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Articles

Are fibrinaloid microclots a cause of autoimmunity in Long Covid and other post-infection diseases?

Douglas B. Kell, Etheresia Pretorius
Journal: Biochemical Journal
Biochem J (2023) 480 (15): 1217–1240.
https://doi.org/10.1042/BCJ20230241
Published: 16 August 2023
View article titled, Are fibrinaloid microclots a cause of autoimmunity in Long Covid and other post-infection diseases?
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Articles

Protein targeting by the itaconate family in immunity and inflammation

Emily A. Day, Luke A.J. O'Neill
Journal: Biochemical Journal
Biochem J (2022) 479 (24): 2499–2510.
https://doi.org/10.1042/BCJ20220364
Published: 22 December 2022
View article titled, Protein targeting by the itaconate family in immunity and inflammation
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Articles

Identification of ester-linked ubiquitylation sites during TLR7 signalling increases the number of inter-ubiquitin linkages from 8 to 12

Elisha H. McCrory, Vyacheslav Akimov, Philip Cohen, Blagoy Blagoev
Journal: Biochemical Journal
Biochem J (2022) 479 (23): 2419–2431.
https://doi.org/10.1042/BCJ20220510
Published: 07 December 2022
View article titled, Identification of ester-linked ubiquitylation sites during TLR7 signalling increases the number of inter-ubiquitin linkages from 8 to 12
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Includes: Supplementary data
Articles

Immunoregulatory signal networks and tumor immune evasion mechanisms: insights into therapeutic targets and agents in clinical development

Qian Wei, Kjetil Taskén
Journal: Biochemical Journal
Biochem J (2022) 479 (20): 2219–2260.
https://doi.org/10.1042/BCJ20210233
Published: 28 October 2022
View article titled, Immunoregulatory signal networks and tumor immune evasion mechanisms: insights into therapeutic targets and agents in clinical development
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Articles

Co-ordinated control of the ADP-heptose/ALPK1 signalling network by the E3 ligases TRAF6, TRAF2/c-IAP1 and LUBAC

Tom Snelling, Natalia Shpiro, Robert Gourlay, Frederic Lamoliatte, Philip Cohen
Journal: Biochemical Journal
Biochem J (2022) 479 (20): 2195–2216.
https://doi.org/10.1042/BCJ20220401
Published: 21 October 2022
View article titled, Co-ordinated control of the ADP-heptose/ALPK1 signalling network by the E3 ligases TRAF6, TRAF2/c-IAP1 and LUBAC
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Includes: Supplementary data
Articles

Mechanisms of TNF-independent RIPK3-mediated cell death

Bart Tummers, Douglas R. Green
Journal: Biochemical Journal
Biochem J (2022) 479 (19): 2049–2062.
https://doi.org/10.1042/BCJ20210724
Published: 14 October 2022
View article titled, Mechanisms of TNF-independent RIPK3-mediated cell death
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Articles

TAK1 protein kinase activity is required for TLR signalling and cytokine production in myeloid cells

Melissa Rodrigues, Tsvetana Petrova, Brendan Tibbs, J. Simon C. Arthur, Philip Cohen
Journal: Biochemical Journal
Biochem J (2022) 479 (17): 1891–1907.
https://doi.org/10.1042/BCJ20220314
Published: 16 September 2022
View article titled, TAK1 protein kinase activity is required for TLR signalling and cytokine production in myeloid cells
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Includes: Supplementary data
Articles

Cell death in skin function, inflammation, and disease

In Collection
Cell death and survival
Holly Anderton, Suhaib Alqudah
Journal: Biochemical Journal
Biochem J (2022) 479 (15): 1621–1651.
https://doi.org/10.1042/BCJ20210606
Published: 05 August 2022
View article titled, Cell death in skin function, inflammation, and disease
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Articles

Endogenous glutamine is rate-limiting for anti-CD3 and anti-CD28 induced CD4 + T-cell proliferation and glycolytic activity under hypoxia and normoxia

