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Articles

Principles of phosphoproteomics and applications in cancer research

Luke Higgins, Henry Gerdes, Pedro R. Cutillas

Biochem J (2023) 480 (6): 403–420.

DOI: https://doi.org/10.1042/BCJ20220220

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...

View article titled, Principles of phosphoproteomics and applications in cancer research

Articles

Characterizing crosstalk in epigenetic signaling to understand disease physiology

Joanna K. Lempiäinen, Benjamin A. Garcia

Biochem J (2023) 480 (1): 57–85.

DOI: https://doi.org/10.1042/BCJ20220550

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...

View article titled, Characterizing crosstalk in epigenetic signaling to understand disease physiology

Articles

Development of a multiplexed targeted mass spectrometry assay for LRRK2-phosphorylated Rabs and Ser910/Ser935 biomarker sites

Raja S. Nirujogi, Francesca Tonelli, Matthew Taylor, Pawel Lis, Alexander Zimprich, Esther Sammler, Dario R. Alessi

Biochem J (2021) 478 (2): 299–326.

DOI: https://doi.org/10.1042/BCJ20200930

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...

View article titled, Development of a multiplexed targeted mass spectrometry assay for LRRK2-phosphorylated Rabs and Ser910/Ser935 biomarker sites

Includes: Supplementary data

Articles

Structure-based enzyme engineering improves donor-substrate recognition of Arabidopsis thaliana glycosyltransferases

Aishat Akere, Serena H. Chen, Xiaohan Liu, Yanger Chen, Sarath Chandra Dantu, Alessandro Pandini, Debsindhu Bhowmik, Shozeb Haider

Biochem J (2020) 477 (15): 2791–2805.

DOI: https://doi.org/10.1042/BCJ20200477

Published: 07 August 2020

... article published by Portland Press Limited on behalf of the Biochemical Society and distributed under the Creative Commons Attribution License 4.0 (CC BY) . deep learning glycosyltransferases mass spectrometry molecular dynamics Glycosyltransferases (GTs) are a large family...

View article titled, Structure-based enzyme engineering improves donor-substrate recognition of Arabidopsis thaliana glycosyltransferases

Includes: Supplementary data

Articles

The molecular chaperone β-casein prevents amorphous and fibrillar aggregation of α-lactalbumin by stabilisation of dynamic disorder

Henry M. Sanders, Blagojce Jovcevski, John A. Carver, Tara L. Pukala

Biochem J (2020) 477 (3): 629–643.

DOI: https://doi.org/10.1042/BCJ20190638

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...

View article titled, The molecular chaperone β-casein prevents amorphous and fibrillar aggregation of α-lactalbumin by stabilisation of dynamic disorder

Includes: Supplementary data

Articles

Nascent SecM chain interacts with outer ribosomal surface to stabilize translation arrest

Mikihisa Muta, Ryo Iizuka, Tatsuya Niwa, Yuanfang Guo, Hideki Taguchi, Takashi Funatsu

Biochem J (2020) 477 (2): 557–566.

DOI: https://doi.org/10.1042/BCJ20190723

Published: 31 January 2020

... the PSIPRED program (v3.3; http://bioinf.cs.ucl.ac.uk/psipred/ ) [ 16 ]. The notable cross-linking product of SecM(Y80Bpa) was analyzed using mass spectrometry to identify the cross-linking partner, because the translation arrest stability of TC-SecM(Y80Bpa) was similar to that of TC-SecM...

View article titled, Nascent SecM chain interacts with outer ribosomal surface to stabilize translation arrest

Includes: Supplementary data

Articles

Phosphorylation of human placental aromatase CYP19A1

Debashis Ghosh, Chinaza Egbuta, Jean E. Kanyo, TuKiet T. Lam

Biochem J (2019) 476 (21): 3313–3331.

DOI: https://doi.org/10.1042/BCJ20190633

Published: 11 November 2019

... activity not only represents a paradigm shift in estrogen-mediated biology, it could also explain unresolved clinical questions such as aromatase inhibitor resistance. androgens cytochrome p450 enzyme activity estrogens mass spectrometry The enzyme aromatase (AROM; CYP19A1...

