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Keywords: mass spectrometry
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Articles
Biochem J (2023) 480 (1): 57–85.
Published: 11 January 2023
... of chromatin-binding proteins where pre-existing epigenetic marks promote or inhibit the writing of new marks. The recent technical advances in mass spectrometry (MS) -based proteomic methods and in genome-wide DNA sequencing approaches have broadened our understanding of epigenetic networks greatly. However...
Articles
Biochem J (2021) 478 (2): 299–326.
Published: 22 January 2021
... their Switch-II motif, impacting interaction with effectors. We describe and validate a new, multiplexed targeted mass spectrometry assay to quantify endogenous levels of LRRK2-phosphorylated Rab substrates (Rab1, Rab3, Rab8, Rab10, Rab35 and Rab43) as well as total levels of Rabs, LRRK2 and LRRK2...
Includes: Supplementary data
Articles
Biochem J (2020) 477 (15): 2791–2805.
Published: 07 August 2020
... applications. These findings can also serve as basis to study other plant UGTs and thereby advancing UGT enzyme engineering. deep learning glycosyltransferases mass spectrometry molecular dynamics Correspondence: Shozeb Haider ( Shozeb.haider@ucl.ac.uk ) 15 6 2020 8 7 2020 10...
Includes: Supplementary data
Articles
Biochem J (2020) 477 (3): 629–643.
Published: 11 February 2020
... Alzheimer's and Parkinson's diseases. Molecular chaperones are intimately involved in maintaining proteostasis, and their mechanisms of action are in part dependent on the morphology of aggregation-prone proteins. This study utilised native ion mobility–mass spectrometry to provide molecular insights...
Includes: Supplementary data
Articles
Biochem J (2020) 477 (2): 557–566.
Published: 31 January 2020
... ]. cross-linking mass spectrometry mutational analysis ribosomes SecM translation arrest Translation is a fundamental biological process via which ribosomes decode genetic information in mRNA and convert it into amino acid sequences that form proteins. The process is strategically regulated...
Includes: Supplementary data
Articles
Biochem J (2019) 476 (21): 3313–3331.
Published: 11 November 2019
... Hospital, University of Toronto, Toronto, ON, Canada © 2019 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2019 androgens cytochrome p450 enzyme activity estrogens mass spectrometry The enzyme aromatase (AROM; CYP19A1 ), an integral membrane...
Includes: Supplementary data
Articles
Biochem J (2019) 476 (13): 1911–1926.
Published: 02 July 2019
... states. The spatiotemporal regulation of ERK activity has been extensively studied. However, scarce information has been available regarding the quality control of the kinases to scavenge malfunctioning ERKs. Using site-specific mutagenesis and mass spectrometry, we found that the disruption...
Includes: Supplementary data
Articles
Biochem J (2019) 476 (6): 975–989.
Published: 22 March 2019
... between the homologues, particularly in the centre of the ring and the secondary metal-binding site, which is not conserved across the homologues. Solution and native mass spectrometry analyses highlight that the stability of the protein quaternary structure differs between EncFtn proteins from different...
Includes: Supplementary data
Articles
Biochem J (2019) 476 (2): 307–332.
Published: 25 January 2019
... the active site and their structural changes explain why a competent active site is not present in the monomeric form. Native mass spectrometry studies confirm that the zebrafish SCP2-thiolase (type-1) as well as its human homolog are weak transient dimers in solution. The crystallographic binding studies...
Includes: Multimedia, Supplementary data
Articles
Biochem J (2018) 475 (23): 3827–3846.
Published: 10 December 2018
... finger domain. The catalytic activity of TIPARP was resistant to meta-iodobenzylguanidine but sensitive to iodoacetamide and hydroxylamine, implicating cysteines and acidic side chains as ADP-ribosylated target residues. Mass spectrometry identified multiple ADP-ribosylated peptides in TIPARP and AHR...
Includes: Supplementary data
Articles
Biochem J (2018) 475 (17): 2819–2830.