Jonas A. Wik, Azazul Chowdhury, Shrikant Kolan, Nasser E. Bastani, Gaoyang Li, Kazi Alam, Franco Grimolizzi, Bjørn S. Skålhegg
Journal: Biochemical Journal
Biochem J (2022) 479 (11): 1221–1235.
https://doi.org/10.1042/BCJ20220144
Published: 13 June 2022
View article titled, Endogenous glutamine is rate-limiting for anti-CD3 and anti-CD28 induced CD4 + T-cell proliferation and glycolytic activity under hypoxia and normoxia
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Includes: Supplementary data
Articles

No longer married to inflammasome signaling: the diverse interacting pathways leading to pyroptotic cell death

In Collection
Cell death and survival
Ashley Weir, James E. Vince
Journal: Biochemical Journal
Biochem J (2022) 479 (10): 1083–1102.
https://doi.org/10.1042/BCJ20210711
Published: 24 May 2022
View article titled, No longer married to inflammasome signaling: the diverse interacting pathways leading to pyroptotic cell death
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Articles

Sialylation-dependent pharmacokinetics and differential complement pathway inhibition are hallmarks of CR1 activity in vivo

Sandra Wymann, Marcel Mischnik, David Leong, Subhajit Ghosh, Xiahui Tan, Helen Cao, Benjamin Kuehnemuth, Glenn A. Powers, Partho Halder, Mitchell J. de Souza, Hannah S. James, Vesna Tomasetig, Holger Lind, Paolo Rossato, Catherine M. Owczarek, Saw Yen Ow, Steven K. Dower, Adriana Baz Morelli, Tony Rowe, Matthew P. Hardy
Journal: Biochemical Journal
Biochem J (2022) 479 (9): 1007–1030.
https://doi.org/10.1042/BCJ20220054
Published: 13 May 2022
View article titled, Sialylation-dependent pharmacokinetics and differential complement pathway inhibition are hallmarks of CR1 activity in vivo
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Includes: Supplementary data
Articles

RIP1 post-translational modifications

In Collection
Cell death and survival
Eugene Varfolomeev, Domagoj Vucic
Journal: Biochemical Journal
Biochem J (2022) 479 (9): 929–951.
https://doi.org/10.1042/BCJ20210725
Published: 06 May 2022
View article titled, RIP1 post-translational modifications
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Articles

Activation and manipulation of inflammasomes and pyroptosis during bacterial infections

In Collection
Cell death and survival
Elliott M. Bernard, Petr Broz
Journal: Biochemical Journal
Biochem J (2022) 479 (7): 867–882.
https://doi.org/10.1042/BCJ20220051
Published: 19 April 2022
View article titled, Activation and manipulation of inflammasomes and pyroptosis during bacterial infections
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Articles

Immunothrombosis and the molecular control of tissue factor by pyroptosis: prospects for new anticoagulants

Tristram A. J. Ryan, Roger J. S. Preston, Luke A. J. O'Neill
Journal: Biochemical Journal
Biochem J (2022) 479 (6): 731–750.
https://doi.org/10.1042/BCJ20210522
Published: 28 March 2022
View article titled, Immunothrombosis and the molecular control of tissue factor by pyroptosis: prospects for new anticoagulants
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Articles

Regulation of the release of damage-associated molecular patterns from necroptotic cells

In Collection
Cell death and survival
Hiroyasu Nakano, Shin Murai, Kenta Moriwaki
Journal: Biochemical Journal
Biochem J (2022) 479 (5): 677–685.
https://doi.org/10.1042/BCJ20210604
Published: 16 March 2022
View article titled, Regulation of the release of damage-associated molecular patterns from necroptotic cells
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Includes: Supplementary data
Articles

Programmed cell death: the pathways to severe COVID-19?

In Collection
Cell death and survival , Coronavirus
Stefanie M. Bader, James P. Cooney, Marc Pellegrini, Marcel Doerflinger
Journal: Biochemical Journal
Biochem J (2022) 479 (5): 609–628.
https://doi.org/10.1042/BCJ20210602
Published: 04 March 2022
View article titled, Programmed cell death: the pathways to severe COVID-19?
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Articles

Adaptor protein 3BP2 regulates dectin-1-mediated cellular signalling to induce cytokine expression and NF-κB activation

