IgG light chain-independent secretion of heavy chain dimers: consequence for therapeutic antibody production and design
Rodent monoclonal antibodies with specificity towards important biological targets are developed for therapeutic use by a process of humanisation. This process involves the creation of molecules, which retain the specificity of the rodent antibody but contain predominantly human coding sequence. Here, we show that some humanised heavy chains (HCs) can fold, form dimers and be secreted even in the absence of a light chain (LC). Quality control of recombinant antibody assembly in vivo is thought to rely upon folding of the HC CH1 domain. This domain acts as a switch for secretion, only folding upon interaction with the LC CL...
Source: Biochemical Journal - September 7, 2017 Category: Biochemistry Authors: Stoyle, C. L., Stephens, P. E., Humphreys, D. P., Heywood, S., Cain, K., Bulleid, N. J. Tags: Research Articles Source Type: research

N-Glycosylation is required for FDNC5 stabilization and irisin secretion
Irisin, a myokine derived from the extracellular domain of FNDC5, has been shown to mediate thermogenesis of white adipose tissue. Biochemical data have shown that N-glycosylation of FNDC5 is unlikely to affect ligand or receptor activation of irisin. The N-glycosylation of FNDC5 remains poorly understood. In the present study, we analysed N-glycosylation sites of FNDC5 and found that two potential N-glycosylation sites (Asn36 and Asn81) could indeed be occupied by N-glycan. Furthermore we showed that the lack of N-glycosylation decreases the secretion of irisin, which is relevant to the instability of FNDC5 and the defici...
Source: Biochemical Journal - September 7, 2017 Category: Biochemistry Authors: Nie, Y., Liu, D. Tags: Research Articles Source Type: research

The functions of Reelin in membrane trafficking and cytoskeletal dynamics: implications for neuronal migration, polarization and differentiation
Reelin is a large extracellular matrix protein with relevant roles in mammalian central nervous system including neurogenesis, neuronal polarization and migration during development; and synaptic plasticity with its implications in learning and memory, in the adult. Dysfunctions in reelin signaling are associated with brain lamination defects such as lissencephaly, but also with neuropsychiatric diseases like autism, schizophrenia and depression as well with neurodegeneration. Reelin signaling involves a core pathway that activates upon reelin binding to its receptors, particularly ApoER2 (apolipoprotein E receptor 2)/LRP8...
Source: Biochemical Journal - September 7, 2017 Category: Biochemistry Authors: Santana, J., Marzolo, M.-P. Tags: Review Articles Source Type: research

Intrinsic disorder in the partitioning protein KorB persists after co-operative complex formation with operator DNA and KorA
The ParB protein, KorB, from the RK2 plasmid is required for DNA partitioning and transcriptional repression. It acts co-operatively with other proteins, including the repressor KorA. Like many multifunctional proteins, KorB contains regions of intrinsically disordered structure, existing in a large ensemble of interconverting conformations. Using NMR spectroscopy, circular dichroism and small-angle neutron scattering, we studied KorB selectively within its binary complexes with KorA and DNA, and within the ternary KorA/KorB/DNA complex. The bound KorB protein remains disordered with a mobile C-terminal domain and no chang...
Source: Biochemical Journal - August 30, 2017 Category: Biochemistry Authors: Hyde, E. I., Callow, P., Rajasekar, K. V., Timmins, P., Patel, T. R., Siligardi, G., Hussain, R., White, S. A., Thomas, C. M., Scott, D. J. Tags: Research Articles Source Type: research

