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The uncharacterized protein ZNF200 interacts with PRMT3 and aids its stability and nuclear translocation

Somlee Gupta, Mamta Verma, Rajashekar Varma Kadumuri, Namita Chutani, Mohd. Imran K. Khan, Sreenivas Chavali, Arunkumar Dhayalan

Biochem J (2024) 481 (23): 1723–1740.

https://doi.org/10.1042/BCJ20240476

Published: 21 November 2024

..., leading to the increased levels of global H4R3me2a modifications. Besides regulating cellular functions by methylating substrate proteins, PRMT3 also affects diverse functions mediated by protein-protein interactions [ 7 , 8 , 10–12 , 22 , 26 ]. Here, we aimed to identify new interactors...

View articletitled, The uncharacterized protein ZNF200 interacts with PRMT3 and aids its stability and nuclear translocation

Includes: Supplementary data

Articles

Exploring the dynamics and interactions of the N-myc transactivation domain through solution nuclear magnetic resonance spectroscopy

Ewa Rejnowicz, Matthew Batchelor, Eoin Leen, Mohd Syed Ahangar, Selena G. Burgess, Mark W. Richards, Arnout P. Kalverda, Richard Bayliss

Biochem J (2024) 481 (21): 1535–1556.

https://doi.org/10.1042/BCJ20240248

Published: 21 October 2024

... disordered region culminating in the transactivation domain (TAD). The TAD participates in many protein–protein interactions, notably with kinases that promote stability (Aurora-A) or degradation (ERK1, GSK3) via the ubiquitin-proteasome system. We probed the structure, dynamics and interactions of N-myc TAD...

View articletitled, Exploring the dynamics and interactions of the N-myc transactivation domain through solution nuclear magnetic resonance spectroscopy

Includes: Supplementary data

Articles

Biophysical and structural analyses of the interaction between the SHANK1 PDZ domain and an internal SLiM

Yue Li, Chi H. Trinh, Amanda Acevedo-Jake, Diana Gimenez, Stuart L. Warriner, Andrew J. Wilson

Biochem J (2024) 481 (14): 945–955.

https://doi.org/10.1042/BCJ20240126

Published: 10 July 2024

... under a transformative agreement with JISC. PDZ domains peptide interacting motifs protein–protein interactions The SHANK (SH3 and multiple ankyrin repeat domain) protein acts as a scaffolding protein located at excitatory glutamatergic synapses (Figure 1); it plays a crucial role...

View articletitled, Biophysical and structural analyses of the interaction between the SHANK1 PDZ domain and an internal SLiM

Includes: Supplementary data

Articles

The C-terminal sequences of Bcl-2 family proteins mediate interactions that regulate cell death

In Collection

Cell death and survival

Dang Nguyen, Elizabeth Osterlund, Justin Kale, David W. Andrews

Biochem J (2024) 481 (14): 903–922.

https://doi.org/10.1042/BCJ20210352

Published: 10 July 2024

... on behalf of the Biochemical Society and distributed under the Creative Commons Attribution License 4.0 (CC BY) . apoptosis Bax Bcl-2 BH3-only proteins protein–protein interactions transmembrane domain When a eukaryotic cell is faced with overwhelming cellular stress that surpasses...

View articletitled, The C-terminal sequences of Bcl-2 family proteins mediate interactions that regulate cell death

Articles

Comprehensive comparative assessment of the Arabidopsis thaliana MLO2–CALMODULIN2 interaction by various in vitro and in vivo protein–protein interaction assays

Kira von Bongartz, Björn Sabelleck, Anežka Baquero Forero, Hannah Kuhn, Franz Leissing, Ralph Panstruga

Biochem J (2023) 480 (20): 1615–1638.

https://doi.org/10.1042/BCJ20230255

Published: 13 October 2023

... key amino acid residues in the barley Mlo calmodulin-binding domain (CAMBD) that, when mutated, affect the MLO–CAM association. We here tested the respective interaction between Arabidopsis thaliana MLO2 and CAM2 using seven different types of in vitro and in vivo protein–protein interaction assays...

View articletitled, Comprehensive comparative assessment of the Arabidopsis thaliana MLO2–CALMODULIN2 interaction by various in vitro and in vivo protein–protein interaction assays

Includes: Supplementary data

Articles

Classification of Cushing's syndrome PKAc mutants based upon their ability to bind PKI

In Collection

Cell signaling in the 21st century

Mitchell H. Omar, Maryanne Kihiu, Dominic P. Byrne, Kyung-Soon Lee, Tyler M. Lakey, Erik Butcher, Patrick A. Eyers, John D. Scott

Biochem J (2023) 480 (12): 875–890.

https://doi.org/10.1042/BCJ20230183

Published: 22 June 2023

... conducted by five independent groups identified mutations in protein kinase A catalytic subunits (PKAc) that drive adrenal Cushing's syndrome [ 12–18 ]. Most PKAc mutations cluster where the kinase domain interfaces with its regulatory (R) subunits [ 19 ]. This protein–protein interaction is not only...