Kazuyasu Chihara, Yuri Chihara, Kenji Takeuchi, Kiyonao Sada
Journal: Biochemical Journal
Biochem J (2022) 479 (4): 503–523.
https://doi.org/10.1042/BCJ20210707
Published: 23 February 2022
View article titled, Adaptor protein 3BP2 regulates dectin-1-mediated cellular signalling to induce cytokine expression and NF-κB activation
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Includes: Supplementary data
Articles

A central role for amyloid fibrin microclots in long COVID/PASC: origins and therapeutic implications

In Collection
Coronavirus
Douglas B. Kell, Gert Jacobus Laubscher, Etheresia Pretorius
Journal: Biochemical Journal
Biochem J (2022) 479 (4): 537–559.
https://doi.org/10.1042/BCJ20220016
Published: 23 February 2022
View article titled, A central role for amyloid fibrin microclots in long COVID/PASC: origins and therapeutic implications
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Articles

Proteomic analysis in primary T cells reveals IL-7 alters T cell receptor thresholding via CYTIP/cytohesin/LFA-1 localisation and activation

Rayner M. L. Queiroz, Siân C. Piper, Johanna S. Rees, Sam Strickson, Emmanuel Briend, Choon Pei Low, G. John Ferguson, Kathryn S. Lilley, Antony P. Jackson, Donna K. Finch
Journal: Biochemical Journal
Biochem J (2022) 479 (3): 225–243.
https://doi.org/10.1042/BCJ20210313
Published: 04 February 2022
View article titled, Proteomic analysis in primary T cells reveals IL-7 alters T cell receptor thresholding via CYTIP/cytohesin/LFA-1 localisation and activation
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Includes: Supplementary data
Articles

TAT–RHIM: a more complex issue than expected

In Collection
Cell death and survival
Benedikt Kolbrink, Theresa Riebeling, Nikolas K. Teiwes, Claudia Steinem, Hubert Kalbacher, Ulrich Kunzendorf, Stefan Krautwald
Journal: Biochemical Journal
Biochem J (2022) 479 (3): 259–272.
https://doi.org/10.1042/BCJ20210677
Published: 04 February 2022
View article titled, TAT–RHIM: a more complex issue than expected
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Articles

IKKα plays a major role in canonical NF-κB signalling in colorectal cells

In Collection
Cell death and survival
Jack A. Prescott, Kathryn Balmanno, Jennifer P. Mitchell, Hanneke Okkenhaug, Simon J. Cook
Journal: Biochemical Journal
Biochem J (2022) 479 (3): 305–325.
https://doi.org/10.1042/BCJ20210783
Published: 04 February 2022
View article titled, IKKα plays a major role in canonical NF-κB signalling in colorectal cells
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Includes: Supplementary data
Articles

Systems approaches to investigate the role of NF-κB signaling in aging

In Collection
Towards systems biochemistry
Masatoshi Haga, Mariko Okada
Journal: Biochemical Journal
Biochem J (2022) 479 (2): 161–183.
https://doi.org/10.1042/BCJ20210547
Published: 28 January 2022
View article titled, Systems approaches to investigate the role of NF-κB signaling in aging
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Articles

Mechanistic diversity in MHC class I antigen recognition

Camila R. R. Barbosa, Justin Barton, Adrian J. Shepherd, Michele Mishto
Journal: Biochemical Journal
Biochem J (2021) 478 (24): 4187–4202.
https://doi.org/10.1042/BCJ20200910
Published: 23 December 2021
View article titled, Mechanistic diversity in MHC class I antigen recognition
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Articles

NAD + -consuming enzymes in immune defense against viral infection

Jialin Shang, Michael R. Smith, Ananya Anmangandla, Hening Lin
Journal: Biochemical Journal
Biochem J (2021) 478 (23): 4071–4092.
https://doi.org/10.1042/BCJ20210181
Published: 06 December 2021
View article titled, NAD + -consuming enzymes in immune defense against viral infection
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Articles

Fetuin-A regulates adipose tissue macrophage content and activation in insulin resistant mice through MCP-1 and iNOS: involvement of IFNγ-JAK2-STAT1 pathway