View article titled, Phosphorylation of human placental aromatase CYP19A1

Includes: Supplementary data

Articles

Nitration-induced ubiquitination and degradation control quality of ERK1

Yuanya Zhang, Xiahe Huang, Jinlong Wang, Xiaorong Wang, Xiaofei Liu, Yuhang Chen, Wu Xu, Yingchun Wang

Biochem J (2019) 476 (13): 1911–1926.

DOI: https://doi.org/10.1042/BCJ20190240

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...

View article titled, Nitration-induced ubiquitination and degradation control quality of ERK1

Includes: Supplementary data

Articles

Conservation of the structural and functional architecture of encapsulated ferritins in bacteria and archaea

Didi He, Cecilia Piergentili, Jennifer Ross, Emma Tarrant, Laura R. Tuck, C. Logan Mackay, Zak McIver, Kevin J. Waldron, David J. Clarke, Jon Marles-Wright

Biochem J (2019) 476 (6): 975–989.

DOI: https://doi.org/10.1042/BCJ20180922

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...

View article titled, Conservation of the structural and functional architecture of encapsulated ferritins in bacteria and archaea

Includes: Supplementary data

Articles

The peroxisomal zebrafish SCP2-thiolase (type-1) is a weak transient dimer as revealed by crystal structures and native mass spectrometry

Tiila-Riikka Kiema, Chandan J. Thapa, Mikko Laitaoja, Werner Schmitz, Mirko M. Maksimainen, Toshiyuki Fukao, Juha Rouvinen, Janne Jänis, Rik K. Wierenga

Biochem J (2019) 476 (2): 307–332.

DOI: https://doi.org/10.1042/BCJ20180788

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...

View article titled, The peroxisomal zebrafish SCP2-thiolase (type-1) is a weak transient dimer as revealed by crystal structures and native mass spectrometry

Includes: Multimedia, Supplementary data

Articles

Characterization of TCDD-inducible poly-ADP-ribose polymerase (TIPARP/ARTD14) catalytic activity

Alvin Gomez, Christian Bindesbøll, Somisetty V. Satheesh, Giulia Grimaldi, David Hutin, Laura MacPherson, Shaimaa Ahmed, Laura Tamblyn, Tiffany Cho, Hilde Irene Nebb, Anders Moen, Jan Haug Anonsen, Denis M. Grant, Jason Matthews

Biochem J (2018) 475 (23): 3827–3846.

DOI: https://doi.org/10.1042/BCJ20180347

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...

View article titled, Characterization of TCDD-inducible poly-ADP-ribose polymerase (TIPARP/ARTD14) catalytic activity

Includes: Supplementary data

Articles

The D′ domain of von Willebrand factor requires the presence of the D3 domain for optimal factor VIII binding

Małgorzata A. Przeradzka, Henriet Meems, Carmen van der Zwaan, Eduard H.T.M. Ebberink, Maartje van den Biggelaar, Koen Mertens, Alexander B. Meijer

Biochem J (2018) 475 (17): 2819–2830.

DOI: https://doi.org/10.1042/BCJ20180431

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...

View article titled, The D′ domain of von Willebrand factor requires the presence of the D3 domain for optimal factor VIII binding

Articles

Deubiquitinating enzyme USP9X regulates cellular clock function by modulating the ubiquitination and degradation of a core circadian protein BMAL1

Yang Zhang, Chunyan Duan, Jing Yang, Suping Chen, Qing Liu, Liang Zhou, Zhengyun Huang, Ying Xu, Guoqiang Xu

Biochem J (2018) 475 (8): 1507–1522.

DOI: https://doi.org/10.1042/BCJ20180005

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...

View article titled, Deubiquitinating enzyme USP9X regulates cellular clock function by modulating the ubiquitination and degradation of a core circadian protein BMAL1

Includes: Supplementary data

Articles

Identification of progesterone receptor membrane component-1 as an interaction partner and possible regulator of fatty acid 2-hydroxylase

Robert Hardt, Dominic Winter, Volkmar Gieselmann, Matthias Eckhardt

Biochem J (2018) 475 (5): 853–871.