Published: 11 September 2018
... for FVIII binding. Subsequent deletion of the other subdomains from D3 resulted in a progressive decrease in FVIII-binding affinity. Chemical footprinting mass spectrometry suggested increased conformational changes at the N-terminal side of D3 upon subsequent subdomain deletions at the C-terminal side...
Articles
Biochem J (2018) 475 (8): 1507–1522.
Published: 30 April 2018
... and mass spectrometry analysis to identify probable ubiquitin carboxyl-terminal hydrolase FAF-X (USP9X) as an interacting protein of the core clock protein aryl hydrocarbon receptor nuclear translocator-like protein 1 (ARNTL or BMAL1). Through biochemical experiments, we discover that USP9X reduces BMAL1...
Includes: Supplementary data
Articles
Biochem J (2018) 475 (5): 853–871.
Published: 06 March 2018
..., quantitative mass spectrometry using stable isotope labeling of cells was combined with formaldehyde cross-linking and proximity biotinylation, respectively. Besides other enzymes involved in sphingolipid synthesis and intermembrane transfer of ceramide, and putative redox partners of FA2H, progesterone...
Articles
Biochem J (2017) 474 (22): 3719–3732.
Published: 01 November 2017
... 2017 © 2017 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2017 angiogenesis mass spectrometry metalloproteases protein degradation syndecans Syndecans (SDCs), including SDC1–4, are transmembrane proteoglycans that contain...
Includes: Supplementary data
Articles
Biochem J (2017) 474 (16): 2779–2784.
Published: 07 August 2017
... effector protein activity remains an important step to understanding the subversion of host cell biology during pathogen infection and although molecular biology and immunochemistry remain critical tools for gaining insights into bacterial effector functions, increasingly mass spectrometry (MS...
Articles
Biochem J (2016) 473 (21): 3979–3995.
Published: 27 October 2016
... Society and distributed under the Creative Commons Attribution License 4.0 (CC BY) . extracellular matrix mass spectrometry matrisome proteomics tissue extraction The extracellular matrix (ECM) in the tissue microenvironment is a complex and heterogeneous collection of proteins...
Includes: Supplementary data
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Biochem J (2016) 473 (19): 3159–3175.
Published: 27 September 2016
... biochemistry with differential scanning fluorimetry (DSF) and ion mobility–mass spectrometry (IM–MS) to evaluate effects of phosphorylation and structure on the ligand binding, dynamics and stability of components of heteromeric PKA protein complexes in vitro . We uncover dynamic, conformationally distinct...
Includes: Supplementary data
Articles
Biochem J (2016) 473 (12): 1805–1819.
Published: 10 June 2016
... coupled with mass spectrometry (MS), to probe the structural rearrangements and to identify protein interfaces. The footprint of C3b on the FH surface matches existing crystal structures of C3b complexed with the N- and C-terminal fragments of FH. In addition, we revealed the position of the central...
Articles
Biochem J (2016) 473 (6): 789–796.
Published: 10 March 2016
... for coping with heat stress in this nematode. ascaroside Caenorhabditis elegans daumone heat stress HSF-1 mass spectrometry pheromone Environmental stresses significantly influence animals' behaviour and metabolism. The responses to such stresses can vary depending on the responding animal...
Includes: Supplementary data
Articles
Biochem J (2016) 473 (3): 321–334.
Published: 25 January 2016
.... intramembrane-cleaving protease lipid microenvironment lipid species mass spectrometry proteoliposomes quantitative shotgun lipidomics γ-secretase The neuropathological feature of Alzheimer's disease (AD) is the extracellular deposition of 40–43 amino acid (a.a.) long amyloid-β (Aβ) peptides...
Includes: Supplementary data
Articles
Biochem J (2015) 472 (2): e25–e26.
Published: 13 November 2015
... of Mariappa et al. advances the field. glycosylation mass spectrometry OGA O-linked N -acetylglucosamine (O-GlcNAc) Cells employ a large selection of post-translational modifications (PTMs) to dynamically alter the activity of proteins. One of the most common is the addition of a single N...
