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Articles

Distinct phosphorylation signals drive acceptor versus free ubiquitin chain targeting by parkin

Karen M. Dunkerley, Anne C. Rintala-Dempsey, Giulia Salzano, Roya Tadayon, Dania Hadi, Kathryn R. Barber, Helen Walden, Gary S. Shaw

Biochem J (2022) 479 (6): 751–766.

DOI: https://doi.org/10.1042/BCJ20210741

Published: 28 March 2022

... structure protein–protein interactions ubiquitin ubiquitin ligases Parkinson's disease (PD) affects ∼1% of the world's population [ 1 ]. Though age of onset and disease severity can vary greatly among patients, there is increasing evidence that implicates mitochondrial dysfunction as a major...

View article titled, Distinct phosphorylation signals drive acceptor versus free ubiquitin chain targeting by parkin

Includes: Supplementary data

Articles

α-Helix stabilization by co-operative side chain charge-reinforced interactions to phosphoserine in a basic kinase-substrate motif

Matthew Batchelor, Robert S. Dawber, Andrew J. Wilson, Richard Bayliss

Biochem J (2022) 479 (5): 687–700.

DOI: https://doi.org/10.1042/BCJ20210812

Published: 16 March 2022

...Matthew Batchelor; Robert S. Dawber; Andrew J. Wilson; Richard Bayliss How cellular functions are regulated through protein phosphorylation events that promote or inhibit protein–protein interactions (PPIs) is key to understanding regulatory molecular mechanisms. Whilst phosphorylation can...

View article titled, α-Helix stabilization by co-operative side chain charge-reinforced interactions to phosphoserine in a basic kinase-substrate motif

Includes: Supplementary data

Articles

Reconstitution of the DTX3L–PARP9 complex reveals determinants for high-affinity heterodimerization and multimeric assembly

Yashwanth Ashok, Carlos Vela-Rodríguez, Chunsong Yang, Heli I. Alanen, Fan Liu, Bryce M. Paschal, Lari Lehtiö

Biochem J (2022) 479 (3): 289–304.

DOI: https://doi.org/10.1042/BCJ20210722

Published: 04 February 2022

... 2022 adenosine diphosphate ribose post-translational modification protein–protein interactions ubiquitin ligases Ubiquitination is a reversible post-translational protein modification that results in the addition of a small protein called ubiquitin (Ub) to lysine residues in target...

View article titled, Reconstitution of the DTX3L–PARP9 complex reveals determinants for high-affinity heterodimerization and multimeric assembly

Includes: Supplementary data

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

... 2022 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2022 protein–protein interactions proteomics proximity ligation assay transcription factor T-box ( Tbx ) genes encode a large family of proteins that are characterized by a conserved DNA...

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

Includes: Supplementary data

Articles

Orchestrating serine/threonine phosphorylation and elucidating downstream effects by short linear motifs

Johanna Kliche, Ylva Ivarsson

Biochem J (2022) 479 (1): 1–22.

DOI: https://doi.org/10.1042/BCJ20200714

Published: 06 January 2022

...Johanna Kliche; Ylva Ivarsson Cellular function is based on protein–protein interactions. A large proportion of these interactions involves the binding of short linear motifs (SLiMs) by folded globular domains. These interactions are regulated by post-translational modifications...

View article titled, Orchestrating serine/threonine phosphorylation and elucidating downstream effects by short linear motifs

Articles

Quantitative characterization of tetraspanin 8 homointeractions in the plasma membrane

Daniel Wirth, Ece Özdemir, Christopher King, Lena Ahlswede, Dirk Schneider, Kalina Hristova

Biochem J (2021) 478 (19): 3643–3654.

DOI: https://doi.org/10.1042/BCJ20210459

Published: 14 October 2021

... regulator of cell signaling. Correspondence: Kalina Hristova ( kh@jhu.edu ) 18 6 2021 13 9 2021 15 9 2021 15 9 2021 © 2021 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2021 membrane proteins protein-protein interactions...

View article titled, Quantitative characterization of tetraspanin 8 homointeractions in the plasma membrane

Articles

SMCHD1's ubiquitin-like domain is required for N-terminal dimerization and chromatin localization

Alexandra D. Gurzau, Christopher R. Horne, Yee-Foong Mok, Megan Iminitoff, Tracy A. Willson, Samuel N. Young, Marnie E. Blewitt, James M. Murphy

Biochem J (2021) 478 (13): 2555–2569.

DOI: https://doi.org/10.1042/BCJ20210278

Published: 09 July 2021

... of Melbourne in an all-inclusive Read & Publish pilot with Portland Press and the Biochemical Society under a transformative agreement with CAUL. GHKL ATPase nucleic acid binding proteins protein–protein interactions SMC proteins UBL domain In 2008, SMCHD1 was identified...