The helicase, DDX3X, interacts with poly(A)-binding protein 1 (PABP1) and caprin-1 at the leading edge of migrating fibroblasts and is required for efficient cell spreading
DDX3X, a helicase, can interact directly with mRNA and translation initiation factors, regulating the selective translation of mRNAs that contain a structured 5' untranslated region. This activity modulates the expression of mRNAs controlling cell cycle progression and mRNAs regulating actin dynamics, contributing to cell adhesion and motility. Previously, we have shown that ribosomes and translation initiation factors localise to the leading edge of migrating fibroblasts in loci enriched with actively translating ribosomes, thereby promoting steady-state levels of ArpC2 and Rac1 proteins at the leading edge of cells durin...
Source: Biochemical Journal - August 30, 2017 Category: Biochemistry Authors: Copsey, A. C., Cooper, S., Parker, R., Lineham, E., Lapworth, C., Jallad, D., Sweet, S., Morley, S. J. Tags: Research Articles Source Type: research

Glycerol-3-phosphate acyltransferase 2 is essential for normal spermatogenesis
Glycerol-3-phosphate acyltransferases (GPATs) catalyze the first and rate-limiting step in the de novo glycerolipid synthesis. The GPAT2 isoform differs from the other isoforms because its expression is restricted to male germ cells and cancer cells. It has been recently reported that GPAT2 expression in mouse testis fluctuates during sexual maturation and that it is regulated by epigenetic mechanisms in combination with vitamin A derivatives. Despite progress made in this field, information about GPAT2 role in the developing male germ cells remains unclear. The aim of the present study was to confirm the hypothesis that G...
Source: Biochemical Journal - August 30, 2017 Category: Biochemistry Authors: Garcia-Fabiani, M. B., Montanaro, M. A., Stringa, P., Lacunza, E., Cattaneo, E. R., Santana, M., Pellon-Maison, M., Gonzalez-Baro, M. R. Tags: Research Articles Source Type: research

From B to A: making an essential cofactor in a human parasite
Trypanosomatids are parasitic eukaryotic organisms that cause human disease. These organisms have complex lifestyles; cycling between vertebrate and insect hosts and alternating between two morphologies; a replicating form and an infective, nonreplicating one. Because trypanosomatids are one of the few organisms that do not synthesize the essential cofactor, heme, these parasites sequester the most common form, heme B, from their hosts. Once acquired, the parasites derivatize heme B to heme A by two sequential enzyme reactions. Although heme C is found in many cytochrome c and c1 proteins, heme A is the cofactor of only on...
Source: Biochemical Journal - August 30, 2017 Category: Biochemistry Authors: Morrissette, N. S., Goulding, C. W. Tags: Commentaries Source Type: research

A ligand divided: antagonist, agonist and analog control
Inhibiting receptor tyrosine kinases has been a cornerstone of cancer therapeutics for decades. Treatment strategies largely involve small-molecule kinase inhibitors and monoclonal antibodies. For receptors activated by constitutively dimeric ligands, another potential mechanism of inhibition exists: developing monomeric ligands that prevent receptor dimerization. In a recent issue of the Biochemical Journal, Zur et al. [Biochem. J. (2017) 474, 2601–2617] describe the details of creating such an inhibitor directed toward the macrophage colony-stimulating factor receptor, c-FMS. In the process of teasing apart the lig...
Source: Biochemical Journal - August 30, 2017 Category: Biochemistry Authors: Klein, D. E. Tags: Commentaries Source Type: research

Activation mechanisms of the E3 ubiquitin ligase parkin
Monogenetic, familial forms of Parkinson's disease (PD) only account for 5–10% of the total number of PD cases, but analysis of the genes involved therein is invaluable to understanding PD-associated neurodegenerative signaling. One such gene, parkin, encodes a 465 amino acid E3 ubiquitin ligase. Of late, there has been considerable interest in the role of parkin signaling in PD and in identifying its putative substrates, as well as the elucidation of the mechanisms through which parkin itself is activated. Its dysfunction underlies both inherited and idiopathic PD-associated neurodegeneration. Here, we review recent...
Source: Biochemical Journal - August 30, 2017 Category: Biochemistry Authors: Panicker, N., Dawson, V. L., Dawson, T. M. Tags: Review Articles Source Type: research

