and GTP are required for the folding of α- and β-tubulin subunits and assembly into heterodimers. We recently described the purification of a novel trimer, TBCD•ARL2•β-tubulin...
September 29, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28966665/si-traceable-determination-of-arsenic-species-in-kelp-thallus-laminariae
#15
Lee L Yu, Rachel C Stanoyevitch, Rolf Zeisler
A dietary supplement, kelp contains a significant amount of arsenic that is mostly arsenosugars. The determination of arsenosugars is difficult due to a lack of arsenosugar calibration standard, because arsenosugar compounds are not commercially available. This work reports the determination of arsenicals in a kelp extract with traceability to the International System of Units (SI). The hydrophilic fraction of arsenicals was reproducibly extracted from a candidate Standard Reference Material (SRM) 3232 Kelp Powder (Thallus Laminariae) in development at the National Institute of Standards and Technology (NIST)...
August 2017: Analytical Methods: Advancing Methods and Applications
https://www.readbyqxmd.com/read/28956290/ion-mobility-spectrometry-mass-spectrometry-coupled-with-gas-phase-hydrogen-deuterium-exchange-for-metabolomics-analyses
#16
Hossein Maleki, Ahmad K Karanji, Sandra Majuta, Megan M Maurer, Stephen J Valentine
Ion mobility spectrometry-mass spectrometry (IMS-MS) in combination with gas-phase hydrogen/deuterium exchange (HDX) and collision-induced dissociation (CID) is evaluated as an analytical method for small-molecule standard and mixture characterization. Experiments show that compound ions exhibit unique HDX reactivities that can be used to distinguish different species. Additionally, it is shown that gas-phase HDX kinetics can be exploited to provide even further distinguishing capabilities by using different partial pressures of reagent gas...
September 27, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28933661/suppressing-allostery-in-epitope-mapping-experiments-using-millisecond-hydrogen-deuterium-exchange-mass-spectrometry
#17
Bin Deng, Shaolong Zhu, Andrew M Macklin, Jianrong Xu, Cristina Lento, Adnan Sljoka, Derek J Wilson
Localization of the interface between the candidate antibody and its antigen target, commonly known as epitope mapping, is a critical component of the development of therapeutic monoclonal antibodies. With the recent availability of commercial automated systems, hydrogen / deuterium eXchange (HDX) is rapidly becoming the tool for mapping epitopes preferred by researchers in both industry and academia. However, this approach has a significant drawback in that it can be confounded by 'allosteric' structural and dynamic changes that result from the interaction, but occur far from the point(s) of contact...
September 21, 2017: MAbs
https://www.readbyqxmd.com/read/28933642/epitope-characterization-of-anti-jam-a-antibodies-using-orthogonal-mass-spectrometry-and-surface-plasmon-resonance-approaches
#18
Guillaume Terral, Thierry Champion, François Debaene, Olivier Colas, Maxime Bourguet, Elsa Wagner-Rousset, Nathalie Corvaia, Alain Beck, Sarah Cianferani
Junctional adhesion molecule-A (JAM-A) is an adherens and tight junction protein expressed by endothelial and epithelial cells and associated with cancer progression. We present here the extensive characterization of immune complexes involving JAM-A antigen and three monoclonal antibodies (mAbs), including hz6F4-2, a humanized version of anti-tumoral 6F4 mAb identified by a functional and proteomic approach in our laboratory. A specific workflow that combines orthogonal approaches has been designed to determine binding stoichiometries along with JAM-A epitope mapping determination at high resolution for these three mAbs...
September 21, 2017: MAbs
https://www.readbyqxmd.com/read/28905070/sodium-cationized-carbohydrate-gas-phase-fragmentation-chemistry-influence-of-glycosidic-linkage-position
#19
Jordan M Rabus, Maha T Abutokaikah, Reginald T Ross, Benjamin J Bythell
We investigate the gas-phase structures and fragmentation chemistry of two isomeric sodium-cationized carbohydrates using combined tandem mass spectrometry, hydrogen/deuterium exchange experiments, and computational methods. Our model systems are the glucose-based disaccharide analytes cellobiose (β-d-glucopyranosyl-(1 → 4)-d-glucose) and gentiobiose (β-d-glucopyranosyl-(1 → 6)-d-glucose). These analytes show substantially different tandem mass spectra. We characterize the rate-determining barriers to both the glycosidic and structurally-informative cross-ring bond cleavages...
September 27, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28901129/peptide-level-interactions-between-proteins-and-small-molecule-drug-candidates-by-two-hydrogen-deuterium-exchange-ms-based-methods-the-example-of-apolipoprotein-e3
#20
Hanliu Wang, Don L Rempel, Daryl Giblin, Carl Frieden, Michael L Gross
We describe a platform utilizing two methods based on hydrogen-deuterium exchange (HDX) coupled with mass spectrometry (MS) to characterize interactions between a protein and a small-molecule ligand. The model system is apolipoprotein E3 (apoE3) and a small-molecule drug candidate. We extended PLIMSTEX (protein-ligand interactions by mass spectrometry, titration, and H/D exchange) to the regional level by incorporating enzymatic digestion to acquire binding information for peptides. In a single experiment, we not only identified putative binding sites, but also obtained affinities of 6...
October 17, 2017: Analytical Chemistry
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