DOI: https://doi.org/10.1042/BCJ20170963

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...

View article titled, Identification of progesterone receptor membrane component-1 as an interaction partner and possible regulator of fatty acid 2-hydroxylase

Articles

Processing of syndecan-2 by matrix metalloproteinase-14 and effect of its cleavage on VEGF-induced tube formation of HUVECs

Young Hun Lee, Jun Hyoung Park, Dong Huey Cheon, Taeyoung Kim, Yae Eun Park, Eok-Soo Oh, Ji Eun Lee, Seung-Taek Lee

Biochem J (2017) 474 (22): 3719–3732.

DOI: https://doi.org/10.1042/BCJ20170340

Published: 01 November 2017

... 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 and cell...

View article titled, Processing of syndecan-2 by matrix metalloproteinase-14 and effect of its cleavage on VEGF-induced tube formation of HUVECs

Includes: Supplementary data

Articles

The role of mass spectrometry analysis in bacterial effector characterization

Nichollas E. Scott, Elizabeth L. Hartland

Biochem J (2017) 474 (16): 2779–2784.

DOI: https://doi.org/10.1042/BCJ20160797

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...

View article titled, The role of mass spectrometry analysis in bacterial effector characterization

Articles

Comparative proteomic assessment of matrisome enrichment methodologies

Lukas Krasny, Angela Paul, Patty Wai, Beatrice A. Howard, Rachael C. Natrajan, Paul H. Huang

Biochem J (2016) 473 (21): 3979–3995.

DOI: https://doi.org/10.1042/BCJ20160686

Published: 27 October 2016

... by trypsin. extracellular matrix mass spectrometry matrisome proteomics tissue extraction Decellularisation involves the use of weak detergents, trypsinization or low ionic strength buffers to disrupt cell membranes leading to the release of intracellular proteins into solution while...

View article titled, Comparative proteomic assessment of matrisome enrichment methodologies

Includes: Supplementary data

Articles

cAMP-dependent protein kinase (PKA) complexes probed by complementary differential scanning fluorimetry and ion mobility–mass spectrometry

Dominic P. Byrne, Matthias Vonderach, Samantha Ferries, Philip J. Brownridge, Claire E. Eyers, Patrick A. Eyers

Biochem J (2016) 473 (19): 3159–3175.

DOI: https://doi.org/10.1042/BCJ20160648

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...

View article titled, cAMP-dependent protein kinase (PKA) complexes probed by complementary differential scanning fluorimetry and ion mobility–mass spectrometry

Includes: Supplementary data

Articles

Probing the solution structure of Factor H using hydroxyl radical protein footprinting and cross-linking

Anna Baud, Florence Gonnet, Isabelle Salard, Maxime Le Mignon, Alexandre Giuliani, Pascal Mercère, Bianca Sclavi, Régis Daniel

Biochem J (2016) 473 (12): 1805–1819.

DOI: https://doi.org/10.1042/BCJ20160225

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...

View article titled, Probing the solution structure of Factor H using hydroxyl radical protein footprinting and cross-linking

Articles

HSF-1 is involved in regulation of ascaroside pheromone biosynthesis by heat stress in Caenorhabditis elegans

Hyoe-Jin Joo, Saeram Park, Kwang-Youl Kim, Mun-Young Kim, Heekyeong Kim, Donha Park, Young-Ki Paik

Biochem J (2016) 473 (6): 789–796.

DOI: https://doi.org/10.1042/BJ20150938

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...

View article titled, HSF-1 is involved in regulation of ascaroside pheromone biosynthesis by heat stress in Caenorhabditis elegans

Includes: Supplementary data

Articles

The lipidome associated with the γ-secretase complex is required for its integrity and activity

Sophie Ayciriex, Hermeto Gerber, Guillermo M. Garcia Osuna, Mohamed Chami, Henning Stahlberg, Andrej Shevchenko, Patrick C. Fraering

Biochem J (2016) 473 (3): 321–334.

DOI: https://doi.org/10.1042/BJ20150448

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...