Articles
Biochem J (2015) 472 (2): 239–248.
Published: 13 November 2015
... Limited 2015 We utilized multiplexed mass spectrometry-based assays to characterize the lysine specificity of Piccolo NuA4 during nucleosome assembly. Although Piccolo NuA4 preferentially acetylates histone H4 (H4K12) regardless of the histone complex, DNA abates histone acetylation, except...
Includes: Supplementary data
Articles
Biochem J (2015) 471 (3): 347–356.
Published: 16 October 2015
... properties of mammalian metallothionein (MT). binding affinity competition domain specificity mass spectrometry metallothionein zinc Metallothioneins are a cysteine-rich family of proteins that are involved in the homoeostatic control of essential metals and the detoxification of toxic...
Includes: Supplementary data
Articles
Biochem J (2015) 469 (3): 409–420.
Published: 23 July 2015
...-deficient S336A mutant displayed normal interaction with PCTAIRE-1. Unbiased mass spectrometry and targeted mutagenesis analysis of cyclin Y identified key phosphorylation sites (Ser 100 and Ser 326 ) required for 14-3-3 binding. Recombinant WT cyclin Y, but not a S100A/S326A mutant, prepared in COS-1 cells...
Includes: Supplementary data
Articles
Biochem J (2015) 468 (1): 65–72.
Published: 05 May 2015
... to screen protein complexes for critical interactive lysine residues. footprinting low-density lipoprotein (LDL) receptor-related protein ligand binding mass spectrometry receptor-associated protein tandem mass tag The assembly of a protein complex is a key event in almost all biological...
Includes: Supplementary data
Articles
Biochem J (2015) 468 (1): 87–98.
Published: 05 May 2015
... intermediate. Herein, we use zero-length chemical cross-linking and homology modelling to create an experimentally validated solution structure of the protein's reduced form. antioxidant enzyme conformational changes mass spectrometry peroxiredoxin solution structure zero-length chemical cross...
Articles
Biochem J (2014) 461 (2): 315–322.
Published: 26 June 2014
..., Vps15, Beclin-1 and Atg14L, but not UVRAG. NRBF2 binds directly to Vps15 and is required for autophagy initiation in starved cells. autophagy human vacuolar protein sorting 34 (hVps34) macroautophagy mass spectrometry nuclear receptor-binding factor 2 (NRBF2) vacuolar protein sorting 34...
Articles
Biochem J (2013) 455 (3): 273–284.
Published: 10 October 2013
.... In the present paper, we highlight the importance of the Csa family of staphylococcal specific antigens as novel vaccine candidates. conserved staphylococcal antigen (Csa) DUF576 mass spectrometry Staphylococcus aureus tandem lipoprotein vaccine Staphylococcus aureus is a commensal...
Includes: Supplementary data
Articles
Biochem J (2013) 454 (3): 501–513.
Published: 29 August 2013
... approaches, DDR2-specific signalling components such as SHP-2 were identified. We further demonstrate that SHP-2 is phosphorylated by a subset of DDR2 lung cancer mutants. cell signalling collagen discoidin domain receptor lung cancer mass spectrometry phosphoproteomics Collagen...
Includes: Supplementary data
Articles
Biochem J (2013) 452 (2): 259–269.
Published: 10 May 2013
... should be addressed (email chi.hung.siu@utoronto.ca ). 1 11 2012 7 3 2013 12 3 2013 12 3 2013 © The Authors Journal compilation © 2013 Biochemical Society 2013 cell adhesion molecule Dictyostelium discoideum heterophilic interaction IPT/TIG domain mass...
Includes: Supplementary data
Articles
Biochem J (2013) 452 (1): 87–95.
