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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
#1
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/28105936/pathways-of-aging-comparative-analysis-of-gene-signatures-in-replicative-senescence-and-stress-induced-premature-senescence
#2
Kamil C Kural, Neetu Tandon, Mikhail Skoblov, Olga V Kel-Margoulis, Ancha V Baranova
BACKGROUND: In culturing normal diploid cells, senescence may either happen naturally, in the form of replicative senescence, or it may be a consequence of external challenges such as oxidative stress. Here we present a comparative analysis aimed at reconstruction of molecular cascades specific for replicative (RS) and stressinduced senescence (SIPS) in human fibroblasts. RESULTS: An involvement of caspase-3/keratin-18 pathway and serine/threonine kinase Aurora A/ MDM2 pathway was shared between RS and SIPS...
December 28, 2016: BMC Genomics
https://www.readbyqxmd.com/read/28063489/using-hydrogen-deuterium-exchange-mass-spectrometry-to-examine-protein-membrane-interactions
#3
O Vadas, M L Jenkins, G L Dornan, J E Burke
Many fundamental cellular processes are controlled via assembly of a network of proteins at membrane surfaces. The proper recruitment of proteins to membranes can be controlled by a wide variety of mechanisms, including protein lipidation, protein-protein interactions, posttranslational modifications, and binding to specific lipid species present in membranes. There are, however, only a limited number of analytical techniques that can study the assembly of protein-membrane complexes at the molecular level. A relatively new addition to the set of techniques available to study these protein-membrane systems is the use of hydrogen-deuterium exchange mass spectrometry (HDX-MS)...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28052237/defining-a-viral-membrane-remodeling-complex-on-an-atomic-level
#4
Mary F Roberts
The Aichi RNA virus remodels host membranes by conscripting two host proteins, PI4KIIIβ (to generate PI4P in the remodeled vesicle) and ACBD3 (that tightly binds PI4KIIIβ), and localizing them on target membranes via Aichi protein 3A. In this issue of Structure, McPhail et al. (2017) reveal structural glimpses of the interfaces involved in this protein threesome using HDX-MS.
January 3, 2017: Structure
https://www.readbyqxmd.com/read/28008853/ric-8a-a-g-protein-chaperone-with-nucleotide-exchange-activity-induces-long-range-secondary-structure-changes-in-g%C3%AE
#5
Ravi Kant, Baisen Zeng, Celestine J Thomas, Brian Bothner, Stephen R Sprang
Cytosolic Ric-8A has guanine nucleotide exchange factor (GEF) activity and is a chaperone for several classes of heterotrimeric G protein α subunits in vertebrates. Using Hydrogen-Deuterium Exchange-Mass Spectrometry (HDX-MS) we show that Ric-8A disrupts the secondary structure of the Gα Ras-like domain that girds the guanine nucleotide-binding site, and destabilizes the interface between the Gαi1 Ras and helical domains, allowing domain separation and nucleotide release. These changes are largely reversed upon binding GTP and dissociation of Ric-8A...
December 23, 2016: ELife
https://www.readbyqxmd.com/read/28000716/%C3%AE-subunit-myristoylation-functions-as-an-energy-sensor-by-modulating-the-dynamics-of-amp-activated-protein-kinase
#6
Nada Ali, Naomi Ling, Srinath Krishnamurthy, Jonathan S Oakhill, John W Scott, David I Stapleton, Bruce E Kemp, Ganesh Srinivasan Anand, Paul R Gooley
The heterotrimeric AMP-activated protein kinase (AMPK), consisting of α, β and γ subunits, is a stress-sensing enzyme that is activated by phosphorylation of its activation loop in response to increases in cellular AMP. N-terminal myristoylation of the β-subunit has been shown to suppress Thr172 phosphorylation, keeping AMPK in an inactive state. Here we use amide hydrogen-deuterium exchange mass spectrometry (HDX-MS) to investigate the structural and dynamic properties of the mammalian myristoylated and non-myristoylated inactivated AMPK (D139A) in the presence and absence of nucleotides...
