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Hydrogen exchange mass spectrometry

Dezhao Liu, Tavs Nyord, Li Rong, Anders Feilberg
Volatile organic compounds (VOC) and hydrogen sulfide are emitted from land spreading of manure slurry to the atmosphere and contribute to odour nuisance, particle formation and tropospheric ozone formation. Data on emissions is almost non-existing partly due to lack of suitable quantitative methods for measuring emissions in full scale. Here we present a method based on application of wind tunnels for simulation of air exchange combined with the use of online mass spectrometry (PTR-MS). The focus was on odorous VOC but all relevant VOC were included...
October 15, 2018: Science of the Total Environment
Manoj Kumar Sriramoju, Tzu-Jing Yang, Shang-Te Danny Hsu
Ornithine transcarbamylases (OTCs) are conserved enzymes involved in arginine biosynthesis in microbes and the urea cycle in mammals. Recent bioinformatics analyses identified two unique OTC variants, N-succinyl-l-ornithine transcarbamylase from Bacteroides fragilis (BfSOTC) and N-acetyl-l-ornithine transcarbamylase from Xanthomonas campestris (XcAOTC). These two variants diverged from other OTCs during evolution despite sharing the common tertiary and quaternary structures, with the exception that the substrate recognition motifs are topologically knotted...
June 16, 2018: Biochemical and Biophysical Research Communications
Chieh Kao, Ritu Chandna, Abhijeet Ghode, Charlotte Dsouza, Mo Chen, Andreas Larsson, Siau Hoi Lim, Minjun Wang, Zhonglian Cao, Yizhun Zhu, Ganesh S Anand, Ruowen Ge
Glucose regulated protein 78 kDa (GRP78) is a recently emerged target for cancer therapy and a biomarker for cancer prognosis. Overexpression of GRP78 is observed in many types of cancers, with the cell-surface GRP78 being preferentially present in cancer cells and cancer blood vessel endothelial cells. Isthmin (ISM) is a secreted high-affinity proapoptotic protein ligand of cell-surface GRP78 that suppresses angiogenesis and tumor growth in mice. The C-terminal AMOP (adhesion-associated domain in MUC4 and other proteins) domain of ISM is critical in mediating its interaction with human umbilical vein endothelial cells (HUVECs)...
June 12, 2018: EBioMedicine
Rajdeep Das, Amrita Mitra, Gopa Mitra, Dibyajyoti Maity, Vijay Bhat, Debnath Pal, Cecil Ross, Anura V Kurpad, Amit Kumar Mandal
In sickle cell anemia, polymerization of hemoglobin in its deoxy state leads to the formation of insoluble fibres that result in sickling of red blood cells. Stereo-specific binding of isopropyl group of βVal6, the mutated amino acid residue of a tetrameric sickle hemoglobin molecule (HbS), with hydrophobic groove of another HbS tetramer initiates the polymerization. Glutathionylation of βCys93 in HbS was reported to inhibit the polymerization. However, the mechanism of inhibition in polymerization is unknown to date...
June 1, 2018: Biochemical Journal
Britney Johnson, Patrick McConnell, Alex G Kozlov, Marlene Mekel, Timothy M Lohman, Michael L Gross, Gaya K Amarasinghe, John A Cooper
Actin assembly is important for cell motility. The ability of actin subunits to join or leave filaments via the barbed end is critical to actin dynamics. Capping protein (CP) binds to barbed ends to prevent subunit gain and loss and is regulated by proteins that include V-1 and CARMIL. V-1 inhibits CP by sterically blocking one binding site for actin. CARMILs bind at a distal site and decrease the affinity of CP for actin, suggested to be caused by conformational changes. We used hydrogen-deuterium exchange with mass spectrometry (HDX-MS) to probe changes in structural dynamics induced by V-1 and CARMIL binding to CP...
May 29, 2018: Cell Reports
Alessandro T Caputo, Dominic S Alonzi, John L Kiappes, Weston B Struwe, Alice Cross, Souradeep Basu, Benoit Darlot, Pietro Roversi, Nicole Zitzmann
Targeting the host-cell endoplasmic reticulum quality control (ERQC) pathway is an effective broad-spectrum antiviral strategy. The two ER resident α-glucosidases whose sequential action permits entry in this pathway are the targets of glucomimetic inhibitors. Knowledge of the molecular details of the ER α-glucosidase II (α-Glu II) structure was limited. We determined crystal structures of a trypsinolytic fragment of murine α-Glu II, alone and in complex with key catalytic cycle ligands, and four different broad-spectrum antiviral iminosugar inhibitors, two of which are currently in clinical trials against dengue fever...
2018: Advances in Experimental Medicine and Biology
Kunhong Xiao, Yang Zhao, Minjung Choi, Hongda Liu, Adi Blanc, Jiang Qian, Thomas J Cahill, Xue Li, Yunfang Xiao, Lisa J Clark, Sheng Li
Many cellular functions necessitate structural assemblies of two or more associated proteins. The structural characterization of protein complexes using standard methods, such as X-ray crystallography, is challenging. Herein, we describe an orthogonal approach using hydrogen-deuterium-exchange mass spectrometry (HDXMS), cross-linking mass spectrometry (CXMS), and disulfide trapping to map interactions within protein complexes. HDXMS measures changes in solvent accessibility and hydrogen bonding upon complex formation; a decrease in HDX rate could account for newly formed intermolecular or intramolecular interactions...
