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Articles

Principles of phosphoproteomics and applications in cancer research

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Cell signaling in the 21st century

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

... by Portland Press Limited on behalf of the Biochemical Society and distributed under the Creative Commons Attribution License 4.0 (CC BY) . kinase biology mass spectrometry proteomics Cancer is caused by mutations in genes that, in normal cells, regulate fundamental cell biological processes...

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

Articles

The adaptive response to alternative carbon sources in the pathogen Candida albicans involves a remodeling of thiol- and glutathione-dependent redox status

Juliette Bayot, Caroline Martin, Guillaume Chevreux, Jean-Michel Camadro, Françoise Auchère

Biochem J (2023) 480 (3): 197–217.

DOI: https://doi.org/10.1042/BCJ20220505

Published: 07 February 2023

... must adapt to host microenvironments and this adaptive response is crucial for the survival of this organism, as it facilitates the effective assimilation of alternative carbon sources others than glucose. We performed a global proteomic analysis on the global changes in protein abundance in response...

View article titled, The adaptive response to alternative carbon sources in the pathogen Candida albicans involves a remodeling of thiol- and glutathione-dependent redox status

Includes: Supplementary data

Articles

Characterizing crosstalk in epigenetic signaling to understand disease physiology

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Cell signaling in the 21st century

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

Systems approaches to understand oxygen sensing: how multi-omics has driven advances in understanding oxygen-based signalling

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Towards systems biochemistry

Michael Batie, Niall S. Kenneth, Sonia Rocha

Biochem J (2022) 479 (3): 245–257.

DOI: https://doi.org/10.1042/BCJ20210554

Published: 04 February 2022

... synthesis and destruction that together establish changes to the cellular proteome. In this article, we will discuss the advances of our understanding of the cellular oxygen sensing machinery achieved through the application of ‘omics-based experimental approaches. Correspondence: Niall S. Kenneth...

View article titled, Systems approaches to understand oxygen sensing: how multi-omics has driven advances in understanding oxygen-based signalling

Articles

Proteomic analysis identifies ZMYM2 as endogenous binding partner of TBX18 protein in 293 and A549 cells

Timo H.-W. Lüdtke, Marc-Jens Kleppa, Reginaldo Rivera-Reyes, Fairouz Qasrawi, Dervla M. Connaughton, Shirlee Shril, Friedhelm Hildebrandt, Andreas Kispert

Biochem J (2022) 479 (1): 91–109.

DOI: https://doi.org/10.1042/BCJ20210642

Published: 14 January 2022

... in which TBX18 resides to exert its crucial transcriptional function in these embryonic contexts have remained elusive. Here, we used 293 and A549 cells as an accessible cell source to search for endogenous protein interaction partners of TBX18 by an unbiased proteomic approach. We tagged endogenous TBX18...

View article titled, Proteomic analysis identifies ZMYM2 as endogenous binding partner of TBX18 protein in 293 and A549 cells

Includes: Supplementary data

Articles

An ERK5–KLF2 signalling module regulates early embryonic gene expression and telomere rejuvenation in stem cells

Helen A. Brown, Charles A.C. Williams, Houjiang Zhou, Diana Rios-Szwed, Rosalia Fernandez-Alonso, Saria Mansoor, Liam McMulkin, Rachel Toth, Robert Gourlay, Julien Peltier, Nora Dieguez-Martinez, Matthias Trost, Jose M. Lizcano, Marios P. Stavridis, Greg M. Findlay

Biochem J (2021) 478 (23): 4119–4136.

DOI: https://doi.org/10.1042/BCJ20210646

Published: 06 December 2021

... pathway drives transcription of naïve pluripotency genes in mouse Embryonic Stem Cells (mESCs). However, how ERK5 impacts on other aspects of mESC biology has not been investigated. Here, we employ quantitative proteomic profiling to identify proteins whose expression is regulated by the ERK5 pathway...

View article titled, An ERK5–KLF2 signalling module regulates early embryonic gene expression and telomere rejuvenation in stem cells

Articles

Intelligent host engineering for metabolic flux optimisation in biotechnology

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Towards systems biochemistry

Lachlan J. Munro, Douglas B. Kell

Biochem J (2021) 478 (20): 3685–3721.

DOI: https://doi.org/10.1042/BCJ20210535

Published: 21 October 2021

... by the participation of University of Liverpool in an all-inclusive Read & Publish pilot with Portland Press and the Biochemical Society under a transformative agreement with JISC. flux host metabolomics optimisation proteomics transcriptomics Much of microbial biotechnology consists...

View article titled, Intelligent host engineering for metabolic flux optimisation in biotechnology

Articles

Protein tyrosine phosphatases in cell adhesion

Katherine A. Young, Laura Biggins, Hayley J. Sharpe

Biochem J (2021) 478 (5): 1061–1083.