Phosphorylation of AMPK by upstream kinases is required for activity in mammalian cells
We present here the crystal structure of non-phosphorylated Thr172 AMPK in complex with AMP and 991. This structure reveals that the activation loop, as well as the complex overall, is similar to the Thr172 phosphorylated complex. We find that in the presence of AMP and 991 non-phosphorylated Thr172, AMPK is much less active than the Thr172 phosphorylated enzyme. In human cells, the basal level of Thr172 phosphorylation is very low (~1%), but is increased 10-fold by treatment with 2-deoxyglucose. In cells lacking the major Thr172 kinases, LKB1 and CaMKKβ, Thr172 phosphorylation is almost completely abolished, and AMPK...
Source: Biochemical Journal - August 22, 2017 Category: Biochemistry Authors: Willows, R., Sanders, M. J., Xiao, B., Patel, B. R., Martin, S. R., Read, J., Wilson, J. R., Hubbard, J., Gamblin, S. J., Carling, D. Tags: Research Articles Source Type: research

Sialylated glycosylphosphatidylinositols suppress the production of toxic amyloid-{beta} oligomers
The production of amyloid-β (Aβ) is a key factor driving pathogenesis in Alzheimer's disease (AD). Increasing concentrations of soluble Aβ oligomers within the brain lead to synapse degeneration and the progressive dementia characteristic of AD. Since Aβ exists in both disease-relevant (toxic) and non-toxic forms, the factors that affected the release of toxic Aβ were studied in a cell model. 7PA2 cells expressing the human amyloid precursor protein released Aβ oligomers that caused synapse damage when incubated with cultured neurones. These Aβ oligomers had similar potency to soluble A&b...
Source: Biochemical Journal - August 22, 2017 Category: Biochemistry Authors: Nolan, W., McHale-Owen, H., Bate, C. Tags: Research Articles Source Type: research

The antifungal activity of the peptide, periplanetasin-2, derived from American cockroach Periplaneta americana
The cockroach, which is a household insect, is an established model organism in research. Periplanetasin-2, derived from the American cockroach Periplaneta americana, exerted potent antifungal effect against pathogenic fungi without causing hemolysis. Periplanetasin-2 induced oxidative stress by generation of reactive oxygen species (ROS) and lipid peroxidation. Periplanetasin-2 also caused apoptosis by exposure of phosphatidylserine and fragmentation of DNA, exerted in a concentration-dependent manner. Hence, we investigated the mitochondrial apoptotic mechanism of periplanetasin-2 in Candida albicans. After treatment wit...
Source: Biochemical Journal - August 22, 2017 Category: Biochemistry Authors: Yun, J., Hwang, J.-S., Lee, D. G. Tags: Research Articles Source Type: research

Evaluation of ethyl gallate for its antioxidant and anticancer properties against chemical-induced tongue carcinogenesis in mice
Cancer arising in the oral cavity is one of the major causes of mortality worldwide and demands immediate attention. Regardless of the use of advanced treatment for oral cancer, successful treatment resulting in cancer survival is low. Currently available drugs are ineffective and are toxic. Therefore, successful treatment without toxic effects remains essential. This is quite challenging, leading to the identification of natural bioactive compounds for oral cancer treatment. Thus, a plant extract rich in phenolics is preferred for studying the cellular, biochemical and molecular changes associated with oral carcinogenesis...
Source: Biochemical Journal - August 22, 2017 Category: Biochemistry Authors: Mohan, S., Thiagarajan, K., Chandrasekaran, R. Tags: Research Articles Source Type: research