View article titled, The lipidome associated with the γ-secretase complex is required for its integrity and activity

Includes: Supplementary data

Articles

Use of a mutant OGA for detecting O-GlcNAc modified proteins

Robert J. Chalkley

Biochem J (2015) 472 (2): e25–e26.

DOI: https://doi.org/10.1042/BJ20150970

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...

View article titled, Use of a mutant OGA for detecting O-GlcNAc modified proteins

Articles

Site specificity analysis of Piccolo NuA4-mediated acetylation for different histone complexes

Yin-Ming Kuo, Ryan A. Henry, Song Tan, Jacques Côté, Andrew J. Andrews

Biochem J (2015) 472 (2): 239–248.

DOI: https://doi.org/10.1042/BJ20150654

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...

View article titled, Site specificity analysis of Piccolo NuA4-mediated acetylation for different histone complexes

Includes: Supplementary data

Articles

Putting the pieces into place: Properties of intact zinc metallothionein 1A determined from interaction of its isolated domains with carbonic anhydrase

Tyler B.J. Pinter, Martin J. Stillman

Biochem J (2015) 471 (3): 347–356.

DOI: https://doi.org/10.1042/BJ20150676

Published: 16 October 2015

... domain specificity mass spectrometry metallothionein zinc Figure 2 shows the relative populations of each of the zinc species during the stepwise zinc titration that were extracted from the deconvoluted ESI mass spectral data. Figure 2( A) shows that apo-αMT metalates non-co-operatively...

View article titled, Putting the pieces into place: Properties of intact zinc metallothionein 1A determined from interaction of its isolated domains with carbonic anhydrase

Includes: Supplementary data

Articles

Cyclin Y phosphorylation- and 14-3-3-binding-dependent activation of PCTAIRE-1/CDK16

Saifeldin N. Shehata, Maria Deak, Nicholas A. Morrice, Eriko Ohta, Roger W. Hunter, Vera M. Kalscheuer, Kei Sakamoto

Biochem J (2015) 469 (3): 409–420.

DOI: https://doi.org/10.1042/BJ20150486

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...

View article titled, Cyclin Y phosphorylation- and 14-3-3-binding-dependent activation of PCTAIRE-1/CDK16

Includes: Supplementary data

Articles

A novel chemical footprinting approach identifies critical lysine residues involved in the binding of receptor-associated protein to cluster II of LDL receptor-related protein

Esther Bloem, Eduard H.T.M. Ebberink, Maartje van den Biggelaar, Carmen van der Zwaan, Koen Mertens, Alexander B. Meijer

Biochem J (2015) 468 (1): 65–72.

DOI: https://doi.org/10.1042/BJ20140977

Published: 05 May 2015

... cluster II. Our results together further suggest that lysine residues at position 191 of the D2 domain and position 306 of the D3 domain are involved in LRP cluster II binding as well. footprinting low-density lipoprotein (LDL) receptor-related protein ligand binding mass spectrometry receptor...

View article titled, A novel chemical footprinting approach identifies critical lysine residues involved in the binding of receptor-associated protein to cluster II of LDL receptor-related protein

Includes: Supplementary data

Articles

Solution structure of the reduced form of human peroxiredoxin-6 elucidated using zero-length chemical cross-linking and homology modelling

Roland F. Rivera-Santiago, Sandra L. Harper, Suiping Zhou, Sira Sriswasdi, Sheldon I. Feinstein, Aron B. Fisher, David W. Speicher

Biochem J (2015) 468 (1): 87–98.

DOI: https://doi.org/10.1042/BJ20141463

Published: 05 May 2015

.... antioxidant enzyme conformational changes mass spectrometry peroxiredoxin solution structure zero-length chemical cross-linking The SDS/PAGE and trypsin digestion methods have been previously described [ 21 ]. Briefly, samples for the reactions described above were run in SDS/PAGE gels and bands...

View article titled, Solution structure of the reduced form of human peroxiredoxin-6 elucidated using zero-length chemical cross-linking and homology modelling

Articles

NRBF2 regulates macroautophagy as a component of Vps34 Complex I

Yanyan Cao, Yichen Wang, Widian F. Abi Saab, Fajun Yang, Jeffrey E. Pessin, Jonathan M. Backer

Biochem J (2014) 461 (2): 315–322.