Dipanjan Chattopadhyay, Snehasis Das, Suktara Guria, Soumyadeep Basu, Sutapa Mukherjee
Journal: Biochemical Journal
Biochem J (2021) 478 (22): 4027–4043.
https://doi.org/10.1042/BCJ20210442
Published: 26 November 2021
View article titled, Fetuin-A regulates adipose tissue macrophage content and activation in insulin resistant mice through MCP-1 and iNOS: involvement of IFNγ-JAK2-STAT1 pathway
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Includes: Supplementary data
Articles

Regulation of Tim-3 function by binding to phosphatidylserine

Lawrence P. Kane
Journal: Biochemical Journal
Biochem J (2021) 478 (22): 3999–4004.
https://doi.org/10.1042/BCJ20210652
Published: 23 November 2021
View article titled, Regulation of Tim-3 function by binding to phosphatidylserine
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Articles

Phosphatidylserine binding directly regulates TIM-3 function

Courtney M. Smith, Alice Li, Nithya Krishnamurthy, Mark A. Lemmon
Journal: Biochemical Journal
Biochem J (2021) 478 (17): 3331–3349.
https://doi.org/10.1042/BCJ20210425
Published: 14 September 2021
View article titled, Phosphatidylserine binding directly regulates TIM-3 function
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Includes: Supplementary data
Articles

Lactate cross-talk in host–pathogen interactions

Alba Llibre, Frances S. Grudzinska, Matthew K. O'Shea, Darragh Duffy, David R. Thickett, Claudio Mauro, Aaron Scott
Journal: Biochemical Journal
Biochem J (2021) 478 (17): 3157–3178.
https://doi.org/10.1042/BCJ20210263
Published: 07 September 2021
View article titled, Lactate cross-talk in host–pathogen interactions
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Articles

TFEB phosphorylation on Serine 211 is induced by autophagy in human synovial fibroblasts and by p62/SQSTM1 overexpression in HEK293 cells

Biserka Relic, Celine Deroyer, Olivier Malaise, Zelda Plener, Philippe Gillet, Dominique de Seny, Michel G. Malaise
Journal: Biochemical Journal
Biochem J (2021) 478 (16): 3145–3155.
https://doi.org/10.1042/BCJ20210174
Published: 27 August 2021
View article titled, TFEB phosphorylation on Serine 211 is induced by autophagy in human synovial fibroblasts and by p62/SQSTM1 overexpression in HEK293 cells
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Articles

Manipulating the exposome to enable better ageing

Paul G. Shiels, Johanna Painer, Barbara Natterson-Horowitz, Richard J. Johnson, Jaime J. Miranda, Peter Stenvinkel
Journal: Biochemical Journal
Biochem J (2021) 478 (14): 2889–2898.
https://doi.org/10.1042/BCJ20200958
Published: 28 July 2021
View article titled, Manipulating the exposome to enable better ageing
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Articles

Importance of tyrosine phosphorylation for transmembrane signaling in plants

Henning Mühlenbeck, Kyle W. Bender, Cyril Zipfel
Journal: Biochemical Journal
Biochem J (2021) 478 (14): 2759–2774.
https://doi.org/10.1042/BCJ20210202
Published: 23 July 2021
View article titled, Importance of tyrosine phosphorylation for transmembrane signaling in plants
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Articles

Inhibitory feedback control of NF-κB signalling in health and disease

Jack A. Prescott, Jennifer P. Mitchell, Simon J. Cook
Journal: Biochemical Journal
Biochem J (2021) 478 (13): 2619–2664.
https://doi.org/10.1042/BCJ20210139
Published: 16 July 2021
View article titled, Inhibitory feedback control of NF-κB signalling in health and disease
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Articles

FATP4 inactivation in cultured macrophages attenuates M1- and ER stress-induced cytokine release via a metabolic shift towards triacylglycerides

Yuling Zhang, Ning Wu, Hongying Gan-Schreier, Feng Xu, Sabine Tuma-Kellner, Simone Staffer, Jessica Seeßle, Uta Merle, Walee Chamulitrat
Journal: Biochemical Journal
Biochem J (2021) 478 (10): 1861–1877.
https://doi.org/10.1042/BCJ20210155
Published: 18 May 2021
View article titled, FATP4 inactivation in cultured macrophages attenuates M1- and ER stress-induced cytokine release via a metabolic shift towards triacylglycerides
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Includes: Supplementary data
Articles