Published: 25 April 2013
... in proteins. 1 To whom correspondence should be addressed (email rotweinp@ohsu.edu ). 7 12 2012 18 2 2013 6 3 2013 6 3 2013 © The Authors Journal compilation © 2013 Biochemical Society 2013 disulfide bond haemojuvelin iron metabolism mass spectrometry molecular...
Includes: Supplementary data
Articles
Biochem J (2013) 450 (3): 595–605.
Published: 28 February 2013
... Biochemical Society 2013 glutathione islets mass spectrometry NADPH ribose 5-phosphate Type 2 diabetes Pancreatic β-cells continuously monitor the blood glucose level. After a meal, they secrete insulin in response to a rise in the blood glucose level. This triggers the disposal of absorbed...
Includes: Supplementary data
Articles
Biochem J (2012) 448 (1): 83–91.
Published: 18 October 2012
... of this enzyme as a model system for studying the mechanism of action and specificity of photosensitizing agents. acetylcholinesterase (AChE) active-site gorge mass spectrometry N -formylkynurenine singlet oxygen site-specific photo-oxidation The principle biological role of AChE...
Includes: Supplementary data
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Biochem J (2012) 444 (2): 169–181.
Published: 11 May 2012
...@ars.usda.gov or MiernykJ@missouri.edu ). 25 2 2011 22 2 2012 1 3 2012 © The Authors Journal compilation © 2012 Biochemical Society 2012 label-free mass spectrometry post-translational modification protein interaction proteogenomics proteomics The introduction...
Articles
Biochem J (2012) 442 (2): 423–432.
Published: 13 February 2012
... 10 2011 15 11 2011 18 11 2011 18 11 2011 © The Authors Journal compilation © 2012 Biochemical Society 2012 a disintegrin and metalloproteinase with thrombospondin motifs 13 (ADAMTS-13) chronic renal failure mass spectrometry oxidative stress sepsis von Willebrand...
Includes: Supplementary data
Articles
Biochem J (2010) 431 (1): 141–148.
Published: 14 September 2010
... 23 7 2010 © The Authors Journal compilation © 2010 Biochemical Society 2010 docosahexanoic acid lipoxygenase mass spectrometry phospholipid platelet thrombin LOX (lipoxygenase), COX (cyclo-oxygenase) and CYP (cytochrome P450) enzymes oxidize non-esterified arachidonate...
Articles
Biochem J (2010) 429 (2): 359–367.
Published: 28 June 2010
.... 1 To whom correspondence should be addressed (email niclas.karlsson@medkem.gu.se ). 10 3 2010 30 4 2010 5 5 2010 5 5 2010 © The Authors Journal compilation © 2010 Biochemical Society 2010 glycosylation inflammation lubricin mass spectrometry MECA-79 L...
Includes: Supplementary data
Articles
Biochem J (2010) 428 (3): 355–362.
Published: 27 May 2010
... classical late-infantile neuronal ceroid lipofuscinosis (LINCL) glial fibrillary acidic protein (GFAP) lysosome mass spectrometry storage material Fluorescence images were obtained using a confocal laser-scanning microscope (LSM510; Carl Zeiss). For images shown in Figure 4 , conditions were...
Includes: Supplementary data
Articles
Biochem J (2009) 424 (3): 385–398.
Published: 10 December 2009
...Darren Locke; Shengjie Bian; Hong Li; Andrew L. Harris Gap junctions play important roles in auditory function and skin biology; mutations in the Cx26 (connexin26) gene are the predominant cause of inherited non-syndromic deafness and cause disfiguring skin disorders. Mass spectrometry (MS...
Articles
Biochem J (2009) 423 (1): 41–52.
Published: 14 September 2009
... 7 2009 17 7 2009 17 7 2009 © The Authors Journal compilation © 2009 Biochemical Society 2009 Dictyostelium discoideum fucose fucosyltransferase glycan mass spectrometry Cell–cell interactions often rely on the recognition of carbohydrate chains; such interactions...
Includes: Supplementary data
Articles
Biochem J (2009) 420 (1): 57–65.