View article titled, SMCHD1's ubiquitin-like domain is required for N-terminal dimerization and chromatin localization

Includes: Supplementary data

Articles

Identification of the contact region responsible for the formation of the homomeric CYP1A2•CYP1A2 complex

Aratrika Saha, J. Patrick Connick, James R. Reed, Charles S. Lott, Wayne L. Backes

Biochem J (2021) 478 (11): 2163–2178.

DOI: https://doi.org/10.1042/BCJ20210269

Published: 11 June 2021

... CYP1A2 cytochrome p450 NADPH-cytochrome P450 reductase protein–protein interactions Relative protein expression levels were measured using a spectrofluorometer. The photometric measurements of the GFP 2 - and Rluc-tagged proteins were compared with the measurements of a cell transfected...

View article titled, Identification of the contact region responsible for the formation of the homomeric CYP1A2•CYP1A2 complex

Includes: Supplementary data

Articles

On the specificity of protein–protein interactions in the context of disorder

Kaare Teilum, Johan G. Olsen, Birthe B. Kragelund

Biochem J (2021) 478 (11): 2035–2050.

DOI: https://doi.org/10.1042/BCJ20200828

Published: 08 June 2021

..., interpret and speak about their specificity. intrinsically disordered proteins multispecificity multivalency protein–protein interactions specificity structural biology Correspondence: Birthe B. Kragelund ( bbk@bio.ku.dk ) 27 3 2021 14 5 2021 17 5 2021 © 2021...

View article titled, On the specificity of protein–protein interactions in the context of disorder

Articles

Unique C-terminal extension and interactome of Mycobacterium tuberculosis GlmU impacts its in vivo function and the survival of the pathogen

Meetu Agarwal, Vijay Soni, Suresh Kumar, Biplab Singha, Vinay Kumar Nandicoori

Biochem J (2021) 478 (11): 2081–2099.

DOI: https://doi.org/10.1042/BCJ20210170

Published: 08 June 2021

... Medicine, Jamia Hamdard University, New Delhi 110062, India 19 3 2021 1 5 2021 6 5 2021 6 5 2021 © 2021 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2021 cell wall synthesis enzyme activity GlmU protein–protein interactions...

View article titled, Unique C-terminal extension and interactome of Mycobacterium tuberculosis GlmU impacts its in vivo function and the survival of the pathogen

Includes: Supplementary data

Articles

Structural basis of the human Scribble–Vangl2 association in health and disease

Jing Yuan How, Rebecca K. Stephens, Krystle Y.B. Lim, Patrick O. Humbert, Marc Kvansakul

Biochem J (2021) 478 (7): 1321–1332.

DOI: https://doi.org/10.1042/BCJ20200816

Published: 06 April 2021

... polarity crystallography PDZ domain protein–protein interactions Scribble Vangl2 The establishment of cell polarity, defined as the asymmetric distribution of proteins, carbohydrates and lipids within the cell, is a crucial process for the organization and development of all animal tissues [ 1...

View article titled, Structural basis of the human Scribble–Vangl2 association in health and disease

Includes: Supplementary data

Articles

Heteromeric complex formation between human cytochrome P450 CYP1A1 and heme oxygenase-1

J. Patrick Connick, James R. Reed, George F. Cawley, Wayne L. Backes

Biochem J (2021) 478 (2): 377–388.

DOI: https://doi.org/10.1042/BCJ20200768

Published: 27 January 2021

... for POR to function. In addition to these functionally required protein–protein interactions, HO-1 forms homomeric complexes, and several P450s have been shown to form complexes with themselves and with other P450s, raising the question, ‘How are the HO-1 and P450 systems organized in the endoplasmic...

View article titled, Heteromeric complex formation between human cytochrome P450 CYP1A1 and heme oxygenase-1

Includes: Supplementary data

Articles

Identification of a glycan cluster in gp120 essential for irreversible HIV-1 lytic inactivation by a lectin-based recombinantly engineered protein conjugate

Bibek Parajuli, Kriti Acharya, Aakansha Nangarlia, Shiyu Zhang, Bijay Parajuli, Alexej Dick, Brendon Ngo, Cameron F. Abrams, Irwin Chaiken

Biochem J (2020) 477 (21): 4263–4280.

DOI: https://doi.org/10.1042/BCJ20200495

Published: 13 November 2020

... 2020 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2020 Biacore epitope glycosylation isothermal titration calorimetry protein–protein interactions surface plasmon resonance The envelope glycoprotein (Env) of HIV-1 is the important...

View article titled, Identification of a glycan cluster in gp120 essential for irreversible HIV-1 lytic inactivation by a lectin-based recombinantly engineered protein conjugate

Includes: Supplementary data

Articles

2.09 Å Resolution structure of E. coli HigBA toxin–antitoxin complex reveals an ordered DNA-binding domain and intrinsic dynamics in antitoxin

Pankaj Vilas Jadhav, Vikrant Kumar Sinha, Saurabh Chugh, Chaithanya Kotyada, Digvijay Bachhav, Ramandeep Singh, Ulli Rothweiler, Mahavir Singh

Biochem J (2020) 477 (20): 4001–4019.