DOI: https://doi.org/10.1042/BCJ20200511

Published: 10 March 2021

... adhesions that are relatively unexplored. Finally, we reflect on the dysregulation of PTPs and cell adhesions in disease. cell adhesion protein tyrosine phosphatases proteomics signalling Cell adhesions are an essential feature of multicellular life and function as both mechanical links...

View article titled, Protein tyrosine phosphatases in cell adhesion

Includes: Supplementary data

Articles

Temporal modulation of the NF-κB RelA network in response to different types of DNA damage

Amy E. Campbell, Catarina Ferraz Franco, Ling-I Su, Emma K. Corbin, Simon Perkins, Anton Kalyuzhnyy, Andrew R. Jones, Philip J. Brownridge, Neil D. Perkins, Claire E. Eyers

Biochem J (2021) 478 (3): 533–551.

DOI: https://doi.org/10.1042/BCJ20200627

Published: 10 February 2021

... nuclear factor κB phosphorylation/dephosphorylation proteomics RelA, also known as p65, is a key member of the NF-κB family of transcription factors, which serve as ‘master regulators’ of the cellular inflammatory and stress responses, and are key components that maintain tissue homeostasis...

View article titled, Temporal modulation of the NF-κB RelA network in response to different types of DNA damage

Includes: Supplementary data

Articles

Combinations of histone post-translational modifications

Bethany C. Taylor, Nicolas L. Young

Biochem J (2021) 478 (3): 511–532.

DOI: https://doi.org/10.1042/BCJ20200170

Published: 10 February 2021

... 7 2020 13 1 2021 18 1 2021 © 2021 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2021 chromatin histones post-translational modification proteomics The DNA of the eukaryotic genome is packaged and condensed into nucleosomes...

View article titled, Combinations of histone post-translational modifications

Articles

Extracellular signal-regulated kinase (ERK) pathway control of CD8 + T cell differentiation

Marcos P. Damasio, Julia M. Marchingo, Laura Spinelli, Jens L. Hukelmann, Doreen A. Cantrell, Andrew J.M. Howden

Biochem J (2021) 478 (1): 79–98.

DOI: https://doi.org/10.1042/BCJ20200661

Published: 13 January 2021

.... Accordingly, we have used mass spectrometry to explore how ERK signalling pathways control antigen receptor driven proteome restructuring in CD8 + T cells to gain insights about the biological processes controlled by ERKs in primary lymphocytes. Quantitative analysis of >8000 proteins identified 900 ERK...

View article titled, Extracellular signal-regulated kinase (ERK) pathway control of CD8 + T cell differentiation

Includes: Supplementary data

Articles

The composition and turnover of the Arabidopsis thaliana 80S cytosolic ribosome

Karzan Jalal Salih, Owen Duncan, Lei Li, Josua Trösch, A. Harvey Millar

Biochem J (2020) 477 (16): 3019–3032.

DOI: https://doi.org/10.1042/BCJ20200385

Published: 26 August 2020

... proteomics ribosomes The ribosome uses information encoded by messenger RNA (mRNA) to drive peptide-bond formation resulting in protein synthesis. All ribosomes consist of two subunits, a large and small, and each contain ribosomal RNAs (rRNAs) and ribosomal proteins (r-proteins). The 80S eukaryotic...

View article titled, The composition and turnover of the Arabidopsis thaliana 80S cytosolic ribosome

Includes: Supplementary data

Articles

Bioinformatic and experimental evidence for suicidal and catalytic plant THI4s

Jaya Joshi, Guillaume A.W. Beaudoin, Jenelle A. Patterson, Jorge D. García-García, Catherine E. Belisle, Lan-Yen Chang, Lei Li, Owen Duncan, A. Harvey Millar, Andrew D. Hanson

Biochem J (2020) 477 (11): 2055–2069.

DOI: https://doi.org/10.1042/BCJ20200297

Published: 10 June 2020

... was predominantly in desulfurated form, consistent with THI4 having a suicide mechanism in planta . Unexpectedly, transcriptome data mining and deep proteome profiling showed that barley, wheat, and oat have both a widely expressed canonical THI4 with an active-site Cys, and a THI4-like paralog (non-Cys THI4...

View article titled, Bioinformatic and experimental evidence for suicidal and catalytic plant THI4s

Includes: Supplementary data

Articles

Rhodobacter sphaeroides methionine sulfoxide reductase P reduces R - and S -diastereomers of methionine sulfoxide from a broad-spectrum of protein substrates

Lionel Tarrago, Sandrine Grosse, Marina I. Siponen, David Lemaire, Béatrice Alonso, Guylaine Miotello, Jean Armengaud, Pascal Arnoux, David Pignol, Monique Sabaty

Biochem J (2018) 475 (23): 3779–3795.

DOI: https://doi.org/10.1042/BCJ20180706

Published: 06 December 2018

...@cea.fr ) 30 8 2018 26 10 2018 1 11 2018 2 11 2018 © 2018 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2018 enzyme kinetics methionine sulfoxide reductase molybdoenzyme oxidative stress protein oxidation proteomics...