Buddleja thyrsoides Lam. crude extract presents antinociceptive effect on an arthritic pain model in mice
Arthritis is a chronic inflammatory disease which reduces the life quality of affected individuals. Therapeutic tools used for treating inflammatory pain are associated with several undesirable effects. Buddleja thyrsoides Lam., known as ‘Barbasco’ or ‘Cambara’, is mostly used in several disorders and possesses antirheumatic, anti-inflammatory, and analgesic properties. Here, we investigated the antinociceptive and anti-inflammatory effects of the B. thyrsoides crude extract applied orally and topically in acute pain models and an arthritic pain model induced by complete Freund's adjuvant (CFA) paw ...
Source: Biochemical Journal - August 17, 2017 Category: Biochemistry Authors: Fialho, M. F. P., Brusco, I., da Silva Brum, E., Piana, M., Boligon, A. A., Trevisan, G., Oliveira, S. M. Tags: Research Articles Source Type: research

Loss of prion protein is associated with the development of insulin resistance and obesity
Prion protein (PrPC) was initially described due to its involvement in transmissible spongiform encephalopathies. It was subsequently demonstrated to be a cell surface molecule involved in many physiological processes, such as vesicle trafficking. Here, we investigated the roles of PrPC in the response to insulin and obesity development. Two independent PrPC knockout (KO) and one PrPC overexpressing (TG20) mouse models were fed high-fat diets, and the development of insulin resistance and obesity was monitored. PrPC KO mice fed high-fat diets presented all of the symptoms associated with the development of insulin resistan...
Source: Biochemical Journal - August 17, 2017 Category: Biochemistry Authors: de Brito, G., Lupinacci, F. C., Beraldo, F. H., Santos, T. G., Roffe, M., Lopes, M. H., de Lima, V. C., Martins, V. R., Hajj, G. N. Tags: Research Articles Source Type: research

New insight on the S100A1-STIP1 complex highlights the important relationship between allostery and entropy in protein function
Calcium signaling serves as a nexus of many vital cellular processes. Of particular importance is the role the calcium signaling plays in the prevention of protein misfolding, and the S100 family of calcium-binding proteins is a key player in this pathway. While the S100 proteins carry out a range of roles, the interaction of S100A1 and the stress-inducible phosphoprotein 1 (STIP1) has been shown to be particularly important. A recent study by Maciejewski et al. in Biochemical Journal (Biochemical Journal (2017) 474, 1853–1866) revealed new insights into the nature of the S100A1–STIP1 interaction. Not only did ...
Source: Biochemical Journal - August 17, 2017 Category: Biochemistry Authors: Nucci, N. V. Tags: Commentaries Source Type: research

The AAA+ ATPase p97, a cellular multitool
The AAA+ (ATPases associated with diverse cellular activities) ATPase p97 is essential to a wide range of cellular functions, including endoplasmic reticulum-associated degradation, membrane fusion, NF-B (nuclear factor kappa-light-chain-enhancer of activated B cells) activation and chromatin-associated processes, which are regulated by ubiquitination. p97 acts downstream from ubiquitin signaling events and utilizes the energy from ATP hydrolysis to extract its substrate proteins from cellular structures or multiprotein complexes. A multitude of p97 cofactors have evolved which are essential to p97 function. Ubiquitin-inte...
Source: Biochemical Journal - August 17, 2017 Category: Biochemistry Authors: Stach, L., Freemont, P. S. Tags: Review Articles Source Type: research

GFI1 functions in transcriptional control and cell fate determination require SNAG domain methylation to recruit LSD1
(Source: Biochemical Journal)
Source: Biochemical Journal - August 11, 2017 Category: Biochemistry Authors: Velinder, M., Singer, J., Bareyan, D., Meznarich, J., Tracy, C. M., Fulcher, J. M., McClellan, D., Lucente, H., Franklin, S., Sharma, S., Engel, M. E. Tags: Corrections Source Type: research

