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hydrogen deuterium exchange

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https://www.readbyqxmd.com/read/28223522/conformational-dynamics-of-a-neurotransmitter-sodium-symporter-in-a-lipid-bilayer
#1
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...
February 21, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28211014/comprehensive-peptide-ion-structure-studies-using-ion-mobility-techniques-part-1-an-advanced-protocol-for-molecular-dynamics-simulations-and-collision-cross-section-calculation
#2
Samaneh Ghassabi Kondalaji, Mahdiar Khakinejad, Amirmahdi Tafreshian, Stephen J Valentine
Collision cross-section (CCS) measurements with a linear drift tube have been utilized to study the gas-phase conformers of a model peptide (acetyl-PAAAAKAAAAKAAAAKAAAAK). Extensive molecular dynamics (MD) simulations have been conducted to derive an advanced protocol for the generation of a comprehensive pool of in-silico structures; both higher energy and more thermodynamically stable structures are included to provide an unbiased sampling of conformational space. MD simulations at 300 K are applied to the in-silico structures to more accurately describe the gas-phase transport properties of the ion conformers including their dynamics...
February 16, 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
#3
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
#4
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
#5
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 9, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28186093/conformational-changes-in-intact-dengue-virus-reveal-serotype-specific-expansion
#6
Xin-Xiang Lim, Arun Chandramohan, Xin Ying Elisa Lim, Nirmalya Bag, Kamal Kant Sharma, Melissa Wirawan, Thorsten Wohland, Shee-Mei Lok, Ganesh S Anand
Dengue virus serotype 2 (DENV2) alone undergoes structural expansion at 37 °C (associated with host entry), despite high sequence and structural homology among the four known serotypes. The basis for this differential expansion across strains and serotypes is unknown and necessitates mapping of the dynamics of dengue whole viral particles to describe their coordinated motions and conformational changes when exposed to host-like environments. Here we capture the dynamics of intact viral particles of two serotypes, DENV1 and DENV2, by amide hydrogen/deuterium exchange mass spectrometry (HDXMS) and time resolved Förster Resonance Energy Transfer...
February 10, 2017: Nature Communications
https://www.readbyqxmd.com/read/28171682/unusual-electrospray-ionization-induced-fragmentation-structural-elucidation-of-an-in-process-synthetic-intermediate-of-doravirine-mk-1439-using-lc-hrms-ms-and-2d-nmr
#7
Huaming Sheng, Katrina W Lexa, Li-Kang Zhang, Rong-Sheng Yang, Timothy J Wright, Benjamin D Sherry, Roy Helmy, Gary E Martin
RATIONALE: During the development of a novel synthetic route to doravirine; (1), a human immunodeficiency type 1 virus (HIV-1) nonnucleoside reverse transcriptase inhibitor (NNRTI), an unanticipated reaction intermediate, methyl (Z)-2-(3-chloro-5-cyanophenoxy)-5-(3-(3-chloro-5-cyanophenoxy)-2-oxo-4-(trifluoromethyl)pyridin-1(2H)-yl)-5-ethoxy-3-(trifluoromethyl)pent-2-enoate (2), was isolated. Moreover, the unusual ESI induced fragmentation was observed for 2. Hence, efforts were made towards the understanding of the structure of 2, which was crucial for the understanding of the reaction mechanism...
February 7, 2017: Rapid Communications in Mass Spectrometry: RCM
https://www.readbyqxmd.com/read/28170222/nitric-oxide-induced-conformational-changes-govern-h-nox-and-histidine-kinase-interaction-and-regulation-in-shewanella-oneidensis
#8
Minxi Rao, Mark A Herzik, Anthony T Iavarone, Michael A Marletta
Nitric oxide (NO) is implicated in biofilm regulation in several bacterial families via heme-nitric oxide/oxygen binding (H-NOX) protein signaling. The Shewanella oneidensis H-NOX (So H-NOX) is associated with a histidine kinase (So HK) encoded on the same operon, and together form a multi-component signaling network whereby the NO-bound state of So H-NOX inhibits So HK autophosphorylation activity. Although the conformational changes of So H-NOX upon NO binding have been structurally characterized, the mechanism of HK inhibition by NO-bound So H-NOX remains unclear...