DOI: https://doi.org/10.1042/BCJ20200363

Published: 29 October 2020

... by the vendor. All the parameters were kept floating during the data fitting. antibiotic resistance HigBA protein–DNA protein–protein interactions toxin–antitoxin X-ray structure Toxin–antitoxin (TA) systems are pairs of genes that are either located on bacterial plasmids or integrated...

View article titled, 2.09 Å Resolution structure of E. coli HigBA toxin–antitoxin complex reveals an ordered DNA-binding domain and intrinsic dynamics in antitoxin

Includes: Supplementary data

Articles

A structure model explaining the binding between a ubiquitous unconventional G-protein (OsYchF1) and a plant-specific C2-domain protein (OsGAP1) from rice

Ming-Yan Cheung, Jacky Chi-Ki Ngo, Zhongzhou Chen, Qi Jia, Tianjie Li, Yitao Gou, Yi Wang, Hon-Ming Lam

Biochem J (2020) 477 (20): 3935–3949.

DOI: https://doi.org/10.1042/BCJ20200380

Published: 23 October 2020

... of the Biochemical Society 2020 C2-domain protein docking model G-protein protein–protein interactions structure–function relationship The plasmid pGEX-4T-1-OsYchF (6 kb), which contained an OsYchF1 cDNA fragment amplified from the cDNA pool of rice cultivars (SN1033 and JG30) in the pGEX-4T-1...

View article titled, A structure model explaining the binding between a ubiquitous unconventional G-protein (OsYchF1) and a plant-specific C2-domain protein (OsGAP1) from rice

Includes: Supplementary data

Articles

Quantitative mapping of binding specificity landscapes for homologous targets by using a high-throughput method

Lidan Aharon, Shay-Lee Aharoni, Evette S. Radisky, Niv Papo

Biochem J (2020) 477 (9): 1701–1719.

DOI: https://doi.org/10.1042/BCJ20200188

Published: 11 May 2020

...Lidan Aharon; Shay-Lee Aharoni; Evette S. Radisky; Niv Papo To facilitate investigations of protein–protein interactions (PPIs), we developed a novel platform for quantitative mapping of protein binding specificity landscapes, which combines the multi-target screening of a mutagenesis library...

View article titled, Quantitative mapping of binding specificity landscapes for homologous targets by using a high-throughput method

Includes: Supplementary data

Articles

Reading the phosphorylation code: binding of the 14-3-3 protein to multivalent client phosphoproteins

Nikolai N. Sluchanko

Biochem J (2020) 477 (7): 1219–1225.

DOI: https://doi.org/10.1042/BCJ20200084

Published: 09 April 2020

...Nikolai N. Sluchanko Many major protein–protein interaction networks are maintained by ‘hub’ proteins with multiple binding partners, where interactions are often facilitated by intrinsically disordered protein regions that undergo post-translational modifications, such as phosphorylation...

View article titled, Reading the phosphorylation code: binding of the 14-3-3 protein to multivalent client phosphoproteins

Articles

Toward a systems approach to cytochrome P450 ensemble: interactions of CYP2E1 with other P450 species and their impact on CYP1A2

Nadezhda Y. Davydova, Bikash Dangi, Marc A. Maldonado, Nikita E. Vavilov, Victor G. Zgoda, Dmitri R. Davydov

Biochem J (2019) 476 (23): 3661–3685.

DOI: https://doi.org/10.1042/BCJ20190532

Published: 12 December 2019

... for monitoring protein–protein interactions in HLM with various biophysical techniques, as well as for identifying the P450 interaction partners with the technique of molecular fishing. Results of the present study demonstrate high utility of this approach in the studies of interactions between multiple...

View article titled, Toward a systems approach to cytochrome P450 ensemble: interactions of CYP2E1 with other P450 species and their impact on CYP1A2

Includes: Supplementary data

Articles

The role of PTB domain containing adaptor proteins on PICALM-mediated APP endocytosis and localization

Lisa Merthan, Amelie Haller, Dietmar R. Thal, Bjoern von Einem, Christine A.F. von Arnim

Biochem J (2019) 476 (14): 2093–2109.

DOI: https://doi.org/10.1042/BCJ20180840

Published: 31 July 2019

..., with the magnitude of the effect depending on which PTB-AP was co-expressed. Taken together, our results indicate a modulating effect of PTB-APs on PICALM-mediated APP endocytosis and localization. amyloid precursor protein endocytosis PICALM protein–protein interactions PTB-containing adaptor protein...