December 21, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27998708/conformations-of-jnk3%C3%AE-splice-variants-analyzed-by-hydrogen-deuterium-exchange-mass-spectrometry
#7
Ji Young Park, Youngjoo Yun, Ka Young Chung
c-Jun N-terminal kinases (JNKs) are members of the mitogen-activated protein kinase (MAPK) family that regulate apoptosis, inflammation, cytokine production, and metabolism. MAPKs undergo various splicing within their kinase domains. Unlike other MAPKs, JNKs have alternative splicing at the C-terminus, resulting in long and short variants. Functional or conformational effects due to the elongated C-terminal tail in the long splice variants have not been investigated nor has the conformation of the C-terminal tail been analyzed...
December 18, 2016: Journal of Structural Biology
https://www.readbyqxmd.com/read/27992649/kinetic-isotope-effects-and-hydrogen-deuterium-exchange-reveal-large-conformational-changes-during-the-catalysis-of-the-clostridium-acetobutylicum-spore-photoproduct-lyase
#8
Linlin Yang, Jagat Adhikari, Michael L Gross, Lei Li
Spore photoproduct lyase (SPL) catalyzes the direct reversal of a thymine dimer 5-thyminyl-5,6-dihydrothymine (i.e., the spore photoproduct (SP)) to two thymine residues in germinating endospores. Previous studies suggest that SPL from the bacterium Bacillus subtilis (Bs) harbors an unprecedented radical transfer pathway starting with cysteine 141 proceeding through tyrosine 99. However, in SPL from the bacterium C. acetobutylicum (Ca), the cysteine (at position 74) and tyrosine are located on the opposite sides of a substrate binding pocket that has to collapse to bring the two residues into proximity, enabling the C→Y radical passage as implied in SPL(Bs) ...
December 19, 2016: Photochemistry and Photobiology
https://www.readbyqxmd.com/read/27989622/the-molecular-basis-of-aichi-virus-3a-protein-activation-of-phosphatidylinositol-4-kinase-iii%C3%AE-pi4kb-through-acbd3
#9
Jacob A McPhail, Erik H Ottosen, Meredith L Jenkins, John E Burke
Phosphatidylinositol 4-kinase III beta (PI4KIIIβ) is an essential enzyme in mediating membrane transport, and plays key roles in facilitating viral infection. Many pathogenic positive-sense single-stranded RNA viruses activate PI4KIIIβ to generate phosphatidylinositol 4-phosphate (PI4P)-enriched organelles for viral replication. The molecular basis for PI4KIIIβ activation during viral infection has remained largely unclear. We describe the biochemical reconstitution and characterization of the complex of PI4KIIIβ with the Golgi protein Acyl-coenzyme A binding domain containing protein 3 (ACBD3) and Aichi virus 3A protein on membranes...
December 7, 2016: Structure
https://www.readbyqxmd.com/read/27975228/protein-structural-analysis-via-mass-spectrometry-based-proteomics
#10
Antonio Artigues, Owen W Nadeau, Mary Ashley Rimmer, Maria T Villar, Xiuxia Du, Aron W Fenton, Gerald M Carlson
Modern mass spectrometry (MS) technologies have provided a versatile platform that can be combined with a large number of techniques to analyze protein structure and dynamics. These techniques include the three detailed in this chapter: (1) hydrogen/deuterium exchange (HDX), (2) limited proteolysis, and (3) chemical crosslinking (CX). HDX relies on the change in mass of a protein upon its dilution into deuterated buffer, which results in varied deuterium content within its backbone amides. Structural information on surface exposed, flexible or disordered linker regions of proteins can be achieved through limited proteolysis, using a variety of proteases and only small extents of digestion...
2016: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/27959512/distinct-dynamic-modes-enable-the-engagement-of-dissimilar-ligands-in-a-promiscuous-atypical-rna-recognition-motif
#11
Kerene A Brown, Samel Sharifi, Rawaa Hussain, Logan Donaldson, Mark A Bayfield, Derek J Wilson
Conformational dynamics play a critical role in ligand binding, often conferring divergent activities and specificities even in species with highly similar ground-state structures. Here, we employ time-resolved electrospray ionization hydrogen-deuterium exchange (TRESI-HDX) to characterize the changes in dynamics that accompany oligonucleotide binding in the atypical RNA recognition motif (RRM2) in the C-terminal domain (CTD) of human La protein. Using this approach, which is uniquely capable of probing changes in the structure and dynamics of weakly ordered regions of proteins, we reveal that binding of RRM2 to a model 23-mer single-stranded RNA and binding of RRM2 to structured IRES domain IV of the hepatitis C viral (HCV) RNA are driven by fundamentally different dynamic processes...