Published: 28 April 2009
... and reproduction in any medium, provided the original work is properly cited. Arabidopsis gene expression P i starvation mass spectrometry phosphoenolpyruvate carboxylase kinase (PPCK) protein phosphorylation Heterotrophic A. thaliana (cv. Landsberg erecta) suspension cells were...
Includes: Supplementary data
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Biochem J (2007) 407 (1): 41–48.
Published: 12 September 2007
..., Department of Pharmacology, Sherbrooke, Québec, Canada, J1H 5N4. 2 To whom correspondence should be addressed (email gsalvesen@burnham.org ). 8 6 2007 19 7 2007 24 7 2007 24 7 2007 © The Authors Journal compilation © 2007 Biochemical Society 2007 mass spectrometry...
Includes: Supplementary data
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Biochem J (2007) 407 (1): e1.
Published: 12 September 2007
... mbogyo@stanford.edu 13 8 2007 14 8 2007 © The Authors Journal compilation © 2007 Biochemical Society 2007 mass spectrometry methionine aminopeptidase protease proteolysis substrate identification At the time of their discovery over a century ago, proteases were...
Articles
Biochem J (2007) 403 (3): 463–472.
Published: 12 April 2007
... mass spectrometry Monte Carlo simulation protein oxidation radiolytic attack The Biochemical Society, London 2007 26 9 2006 24 1 2007 31 1 2007 31 1 2007 1 To whom correspondence should be addressed (email spotheim@cnrs-orleans.fr ). The headpiece...
Articles
Biochem J (2006) 394 (1): 365–373.
Published: 27 January 2006
... 30 11 2005 9 12 2005 9 12 2005 The Biochemical Society, London 2006 extracellular-signal-regulated kinase 8 (ERK8) mass spectrometry mitogen-activated protein kinase (MAPK) oxidative stress protein phosphatase Many members of the MAPK (mitogen-activated protein...
Articles
Biochem J (2004) 384 (1): 191–199.
Published: 09 November 2004
... to the DDBJ, EMBL, GenBank® and GSDB Nucleotide Sequence Databases under accession number AB114441. acrosome reaction fertilization glycoprotein mass spectrometry sperm zona pellucida 25 2 2004 25 6 2004 20 7 2004 20 7 2004 The Biochemical Society, London 2004...
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Biochem J (2004) 382 (1): 307–314.
Published: 10 August 2004
... (email peepp@staff.ttu.ee ). 5 3 2004 10 5 2004 14 5 2004 14 5 2004 The Biochemical Society, London 2004 co-operative metal binding copper cluster cytochrome c oxidase copper chaperone (Cox17) mass spectrometry charge-state distribution analysis Cytochrome...
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Biochem J (2003) 375 (2): 323–328.
Published: 15 October 2003
...2003 2003 amyloid P component C-reactive protein (CRP) mass spectrometry nanoelectrospray ionization MS (nanoESI MS) pentraxin Abbreviations used: Aβ, β-amyloid peptide; APR, acute-phase reactant; CRP, C-reactive protein; EB, electrospray buffer; ESI, electrospray ionization; SAP...
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Biochem J (2003) 373 (3): 855–863.
Published: 01 August 2003
... 2003 8 5 2003 8 5 2003 The Biochemical Society, London ©2003 2003 chaperone protein growth hormone receptor mass spectrometry protein—protein interaction small glutamine-rich tetratricopeptide repeat-containing protein (SGT) tetratricopeptide repeat Abbreviations...
Articles
Biochem J (2003) 373 (3): 965–971.
Published: 01 August 2003
... 2003 caspase cell death inhibitor of apoptosis protein (IAP) mass spectrometry ubiquitin Abbreviations used: Ac-DEVD-AFC, N -acetyl-Asp-Glu-Val-Asp 7-amino-4-trifluoromethylcoumarin; DTT, dithiothreitol; GST, glutathione S-transferase; IAP, inhibitor of apoptosis protein; BIR...