View article titled, The role of PTB domain containing adaptor proteins on PICALM-mediated APP endocytosis and localization

Includes: Supplementary data

Articles

The ChlD subunit links the motor and porphyrin binding subunits of magnesium chelatase

David A. Farmer, Amanda A. Brindley, Andrew Hitchcock, Philip J. Jackson, Bethany Johnson, Mark J. Dickman, C. Neil Hunter, James D. Reid, Nathan B. P. Adams

Biochem J (2019) 476 (13): 1875–1887.

DOI: https://doi.org/10.1042/BCJ20190095

Published: 02 July 2019

... are currently unknown. While there have been an extensive steady state [ 2 , 4 , 5 , 12 , 13 , 21 – 26 ] and transient [ 27 ] kinetic analyses of MgCH, there is no settled view on the organisation of subunits and the protein–protein interactions representing the minimal catalytic unit. In addition...

View article titled, The ChlD subunit links the motor and porphyrin binding subunits of magnesium chelatase

Includes: Supplementary data

Articles

Designing active RNF4 monomers by introducing a tryptophan: avidity towards E2∼Ub conjugates dictates the activity of ubiquitin RING E3 ligases

Sayani Sarkar, Adaitya Prasad Behera, Prateeka Borar, Prerana Agarwal Banka, Ajit B. Datta

Biochem J (2019) 476 (10): 1465–1482.

DOI: https://doi.org/10.1042/BCJ20180883

Published: 28 May 2019

... Limited on behalf of the Biochemical Society 2019 E2 enzymes isothermal titration calorimetry oligomerization protein–protein interactions ubiquitin ring E3 ligases ubiquitins For FRET-based di-Ub formation assays, two Ub mutants, namely Ub K63C and Ub G75C , were purified and labeled...

View article titled, Designing active RNF4 monomers by introducing a tryptophan: avidity towards E2∼Ub conjugates dictates the activity of ubiquitin RING E3 ligases

Includes: Supplementary data

Articles

Silencing of type II phosphatidylinositol 4-kinase β stabilizes prostate apoptosis response-4 and induces apoptosis in cancer cells

Sonica Chaudhry, Vibhor Joshi, Naveen Bojjireddy, Maikho Thoh, Santosh K. Sandur, Gosukonda Subrahmanyam

Biochem J (2019) 476 (2): 405–419.

DOI: https://doi.org/10.1042/BCJ20180732

Published: 31 January 2019

.... These results suggest that PtdIns 4-kinase II β may be a novel regulator of Par-4 through protein–protein interactions. These studies have potential implications in cancer therapy . Correspondence: Gosukonda Subrahmanyam ( gsm@iitb.ac.in ) 7 9 2018 2 1 2019 3 1 2019 3 1 2019 ©...

View article titled, Silencing of type II phosphatidylinositol 4-kinase β stabilizes prostate apoptosis response-4 and induces apoptosis in cancer cells

Includes: Supplementary data

Articles

Using backbone-cyclized Cys-rich polypeptides as molecular scaffolds to target protein–protein interactions

Dipankar Chaudhuri, Teshome Aboye, Julio A. Camarero

Biochem J (2019) 476 (1): 67–83.

DOI: https://doi.org/10.1042/BCJ20180792

Published: 11 January 2019

... of these relatively new scaffolds have been also found to be highly tolerant to sequence variability, aside from the conserved residues forming the disulfide bonds, able to cross cellular membranes and modulate intracellular protein–protein interactions both in vitro and in vivo . These properties make them ideal...

View article titled, Using backbone-cyclized Cys-rich polypeptides as molecular scaffolds to target protein–protein interactions

Articles

Isoform-specific AMPK association with TBC1D1 is reduced by a mutation associated with severe obesity

In Collection

Editors' pick of research highlights published in the Biochemical Journal in 2018 & 2019

Elaine C. Thomas, Sharon C. Hook, Alexander Gray, Alexandra Chadt, David Carling, Hadi Al-Hasani, Kate J. Heesom, D. Grahame Hardie, Jeremy M. Tavaré

Biochem J (2018) 475 (18): 2969–2983.

DOI: https://doi.org/10.1042/BCJ20180475

Published: 25 September 2018

..., suggesting a tryptophan substitution would alter protein–protein interactions [ 33 ]. However, how this single-point mutation manifests as a severe obesity phenotype is currently unclear. The initial aim of the present study was to identify proteins that bind to the PTB domains of TBC1D1 using Stable...

View article titled, Isoform-specific AMPK association with TBC1D1 is reduced by a mutation associated with severe obesity

Includes: Supplementary data

Articles

Interplay between negative and positive design elements in Gα helical domains of G proteins determines interaction specificity toward RGS2

Mohammad Kasom, Samia Gharra, Isra Sadiya, Meirav Avital-Shacham, Mickey Kosloff

Biochem J (2018) 475 (14): 2293–2304.