View article titled, Rhodobacter sphaeroides methionine sulfoxide reductase P reduces R - and S -diastereomers of methionine sulfoxide from a broad-spectrum of protein substrates

Includes: Supplementary data

Articles

Adipose depot-specific effects of ileal interposition surgery in UCD-T2D rats: unexpected implications for obesity and diabetes

Connie Hung, Casey Bronec, Eleonora Napoli, James Graham, Kimber L. Stanhope, Ilaria Marsilio, Maria Cecilia Giron, Peter J. Havel, Cecilia Giulivi

Biochem J (2018) 475 (3): 649–662.

DOI: https://doi.org/10.1042/BCJ20170899

Published: 14 February 2018

... of the molecular events underlying the effects of IT surgery, we examined the changes in the proteome of four white adipose depots (retroperitoneal, mesenteric, inguinal, and epididymal) and plasma-free fatty acid profile in pre-diabetic rats 1.5 months following IT or sham surgery. The IT-mediated changes were...

View article titled, Adipose depot-specific effects of ileal interposition surgery in UCD-T2D rats: unexpected implications for obesity and diabetes

Includes: Supplementary data

Articles

Engineering oxidative stability in human hemoglobin based on the Hb providence (βK82D) mutation and genetic cross-linking

Michael Brad Strader, Rachel Bangle, Claire J. Parker Siburt, Cornelius L. Varnado, Jayashree Soman, Andres S. Benitez Cardenas, Premila P. Samuel, Eileen W. Singleton, Alvin L. Crumbliss, John S. Olson, Abdu I. Alayash

Biochem J (2017) 474 (24): 4171–4192.

DOI: https://doi.org/10.1042/BCJ20170491

Published: 11 December 2017

... 6 2017 4 10 2017 23 10 2017 25 10 2017 © 2017 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2017 heme hemoglobin modifications oxidation–reduction post-translational proteomics Efforts to develop cell-free adult human...

View article titled, Engineering oxidative stability in human hemoglobin based on the Hb providence (βK82D) mutation and genetic cross-linking

Articles

Redox regulation of a guard cell SNF1-related protein kinase in Brassica napus , an oilseed crop

Mengmeng Zhu, Tong Zhang, Wei Ji, Cecilia Silva-Sanchez, Wen-yuan Song, Sarah M. Assmann, Alice C. Harmon, Sixue Chen

Biochem J (2017) 474 (15): 2585–2599.

DOI: https://doi.org/10.1042/BCJ20170070

Published: 18 July 2017

...Mengmeng Zhu; Tong Zhang; Wei Ji; Cecilia Silva-Sanchez; Wen-yuan Song; Sarah M. Assmann; Alice C. Harmon; Sixue Chen Kinase-mediated phosphorylation is a pivotal regulatory process in stomatal responses to stresses. Through a redox proteomics study, a sucrose non-fermenting 1-related protein...

View article titled, Redox regulation of a guard cell SNF1-related protein kinase in Brassica napus , an oilseed crop

Includes: Supplementary data

Articles

Protein CoAlation: a redox-regulated protein modification by coenzyme A in mammalian cells

In Collection

Awards

Biochem J (2017) 474 (14): 2489–2508.

DOI: https://doi.org/10.1042/BCJ20170129

Published: 11 July 2017

... reveals that protein CoAlation is a widespread post-translational modification which may play an important role in redox regulation under physiological and pathophysiological conditions. coenzyme A metabolic and oxidative stress post-translational modification proteomics Heart perfusion...

View article titled, Protein CoAlation: a redox-regulated protein modification by coenzyme A in mammalian cells

Includes: Supplementary data

Articles

Biochemical and functional characterization of the human tissue kallikrein 9

Panagiota S. Filippou, Sofia Farkona, Davor Brinc, Yijing Yu, Ioannis Prassas, Eleftherios P. Diamandis

Biochem J (2017) 474 (14): 2417–2433.

DOI: https://doi.org/10.1042/BCJ20170174

Published: 06 July 2017

...)] were subjected to further validation. Taken together, our data delineate some functional and biochemical properties of KLK9 for future elucidation of the role of this enzyme in health and disease. biomarkers enzyme kinetics kallikreins proteomics serine protease inhibitors substrate specificity...

View article titled, Biochemical and functional characterization of the human tissue kallikrein 9

Includes: Supplementary data

Articles

Modulation of the specific glutathionylation of mitochondrial proteins in the yeast Saccharomyces cerevisiae under basal and stress conditions

Rachel Gergondey, Camille Garcia, Christophe H. Marchand, Stephane D. Lemaire, Jean-Michel Camadro, Françoise Auchère

Biochem J (2017) 474 (7): 1175–1193.

DOI: https://doi.org/10.1042/BCJ20160927

Published: 15 March 2017

... of glutathionylated proteins in the yeast Saccharomyces cerevisiae and present a detailed proteomic analysis of the targets of protein glutathionylation in cells undergoing constitutive metabolism and after exposure to various stress conditions. This work establishes the physiological importance...