February 7, 2017: Biochemistry
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
#9
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 7, 2017: Biochemistry
https://www.readbyqxmd.com/read/28167786/functional-importance-of-stripping-in-nf%C3%AE%C2%BAb-signaling-revealed-by-a-stripping-impaired-i%C3%AE%C2%BAb%C3%AE-mutant
#10
Holly E Dembinski, Kevin Wismer, Jesse D Vargas, Gajendra W Suryawanshi, Nadja Kern, Gerard Kroon, H Jane Dyson, Alexander Hoffmann, Elizabeth A Komives
Stress-response transcription factors such as NFκB turn on hundreds of genes and must have a mechanism for rapid cessation of transcriptional activation. We recently showed that the inhibitor of NFκB signaling, IκBα, dramatically accelerates the dissociation of NFκB from transcription sites, a process we have called "stripping." To test the role of the IκBα C-terminal PEST (rich in proline, glutamic acid, serine, and threonine residues) sequence in NFκB stripping, a mutant IκBα was generated in which five acidic PEST residues were mutated to their neutral analogs...
February 6, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28167755/conformational-disruption-of-pi3k%C3%AE-regulation-by-immunodeficiency-mutations-in-pik3cd-and-pik3r1
#11
Gillian L Dornan, Braden D Siempelkamp, Meredith L Jenkins, Oscar Vadas, Carrie L Lucas, John E Burke
Activated PI3K Delta Syndrome (APDS) is a primary immunodeficiency disease caused by activating mutations in either the leukocyte-restricted p110δ catalytic (PIK3CD) subunit or the ubiquitously expressed p85α regulatory (PIK3R1) subunit of class IA phosphoinositide 3-kinases (PI3Ks). There are two classes of APDS: APDS1 that arises from p110δ mutations that are analogous to oncogenic mutations found in the broadly expressed p110α subunit and APDS2 that occurs from a splice mutation resulting in p85α with a central deletion (Δ434-475)...
February 6, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28167534/detection-of-lipid-induced-structural-changes-of-the-marburg-virus-matrix-protein-vp40-using-hydrogen-deuterium-exchange-mass-spectrometry
#12
Kaveesha J Wijesinghe, Sarah Urata, Nisha Bhattarai, Edgar E Kooijman, Bernard S Gerstman, Prem P Chapagain, Sheng Li, Robert V Stahelin
Marburg virus (MARV) is a lipid-enveloped virus from the Filoviridae family containing a negative sense RNA genome. One of the seven MARV genes encodes the matrix protein VP40, which forms a matrix layer beneath the plasma membrane inner leaflet to facilitate budding from the host cell. MARV VP40 (mVP40) has been shown to be a dimeric peripheral protein with a broad and flat basic surface that can associate with anionic phospholipids such as phosphatidylserine. While a number of mVP40 cationic residues have been shown to facilitate binding to membranes containing anionic lipids, much less is known on how mVP40 assembles to form the matrix layer following membrane binding...
February 6, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28154854/nanospray-hx-ms-configuration-for-structural-interrogation-of-large-protein-systems
#13
Joey G Sheff, Morgan Hepburn, Yaping Yu, Susan P Lees-Miller, David C Schriemer
Hydrogen-deuterium exchange mass spectrometry (HX-MS) has made important contributions to the study of protein structure and function. Unfortunately, it is not known for low limits of detection, when compared with other forms of peptide-based or bottom-up protein MS methods. Systems perform poorly on sub-pmol quantities of protein states with greater than 300 kDa of unique sequences. The HX-MS analysis of complex protein states would be possible if proteomics-grade configurations could be used reliably, but temperature and temporal constraints have proven to be significant design challenges...
February 3, 2017: Analyst
https://www.readbyqxmd.com/read/28154009/caspase-6-undergoes-a-distinct-helix-strand-interconversion-upon-substrate-binding
#14
Kevin B Dagbay, Nicolas Bolik-Coulon, Sergey N Savinov, Jeanne A Hardy
Caspases are cysteine aspartate proteases that are major players in key cellular processes, including apoptosis and inflammation. Specifically, caspase-6 has also been implicated in playing a unique and critical role in neurodegeneration: however structural similarities between caspase-6 and other caspases have hampered precise targeting of caspase-6. All caspases can exist in a canonical conformation, in which the substrate binds atop a beta-strand platform in the 130's region. This caspase-6 region can also adopt a helical conformation that has not been seen in any other caspases...
