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hydrogen deuterium exchange

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https://www.readbyqxmd.com/read/29150441/co-ii-and-ni-ii-binding-of-the-escherichia-coli-transcriptional-repressor-rcnr-orders-its-n-terminus-alters-helix-dynamics-and-reduces-dna-affinity
#1
Hsin-Ting Huang, Cedric E Bobst, Jeffrey S Iwig, Peter T Chivers, Igor A Kaltashov, Michael J Maroney
RcnR, a transcriptional regulator in Escherichia coli, derepresses the expression of the export proteins RcnAB upon binding Ni(II) or Co(II). Lack of structural information has precluded elucidation of the allosteric basis for the decreased DNA affinity in RcnR's metal-bound states. Here, using hydrogen-deuterium exchange coupled with MS (HDX-MS), we probed the RcnR structure in the presence of DNA, the cognate metal ions Ni(II) and Co(II), or the noncognate metal ion Zn(II). We found that cognate metal binding altered the flexibility from the N-terminus through helix 1 and modulated the RcnR-DNA interaction...
November 17, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29138428/structural-disorder-and-induced-folding-within-two-cereal-aba-stress-and-ripening-asr-proteins
#2
Karama Hamdi, Edoardo Salladini, Darragh P O'Brien, Sébastien Brier, Alexandre Chenal, Ines Yacoubi, Sonia Longhi
Abscisic acid (ABA), stress and ripening (ASR) proteins are plant-specific proteins involved in plant response to multiple abiotic stresses. We previously isolated the ASR genes and cDNAs from durum wheat (TtASR1) and barley (HvASR1). Here, we show that HvASR1 and TtASR1 are consistently predicted to be disordered and further confirm this experimentally. Addition of glycerol, which mimics dehydration, triggers a gain of structure in both proteins. Limited proteolysis showed that they are highly sensitive to protease degradation...
November 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29137992/ir-spectroscopy-analysis-of-pancreatic-lipase-related-protein-2-interaction-with-phospholipids-3-monitoring-dppc-lipolysis-in-mixed-micelles
#3
Eduardo Mateos-Diaz, Priscila Sutto-Ortiz, Moulay Sahaka, Jorge A Rodriguez, Frédéric Carrière
Usual methods for the continuous assay of lipolytic enzyme activities are mainly based on the titration of free fatty acids, surface pressure monitoring or spectrophotometry using substrates labeled with specific probes. These approaches only give a partial information on the chemistry of the lipolysis reaction and additional end-point analyses are often required to quantify both residual substrate and lipolysis products. We used transmission infrared (IR) spectroscopy to monitor simultaneously the hydrolysis of phospholipids by guinea pig pancreatic lipase-related protein 2 (GPLRP2) and the release of lipolysis products...
November 11, 2017: Chemistry and Physics of Lipids
https://www.readbyqxmd.com/read/29135326/hydrogen-deuterium-exchange-mass-spectrometry-and-computational-modeling-reveal-a-discontinuous-epitope-of-an-antibody-tl1a-interaction
#4
Richard Y-C Huang, Stanley R Krystek, Nathan Felix, Robert F Graziano, Mohan Srinivasan, Achal Pashine, Guodong Chen
TL1A, a tumor necrosis factor-like cytokine, is a ligand for the death domain receptor DR3. TL1A, upon binding to DR3, can stimulate lymphocytes and trigger secretion of proinflammatory cytokines. Therefore, blockade of TL1A/DR3 interaction may be a potential therapeutic strategy for autoimmune and inflammatory diseases. Recently, the anti-TL1A monoclonal antibody 1 (mAb1) with a strong potency in blocking the TL1A/DR3 interaction was identified. Here, we report on the use of hydrogen/deuterium exchange mass spectrometry (HDX-MS) to obtain molecular-level details of mAb1's binding epitope on TL1A...
November 14, 2017: MAbs
https://www.readbyqxmd.com/read/29131142/a-consensus-model-of-human-apolipoprotein-a-i-in-its-monomeric-and-lipid-free-state
#5
John T Melchior, Ryan G Walker, Allison L Cooke, Jamie Morris, Mark Castleberry, Thomas B Thompson, Martin K Jones, Hyun D Song, Kerry-Anne Rye, Michael N Oda, Mary G Sorci-Thomas, Michael J Thomas, Jay W Heinecke, Xiaohu Mei, David Atkinson, Jere P Segrest, Sissel Lund-Katz, Michael C Phillips, W Sean Davidson
Apolipoprotein (apo)A-I is an organizing scaffold protein that is critical to high-density lipoprotein (HDL) structure and metabolism, probably mediating many of its cardioprotective properties. However, HDL biogenesis is poorly understood, as lipid-free apoA-I has been notoriously resistant to high-resolution structural study. Published models from low-resolution techniques share certain features but vary considerably in shape and secondary structure. To tackle this central issue in lipoprotein biology, we assembled a team of structural biologists specializing in apolipoproteins and set out to build a consensus model of monomeric lipid-free human apoA-I...