DOI: https://doi.org/10.1042/BCJ20180285

Published: 25 July 2018

... signaling protein–protein interactions Heterotrimeric (αβγ) G proteins are molecular switches that mediate signaling initiated by G protein-coupled receptors (GPCRs) and play central roles in numerous cellular signaling cascades [ 1 – 3 ]. G proteins are activated by the exchange of bound GDP...

View article titled, Interplay between negative and positive design elements in Gα helical domains of G proteins determines interaction specificity toward RGS2

Includes: Supplementary data

Articles

Restricted HIV-1 Env glycan engagement by lectin-reengineered DAVEI protein chimera is sufficient for lytic inactivation of the virus

Bibek Parajuli, Kriti Acharya, Harry C. Bach, Bijay Parajuli, Shiyu Zhang, Amos B. Smith, III, Cameron F. Abrams, Irwin Chaiken

Biochem J (2018) 475 (5): 931–957.

DOI: https://doi.org/10.1042/BCJ20170662

Published: 09 March 2018

... molecular arrangements of Env-DAVEI enabling virolysis and also opens the way to form DAVEI fusions made up of gp120-binding small molecules linked to Trp3 peptide. biacore epitope HIV protein design protein–protein interactions SPR The Env (envelope glycoprotein) of HIV-1 (human...

View article titled, Restricted HIV-1 Env glycan engagement by lectin-reengineered DAVEI protein chimera is sufficient for lytic inactivation of the virus

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

..., the PGRMC1 inhibitor AG-205 significantly reduced synthesis of hydroxylated ceramide and glucosylceramide in FA2H-expressing cells. This suggests that PGRMC1 may regulate FA2H activity, possibly through its heme chaperone activity. heme mass spectrometry protein–protein interactions SILAC...

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

Articles

Globular C1q receptor (p33) binds and stabilizes pro-inflammatory MCP-1: a novel mechanism for regulation of MCP-1 production and function

Emma Anders, Daniel Nebel, Johannes Westman, Heiko Herwald, Bengt-Olof Nilsson, Daniel Svensson

Biochem J (2018) 475 (4): 775–786.

DOI: https://doi.org/10.1042/BCJ20170857

Published: 23 February 2018

... ) 9 11 2017 16 1 2018 18 1 2018 22 1 2018 © 2018 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2018 cytokine gC1qR (gC1qBP) inflammation MCP-1 (CCL2) periodontal ligament cells (PDL cells) protein–protein interactions...

View article titled, Globular C1q receptor (p33) binds and stabilizes pro-inflammatory MCP-1: a novel mechanism for regulation of MCP-1 production and function

Includes: Supplementary data

Articles

Direct visualization of interaction between calmodulin and connexin45

Juan Zou, Mani Salarian, Yanyi Chen, You Zhuo, Nicole E. Brown, John R. Hepler, Jenny J. Yang

Biochem J (2017) 474 (24): 4035–4051.

DOI: https://doi.org/10.1042/BCJ20170426

Published: 27 November 2017

... ) 1 6 2017 12 9 2017 25 9 2017 28 9 2017 © 2017 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2017 calmodulin connexin45 gap junctions intracellular calcium protein–protein interactions regulation Gap junctions formed...

View article titled, Direct visualization of interaction between calmodulin and connexin45

Articles

The spliceosomal proteins PPIH and PRPF4 exhibit bi-partite binding

Caroline Rajiv, S. RaElle Jackson, Simon Cocklin, Elan Z. Eisenmesser, Tara L. Davis

Biochem J (2017) 474 (21): 3689–3704.

DOI: https://doi.org/10.1042/BCJ20170366

Published: 25 October 2017

... processing factor 3 (PRPF3). Destabilization of tri-snRNP results in aberrant mRNA splicing that contributes to the disease. This highlights the contribution of protein–protein interactions to proper spliceosome function, in addition to protein–RNA interactions [ 11 – 14 ]. immunophilins intrinsically...

View article titled, The spliceosomal proteins PPIH and PRPF4 exhibit bi-partite binding

Includes: Supplementary data

Articles

Toward a systems approach to the human cytochrome P450 ensemble: interactions between CYP2D6 and CYP2E1 and their functional consequences

Dmitri R. Davydov, Nadezhda Y. Davydova, John T. Rodgers, Thomas H. Rushmore, Jeffrey P. Jones

Biochem J (2017) 474 (20): 3523–3542.

DOI: https://doi.org/10.1042/BCJ20170543

Published: 10 October 2017

... metabolism membrane proteins protein–protein interactions The system-wide parameters of the drug-metabolizing cascade of human liver are largely determined by the properties of the ensemble of cytochromes P450, which is responsible for metabolism of over 75% of all marketed drugs and new drug...