DOI: https://doi.org/10.1042/BJ20140515

Published: 26 June 2014

..., 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 (Vps34) vacuolar protein sorting 15...

View article titled, NRBF2 regulates macroautophagy as a component of Vps34 Complex I

Articles

Mining the bacterial unknown proteome: identification and characterization of a novel family of highly conserved protective antigens in Staphylococcus aureus

Biochem J (2013) 455 (3): 273–284.

DOI: https://doi.org/10.1042/BJ20130540

Published: 10 October 2013

... antigens as novel vaccine candidates. conserved staphylococcal antigen (Csa) DUF576 mass spectrometry Staphylococcus aureus tandem lipoprotein vaccine Staphylococcus aureus is a commensal bacterium that may colonize over 30% of healthy adults, which is associated with increased risk...

View article titled, Mining the bacterial unknown proteome: identification and characterization of a novel family of highly conserved protective antigens in Staphylococcus aureus

Includes: Supplementary data

Articles

Phosphoproteomics of collagen receptor networks reveals SHP-2 phosphorylation downstream of wild-type DDR2 and its lung cancer mutants

Leo K. Iwai, Leo S. Payne, Maciej T. Luczynski, Francis Chang, Huifang Xu, Ryan W. Clinton, Angela Paul, Edward A. Esposito, Scott Gridley, Birgit Leitinger, Kristen M. Naegle, Paul H. Huang

Biochem J (2013) 454 (3): 501–513.

DOI: https://doi.org/10.1042/BJ20121750

Published: 29 August 2013

... cancer mass spectrometry phosphoproteomics Collagen is the most abundant protein in mammals and plays a critical role in maintaining tissue structural integrity [ 1 ]. There is an increasing appreciation that collagen has additional functions in propagating signal transduction networks which...

View article titled, Phosphoproteomics of collagen receptor networks reveals SHP-2 phosphorylation downstream of wild-type DDR2 and its lung cancer mutants

Includes: Supplementary data

Articles

TgrC1 mediates cell–cell adhesion by interacting with TgrB1 via mutual IPT/TIG domains during development of Dictyostelium discoideum

Gong Chen, Jun Wang, Xiaoqun Xu, Xiangfu Wu, Ruihan Piao, Chi-Hung Siu

Biochem J (2013) 452 (2): 259–269.

DOI: https://doi.org/10.1042/BJ20121674

Published: 10 May 2013

... 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 spectrometry How adhesive...

View article titled, TgrC1 mediates cell–cell adhesion by interacting with TgrB1 via mutual IPT/TIG domains during development of Dictyostelium discoideum

Includes: Supplementary data

Articles

Proteomic analysis and molecular modelling characterize the iron-regulatory protein haemojuvelin/repulsive guidance molecule c

Mahta Nili, Larry David, Johannes Elferich, Ujwal Shinde, Peter Rotwein

Biochem J (2013) 452 (1): 87–95.

DOI: https://doi.org/10.1042/BJ20121845

Published: 25 April 2013

... in proteins. disulfide bond haemojuvelin iron metabolism mass spectrometry molecular modelling protein structure repulsive guidance molecule 1 To whom correspondence should be addressed (email rotweinp@ohsu.edu ). 7 12 2012 18 2 2013 6 3 2013 6 3 2013 ©...

View article titled, Proteomic analysis and molecular modelling characterize the iron-regulatory protein haemojuvelin/repulsive guidance molecule c

Includes: Supplementary data

Articles

Time-resolved metabolomics analysis of β-cells implicates the pentose phosphate pathway in the control of insulin release

Peter Spégel, Vladimir V. Sharoyko, Isabel Goehring, Anders P. H. Danielsson, Siri Malmgren, Cecilia L. F. Nagorny, Lotta E. Andersson, Thomas Koeck, Geoffrey W. G. Sharp, Susanne G. Straub, Claes B. Wollheim, Hindrik Mulder

Biochem J (2013) 450 (3): 595–605.