Opposing forces fight over the same ground to regulate interferon signaling

William L. Blalock
Journal: Biochemical Journal
Biochem J (2021) 478 (10): 1853–1859.
https://doi.org/10.1042/BCJ20210110
Published: 18 May 2021
View article titled, Opposing forces fight over the same ground to regulate interferon signaling
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Articles

Tick–human interactions: from allergic klendusity to the α-Gal syndrome

Alejandro Cabezas-Cruz, Adnan Hodžić, Lourdes Mateos-Hernández, Marinela Contreras, José de la Fuente
Journal: Biochemical Journal
Biochem J (2021) 478 (9): 1783–1794.
https://doi.org/10.1042/BCJ20200915
Published: 14 May 2021
View article titled, Tick–human interactions: from allergic klendusity to the α-Gal syndrome
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Articles

Anti-glycan antibodies: roles in human disease

J. Sebastian Temme, Dorothy L. Butler, Jeffrey C. Gildersleeve
Journal: Biochemical Journal
Biochem J (2021) 478 (8): 1485–1509.
https://doi.org/10.1042/BCJ20200610
Published: 21 April 2021
View article titled, Anti-glycan antibodies: roles in human disease
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Articles

T cells: a dedicated effector kinase pathways for every trait?

Kriti Bahl, Jeroen P. Roose
Journal: Biochemical Journal
Biochem J (2021) 478 (6): 1303–1307.
https://doi.org/10.1042/BCJ20210006
Published: 23 March 2021
View article titled, T cells: a dedicated effector kinase pathways for every trait?
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Articles

Reprogramming the tumor metastasis cascade by targeting galectin-driven networks

Ramiro M. Perrotta, Camila A. Bach, Mariana Salatino, Gabriel A. Rabinovich
Journal: Biochemical Journal
Biochem J (2021) 478 (3): 597–617.
https://doi.org/10.1042/BCJ20200167
Published: 12 February 2021
View article titled, Reprogramming the tumor metastasis cascade by targeting galectin-driven networks
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Articles

Opposite actions of two dsRNA-binding proteins PACT and TRBP on RIG-I mediated signaling

Lauren S. Vaughn, Evelyn Chukwurah, Rekha C. Patel
Journal: Biochemical Journal
Biochem J (2021) 478 (3): 493–510.
https://doi.org/10.1042/BCJ20200987
Published: 05 February 2021
View article titled, Opposite actions of two dsRNA-binding proteins PACT and TRBP on RIG-I mediated signaling
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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
Journal: Biochemical Journal
Biochem J (2021) 478 (1): 79–98.
https://doi.org/10.1042/BCJ20200661
Published: 13 January 2021
View article titled, Extracellular signal-regulated kinase (ERK) pathway control of CD8 + T cell differentiation
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Includes: Supplementary data
Articles

Structure, metabolism and biological functions of steryl glycosides in mammals

Michio Shimamura
Journal: Biochemical Journal
Biochem J (2020) 477 (21): 4243–4261.
https://doi.org/10.1042/BCJ20200532
Published: 13 November 2020
View article titled, Structure, metabolism and biological functions of steryl glycosides in mammals
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Articles

Heat shock protein 90 inhibitors suppress pyroptosis in THP-1 cells

Zhou Zhou, Xiuzhen Li, Yisong Qian, Cynthia Liu, Xiaotian Huang, Mingui Fu
Journal: Biochemical Journal
Biochem J (2020) 477 (20): 3923–3934.
https://doi.org/10.1042/BCJ20200351
Published: 23 October 2020
View article titled, Heat shock protein 90 inhibitors suppress pyroptosis in THP-1 cells
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Articles

Molecular and structural basis for Lewis glycan recognition by a cancer-targeting antibody

Caroline Soliman, Andrew J. Guy, Jia Xin Chua, Mireille Vankemmelbeke, Richard S. McIntosh, Sarah Eastwood, Vi Khanh Truong, Aaron Elbourne, Ian Spendlove, Lindy G. Durrant, Paul A. Ramsland
Journal: Biochemical Journal
Biochem J (2020) 477 (17): 3219–3235.
https://doi.org/10.1042/BCJ20200454
Published: 10 September 2020
View article titled, Molecular and structural basis for Lewis glycan recognition by a cancer-targeting antibody
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Includes: Supplementary data
Articles