View article titled, Modulation of the specific glutathionylation of mitochondrial proteins in the yeast Saccharomyces cerevisiae under basal and stress conditions

Includes: Supplementary data

Articles

Systematic approaches to identify E3 ligase substrates

Mary Iconomou, Darren N. Saunders

Biochem J (2016) 473 (22): 4083–4101.

DOI: https://doi.org/10.1042/BCJ20160719

Published: 10 November 2016

... has expanded by orders of magnitude to now include a significant proportion of the total proteome — with >23 000 individual modification sites mapping to >4600 proteins [ 65 , 66 ]. In particular, integrated approaches combining genetic models (i.e. modulating E3 ligase expression or activity...

View article titled, Systematic approaches to identify E3 ligase substrates

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

... for matrisome enrichment have been developed, it is currently unknown how the performance of these different methodologies compares in the proteomic identification of matrisome components across multiple tissue types. In the present study, we perform a comparative proteomic assessment of two widely used...

View article titled, Comparative proteomic assessment of matrisome enrichment methodologies

Includes: Supplementary data

Articles

The metalloproteases meprin α and meprin β: unique enzymes in inflammation, neurodegeneration, cancer and fibrosis

Claudia Broder, Christoph Becker-Pauly

Biochem J (2013) 450 (2): 253–264.

DOI: https://doi.org/10.1042/BJ20121751

Published: 15 February 2013

..., inflammation, fibrosis and neurodegenerative diseases. Different animal models, as well as proteomics approaches for the identification of protease substrates, have helped to reveal more precise molecular signalling events mediated by meprin activity, such as activation and release of pro-inflammatory...

View article titled, The metalloproteases meprin α and meprin β: unique enzymes in inflammation, neurodegeneration, cancer and fibrosis

Includes: Multimedia, 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

...Jay J. Thelen; Ján A. Miernyk A newcomer to the -omics era, proteomics, is a broad instrument-intensive research area that has advanced rapidly since its inception less than 20 years ago. Although the ‘wet-bench’ aspects of proteomics have undergone a renaissance with the improvement in protein...

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

Articles

A preliminary characterization of the cytosolic glutathione transferase proteome from Drosophila melanogaster

Chonticha Saisawang, Jantana Wongsantichon, Albert J. Ketterman

Biochem J (2012) 442 (1): 181–190.

DOI: https://doi.org/10.1042/BJ20111747

Published: 27 January 2012

... have obtained the 41 transcripts encoding proteins by RT (reverse transcription)–PCR using RNA template from Drosophila S2 cells, an embryonic cell line. This observation suggests that all of the annotated DmGSTs ( D. melanogaster GSTs) in the proteome are expressed in the late embryonic stages of D...

View article titled, A preliminary characterization of the cytosolic glutathione transferase proteome from Drosophila melanogaster

Includes: Supplementary data

Articles

Silencing of hHS6ST2 inhibits progression of pancreatic cancer through inhibition of Notch signalling

Kai Song, Qin Li, Yong-Bo Peng, Jie Li, Kan Ding, Li-Juan Chen, Cheng-Hao Shao, Li-Jun Zhang, Ping Li

Biochem J (2011) 436 (2): 271–282.

DOI: https://doi.org/10.1042/BJ20110297

Published: 13 May 2011

... fluorescence microscope. angiogenesis epithelial–mesenchymal transition (EMT) heparan sulfate Notch pancreatic cancer proteomics 6-O-sulfotransferase Total RNA was extracted according to the manufacturer's instructions, using RNAiso plus reagent (TaKaRa). First-strand cDNA was synthesized...

View article titled, Silencing of hHS6ST2 inhibits progression of pancreatic cancer through inhibition of Notch signalling

Includes: Supplementary data

Articles

Fatty liver is associated with reduced SIRT3 activity and mitochondrial protein hyperacetylation

Agnieszka A. Kendrick, Mahua Choudhury, Shaikh M. Rahman, Carrie E. McCurdy, Marisa Friederich, Johan L. K. Van Hove, Peter A. Watson, Nicholas Birdsey, Jianjun Bao, David Gius, Michael N. Sack, Enxuan Jing, C. Ronald Kahn, Jacob E. Friedman, Karen R. Jonscher

Biochem J (2011) 433 (3): 505–514.

DOI: https://doi.org/10.1042/BJ20100791

Published: 14 January 2011

... of acetylation or SIRTs in pathogenic hepatic fuel metabolism under nutrient excess is unknown. In the present study, we isolated acetylated proteins from total liver proteome and observed 193 preferentially acetylated proteins in mice fed on an HFD (high-fat diet) compared with controls, including 11 proteins...