December 27, 2016: Biochemistry
https://www.readbyqxmd.com/read/27929190/mechanism-and-kinetics-of-tyrosinase-inhibition-by-glycolic-acid-a-study-using-conventional-spectroscopy-methods-and-hydrogen-deuterium-exchange-coupling-with-mass-spectrometry
#12
Da Ma, Zong-Cai Tu, Hui Wang, Lu Zhang, Na He, David Julian McClements
Tyrosinase is an enzyme that promotes enzymatic browning of fruits and vegetables, thereby reducing product quality. A variety of analytical tools were used to characterize the interactions between tyrosinase and a natural tyrosinase inhibitor (glycolic acid). Hydrogen/deuterium exchange coupling with mass spectrometry (HDX-MS) was used to elucidate the interaction mechanism between glycolic acid and tyrosinase. UV-visible, fluorescence and circular dichroism spectroscopy analysis indicated that glycolic acid inhibited tyrosinase activity in a mixed-type manner with an IC50 of 83 ± 14 μM...
December 8, 2016: Food & Function
https://www.readbyqxmd.com/read/27916388/application-of-dual-protease-column-for-hdx-ms-analysis-of-monoclonal-antibodies
#13
Sasidhar N Nirudodhi, Justin B Sperry, Jason C Rouse, James A Carroll
A co-immobilized, dual protease column was developed and implemented to more efficiently digest IgG molecules for hydrogen/deuterium exchange mass spectrometry (HDX-MS). The low-pH proteolytic enzymes pepsin and type XIII protease from Aspergillus were packed into a single column to most effectively combine the complementary specificities. The method was optimized using an IgG2 monoclonal antibody as a substrate because they are known to be more difficult to efficiently digest. The general applicability of the method was then demonstrated using IgG1 and IgG4 mAbs...
February 2017: Journal of Pharmaceutical Sciences
https://www.readbyqxmd.com/read/27879668/structure-functional-basis-of-ion-transport-in-sodium-calcium-exchanger-ncx-proteins
#14
REVIEW
Moshe Giladi, Reut Shor, Michal Lisnyansky, Daniel Khananshvili
The membrane-bound sodium-calcium exchanger (NCX) proteins shape Ca(2+) homeostasis in many cell types, thus participating in a wide range of physiological and pathological processes. Determination of the crystal structure of an archaeal NCX (NCX_Mj) paved the way for a thorough and systematic investigation of ion transport mechanisms in NCX proteins. Here, we review the data gathered from the X-ray crystallography, molecular dynamics simulations, hydrogen-deuterium exchange mass-spectrometry (HDX-MS), and ion-flux analyses of mutants...
November 22, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27879053/n-arylsulfonyl-indolines-as-retinoic-acid-receptor-related-orphan-receptor%C3%A2-%C3%AE-ror%C3%AE-agonists
#15
Christelle Doebelin, Rémi Patouret, Ruben D Garcia-Ordonez, Mi Ra Chang, Venkatasubramanian Dharmarajan, Dana S Kuruvilla, Scott J Novick, Li Lin, Michael D Cameron, Patrick R Griffin, Theodore M Kamenecka
The nuclear retinoic acid receptor-related orphan receptor γ (RORγ; NR1F3) is a key regulator of inflammatory gene programs involved in T helper 17 (TH 17) cell proliferation. As such, synthetic small-molecule repressors (inverse agonists) targeting RORγ have been extensively studied for their potential as therapeutic agents for various autoimmune diseases. Alternatively, enhancing TH 17 cell proliferation through activation (agonism) of RORγ may boost an immune response, thereby offering a potentially new approach in cancer immunotherapy...