DOI: https://doi.org/10.1042/BJ20121349

Published: 28 February 2013

... glutathione islets mass spectrometry NADPH ribose 5-phosphate Type 2 diabetes In the present study, a metabolomics approach was used to examine stimulus–secretion coupling in a clonal insulinoma-derived β-cell, the INS-1 832/13 line [ 17 , 18 ], and in rat islets. To this end, GC–MS-based...

View article titled, Time-resolved metabolomics analysis of β-cells implicates the pentose phosphate pathway in the control of insulin release

Includes: Supplementary data

Articles

Targeted oxidation of Torpedo californica acetylcholinesterase by singlet oxygen: identification of N -formylkynurenine tryptophan derivatives within the active-site gorge of its complex with the photosensitizer Methylene Blue

Mathilde M. Triquigneaux, Marilyn Ehrenshaft, Esther Roth, Israel Silman, Yakov Ashani, Ronald P. Mason, Lev Weiner, Leesa J. Deterding

Biochem J (2012) 448 (1): 83–91.

DOI: https://doi.org/10.1042/BJ20120992

Published: 18 October 2012

... by the manufacturer. acetylcholinesterase (AChE) active-site gorge mass spectrometry N -formylkynurenine singlet oxygen site-specific photo-oxidation The principle biological role of AChE (acetylcholinesterase) is the termination of impulse transmission at cholinergic synapses by rapid hydrolysis...

View article titled, Targeted oxidation of Torpedo californica acetylcholinesterase by singlet oxygen: identification of N -formylkynurenine tryptophan derivatives within the active-site gorge of its complex with the photosensitizer Methylene Blue

Includes: Supplementary data

Articles

The proteomic future: where mass spectrometry should be taking us

Jay J. Thelen, Ján A. Miernyk

Biochem J (2012) 444 (2): 169–181.

DOI: https://doi.org/10.1042/BJ20110363

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 Improvements...

View article titled, The proteomic future: where mass spectrometry should be taking us

Articles

Oxidation of Met 1606 in von Willebrand factor is a risk factor for thrombotic and septic complications in chronic renal failure

Vincenzo De Filippis, Stefano Lancellotti, Fabio Maset, Barbara Spolaore, Nicola Pozzi, Giovanni Gambaro, Laura Oggianu, Lorenzo A. Calò, Raimondo De Cristofaro

Biochem J (2012) 442 (2): 423–432.

DOI: https://doi.org/10.1042/BJ20111798

Published: 13 February 2012

... and metalloproteinase with thrombospondin motifs 13 (ADAMTS-13) chronic renal failure mass spectrometry oxidative stress sepsis von Willebrand factor (vWF) CKD (chronic kidney disease), often requiring HD (haemodialysis) treatment, is a life-threatening disease of outstanding clinical relevance and dramatic...

View article titled, Oxidation of Met 1606 in von Willebrand factor is a risk factor for thrombotic and septic complications in chronic renal failure

Includes: Supplementary data

Articles

Thrombin-activated human platelets acutely generate oxidized docosahexaenoic-acid-containing phospholipids via 12-lipoxygenase

Lloyd T. Morgan, Christopher P. Thomas, Hartmut Kühn, Valerie B. O'Donnell

Biochem J (2010) 431 (1): 141–148.

DOI: https://doi.org/10.1042/BJ20100415

Published: 14 September 2010

... stimulation, and their formation was blocked by calcium chelation. In summary, a new family of oxidized phospholipid was identified in thrombin-activated human platelets. docosahexanoic acid lipoxygenase mass spectrometry phospholipid platelet thrombin LOX (lipoxygenase), COX (cyclo-oxygenase...

View article titled, Thrombin-activated human platelets acutely generate oxidized docosahexaenoic-acid-containing phospholipids via 12-lipoxygenase

Articles

The glycosylation of human synovial lubricin: implications for its role in inflammation

Ruby P. Estrella, John M. Whitelock, Nicolle H. Packer, Niclas G. Karlsson

Biochem J (2010) 429 (2): 359–367.

DOI: https://doi.org/10.1042/BJ20100360

Published: 28 June 2010

...% of the total protein content in SF, and there was no apparent difference detected between OA and RA patients. glycosylation inflammation lubricin mass spectrometry MECA-79 L-selectin Lubricin is a mucin-like molecule encoded by the PRG4 (proteoglycan 4) gene. The protein, also known...