View article titled, Fatty liver is associated with reduced SIRT3 activity and mitochondrial protein hyperacetylation

Includes: Supplementary data

Articles

Identification and characterization of PRG-1 as a neuronal calmodulin-binding protein

Hiroshi Tokumitsu, Naoya Hatano, Mitsumasa Tsuchiya, Saki Yurimoto, Tomohito Fujimoto, Naoki Ohara, Ryoji Kobayashi, Hiroyuki Sakagami

Biochem J (2010) 431 (1): 81–91.

DOI: https://doi.org/10.1042/BJ20100637

Published: 14 September 2010

... with and alter the function of numerous proteins. In the present study, using a newly developed functional proteomic screen of rat brain extracts, we identified PRG-1 (plasticity-related gene-1) as a novel CaM target. A CaM-overlay and an immunoprecipitation assay revealed that PRG-1 is capable of binding the Ca...

View article titled, Identification and characterization of PRG-1 as a neuronal calmodulin-binding protein

Articles

Human Ccr4–Not complexes contain variable deadenylase subunits

Nga-Chi Lau, Annemieke Kolkman, Frederik M. A. van Schaik, Klaas W. Mulder, W. W. M. Pim Pijnappel, Albert J. R. Heck, H. Th. Marc Timmers

Biochem J (2009) 422 (3): 443–453.

DOI: https://doi.org/10.1042/BJ20090500

Published: 27 August 2009

... described. Orthologues of the yeast Ccr4–Not components have been identified in human cells including multiple subunits with mRNA deadenylase activity. In the present study, we examine the composition of the human Ccr4–Not complex in an in-depth proteomic approach using stable cell lines expressing tagged...

View article titled, Human Ccr4–Not complexes contain variable deadenylase subunits

Includes: Supplementary data

Articles

Phosphorylated and non-phosphorylated forms of catechol O -methyltransferase in rat liver, brain and other tissues

Anders Øverbye, Per O. Seglen

Biochem J (2009) 417 (2): 535–545.

DOI: https://doi.org/10.1042/BJ20081284

Published: 23 December 2008

.... catechol O -methyltransferase (COMT) N-acetylation phosphorylation proteomics tissue distribution two-dimensional gel electrophoresis α-Cyano-4-hydroxycinnamic acid, ammonium bicarbonate, ammonium persulfate, Tween 20, Trizma base, EDTA, Bromophenol Blue, glycine, TEMED and glycerol were bought...

View article titled, Phosphorylated and non-phosphorylated forms of catechol O -methyltransferase in rat liver, brain and other tissues

Articles

Genetic disruption of calpain correlates with loss of membrane blebbing and differential expression of RhoGDI-1, cofilin and tropomyosin

Anna K. Larsen, René Lametsch, John S. Elce, Jørgen K. Larsen, Bo Thomsen, Martin R. Larsen, Moira A. Lawson, Peter A. Greer, Per Ertbjerg

Biochem J (2008) 411 (3): 657–666.

DOI: https://doi.org/10.1042/BJ20070522

Published: 14 April 2008

... by time-lapse fluorescence microscopy, and a role of calpain in mediating the formation of sporadic membrane blebs was established. Membrane blebbing was significantly reduced in calpain-knockout cells, and genetic rescue fully restored the wild-type phenotype in knockout cells. Proteomic comparison...

View article titled, Genetic disruption of calpain correlates with loss of membrane blebbing and differential expression of RhoGDI-1, cofilin and tropomyosin

Includes: Multimedia, Supplementary data

Articles

SRP-27 is a novel component of the supramolecular signalling complex involved in skeletal muscle excitation–contraction coupling

Christophe Bleunven, Susan Treves, Xia Jinyu, Elisa Leo, Michel Ronjat, Michel De Waard, Georg Kern, Bernhard E. Flucher, Francesco Zorzato

Biochem J (2008) 411 (2): 343–349.

DOI: https://doi.org/10.1042/BJ20070906

Published: 27 March 2008

... zor@unife.it ). 10 7 2007 23 11 2007 26 11 2007 26 11 2007 © The Authors Journal compilation © 2008 Biochemical Society 2008 calcium expressed sequence tag excitation–contraction coupling proteomics ryanodine receptor sarcoplasmic reticulum The skeletal...

View article titled, SRP-27 is a novel component of the supramolecular signalling complex involved in skeletal muscle excitation–contraction coupling

Includes: Supplementary data

Articles

MARCKS-like protein, a membrane protein identified for its expression in developing neural retina, plays a role in regulating retinal cell proliferation

Jing Zhao, Tomonori Izumi, Kazuto Nunomura, Shinya Satoh, Sumiko Watanabe

Biochem J (2007) 408 (1): 51–59.

DOI: https://doi.org/10.1042/BJ20070826

Published: 29 October 2007

... important for the regulation of organogenesis because some may participate in signal transduction. In the present study, we used proteomics to examine the comprehensive protein expression profile of the membrane fraction in the embryonic and adult mouse retina. We purified the retinal membrane fraction...