November 13, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/29129068/structural-and-functional-characterization-of-a-hole-hole-homodimer-variant-in-a-knob-into-hole-bispecific-antibody
#6
Hui-Min Zhang, Charlene Li, Ming Lei, Victor Lundin, Ho Young Lee, Milady Ninonuevo, Kevin Lin, Guanghui Han, Wendy Sandoval, Dongsheng Lei, Gang Ren, Jennifer Zhang, Hongbin Liu
Bispecific antibodies have great potential to be the next-generation biotherapeutics due to their ability to simultaneously recognize two different targets. Compared to conventional monoclonal antibodies, knob-into-hole bispecific antibodies face unique challenges in production and characterization due to the increase in variant possibilities, such as homodimerization in covalent and non-covalent forms. In this study, a storage- and pH-sensitive hydrophobic interaction chromatography (HIC) profile change was observed for the hole-hole homodimer, and the multiple HIC peaks were explored and shown to be conformational isomers...
November 12, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29127559/a-13-c-detected-15-n-double-quantum-nmr-experiment-to-probe-arginine-side-chain-guanidinium-15-n-%C3%AE-chemical-shifts
#7
Harold W Mackenzie, D Flemming Hansen
Arginine side-chains are often key for enzyme catalysis, protein-ligand and protein-protein interactions. The importance of arginine stems from the ability of the terminal guanidinium group to form many key interactions, such as hydrogen bonds and salt bridges, as well as its perpetual positive charge. We present here an arginine (13)C(ζ)-detected NMR experiment in which a double-quantum coherence involving the two (15)N(η) nuclei is evolved during the indirect chemical shift evolution period. As the precession frequency of the double-quantum coherence is insensitive to exchange of the two (15)N(η); this new approach is shown to eliminate the previously deleterious line broadenings of (15)N(η) resonances caused by the partially restricted rotation about the C(ζ)-N(ε) bond...
November 10, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/29109150/role-of-salt-bridges-in-the-dimer-interface-of-14-3-3%C3%AE-in-dimer-dynamics-n-terminal-%C3%AE-helical-order-and-molecular-chaperone-activity
#8
Joanna M Woodcock, Katy L Goodwin, Jarrod J Sandow, Carl Coolen, Matthew A Perugini, Andrew I Webb, Stuart M Pitson, Angel F Lopez, John A Carver
The 14-3-3 family of intracellular proteins are dimeric, multi-functional adaptor proteins that bind to and regulate the activities of many important signaling proteins. The subunits within 14-3-3 dimers are predicted to be stabilized by salt bridges that are largely conserved across the 14-3-3 protein family and allow the different isoforms to form heterodimers. Here, we have examined the contributions of conserved salt-bridging residues in stabilizing the dimeric state of 14-3-3ζ. Using analytical ultracentrifugation, our results revealed that Asp-21 and Glu-89 both play key roles in dimer dynamics and contribute to dimer stability...
November 6, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29107538/hybrid-structure-of-the-raga-c-ragulator-mtorc1-activation-complex
#9
Ming-Yuan Su, Kyle L Morris, Do Jin Kim, Yangxue Fu, Rosalie Lawrence, Goran Stjepanovic, Roberto Zoncu, James H Hurley
The lysosomal membrane is the locus for sensing cellular nutrient levels, which are transduced to mTORC1 via the Rag GTPases and the Ragulator complex. The crystal structure of the five-subunit human Ragulator at 1.4 Å resolution was determined. Lamtor1 wraps around the other four subunits to stabilize the assembly. The Lamtor2:Lamtor3 dimer stacks upon Lamtor4:Lamtor5 to create a platform for Rag binding. Hydrogen-deuterium exchange was used to map the Rag binding site to the outer face of the Lamtor2:Lamtor3 dimer and to the N-terminal intrinsically disordered region of Lamtor1...
October 25, 2017: Molecular Cell
https://www.readbyqxmd.com/read/29099587/combining-h-d-exchange-mass-spectrometry-and-computational-docking-to-derive-the-structure-of-protein-protein-complexes
#10
Victoria A Roberts, Michael E Pique, Simon Hsu, Sheng Li
Protein-protein interactions are essential for biological function, but structures of protein-protein complexes are difficult to obtain experimentally. To derive the protein complex of the DNA-repair enzyme human uracil-DNA-glycosylase (hUNG) with its protein inhibitor (UGI), we combined rigid-body computational docking with hydrogen/deuterium exchange mass spectrometry (DXMS). Computational docking of the unbound protein structures provides a list of possible three-dimensional models of the complex; DXMS identifies solvent-protected protein residues...