December 6, 2016: ChemMedChem
https://www.readbyqxmd.com/read/27870250/new-insights-into-interactions-between-the-nucleotide-binding-domain-of-cftr-and-keratin-8
#16
Aiswarya Premchandar, Anna Kupniewska, Arkadiusz Bonna, Grazyna Faure, Tomasz Fraczyk, Ariel Roldan, Brice Hoffmann, Mélanie Faria da Cunha, Harald Herrmann, Gergely L Lukacs, Aleksander Edelman, Michał Dadlez
The intermediate filament protein keratin 8 (K8) interacts with the nucleotide-binding domain 1 (NBD1) of the cystic fibrosis transmembrane regulator (CFTR) with phenylalanine 508 deletion (ΔF508), and this interaction hampers the biogenesis of functional ΔF508-CFTR and its insertion into the plasma membrane. Interruption of this interaction may constitute a new therapeutic target for cystic fibrosis patients bearing the ΔF508 mutation. Here we aimed to determine the binding surface between these two proteins, to facilitate the design of the interaction inhibitors...
November 21, 2016: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/27851982/interdomain-electron-transfer-in-cellobiose-dehydrogenase-is-governed-by-surface-electrostatics
#17
Alan Kadek, Daniel Kavan, Julien Marcoux, Johann Stojko, Alfons K G Felice, Sarah Cianférani, Roland Ludwig, Petr Halada, Petr Man
BACKGROUND: Cellobiose dehydrogenase (CDH) is a fungal extracellular oxidoreductase which fuels lytic polysaccharide monooxygenase with electrons during cellulose degradation. Interdomain electron transfer between the flavin and cytochrome domain in CDH, preceding the electron flow to lytic polysaccharide monooxygenase, is known to be pH dependent, but the exact mechanism of this regulation has not been experimentally proven so far. METHODS: To investigate the structural aspects underlying the domain interaction in CDH, hydrogen/deuterium exchange (HDX-MS) with improved proteolytic setup (combination of nepenthesin-1 with rhizopuspepsin), native mass spectrometry with ion mobility and electrostatics calculations were used...
February 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27846722/-utilization-of-hydrogen-deuterium-exchange-in-biopharmaceutical-industry
#18
D Coufalová, B Vojtěšek, L Hernychova
BACKGROUND: The development of biopharmaceutics is the fastest growing segment of the present pharmaceutical industry. The analysis of proteins therapeutics is a challenging task due to their large size and complexity of spatial structure. Any changes in the primary, secondary, tertiary or quaternary protein structure can have huge impact on their function, efficiency and toxicity. Mass spectrometry proved itself to be a powerful tool for analysis of primary protein structure (amino acid sequence) and thanks to the development of new techniques in last years it is able to analyse higher order protein structures...
2016: Klinická Onkologie: Casopis Ceské a Slovenské Onkologické Spolecnosti
https://www.readbyqxmd.com/read/27832483/7tm-domain-structure-of-adhesion-gpcrs
#19
Chris de Graaf, Saskia Nijmeijer, Steffen Wolf, Oliver P Ernst
Schematic presentation of the overall adhesion G Protein-Coupled Receptor (aGPCR) structure and functional domains, covering an extracellular N-terminal fragment (NTF), a membrane-spanning C-terminal fragment (CTF) and a GPCR proteolysis site (GPS). (Left side) aGPCR model constructed based on the seven-transmembrane (7TM) structure (blue) of secretin family glucagon receptor (GCGR) (PDB, 4L6R) [11] and the GPCR autoproteolysis inducing (GAIN) domain (magenta) structure of latrophilin 1 (PDB, 4DLQ) [9]...
2016: Handbook of Experimental Pharmacology
https://www.readbyqxmd.com/read/27807976/a-residue-resolved-bayesian-approach-to-quantitative-interpretation-of-hydrogen-deuterium-exchange-from-mass-spectrometry-application-to-characterizing-protein-ligand-interactions
#20
Daniel John Saltzberg, Howard B Broughton, Riccardo Pellarin, Michael J Chalmers, Alfonso Espada, Jeffrey A Dodge, Bruce D Pascal, Patrick R Griffin, Christine Humblet, Andrej Sali
Characterization of interactions between proteins and other molecules is crucial for understanding the mechanisms of action of biological systems and, thus, drug discovery. An increasingly useful approach to mapping these interactions is measurement of hydrogen/deuterium exchange (HDX) using mass spectrometry (HDX-MS), which measures the time-resolved deuterium incorporation of peptides obtained by enzymatic digestion of the protein. Comparison of exchange rates between apo- and ligand-bound conditions results in a mapping of the differential HDX (ΔHDX) of the ligand...
November 3, 2016: Journal of Physical Chemistry. B
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