June 2018: Nature Protocols
Chien-Ning Hsu, Wan-Tz Lai, Yu-Ju Lin, You-Lin Tain
Hypertension can originate from pre- and post-natal insults. High-fat (HF) diet and prenatal dexamethasone (DEX) exposure are both involved in hypertension of developmental origins. We examined whether postnatal HF diet sex-specifically increases the vulnerability to prenatal DEX exposure-induced programmed hypertension in adult offspring. Additionally, we sought to identify candidate proteins involved in programmed hypertension through a mass spectrometry-based quantitative proteomic approach. Male and female offspring were studied separately: control, DEX, HF, and DEX + HF (n=8/group)...
April 22, 2018: Journal of Nutritional Biochemistry
Nathan Will, Kwangwoon Lee, Fatlum Hajredini, David H Giles, Rinat R Abzalimov, Michael Clarkson, Kevin N Dalby, Ranajeet Ghose
Eukaryotic elongation factor 2 kinase (eEF-2K), the only known calmodulin (CaM) activated α-kinase, phosphorylates eukaryotic elongation factor 2 (eEF-2) on a specific threonine (Thr-56) diminishing its affinity for the ribosome and reducing the rate of nascent chain elongation during translation. Despite its critical cellular role, the precise mechanisms underlying the CaM-mediated activation of eEF-2K remain poorly defined. Here, employing a minimal eEF-2K construct (TR) that exhibits activity comparable to the wild-type enzyme and is fully activated by CaM in vitro and in cells, and using a variety of complimentary biophysical techniques in combination with computational modeling, we provide a structural mechanism by which CaM activates eEF-2K...
May 22, 2018: Journal of Molecular Biology
Priscilla L S Boon, Wuan Geok Saw, Xin Xiang Lim, Palur Venkata Raghuvamsi, Roland G Huber, Jan K Marzinek, Daniel A Holdbrook, Ganesh S Anand, Gerhard Grüber, Peter J Bond
The 11 kDa, positively charged dengue capsid protein (C protein) exists stably as a homodimer and co-localizes with the viral genome within mature viral particles. Its core is composed of four alpha helices encompassing a small hydrophobic patch that may interact with lipids, but approximately 20% of the protein at the N-terminus is intrinsically disordered, making it challenging to elucidate its conformational landscape. Here, we combine small-angle X-ray scattering (SAXS), amide hydrogen-deuterium exchange mass spectrometry (HDXMS), and atomic-resolution molecular dynamics (MD) simulations to probe the dynamics of dengue C proteins...
May 24, 2018: ACS Chemical Biology
Regina Feil, John Edward Lunn
Sugars are simple carbohydrates composed primarily of carbon, hydrogen, and oxygen. They play a central role in metabolism as sources of energy and as building blocks for synthesis of structural and nonstructural polymers. Many different techniques have been used to measure sugars, including refractometry, colorimetric and enzymatic assays, gas chromatography, high-performance liquid chromatography, and nuclear magnetic resonance spectroscopy. In this chapter we describe a method that combines an initial separation of sugars by high-performance anion-exchange chromatography (HPAEC) with detection and quantification by tandem mass spectrometry (MS/MS)...
2018: Methods in Molecular Biology
Patrick S Merkle, Kamil Gotfryd, Michel A Cuendet, Katrine Z Leth-Espensen, Ulrik Gether, Claus J Loland, Kasper D Rand
LeuT, a prokaryotic member of the neurotransmitter:sodium symporter (NSS) family, is an established structural model for mammalian NSS counterparts. We investigate the substrate translocation mechanism of LeuT by measuring the solution-phase structural dynamics of the transporter in distinct functional states by hydrogen/deuterium exchange mass spectrometry (HDX-MS). Our HDX-MS data pinpoint LeuT segments involved in substrate transport and reveal for the first time a comprehensive and detailed view of the dynamics associated with transition of the transporter between outward- and inward-facing configurations in a Na+ - and K+ -dependent manner...
May 2018: Science Advances
Ulrik H Mistarz, Kasper D Rand
Gas-phase hydrogen/deuterium exchange measured by mass spectrometry in a millisecond timeframe after ESI (gas-phase HDX-MS) is a fast and sensitive, yet unharnessed method to analyze the primary- and higher-order structure, intramolecular and intermolecular interactions, surface properties, and charge location of peptides and proteins. During a gas-phase HDX-MS experiment, heteroatom-bound non-amide hydrogens are made to exchange with deuterium during a millisecond timespan after electrospray ionization (ESI) by reaction with the highly basic reagent ND3 , enabling conformational analysis of protein states that are pertinent to the native solution-phase...