View articletitled, Classification of Cushing's syndrome PKAc mutants based upon their ability to bind PKI

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.

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 articletitled, 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.

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 articletitled, 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.

https://doi.org/10.1042/BCJ20210722

Published: 04 February 2022

... Press Limited on behalf of the Biochemical Society 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...

View articletitled, 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.

https://doi.org/10.1042/BCJ20210642

Published: 14 January 2022

... 2021 15 12 2021 21 12 2021 22 12 2021 © 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...

View articletitled, 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.

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 articletitled, 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.

https://doi.org/10.1042/BCJ20210459

Published: 14 October 2021

... regulator of cell signaling. membrane proteins protein-protein interactions tetraspanins Tetraspanins (Tspans) are widely expressed membrane proteins of 200–350 amino acids that cross the cell membrane four times [ 1 ]. They are involved in diverse cellular processes, such as cell proliferation...

View articletitled, 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.

https://doi.org/10.1042/BCJ20210278

Published: 09 July 2021

... by the participation of the University 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...

View articletitled, 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.

https://doi.org/10.1042/BCJ20210269

Published: 11 June 2021

...–protein interactions The cytochrome P450s (P450s) involved in drug and xenobiotic metabolism are heme-containing, membrane-bound enzymes that reside primarily in the endoplasmic reticulum of cells in the liver, spleen and small intestine. These enzymes act as monooxygenases and obtain electrons...

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

Includes: Supplementary data

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.

https://doi.org/10.1042/BCJ20210170

Published: 08 June 2021

..., 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 articletitled, 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

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.

https://doi.org/10.1042/BCJ20200828

Published: 08 June 2021

... under the Creative Commons Attribution License 4.0 (CC BY-NC-ND) . intrinsically disordered proteins multispecificity multivalency protein–protein interactions specificity structural biology Molecular communication is at the base of life, and to understand life, we need to understand...

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

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.

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 articletitled, 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.

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 articletitled, 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.

https://doi.org/10.1042/BCJ20200495

Published: 13 November 2020

... Society 2020 Biacore epitope glycosylation isothermal titration calorimetry protein–protein interactions surface plasmon resonance The envelope glycoprotein (Env) of HIV-1 is the important for recognition of virus by the receptor of host T-cells (CD4, CCR5 and CXCR4) [ 1 ]. The initial...

View articletitled, 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.

https://doi.org/10.1042/BCJ20200363

Published: 29 October 2020

... 30 9 2020 1 10 2020 © 2020 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2020 antibiotic resistance HigBA protein–DNA protein–protein interactions toxin–antitoxin X-ray structure Toxin–antitoxin (TA) systems are pairs of genes...

View articletitled, 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.

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 We previously solved the crystal structures of an unconventional G-protein in rice, OsYchF1, and its regulator, OsGAP1, which is a C2-domain protein [ 1 , 2...

View articletitled, 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.

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 articletitled, 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.

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 articletitled, 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.

https://doi.org/10.1042/BCJ20190532

Published: 12 December 2019

... advantage of this strategy is its applicability for incorporating genetically or chemically modified proteins. This includes the incorporation of proteins bearing fluorescent probes and light-activating cross-linkers. Therefore, this strategy may be used for monitoring protein–protein interactions in HLM...

View articletitled, 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.

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 articletitled, 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.

https://doi.org/10.1042/BCJ20190095

Published: 02 July 2019

... Attribution License 4.0 (CC BY) . AAA proteins integrins protein–protein interactions tetrapyrroles The first committed step in the biosynthesis of chlorophyll is catalysed by magnesium chelatase (MgCH; E.C.6.6.1.1), a large, multisubunit enzyme which catalyses the insertion of a Mg 2+ ion...

View articletitled, 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.

https://doi.org/10.1042/BCJ20180883

Published: 28 May 2019

... , whereas the ‘linchpin’ arginine is found at the ‘+1’ position ( Figure 1B ). © 2019 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2019 E2 enzymes isothermal titration calorimetry oligomerization protein–protein interactions ubiquitin ring E3 ligases...

View articletitled, 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.

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 ( [email protected] ) MCF-7 cells and MCF-10A cells were obtained from National...

View articletitled, 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.

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 articletitled, 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.

https://doi.org/10.1042/BCJ20180475

Published: 25 September 2018

... 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 Isotope Labelling by Amino...

View articletitled, 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.

https://doi.org/10.1042/BCJ20180285

Published: 25 July 2018

... 2018 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2018 G proteins GTPases intracellular signaling protein–protein interactions Heterotrimeric (αβγ) G proteins are molecular switches that mediate signaling initiated by G protein-coupled...

View articletitled, 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.

https://doi.org/10.1042/BCJ20170662

Published: 09 March 2018

... 2018 biacore epitope HIV protein design protein–protein interactions SPR We previously found that the high mannose-binding sites of Env can be used by bifunctional chimeras denoted DAVEIs (dual action virus entry inhibitors) to lytically inactivate HIV-1 virions independent of host...