Pro4 prolyl peptide bond isomerization in human galectin-7 modulates the monomer-dimer equilibrum to affect function

Michelle C. Miller, Irina V. Nesmelova, Vladimir A. Daragan, Hans Ippel, Malwina Michalak, Aurelio Dregni, Herbert Kaltner, Jürgen Kopitz, Hans-Joachim Gabius, Kevin H. Mayo
Journal: Biochemical Journal
Biochem J (2020) 477 (17): 3147–3165.
https://doi.org/10.1042/BCJ20200499
Published: 04 September 2020
View article titled, Pro4 prolyl peptide bond isomerization in human galectin-7 modulates the monomer-dimer equilibrum to affect function
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Includes: Supplementary data
Articles

ALG2 Influences T cell apoptosis by regulating FASLG intracellular transportation

Wangsheng Ji, Yang Xin, Lianfei Zhang, Xinqi Liu
Journal: Biochemical Journal
Biochem J (2020) 477 (16): 3105–3121.
https://doi.org/10.1042/BCJ20200028
Published: 28 August 2020
View article titled, ALG2 Influences T cell apoptosis by regulating FASLG intracellular transportation
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Articles

Membrane-associated RING-CH (MARCH) proteins down-regulate cell surface expression of the interleukin-6 receptor alpha chain (IL6Rα)

Jeffrey J. Babon, Dina Stockwell, Ladina DiRago, Jian-Guo Zhang, Artem Laktyushin, Jose Villadangos, Alan Ching, Satoshi Ishido, Douglas J. Hilton, Warren S. Alexander, Nicos A. Nicola
Journal: Biochemical Journal
Biochem J (2019) 476 (19): 2869–2882.
https://doi.org/10.1042/BCJ20190577
Published: 11 October 2019
View article titled, Membrane-associated RING-CH (MARCH) proteins down-regulate cell surface expression of the interleukin-6 receptor alpha chain (IL6Rα)
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Includes: Supplementary data
Articles

Gelatinase B/matrix metalloproteinase-9 and other neutrophil proteases switch off interleukin-2 activity

Vasily Rybakin, Melissa Stas, Estefania Ugarte-Berzal, Sam Noppen, Jennifer Vandooren, Ilse Van Aelst, Sandra Liekens, Paul Proost, Ghislain Opdenakker
Journal: Biochemical Journal
Biochem J (2019) 476 (15): 2191–2208.
https://doi.org/10.1042/BCJ20180382
Published: 09 August 2019
View article titled, Gelatinase B/matrix metalloproteinase-9 and other neutrophil proteases switch off interleukin-2 activity
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Includes: Supplementary data
Articles

Signalling circuits that direct early B-cell development

Georg Petkau, Martin Turner
Journal: Biochemical Journal
Biochem J (2019) 476 (5): 769–778.
https://doi.org/10.1042/BCJ20180565
Published: 06 March 2019
View article titled, Signalling circuits that direct early B-cell development
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Articles

Potential role of a series of lysine-/leucine-rich antimicrobial peptide in inhibiting lipopolysaccharide-induced inflammation

Weibing Dong, Xin Zhu, Xuan Zhou, Ying Yang, Xin Yan, Li Sun, Dejing Shang
Journal: Biochemical Journal
Biochem J (2018) 475 (22): 3687–3706.
https://doi.org/10.1042/BCJ20180483
Published: 30 November 2018
View article titled, Potential role of a series of lysine-/leucine-rich antimicrobial peptide in inhibiting lipopolysaccharide-induced inflammation
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Includes: Supplementary data
Articles

DDX3 directly facilitates IKKα activation and regulates downstream signalling pathways

Anthony Fullam, Lili Gu, Yvette Höhn, Martina Schröder
Journal: Biochemical Journal
Biochem J (2018) 475 (22): 3595–3607.
https://doi.org/10.1042/BCJ20180163
Published: 20 November 2018
View article titled, DDX3 directly facilitates IKKα activation and regulates downstream signalling pathways
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Includes: Supplementary data