February 2, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28147229/identification-and-structural-characterization-of-the-precursor-conformation-of-the-prion-protein-which-directly-initiates-misfolding-and-oligomerization
#15
Roumita Moulick, Jayant B Udgaonkar
To identify and structurally characterize the precursor conformation of the prion protein (PrP), from which misfolding and aggregation directly commence, has been a long-standing goal. Misfolding converts the α-helical, non-pathogenic functional form of PrP to pathogenic, β-structured oligomeric and amyloidogenic forms, which are the cause of prion diseases. Susceptibility to sporadic prion disease correlates well with the propensity of PrP to misfold to cytotoxic, proteinase K resistant oligomeric conformations at low pH...
January 29, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28146350/organocatalytic-imidazolium-ionic-liquids-h-d-exchange-catalysts
#16
Marcileia Zanatta, Francisco P Dos Santos, Cristina Biehl, Graciane Marin, Gunter Ebeling, Paulo A Netz, Jairton Dupont
Simple 1,2,3-trialkylimidazolium cation associated with basic anions, such as hydrogen carbonate, prolinate, and imidazolate, is an active catalyst for the H/D exchange reaction of various substrates using CDCl3 as D source, without the addition of any extra bases or metal. High deuterium incorporation (up to 49%) in acidic C-H bonds of ketone and alkyne substrates (pKa from 18.7 to 28.8) was found at room temperature. The reaction proceeds through the fast and reversible deuteration of the 2-methyl H of the imidazolium cation followed by D transfer to the substrate...
February 14, 2017: Journal of Organic Chemistry
https://www.readbyqxmd.com/read/28137577/analysis-of-translocation-competent-secretory-proteins-by-hdx-ms
#17
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/28110498/neutral-losses-of-sodium-benzoate-and-benzoic-acid-in-the-fragmentation-of-the-m%C3%A2-%C3%A2-na-ions-of-methoxyfenozide-and-tebufenozide-via-intramolecular-rearrangement-in-electrospray-ionization-tandem-mass-spectrometry
#18
Yunfeng Chai, Guanwei Gao, Shanshan Shen, Xin Liu, Chengyin Lu
RATIONALE: Electrospray ionization (ESI) tandem mass spectrometry can be applied to determine structural information about organic compounds. The [M + Na](+) ion is one of the major precursor ions in ESI mass spectrometry, but its fragmentation mechanism study is still insufficient. This study reveals the interesting fragmentation reactions of the [M + Na](+) ions of methoxyfenozide and tebufenozide. METHODS: The fragmentations of the [M + Na](+) , [M + Li](+) , and [M + H](+) ions of methoxyfenozide and tebufenozide were studied using a hybrid quadrupole-orbitrap mass spectrometer and an ion trap mass spectrometer...
February 15, 2017: Rapid Communications in Mass Spectrometry: RCM
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
#19
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/28096372/helical-structure-stability-and-dynamics-in-human-apolipoprotein-e3-and-e4-by-hydrogen-exchange-and-mass-spectrometry
#20
Palaniappan S Chetty, Leland Mayne, Sissel Lund-Katz, S Walter Englander, Michael C Phillips
Apolipoprotein E (apoE) plays a critical role in cholesterol transport in both peripheral circulation and brain. Human apoE is a polymorphic 299-residue protein in which the less common E4 isoform differs from the major E3 isoform only by a C112R substitution. ApoE4 interacts with lipoprotein particles and with the amyloid-β peptide, and it is associated with increased incidence of cardiovascular and Alzheimer's disease. To understand the structural basis for the differences between apoE3 and E4 functionality, we used hydrogen-deuterium exchange coupled with a fragment separation method and mass spectrometric analysis to compare their secondary structures at near amino acid resolution...
January 31, 2017: Proceedings of the National Academy of Sciences of the United States of America
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