May 10, 2018: Methods: a Companion to Methods in Enzymology
Apurva S More, Ronald T Toth, Solomon Z Okbazghi, C Russell Middaugh, Sangeeta B Joshi, Thomas J Tolbert, David B Volkin, David D Weis
We have utilized hydrogen exchange-mass spectrometry (HX-MS) to characterize local backbone flexibility of four well-defined IgG1-Fc glycoforms expressed and purified from Pichia pastoris, two of which were prepared using subsequent in vitro enzymatic treatments. Progressively decreasing the size of the N-linked N297 oligosaccharide from high mannose (Man8-Man12), to Man5, to GlcNAc, to non-glycosylated N297Q resulted in progressive increases in backbone flexibility. Comparison of these results with recently published physicochemical stability and Fcγ receptor binding data with the same set of glycoproteins provide improved insights into correlations between glycan structure and these pharmaceutical properties...
May 8, 2018: Journal of Pharmaceutical Sciences
Amberley Stephens, Nadezhda Nespovitaya, Maria Zacharopoulou, Clemens F Kaminski, Jonathan James Phillips, Gabriele S Kaminski Schierle
Understanding the mechanisms behind amyloid protein aggregation in diseases such as Parkinson's and Alzheimer's disease is often hampered by the reproducibility of in vitro assays. Yet, understanding the basic mechanisms of protein misfolding is essential for the development of novel therapeutic strategies. We show here, that for the amyloid protein alpha-synuclein (aSyn), a protein involved in Parkinson's disease (PD), chromatographic buffers and storage conditions can significantly interfere with the overall structure of the protein and thus affect protein aggregation kinetics...
May 11, 2018: Analytical Chemistry
Richard Y-C Huang, Steven R O'Neil, Daša Lipovšek, Guodong Chen
Higher-order structure (HOS) characterization of therapeutic protein-drug conjugates for comprehensive assessment of conjugation-induced protein conformational changes is an important consideration in the biopharmaceutical industry to ensure proper behavior of protein therapeutics. In this study, conformational dynamics of a small therapeutic protein, adnectin 1, together with its drug conjugate were characterized by hydrogen/deuterium exchange mass spectrometry (HDX-MS) with different spatial resolutions. Top-down HDX allows detailed assessment of the residue-level deuterium content in the payload conjugation region...
May 7, 2018: Journal of the American Society for Mass Spectrometry
Kyle W Anderson, Elyssia S Gallagher, Jeffrey W Hudgens
Membrane proteins are currently the most common targets for pharmaceuticals. However, characterization of their structural dynamics by hydrogen/deuterium exchange mass spectrometry (HDX-MS) is sparse due to insufficient automated methods to handle full-length membrane proteins in lipid bilayers. Additionally, membrane lipids used to mimic the membrane environment and to solubilize membrane proteins can impair chromatography performance and cause ion suppression in the mass spectrometer. The workflow discussed herein advances HDX-MS capabilities and other MS applications for membrane proteins by providing a fully automated method for HDX-MS analysis based on a phospholipid removal scheme compatible with robotic handling...
June 5, 2018: Analytical Chemistry
Luke Berry, Angela Patterson, Natasha Pence, John W Peters, Brian Bothner
The protocol detailed here describes a way to perform hydrogen deuterium exchange coupled to mass spectrometry (HDX-MS) on oxygen sensitive proteins. HDX-MS is a powerful tool for studying the protein structure-function relationship. Applying this technique to anaerobic proteins provides insight into the mechanism of proteins that perform oxygen sensitive chemistry. A problem when using HDX-MS to study anaerobic proteins is that there are many parts that require constant movement into and out of an anaerobic chamber...
March 20, 2018: Bio-protocol
Irina Oganesyan, Cristina Lento, Derek J Wilson
Hydrogen/deuterium exchange (HDX) mass spectrometry (MS) emerged as a tool for biochemistry and structural biology around 25 years ago. It has since become a key approach for studying protein dynamics, protein-ligand interactions, membrane proteins and intrinsically disordered proteins (IDPs). In HDX labeling, proteins are exposed to deuterated solvent (usually D2 O) for a variable 'labeling time', resulting in isotope exchange of unprotected labile protons on the amide backbone and amino acid side chains...
April 26, 2018: Methods: a Companion to Methods in Enzymology
M Rafalik, M Spodzieja, A S Kołodziejczyk, S Rodziewicz-Motowidło, A Szymańska, A Grubb, P Czaplewska
Human cystatin C (hCC) is a cysteine proteinase inhibitor involved in pathophysiological processes of dimerization and amyloid formation. These processes are directly associated with a number of neurodegenerative disorders such as Alzheimer disease or hereditary cystatin C amyloid angiopathy (HCCAA). One of the ideas on how to prevent amyloid formation is to use immunotherapy. HCC3 is one of a group of antibodies binding to hCC and reducing the in vitro formation of cystatin C dimers. Therefore, identification of the binding sites in the hCC-HCC3 complex may facilitate a search of effective drugs against HCCAA as well as understanding the mechanisms of neurodegenerative disorders...
April 22, 2018: Journal of Proteomics
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