November 16, 2017: Biochemistry
https://www.readbyqxmd.com/read/29098736/structural-characterization-of-the-catalytic-%C3%AE-and-regulatory-%C3%AE-subunits-of-phosphorylase-kinase-in-the-context-of-the-hexadecameric-enzyme-complex
#11
Mary Ashley Rimmer, Owen W Nadeau, Antonio Artigues, Gerald M Carlson
In the tightly regulated glycogenolysis cascade, the breakdown of glycogen to glucose-1-phosphate, phosphorylase kinase (PhK) plays a key role in the regulating the activity of glycogen phosphorylase. PhK is a 1.3 MDa hexadecamer, with four copies each of four different subunits (α, β, γ and δ), making the study of its structure challenging. Using hydrogen-deuterium exchange, we have analyzed the regulatory β subunit and the catalytic γ subunit in the context of the intact non-activated PhK complex, to study the structure of these subunits and identify regions of surface exposure...
November 3, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/29098725/the-structure-of-the-large-regulatory-%C3%AE-subunit-of-phosphorylase-kinase-examined-by-modeling-and-hydrogen-deuterium-exchange
#12
Mary Ashley Rimmer, Owen W Nadeau, Jianyi Yang, Antonio Artigues, Yang Zhang, Gerald M Carlson
Phosphorylase kinase (PhK), a 1.3 MDa regulatory enzyme complex in the glycogenolysis cascade, has four copies each of four subunits, (αβγδ)4 , and 325 kDa of unique sequence (the mass of an αβγδ protomer). The α, β and δ subunits are regulatory, and contain allosteric activation sites that stimulate the activity of the catalytic γ subunit in response to diverse signaling molecules. Due to its size and complexity, no high resolution structures have been solved for the intact complex or its regulatory α and β subunits...
November 3, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/29092908/coordination-and-redox-state-dependent-structural-changes-of-the-heme-based-oxygen-sensor-afgchk-associated-with-intraprotein-signal-transduction
#13
Martin Stranava, Petr Man, Tereza Skalova, Petr Kolenko, Jan Blaha, Veronika Fojtikova, Vaclav Martinek, Jan Dohnalek, Alzbeta Lengalova, Michal Rosulek, Toru Shimizu, Marketa Martinkova
The heme-based oxygen sensor histidine kinase AfGcHK is part of a two-component signal transduction system in bacteria. O2 binding to the Fe(II) heme complex of its N-terminal globin domain strongly stimulates autophosphorylation at His-183 in its C-terminal kinase domain. The 6-coordinate heme Fe(III)-OH- and -CN- complexes of AfGcHK are also active, but the 5-coordinate heme Fe(II) complex and the heme-free apo-form are inactive. Here, we determined the crystal structures of the isolated dimeric globin domains of the active Fe(III)-CN- and inactive 5-coordinate Fe(II) forms, revealing striking structural differences on the heme-proximal side of the globin domain...
November 1, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29080206/structural-dynamics-of-the-gw182-silencing-domain-including-its-rna-recognition-motif-rrm-revealed-by-hydrogen-deuterium-exchange-mass-spectrometry
#14
Maja K Cieplak-Rotowska, Krzysztof Tarnowski, Marcin Rubin, Marc R Fabian, Nahum Sonenberg, Michal Dadlez, Anna Niedzwiecka
The human GW182 protein plays an essential role in micro(mi)RNA-dependent gene silencing. miRNA silencing is mediated, in part, by a GW182 C-terminal region called the silencing domain, which interacts with the poly(A) binding protein and the CCR4-NOT deadenylase complex to repress protein synthesis. Structural studies of this GW182 fragment are challenging due to its predicted intrinsically disordered character, except for its RRM domain. However, detailed insights into the properties of proteins containing disordered regions can be provided by hydrogen-deuterium exchange mass spectrometry (HDX/MS)...
October 27, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/29080204/design-and-validation-of-in-source-atmospheric-pressure-photoionization-hydrogen-deuterium-exchange-mass-spectrometry-with-continuous-feeding-of-d2o
#15
Thamina Acter, Seulgidaun Lee, Eunji Cho, Maeng-Joon Jung, Sunghwan Kim
In this study, continuous in-source hydrogen/deuterium exchange (HDX) atmospheric pressure photoionization (APPI) mass spectrometry (MS) with continuous feeding of D2O was developed and validated. D2O was continuously fed using a capillary line placed on the center of a metal plate positioned between the UV lamp and nebulizer. The proposed system overcomes the limitations of previously reported APPI HDX-MS approaches where deuterated solvents were premixed with sample solutions before ionization. This is particularly important for APPI because solvent composition can greatly influence ionization efficiency as well as the solubility of analytes...