View article titled, MARCKS-like protein, a membrane protein identified for its expression in developing neural retina, plays a role in regulating retinal cell proliferation

Articles

Biochemical characterization and lysosomal localization of the mannose-6-phosphate protein p76 (hypothetical protein LOC196463)

Anaïs G. Jensen, Magali Chemali, Agnès Chapel, Sylvie Kieffer-Jaquinod, Michel Jadot, Jérôme Garin, Agnès Journet

Biochem J (2007) 402 (3): 449–458.

DOI: https://doi.org/10.1042/BJ20061205

Published: 26 February 2007

... targeting towards the lysosome. This characteristic was exploited to identify novel soluble lysosomal proteins by proteomic analysis of Man6P proteins purified from a human cell line. Among the proteins identified during the course of the latter study [Journet, Chapel, Kieffer, Roux and Garin (2002...

View article titled, Biochemical characterization and lysosomal localization of the mannose-6-phosphate protein p76 (hypothetical protein LOC196463)

Includes: Supplementary data

Articles

Comparing calpain- and caspase-3-mediated degradation patterns in traumatic brain injury by differential proteome analysis

Ming Cheng Liu, Veronica Akle, Wenrong Zheng, Jitendra R. Dave, Frank C. Tortella, Ronald L. Hayes, Kevin K. W. Wang

Biochem J (2006) 394 (3): 715–725.

DOI: https://doi.org/10.1042/BJ20050905

Published: 24 February 2006

... produced αII-spectrin BDPs (breakdown products) following TBI. In the present study, we attempted to identify a comprehensive set of protease substrates (degradome) for calpains and caspase-3. We further hypothesized that the TBI differential proteome is likely to overlap significantly with the calpain...

View article titled, Comparing calpain- and caspase-3-mediated degradation patterns in traumatic brain injury by differential proteome analysis

Includes: Supplementary data

Articles

Induction of the permeability transition and cytochrome c release by 15-deoxy-Δ 12,14 -prostaglandin J 2 in mitochondria

Aimee Landar, Sruti Shiva, Anna-Liisa Levonen, Joo-Yeun Oh, Corinne Zaragoza, Michelle S. Johnson, Victor M. Darley-Usmar

Biochem J (2006) 394 (1): 185–195.

DOI: https://doi.org/10.1042/BJ20051259

Published: 27 January 2006

.... The mechanisms involved are consistent with direct modification of protein thiols in the mitochondrion, rather than secondary formation of reactive oxygen species or lipid peroxidation. Using proteomic analysis in combination with biotinylated 15d-PGJ 2 , we were able to identify 17 potential targets...

View article titled, Induction of the permeability transition and cytochrome c release by 15-deoxy-Δ 12,14 -prostaglandin J 2 in mitochondria

Articles

Identification of a mitochondrial transporter for pyrimidine nucleotides in Saccharomyces cerevisiae : bacterial expression, reconstitution and functional characterization

Carlo Marya Thomas Marobbio, Maria Antonietta Di Noia, Ferdinando Palmieri

Biochem J (2006) 393 (2): 441–446.

DOI: https://doi.org/10.1042/BJ20051284

Published: 23 December 2005

.... Umansky L. Drawid A. Jansen R. Liu Y. Subcellular localization of the yeast proteome Genes Dev. 2002 16 707 719 2 Amutha B. Pain D. Nucleoside diphosphate kinase of Saccharomyces cerevisiae, Ynk1p: localization to the mitochondrial intermembrane space Biochem. J...

View article titled, Identification of a mitochondrial transporter for pyrimidine nucleotides in Saccharomyces cerevisiae : bacterial expression, reconstitution and functional characterization

Articles

Proteomic analysis of mouse kidney peroxisomes: identification of RP2p as a peroxisomal nudix hydrolase with acyl-CoA diphosphatase activity

Rob Ofman, Dave Speijer, René Leen, Ronald J. A. Wanders

Biochem J (2006) 393 (2): 537–543.

DOI: https://doi.org/10.1042/BJ20050893

Published: 23 December 2005

...Rob Ofman; Dave Speijer; René Leen; Ronald J. A. Wanders Proteomic analysis of mouse kidney peroxisomes resulted in the identification of a novel nudix hydrolase designated RP2p, which is encoded by the D7RP2e gene. RP2p consists of 357 amino acids and contains two conserved domains: a nudix...

View article titled, Proteomic analysis of mouse kidney peroxisomes: identification of RP2p as a peroxisomal nudix hydrolase with acyl-CoA diphosphatase activity

Articles

Poly(ADP-ribose) glycohydrolase is a component of the FMRP-associated messenger ribonucleoparticles

Jean-Philippe Gagné, Marie-Ève Bonicalzi, Pierre Gagné, Marie-Ève Ouellet, Michael J. Hendzel, Guy G. Poirier

Biochem J (2005) 392 (3): 499–509.

DOI: https://doi.org/10.1042/BJ20050792

Published: 06 December 2005

... suggests that poly(ADP-ribosyl)ation could have a much broader impact on cellular functions. To elucidate the roles that could be played by PARG, we performed a proteomic identification of PARG-interacting proteins by mass spectrometric analysis of PARG pulled-down proteins. In the present paper, we report...