View article titled, The glycosylation of human synovial lubricin: implications for its role in inflammation

Includes: Supplementary data

Articles

Glial fibrillary acidic protein is elevated in the lysosomal storage disease classical late-infantile neuronal ceroid lipofuscinosis, but is not a component of the storage material

Su Xu, David E. Sleat, Michel Jadot, Peter Lobel

Biochem J (2010) 428 (3): 355–362.

DOI: https://doi.org/10.1042/BJ20100128

Published: 27 May 2010

... classical late-infantile neuronal ceroid lipofuscinosis (LINCL) glial fibrillary acidic protein (GFAP) lysosome mass spectrometry storage material The neuronal ceroid lipofuscinoses (NCLs) are a group of hereditary neurodegenerative diseases that primarily affect children and adolescents [ 1...

View article titled, Glial fibrillary acidic protein is elevated in the lysosomal storage disease classical late-infantile neuronal ceroid lipofuscinosis, but is not a component of the storage material

Includes: Supplementary data

Articles

Post-translational modifications of connexin26 revealed by mass spectrometry

Darren Locke, Shengjie Bian, Hong Li, Andrew L. Harris

Biochem J (2009) 424 (3): 385–398.

DOI: https://doi.org/10.1042/BJ20091140

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...

View article titled, Post-translational modifications of connexin26 revealed by mass spectrometry

Articles

Development of Dictyostelium discoideum is associated with alteration of fucosylated N-glycan structures

Birgit Schiller, Alba Hykollari, Josef Voglmeir, Gerald Pöltl, Karin Hummel, Ebrahim Razzazi-Fazeli, Rudolf Geyer, Iain B. H. Wilson

Biochem J (2009) 423 (1): 41–52.

DOI: https://doi.org/10.1042/BJ20090786

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...

View article titled, Development of Dictyostelium discoideum is associated with alteration of fucosylated N-glycan structures

Includes: Supplementary data

Articles

In vivo regulatory phosphorylation of the phosphoenolpyruvate carboxylase AtPPC1 in phosphate-starved Arabidopsis thaliana

Allison L. Gregory, Brenden A. Hurley, Hue T. Tran, Alexander J. Valentine, Yi-Min She, Vicki L. Knowles, William C. Plaxton

Biochem J (2009) 420 (1): 57–65.

DOI: https://doi.org/10.1042/BJ20082397

Published: 28 April 2009

... ). 19 12 2008 10 2 2009 19 2 2009 19 2 2009 Arabidopsis gene expression P i starvation mass spectrometry phosphoenolpyruvate carboxylase kinase (PPCK) protein phosphorylation Heterotrophic A. thaliana (cv. Landsberg erecta) suspension cells were maintained...

View article titled, In vivo regulatory phosphorylation of the phosphoenolpyruvate carboxylase AtPPC1 in phosphate-starved Arabidopsis thaliana

Includes: Supplementary data

Articles

Profiling constitutive proteolytic events in vivo

John C. Timmer, Mari Enoksson, Eric Wildfang, Wenhong Zhu, Yoshinobu Igarashi, Jean-Benard Denault, Yuliang Ma, Benjamin Dummitt, Yie-Hwa Chang, Alan E. Mast, Alexey Eroshkin, Jeffrey W. Smith, W. Andy Tao, Guy S. Salvesen

Biochem J (2007) 407 (1): 41–48.

DOI: https://doi.org/10.1042/BJ20070775

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...

View article titled, Profiling constitutive proteolytic events in vivo

Includes: Supplementary data

Articles

Finding the needles in the haystack: mapping constitutive proteolytic events in vivo

Matthew Bogyo

Biochem J (2007) 407 (1): e1.

DOI: https://doi.org/10.1042/BJ20071096

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...

View article titled, Finding the needles in the haystack: mapping constitutive proteolytic events in vivo

Articles

Radiation-induced oxidative damage to the DNA-binding domain of the lactose repressor

Nathalie Gillard, Stephane Goffinont, Corinne Buré, Marie Davidkova, Jean-Claude Maurizot, Martine Cadene, Melanie Spotheim-Maurizot

Biochem J (2007) 403 (3): 463–472.