View articletitled, 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.

https://doi.org/10.1042/BCJ20170963

Published: 06 March 2018

... Society 2018 heme mass spectrometry protein–protein interactions SILAC sphingolipids Fatty acid 2-hydroxylase (FA2H; EC 1.14.18.6), an enzyme of the endoplasmic reticulum (ER), is required for synthesis of 2-hydroxylated sphingolipids in the nervous system and other organs (for review...

View articletitled, 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.

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 articletitled, 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.

https://doi.org/10.1042/BCJ20170426

Published: 27 November 2017

...-naphthalenesulfonamide hydrochloride] (50 μM) for 20, 10, and 30 min, respectively, before BRET measurement. The average BRET signals from three experiments were plotted as a function of the ratio of acceptor over the donor. calmodulin connexin45 gap junctions intracellular calcium protein–protein interactions...

View articletitled, 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.

https://doi.org/10.1042/BCJ20170366

Published: 25 October 2017

... with pre-mRNA 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 ]. We first...

View articletitled, 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.

https://doi.org/10.1042/BCJ20170543

Published: 10 October 2017

... ensemble and suggest a role of interactions of CYP2E1 with CYP2D6 in pharmacologically important instances of alcohol–drug interactions. allosteric regulation cytochrome P450 drug metabolism membrane proteins protein–protein interactions Correspondence: Dmitri R. Davydov ( dmrdavyd...

View articletitled, 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.

https://doi.org/10.1042/BCJ20170281

Published: 31 August 2017

... interactions protein–protein interactions small-angle scattering transcription regulation To ensure the correct partitioning of chromosomes before cell division, most bacteria use a type Ia partitioning system consisting of a DNA-binding protein from the ParB family; a filament-forming ATPase from...

View articletitled, 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.

https://doi.org/10.1042/BCJ20170276

Published: 21 July 2017

... equally 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...

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

Includes: Supplementary data

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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.

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 The plant homeodomain (PHD) finger is one of the largest families of epigenetic reader domains present in chromatin...

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

Includes: Supplementary data

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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.

https://doi.org/10.1042/BCJ20160832

Published: 19 April 2017

...–protein interactions proteolysis transcription factors The Dok (downstream of kinase) family of adapter proteins consists of seven related proteins characterized by an N-terminal tandem of conserved pleckstrin homology (PH) and phosphotyrosine-binding (PTB) domains linked to more divergent C...

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

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.

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 SAT with an Ile at its C-terminus has previously been observed to interact with OASS in other organisms [ 12 , 30 , 31 ]. The binding characteristics of mutant BaOASS...

View articletitled, 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

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.

https://doi.org/10.1042/BCJ20161078

Published: 23 March 2017

... Ottmann ( [email protected] ) 11 12 2016 9 2 2017 14 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 Parkinson's disease (PD...

View articletitled, Structural interface between LRRK2 and 14-3-3 protein

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.

https://doi.org/10.1042/BCJ20160849

Published: 03 February 2017

... BY) . cAMP cyclic nucleotide phosphodiesterases protein–protein interactions We, and others, have successfully used a peptide array approach to delineate various protein–protein interaction surfaces (see, for example, [ 1 , 34 , 35 , 37 ]). This provides a novel and powerful technology...

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

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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.

https://doi.org/10.1042/BCJ20160312

Published: 27 September 2016

...–protein interactions sodium channel sodium chloride cotransporter transport Hypertension affects ∼1 billion individuals worldwide [ 1 ]. In the USA, almost one-third of the adult population has hypertension [ 2 ]. The key role of kidney sodium reabsorption in the development of hypertension...

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

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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.

https://doi.org/10.1042/BCJ20160159

Published: 27 September 2016

... with 1 M H 2 SO 4 , and an endpoint measurement of HRP activity at 450 nm was made using a SpectraMax M2e plate reader (Molecular Devices). All steps were performed at room temperature. allosteric regulation antibodies protein aggregation protein conformation protein–protein interactions...

View articletitled, 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.

https://doi.org/10.1042/BJ20141198

Published: 19 June 2015

... interface. Peptide binding affects positions distal from the binding groove through a network of residues undergoing subtle changes of conformation and dynamics. intradomain energetic connectivity PDZ domains pre-steady-state kinetics protein–protein interactions Microtubule-associated...

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

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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.

https://doi.org/10.1042/BJ20120636

Published: 28 August 2012

... 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 compounds. Although the interactions between NADPH–POR (cytochrome P450 reductase) and P450 necessary for mono-oxygenase function...

View articletitled, 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.

https://doi.org/10.1042/BJ20061549

Published: 26 February 2007

... 2006 The Biochemical Society, London 2007 CCAAT/enhancer-binding protein α (C/EBPα) phosphoenolpyruvate carboxykinase (PEPCK) protein–protein interactions short heterodimer partner (SHP) transcriptional repression PEPCK (phosphoenolpyruvate carboxykinase) is an enzyme...

View articletitled, 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.

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 articletitled, 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

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