View article titled, Toward a systems approach to the human cytochrome P450 ensemble: interactions between CYP2D6 and CYP2E1 and their functional consequences

Articles

Intrinsic disorder in the partitioning protein KorB persists after co-operative complex formation with operator DNA and KorA

Eva I. Hyde, Philip Callow, Karthik V. Rajasekar, Peter Timmins, Trushar R. Patel, Giuliano Siligardi, Rohanah Hussain, Scott A. White, Christopher M. Thomas, David J. Scott

Biochem J (2017) 474 (18): 3121–3135.

DOI: https://doi.org/10.1042/BCJ20170281

Published: 31 August 2017

... BY) . circular dichroism intrinsically disordered proteins protein–DNA interactions protein–protein interactions small-angle scattering transcription regulation Correspondence: David J. Scott ( david.scott@nottingham.ac.uk ) or Eva I. Hyde ( e.i.hyde@bham.ac.uk ) * Present address: Department...

View article titled, Intrinsic disorder in the partitioning protein KorB persists after co-operative complex formation with operator DNA and KorA

Includes: Supplementary data

Articles

Engineering a monomeric variant of macrophage colony-stimulating factor (M-CSF) that antagonizes the c-FMS receptor

Yuval Zur, Lior Rosenfeld, Anna Bakhman, Stefan Ilic, Hezi Hayun, Anat Shahar, Barak Akabayov, Mickey Kosloff, Noam Levaot, Niv Papo

Biochem J (2017) 474 (15): 2601–2617.

DOI: https://doi.org/10.1042/BCJ20170276

Published: 21 July 2017

... to this work. 12 4 2017 22 6 2017 26 6 2017 27 6 2017 © 2017 The Author(s); published by Portland Press Limited on behalf of the Biochemical Society 2017 drug design osteoclasts protein–protein interactions rational protein engineering receptor tyrosine kinases X-ray...

View article titled, Engineering a monomeric variant of macrophage colony-stimulating factor (M-CSF) that antagonizes the c-FMS receptor

Includes: Supplementary data

Articles

Structural basis of molecular recognition of helical histone H3 tail by PHD finger domains

Alessio Bortoluzzi, Anastasia Amato, Xavier Lucas, Manuel Blank, Alessio Ciulli

Biochem J (2017) 474 (10): 1633–1651.

DOI: https://doi.org/10.1042/BCJ20161053

Published: 04 May 2017

... Society and distributed under the Creative Commons Attribution License 4.0 (CC BY) . epigenetics histone binding PHD finger protein–protein interactions reader domains Members of the BAZ family of proteins, which includes BAZ1A, also known as Acf1 [ 21 , 22 ], BAZ1B, also known...

View article titled, Structural basis of molecular recognition of helical histone H3 tail by PHD finger domains

Includes: Supplementary data

Articles

Binding and inhibition of the ternary complex factor Elk-4/Sap1 by the adapter protein Dok-4

Erika Hooker, Cindy Baldwin, Victoria Roodman, Anupam Batra, Naajia Nur Isa, Tomoko Takano, Serge Lemay

Biochem J (2017) 474 (9): 1509–1528.

DOI: https://doi.org/10.1042/BCJ20160832

Published: 19 April 2017

... possible interactions were screened with and without co-expression of Lyn tyrosine kinase, respectively. adaptor proteins protein–protein interactions proteolysis transcription factors The Dok (downstream of kinase) family of adapter proteins consists of seven related proteins characterized...

View article titled, Binding and inhibition of the ternary complex factor Elk-4/Sap1 by the adapter protein Dok-4

Includes: Supplementary data

Articles

Structural interface between LRRK2 and 14-3-3 protein

Loes M. Stevers, Rens M.J.M. de Vries, Richard G. Doveston, Lech-Gustav Milroy, Luc Brunsveld, Christian Ottmann

Biochem J (2017) 474 (7): 1273–1287.

DOI: https://doi.org/10.1042/BCJ20161078

Published: 23 March 2017

... 2 2017 15 2 2017 crystallography Parkinson's disease protein–protein interactions © 2017 The Author(s); published by Portland Press Limited on behalf of the Biochemical Society 2017 Correspondence: Christian Ottmann ( c.ottmann@tue.nl ) Parkinson's disease (PD...

View article titled, Structural interface between LRRK2 and 14-3-3 protein

Includes: Supplementary data

Articles

Structure-based mutational studies of O -acetylserine sulfhydrylase reveal the reason for the loss of cysteine synthase complex formation in Brucella abortus

Sudhaker Dharavath, Isha Raj, Samudrala Gourinath

Biochem J (2017) 474 (7): 1221–1239.

DOI: https://doi.org/10.1042/BCJ20161062

Published: 23 March 2017

... of the Biochemical Society 2017 active site cysteine synthase complex O -acetyl serine sulfydrylase protein–protein interactions The SAT C-terminal tail plays a crucial role in the formation of the CSC since this tail binds to the active site of OASS. This role for the SAT C-terminal tail has been...