October 27, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/29078272/ligand-induced-conformational-dynamics-of-the-escherichia-coli-na-h-antiporter-nhaa-revealed-by-hydrogen-deuterium-exchange-mass-spectrometry
#16
Martin Lorenz Eisinger, Aline Ricarda Dörrbaum, Hartmut Michel, Etana Padan, Julian David Langer
Na(+)/H(+) antiporters comprise a family of membrane proteins evolutionarily conserved in all kingdoms of life and play an essential role in cellular ion homeostasis. The NhaA crystal structure of Escherichia coli has become the paradigm for this class of secondary active transporters. However, structural data are only available at low pH, where NhaA is inactive. Here, we adapted hydrogen/deuterium-exchange mass spectrometry (HDX-MS) to analyze conformational changes in NhaA upon Li(+) binding at physiological pH...
October 31, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29076608/efficient-water-reduction-with-sp3-sp3-diboron-4-compounds-application-to-hydrogenations-h-d-exchange-reactions-and-carbonyl-reductions
#17
Troels Skrydstrup, Mathias Flinker, Hongfei Yin, René Juhl, Espen Eikeland, Jacob Overgaard, Dennis Nielsen
A series of crystalline sp3-sp3 diboron(4) compounds were synthesized and shown to promote the facile reduction of water with dihydrogen formation. The application of these diborons as simple and effective dihydrogen and dideuterium sources was demonstrated by conducting a series of selective reductions of alkynes and alkenes and hydrogen-deuterium exchange reactions with two-chamber reactors. Finally, as the water reduction reaction generates an intermediate borohydride species, a range of aldehydes and ketones could be reduced with water as the hydride source...
October 27, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/29070678/dnac-the-indispensable-companion-of-dnab-helicase-controls-the-accessibility-of-dnab-helicase-by-primase
#18
Magdalena M Felczak, Sundari Chodavarapu, Jon M Kaguni
Former studies relying on hydrogen/deuterium exchange analysis suggest that DnaC bound to DnaB alters the conformation of the N-terminal domain (NTD) of DnaB to impair the ability of this DNA helicase to interact with primase. Supporting this idea, the work described herein based on biosensor experiments and enzyme-linked immunosorbent assays shows that the DnaB-DnaC complex binds poorly to primase in comparison with DnaB alone. Using a structural model of DnaB complexed with the C-terminal domain (CTD) of primase, we found that Ile-85 is located at the interface in the NTD of DnaB that contacts primase...
October 25, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29058415/online-simultaneous-hydrogen-deuterium-exchange-of-multitarget-gas-phase-molecules-by-electrospray-ionization-mass-spectrometry-coupled-with-gas-chromatography
#19
Eun Sook Jeong, Eunju Cha, Sangwon Cha, Sunghwan Kim, Han Bin Oh, Oh-Seung Kwon, Jaeick Lee
In this study, a hydrogen/deuterium (H/D) exchange method using gas chromatography-electrospray ionization/mass spectrometry (GC-ESI/MS) was first investigated as a novel tool for online H/D exchange of multitarget analytes. The GC and ESI source were combined with a homemade heated column transfer line. GC-ESI/MS-based H/D exchange occurs in an atmospheric pressure ion source as a result of reacting the gas-phase analyte eluted from GC with charged droplets of deuterium oxide infused as the ESI spray solvent...
October 31, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29056864/understanding-curli-amyloid-protein-aggregation-by-hydrogen-deuterium-exchange-and-mass-spectrometry
#20
Hanliu Wang, Qin Shu, Don L Rempel, Carl Frieden, Michael L Gross
Bacteria within Curli biofilms are protected from environmental pressures (e.g., disinfectants, antibiotics), and this is responsible for intractable infections. Understanding aggregation of the major protein component of Curli, CsgA, may uncover disease-associated amyloidogenesis mechanisms. Here, we report the application of pulsed hydrogen-deuterium exchange and mass spectrometry (HDX-MS) to study CsgA aggregation, thereby obtaining region-specific information. By following time-dependent peptide signal depletion, presumably a result of insoluble fibril formation, we acquired sigmoidal profiles that are specific for regions (region-specific) of the protein...
September 2017: International Journal of Mass Spectrometry
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