View article titled, Poly(ADP-ribose) glycohydrolase is a component of the FMRP-associated messenger ribonucleoparticles

Articles

Spotting new DNA damage-responsive chromatin-binding proteins

Benjamin N. WARDLEWORTH, Jessica A. DOWNS

Biochem J (2005) 388 (1): e1.

DOI: https://doi.org/10.1042/BJ20050503

Published: 10 May 2005

... picture of the cellular responses to DNA damage. In this issue of the Biochemical Journal , a proteomics approach was used by Lee et al. to identify proteins that bind to chromatin in a DNA damage-inducible manner. The proteins identified, nucleophosmin, hnRNP C1 (heterogeneous nuclear ribonucleoprotein...

View article titled, Spotting new DNA damage-responsive chromatin-binding proteins

Articles

A proteomics approach for the identification of nucleophosmin and heterogeneous nuclear ribonucleoprotein C1/C2 as chromatin-binding proteins in response to DNA double-strand breaks

Seung Yun LEE, Ji-Hye PARK, Sungsu KIM, Eun-Jung PARK, Yungdae YUN, Jongbum KWON

Biochem J (2005) 388 (1): 7–15.

DOI: https://doi.org/10.1042/BJ20042033

Published: 10 May 2005

... severe to be tolerated. Evidence indicates that, upon generation of DNA DSBs, many nuclear proteins that are involved in DNA repair and checkpoints are recruited to chromatin around the DNA lesions. In the present study we used a proteomics approach to identify DNA-damage-induced chromatin-binding...

View article titled, A proteomics approach for the identification of nucleophosmin and heterogeneous nuclear ribonucleoprotein C1/C2 as chromatin-binding proteins in response to DNA double-strand breaks

Articles

Mechanisms of the interaction of nitroxyl with mitochondria

Sruti SHIVA, Jack H. CRAWFORD, Anup RAMACHANDRAN, Erin K. CEASER, Tess HILLSON, Paul S. BROOKES, Rakesh P. PATEL, Victor M. DARLEY-USMAR

Biochem J (2004) 379 (2): 359–366.

DOI: https://doi.org/10.1042/bj20031758

Published: 15 April 2004

... modification of specific cysteine residues in the proteins. Using a proteomics approach, extensive modification of mitochondrial protein thiols was demonstrated. From these data it is evident that HNO interacts with mitochondria through mechanisms distinct from those of either NO • or peroxynitrite, including...

View article titled, Mechanisms of the interaction of nitroxyl with mitochondria

Articles

14-3-3-affinity purification of over 200 human phosphoproteins reveals new links to regulation of cellular metabolism, proliferation and trafficking

Mercedes POZUELO RUBIO, Kathryn M. GERAGHTY, Barry H. C. WONG, Nicola T. WOOD, David G. CAMPBELL, Nick MORRICE, Carol MACKINTOSH

Biochem J (2004) 379 (2): 395–408.

DOI: https://doi.org/10.1042/bj20031797

Published: 15 April 2004

... 11 2003 26 1 2004 27 1 2004 27 1 2004 The Biochemical Society, London ©2004 2004 affinity chromatography cell proliferation folate metabolism 14-3-3 protein proteomics purine biosynthesis Abbreviations used: BAD, B cl-2/Bcl-X L - a ntagonist, causing cell d...

View article titled, 14-3-3-affinity purification of over 200 human phosphoproteins reveals new links to regulation of cellular metabolism, proliferation and trafficking

Articles

Identification of the human mitochondrial S-adenosylmethionine transporter: bacterial expression, reconstitution, functional characterization and tissue distribution

G. AGRIMI, M. A. Di NOIA, C. M. T. MAROBBIO, G. FIERMONTE, F. M. LASORSA, F. PALMIERI

Biochem J (2004) 379 (1): 183–190.

DOI: https://doi.org/10.1042/bj20031664

Published: 01 April 2004

... reserved for the gene encoding SAMC. 31 10 2003 10 12 2003 16 12 2003 16 12 2003 The Biochemical Society, London ©2004 2004 mitochondria mitochondrial carrier proteomics S -adenosylmethionine carrier transport Abbreviations used: BFP, blue fluorescent...

View article titled, Identification of the human mitochondrial S-adenosylmethionine transporter: bacterial expression, reconstitution, functional characterization and tissue distribution

Articles

Cellular mechanisms of redox cell signalling: role of cysteine modification in controlling antioxidant defences in response to electrophilic lipid oxidation products

Anna-Liisa LEVONEN, Aimee LANDAR, Anup RAMACHANDRAN, Erin K. CEASER, Dale A. DICKINSON, Giuseppe ZANONI, Jason D. MORROW, Victor M. DARLEY-USMAR

Biochem J (2004) 378 (2): 373–382.