View article titled, Structure-based mutational studies of O -acetylserine sulfhydrylase reveal the reason for the loss of cysteine synthase complex formation in Brucella abortus

Includes: Supplementary data

Articles

Identification of a multifunctional docking site on the catalytic unit of phosphodiesterase-4 (PDE4) that is utilised by multiple interaction partners

Kirsty F. Houslay, Frank Christian, Ruth MacLeod, David R. Adams, Miles D. Houslay, George S. Baillie

Biochem J (2017) 474 (4): 597–609.

DOI: https://doi.org/10.1042/BCJ20160849

Published: 03 February 2017

... BY) . cAMP cyclic nucleotide phosphodiesterases protein–protein interactions The p38 MAPK signalling cascade is a key signal transduction pathway involved in the control of cellular immune, inflammatory and stress responses [ 31 ]. Activated p38 MAPK exerts important effects on cell functioning...

View article titled, Identification of a multifunctional docking site on the catalytic unit of phosphodiesterase-4 (PDE4) that is utilised by multiple interaction partners

Articles

The sodium chloride cotransporter (NCC) and epithelial sodium channel (ENaC) associate

Abinash C. Mistry, Brandi M. Wynne, Ling Yu, Viktor Tomilin, Qiang Yue, Yiqun Zhou, Otor Al-Khalili, Rickta Mallick, Hui Cai, Abdel A. Alli, Benjamin Ko, Alexa Mattheyses, Hui-Fang Bao, Oleh Pochynyuk, Franziska Theilig, Douglas C. Eaton, Robert S. Hoover

Biochem J (2016) 473 (19): 3237–3252.

DOI: https://doi.org/10.1042/BCJ20160312

Published: 27 September 2016

... that there are functional consequences of this interaction, with inhibition of NCC affecting the function of ENaC. This novel finding of an association between ENaC and NCC could alter our understanding of salt transport in the distal tubule. ion channels protein–protein interactions sodium channel sodium chloride...

View article titled, The sodium chloride cotransporter (NCC) and epithelial sodium channel (ENaC) associate

Articles

An antibody that prevents serpin polymerisation acts by inducing a novel allosteric behaviour

Neda Motamedi-Shad, Alistair M. Jagger, Maximilian Liedtke, Sarah V. Faull, Arjun Scott Nanda, Enrico Salvadori, Joshua L. Wort, Christopher W.M. Kay, Narinder Heyer-Chauhan, Elena Miranda, Juan Perez, Adriana Ordóñez, Imran Haq, James A. Irving, David A. Lomas

Biochem J (2016) 473 (19): 3269–3290.

DOI: https://doi.org/10.1042/BCJ20160159

Published: 27 September 2016

... the maximum. The midpoint of denaturation ( T m ) was determined from the optimum fit of an equation describing two-state unfolding [ 39 , 51 , 52 ]: allosteric regulation antibodies protein aggregation protein conformation protein–protein interactions serpin α 1 -Antitrypsin (α 1...

View article titled, An antibody that prevents serpin polymerisation acts by inducing a novel allosteric behaviour

Includes: Supplementary data

Articles

Deciphering the unconventional peptide binding to the PDZ domain of MAST2

Florent Delhommel, Alain Chaffotte, Elouan Terrien, Bertrand Raynal, Henri Buc, Muriel Delepierre, Florence Cordier, Nicolas Wolff

Biochem J (2015) 469 (1): 159–168.

DOI: https://doi.org/10.1042/BJ20141198

Published: 19 June 2015

... be addressed (email nicolas.wolff@pasteur.fr ). 24 9 2014 17 4 2015 5 5 2015 5 5 2015 © 2015 Authors; published by Portland Press Limited 2015 intradomain energetic connectivity PDZ domains pre-steady-state kinetics protein–protein interactions Microtubule...

View article titled, Deciphering the unconventional peptide binding to the PDZ domain of MAST2

Articles

Effect of homomeric P450–P450 complexes on P450 function

James R. Reed, J. Patrick Connick, Dongmei Cheng, George F. Cawley, Wayne L. Backes

Biochem J (2012) 446 (3): 489–497.

DOI: https://doi.org/10.1042/BJ20120636

Published: 28 August 2012

... bioluminescence resonance energy transfer (BRET) cytochrome P450 enzyme kinetics homomeric P450–P450 complexes protein cross-linking protein–protein interactions Cytochrome P450 plays a major role in the metabolism of a wide variety of drugs and other xenobiotics as well as numerous endogenous...

View article titled, Effect of homomeric P450–P450 complexes on P450 function

Includes: Supplementary data

Articles

Transcriptional repression of the gluconeogenic gene PEPCK by the orphan nuclear receptor SHP through inhibitory interaction with C/EBPα

Min Jung Park, Hee Jeong Kong, Hye Young Kim, Hyeong Hoe Kim, Joon Hong Kim, Jae Hun Cheong

Biochem J (2007) 402 (3): 567–574.

