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Keywords: mass spectrometry
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Biochem J (2023) 480 (16): 1241–1265.
Published: 23 August 2023
...Naoya Kitamura; James J. Galligan Post-translational modifications (PTMs) provide a rapid response to stimuli, finely tuning metabolism and gene expression and maintain homeostasis. Advances in mass spectrometry over the past two decades have significantly expanded the list of known PTMs in biology...
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Biochem J (2023) 480 (6): 403–420.
Published: 24 March 2023
... has been used, and can be used in the future, for cancer research. Challenges still exist in mass spectrometry phosphoproteomics and in the software required to provide biological information from these datasets. Nevertheless, improvements in mass spectrometers with enhanced scan rates, separation...
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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...
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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
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Biochem J (2020) 477 (2): 557–566.
Published: 31 January 2020
... 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 to ensure...
Includes: Supplementary data
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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
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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
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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
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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
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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...
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Biochem J (2017) 474 (22): 3719–3732.
Published: 01 November 2017
... 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 glycosaminoglycan chains. SDCs participate in cell adhesion...
Includes: Supplementary data
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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...
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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 (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...
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Biochem J (2016) 473 (6): 789–796.
Published: 10 March 2016
...) and then monitored by a positive electrospray ionization detector in the MRM (multiple-reaction monitoring) mode using stable deuterated isotope-containing ascarosides 1, 2, and 3 as an internal standard (see [ 14 ] for details). ascaroside Caenorhabditis elegans daumone heat stress HSF-1 mass...
Includes: Supplementary data
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Biochem J (2016) 473 (3): 321–334.
Published: 25 January 2016
... and quantified a constellation of endogenous lipid species specifically associated with the γ-secretase complex and required for its integrity and activity. intramembrane-cleaving protease lipid microenvironment lipid species mass spectrometry proteoliposomes quantitative shotgun lipidomics γ...
Includes: Supplementary data
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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
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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...
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Biochem J (2015) 471 (3): 347–356.
Published: 16 October 2015
..., until no PDA was detected in the filtrate. The concentration of the apo-CA was determined immediately prior to MS experiments using UV-visible absorption spectroscopy (ε 280nm =54000 M −1 ·cm −1 ) [ 38 , 39 ]. binding affinity competition domain specificity mass spectrometry metallothionein...
Includes: Supplementary data
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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...
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Biochem J (2014) 461 (2): 315–322.
Published: 26 June 2014
... 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 (Vps34) vacuolar protein sorting 15 (Vps15...
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Biochem J (2013) 452 (2): 259–269.
Published: 10 May 2013
... Harris for advice and invaluable suggestions and members of the Siu laboratory for discussion. We thank Mr Li Zhang and Dr Paul Taylor of the Mass Spectrometry Facility at the Advanced Protein Technology Centre of the Hospital for Sick Children for performing the MS analysis. Confocal microscopy...
Includes: Supplementary data
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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...
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Biochem J (2012) 444 (2): 169–181.
Published: 11 May 2012
...@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 of proteomics as ‘the next big...
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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...
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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...
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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...
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Biochem J (2007) 407 (1): 41–48.
Published: 12 September 2007
... processing of mitochondrial transit peptides in yeast, mouse and human samples. Taken together, our results demonstrate how to rapidly distinguish real proteolysis that occurs in vivo from the predictions based on in vitro experiments. mass spectrometry methionine aminopeptidase (MetAP) mitochondrial...
Includes: Supplementary data
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Biochem J (2007) 407 (1): e1.
Published: 12 September 2007
... that this methodology provides a comprehensive map of constitutive trimming events mediated by regulatory proteases such as methionine aminopeptidase. This study also identifies previously uncharacterized processing events that highlight potential novel regulatory mechanisms mediated by proteolysis. mass...
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Biochem J (2007) 403 (3): 463–472.
Published: 12 April 2007
... processed further using Data Analysis software from Bruker. 26 9 2006 24 1 2007 31 1 2007 31 1 2007 The Biochemical Society, London 2007 ionizing radiation lactose repressor mass spectrometry Monte Carlo simulation protein oxidation radiolytic attack Exposure...
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Biochem J (2006) 394 (1): 365–373.
Published: 27 January 2006
... should be addressed (email i.klevernic@dundee.ac.uk ). 5 8 2005 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...
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Biochem J (2004) 382 (1): 307–314.
Published: 10 August 2004
..., an excitation slit width of 5 nm and an emission slit width of 20 nm. 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...
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