DOI: https://doi.org/10.1042/bj20031049

Published: 01 March 2004

... redox cell signalling thiol modification proteomics Abbreviations used: AP-1, activator protein 1; ARE, antioxidant-responsive element; 15-A 2t -isoP, 15-A 2t -isoprostane; BIAM, biotin-conjugated iodoacetamide; cyPG, cyclopentenone prostaglandin; PGJ, prostaglandin J; 15d-PGJ 2 , 15-deoxy-Δ...

View article titled, Cellular mechanisms of redox cell signalling: role of cysteine modification in controlling antioxidant defences in response to electrophilic lipid oxidation products

Articles

Bioinformatic analysis of the nucleolus

Anthony K. L. LEUNG, Jens S. ANDERSEN, Matthias MANN, Angus I. LAMOND

Biochem J (2003) 376 (3): 553–569.

DOI: https://doi.org/10.1042/bj20031169

Published: 15 December 2003

... of the human nucleolar proteome has been expanded dramatically by the two recent MS studies on isolated nucleoli from HeLa cells [Andersen, Lyon, Fox, Leung, Lam, Steen, Mann and Lamond (2002) Curr. Biol. 12 , 1–11; Scherl, Coute, Deon, Calle, Kindbeiter, Sanchez, Greco, Hochstrasser and Diaz (2002) Mol. Biol...

View article titled, Bioinformatic analysis of the nucleolus

Includes: Multimedia, Supplementary data

Articles

Okadaic acid-induced, naringin-sensitive phosphorylation of glycine N-methyltransferase in isolated rat hepatocytes

Michael T. N. MØLLER, Hamid R. SAMARI, Monica FENGSRUD, Per E. STRØMHAUG, Anne C. ØSTVOLD, Per O. SEGLEN

Biochem J (2003) 373 (2): 505–513.

DOI: https://doi.org/10.1042/bj20030502

Published: 15 July 2003

... phosphatase inhibitor okadaic acid, was found to induce an overphosphorylation of GNMT, as shown by proteomic analysis. The analysis comprised two-dimensional gel electrophoretic separation of 32 P-labelled phosphoproteins and identification of individual protein spots by matrix-assisted laser-desorption...

View article titled, Okadaic acid-induced, naringin-sensitive phosphorylation of glycine N-methyltransferase in isolated rat hepatocytes

Articles

Extensive temporally regulated reorganization of the lipid raft proteome following T-cell antigen receptor triggering

Luca BINI, Sonia PACINI, Sabrina LIBERATORI, Silvia VALENSIN, Michela PELLEGRINI, Roberto RAGGIASCHI, Vitaliano PALLINI, Cosima T. BALDARI

Biochem J (2003) 369 (2): 301–309.

DOI: https://doi.org/10.1042/bj20020503

Published: 15 January 2003

...Luca BINI; Sonia PACINI; Sabrina LIBERATORI; Silvia VALENSIN; Michela PELLEGRINI; Roberto RAGGIASCHI; Vitaliano PALLINI; Cosima T. BALDARI Signalling by immunoreceptors is orchestrated at specific plasma membrane microdomains, referred to as lipid rafts. Here we present a proteomics approach...

View article titled, Extensive temporally regulated reorganization of the lipid raft proteome following T-cell antigen receptor triggering

Articles

A method for detection of overoxidation of cysteines: peroxiredoxins are oxidized in vivo at the active-site cysteine during oxidative stress

Elsa WAGNER, Sylvie LUCHE, Lucia PENNA, Mireille CHEVALLET, Alain van DORSSELAER, Emmanuelle LEIZE-WAGNER, Thierry RABILLOUD

Biochem J (2002) 366 (3): 777–785.

DOI: https://doi.org/10.1042/bj20020525

Published: 15 September 2002

... damage to the cells. 1 To whom correspondence should be addressed (e-mail Thierry.Rabilloud@cea.fr ). 4 4 2002 30 5 2002 11 6 2002 11 6 2002 The Biochemical Society, London ©2002 2002 cysteic acid mass spectrometry (MS) post-translational modification proteomics...

View article titled, A method for detection of overoxidation of cysteines: peroxiredoxins are oxidized in vivo at the active-site cysteine during oxidative stress

Articles

Molecular and immunological characterization and IgE epitope mapping of Pen n 18, a major allergen of Penicillium notatum

Chia-Jung YU, Yen-Ming CHEN, Song-Nan SU, Farhad FOROUHAR, Shu-Hua LEE, Lu-Ping CHOW

Biochem J (2002) 363 (3): 707–715.

DOI: https://doi.org/10.1042/bj3630707

Published: 24 April 2002

... Nucleotide Sequence Database under accession number AF264027. 12 10 2001 15 1 2002 1 2 2002 The Biochemical Society, London ©2002 2002 IgE-binding epitope proteomics vacuolar serine protease Abbreviations used: MALDI-TOF MS, matrix-assisted laser-desorption...

View article titled, Molecular and immunological characterization and IgE epitope mapping of Pen n 18, a major allergen of Penicillium notatum

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