DOI: https://doi.org/10.1042/BJ20061549

Published: 26 February 2007

... independent experiments. ( B ) SHP inhibits the protein–protein interaction between C/EBPα and RFC140. GST fusions to the C/EBPα-interaction region (residues 151–545) of RFC140 were purified from E. coli . C/EBPα was in vitro translated in the presence of 35 S-methionine and then incubated...

View article titled, Transcriptional repression of the gluconeogenic gene PEPCK by the orphan nuclear receptor SHP through inhibitory interaction with C/EBPα

Articles

Phosphorylation of 20S proteasome alpha subunit C8 (alpha7) stabilizes the 26S proteasome and plays a role in the regulation of proteasome complexes by gamma-interferon

Suchira BOSE, Fiona L. L. STRATFORD, Kerry I. BROADFOOT, Grant G. F. MASON, A. Jennifer RIVETT

Biochem J (2004) 378 (1): 177–184.

DOI: https://doi.org/10.1042/bj20031122

Published: 15 February 2004

..., protein complexes, protein degradation, protein protein interactions. INTRODUCTION Proteasomes are multimeric proteinase complexes which play a central role in protein degradation in animal cells. They are involved in many basic cellular processes including the cell cycle, apoptosis, the stress response...

View article titled, Phosphorylation of 20S proteasome alpha subunit C8 (alpha7) stabilizes the 26S proteasome and plays a role in the regulation of proteasome complexes by gamma-interferon

Articles

Interaction between the individual isoenzymes of pyruvate dehydrogenase kinase and the inner lipoyl-bearing domain of transacetylase component of pyruvate dehydrogenase complex

Alina TUGANOVA, Igor BOULATNIKOV, Kirill M. POPOV

Biochem J (2002) 366 (1): 129–136.

DOI: https://doi.org/10.1042/bj20020301

Published: 15 August 2002

...Alina TUGANOVA; Igor BOULATNIKOV; Kirill M. POPOV Protein—protein interactions play an important role in the regulation of enzymic activity of pyruvate dehydrogenase kinase (PDK). It is generally believed that the binding of PDK to the inner lipoyl-bearing domain L2 of the transacetylase component...

View article titled, Interaction between the individual isoenzymes of pyruvate dehydrogenase kinase and the inner lipoyl-bearing domain of transacetylase component of pyruvate dehydrogenase complex

Articles

Characterization of monoclonal antibodies against Escherichia coli core RNA polymerase

Jöelle ROUBY, Martine PUGNIERE, Jean-Claude MANI, Claude GRANIER, Pierrette MONMOUTON, Stephane THEULIER SAINT GERMAIN, Jean-Paul LEONETTI

Biochem J (2002) 361 (2): 347–354.

DOI: https://doi.org/10.1042/bj3610347

Published: 08 January 2002

... correspondence should be addressed (e-mail jp_leo@yahoo.com ). 14 5 2001 9 10 2001 5 11 2001 The Biochemical Society, London ©2002 2002 inhibitor protein–protein interactions σ70 transcription SPR Abbreviations used: mAb, monoclonal antibody; Ni-NTA, Ni 2...

View article titled, Characterization of monoclonal antibodies against Escherichia coli core RNA polymerase

Articles

The result of equilibrium-constant calculations strongly depends on the evaluation method used and on the type of experimental errors

Hendrik FUCHS, Reinhard GESSNER

Biochem J (2001) 359 (2): 411–418.

DOI: https://doi.org/10.1042/bj3590411

Published: 08 October 2001

...Hendrik FUCHS; Reinhard GESSNER The determination of equilibrium constants is a widespread tool both to understand and to characterize protein–protein interactions. A variety of different methods, among them Scatchard analysis, is used to calculate these constants. Although more than 1000 articles...

View article titled, The result of equilibrium-constant calculations strongly depends on the evaluation method used and on the type of experimental errors

Articles

Analysis of a two-domain binding site for the urokinase-type plasminogen activator–plasminogen activator inhibitor-1 complex in low-density-lipoprotein-receptor-related protein

Olav M. ANDERSEN, Helle H. PETERSEN, Christian JACOBSEN, S⊘ren K. MOESTRUP, Michael ETZERODT, Peter A. ANDREASEN, Hans C. THØGERSEN

Biochem J (2001) 357 (1): 289–296.

DOI: https://doi.org/10.1042/bj3570289

Published: 25 June 2001

... be addressed (e-mail hct@biobase.dk ). 23 1 2001 29 3 2001 23 4 2001 The Biochemical Society, London ©2001 2001 complement-type repeat protein–protein interactions receptor-associated protein Abbreviations used: LDLR, low-density-lipoprotein receptor; LRP, α 2...

View article titled, Analysis of a two-domain binding site for the urokinase-type plasminogen activator–plasminogen activator inhibitor-1 complex in low-density-lipoprotein-receptor-related protein

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