DOI: https://doi.org/10.1042/BJ20061466

Published: 12 April 2007

... be addressed (email spotheim@cnrs-orleans.fr ). ionizing radiation lactose repressor mass spectrometry Monte Carlo simulation protein oxidation radiolytic attack 26 9 2006 24 1 2007 31 1 2007 31 1 2007 The Biochemical Society, London 2007 The side-chain...

View article titled, Radiation-induced oxidative damage to the DNA-binding domain of the lactose repressor

Articles

Characterization of the reversible phosphorylation and activation of ERK8

Iva V. Klevernic, Margaret J. Stafford, Nicholas Morrice, Mark Peggie, Simon Morton, Philip Cohen

Biochem J (2006) 394 (1): 365–373.

DOI: https://doi.org/10.1042/BJ20051288

Published: 27 January 2006

... 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 kinase) subfamily are components of protein kinase cascades...

View article titled, Characterization of the reversible phosphorylation and activation of ERK8

Articles

A newly identified zona pellucida glycoprotein, ZPD, and dimeric ZP1 of chicken egg envelope are involved in sperm activation on sperm–egg interaction

Hiroki OKUMURA, Yoshinori KOHNO, Yuki IWATA, Hitoshi MORI, Naohito AOKI, Chihiro SATO, Ken KITAJIMA, Daita NADANO, Tsukasa MATSUDA

Biochem J (2004) 384 (1): 191–199.

DOI: https://doi.org/10.1042/BJ20040299

Published: 09 November 2004

... Sequence Databases under accession number AB114441. 25 2 2004 25 6 2004 20 7 2004 20 7 2004 The Biochemical Society, London 2004 acrosome reaction fertilization glycoprotein mass spectrometry sperm zona pellucida Fertilization is composed of multiple...

View article titled, A newly identified zona pellucida glycoprotein, ZPD, and dimeric ZP1 of chicken egg envelope are involved in sperm activation on sperm–egg interaction

Articles

Metal-binding mechanism of Cox17, a copper chaperone for cytochrome c oxidase

Peep PALUMAA, Liina KANGUR, Anastassia VORONOVA, Rannar SILLARD

Biochem J (2004) 382 (1): 307–314.

DOI: https://doi.org/10.1042/BJ20040360

Published: 10 August 2004

... be addressed (email peepp@staff.ttu.ee ). 5 3 2004 10 5 2004 14 5 2004 14 5 2004 co-operative metal binding copper cluster cytochrome c oxidase copper chaperone (Cox17) mass spectrometry charge-state distribution analysis The Biochemical Society, London 2004...

View article titled, Metal-binding mechanism of Cox17, a copper chaperone for cytochrome c oxidase

Articles

Investigating interactions of the pentraxins serum amyloid P component and C-reactive protein by mass spectrometry

J. Andrew AQUILINA, Carol V. ROBINSON

Biochem J (2003) 375 (2): 323–328.

DOI: https://doi.org/10.1042/bj20030541

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...

View article titled, Investigating interactions of the pentraxins serum amyloid P component and C-reactive protein by mass spectrometry

Articles

Small glutamine-rich tetratricopeptide repeat-containing protein (SGT) interacts with the ubiquitin-dependent endocytosis (UbE) motif of the growth hormone receptor

Julia A. SCHANTL, Marcel ROZA, Ad P. De JONG, Ger J. STROUS

Biochem J (2003) 373 (3): 855–863.

DOI: https://doi.org/10.1042/bj20021591

Published: 01 August 2003

.... Binding studies showed that the first TPR motif of SGT interacts with the UbE motif of the GHR. Taken together, these data show that SGT is a GHR-interacting protein, which binds independent of the ubiquitin-conjugating system. Key words: chaperone protein, growth hormone receptor, mass spectrometry...

View article titled, Small glutamine-rich tetratricopeptide repeat-containing protein (SGT) interacts with the ubiquitin-dependent endocytosis (UbE) motif of the growth hormone receptor

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