The dual-function chaperone HycH improves assembly of the formate hydrogenlyase complex
The assembly of multi-protein complexes requires the concerted synthesis and maturation of its components and subsequently their co-ordinated interaction. The membrane-bound formate hydrogenlyase (FHL) complex is the primary hydrogen-producing enzyme in Escherichia coli and is composed of seven subunits mostly encoded within the hycA-I operon for [NiFe]-hydrogenase-3 (Hyd-3). The HycH protein is predicted to have an accessory function and is not part of the final structural FHL complex. In this work, a mutant strain devoid of HycH was characterised and found to have significantly reduced FHL activity due to the instability...
Source: Biochemical Journal - August 11, 2017 Category: Biochemistry Authors: Lindenstrauss, U., Skorupa, P., McDowall, J. S., Sargent, F., Pinske, C. Tags: Research Articles Source Type: research

The role of interactions of long non-coding RNAs and heterogeneous nuclear ribonucleoproteins in regulating cellular functions
Long non-coding RNAs (lncRNAs) are emerging as critical regulators of various biological processes and human diseases. The mechanisms of action involve their interactions with proteins, RNA and genomic DNA. Most lncRNAs display strong nuclear localization. Heterogeneous nuclear ribonucleoproteins (hnRNPs) are a large family of RNA-binding proteins that are important for multiple aspects of nucleic acid metabolism. hnRNPs are also predominantly expressed in the nucleus. This review discusses the interactions of lncRNAs and hnRNPs in regulating gene expression at transcriptional and post-transcriptional levels or by changing...
Source: Biochemical Journal - August 11, 2017 Category: Biochemistry Authors: Sun, X., Haider Ali, M. S. S., Moran, M. Tags: Review Articles Source Type: research

Phosphatases and solid tumors: focus on glioblastoma initiation, progression and recurrences
Phosphatases and cancer have been related for many years now, as these enzymes regulate key cellular functions, including cell survival, migration, differentiation and proliferation. Dysfunctions or mutations affecting these enzymes have been demonstrated to be key factors for oncogenesis. The aim of this review is to shed light on the role of four different phosphatases (PTEN, PP2A, CDC25 and DUSP1) in five different solid tumors (breast cancer, lung cancer, pancreatic cancer, prostate cancer and ovarian cancer), in order to better understand the most frequent and aggressive primary cancer of the central nervous system, g...
Source: Biochemical Journal - August 11, 2017 Category: Biochemistry Authors: Dedobbeleer, M., Willems, E., Freeman, S., Lombard, A., Goffart, N., Rogister, B. Tags: Review Articles Source Type: research

Correction: EGFR-mediated expression of aquaporin-3 is involved in human skin fibroblast migration
(Source: Biochemical Journal)
Source: Biochemical Journal - August 10, 2017 Category: Biochemistry Authors: Cao, C., Sun, Y., Healey, S., Bi, Z., Hu, G., Wan, S., Kouttab, N., Chu, W., Wan, Y. Tags: Corrections Source Type: research

Protein CoAlation: a redox-linked post-translational modification
Regulation of metabolic pathways by signal transduction and transcriptional cascades can alter cellular levels of metabolites. Metabolites themselves can also have regulatory activity as shown in a new study published in the Biochemical Journal. Tsuchiya et al. describe a novel antibody and mass spectrometry-based method for identifying proteins that are reversibly modified with Coenzyme A (CoA). Analysis of the ‘CoAlated proteome’ under conditions of oxidative and metabolic stress revealed a bias towards the modification of metabolic enzymes by CoA. Furthermore, CoAlation was shown to alter the activity of tar...
Source: Biochemical Journal - August 10, 2017 Category: Biochemistry Authors: Ley, S. C., de Carvalho, L. P. S. Tags: Commentaries Source Type: research

A strictly monofunctional bacterial hydroxymethylpyrimidine phosphate kinase precludes damaging errors in thiamin biosynthesis
The canonical kinase (ThiD) that converts the thiamin biosynthesis intermediate hydroxymethylpyrimidine (HMP) monophosphate into the diphosphate can also very efficiently convert free HMP into the monophosphate in prokaryotes, plants, and fungi. This HMP kinase activity enables salvage of HMP, but it is not substrate-specific and so allows toxic HMP analogs and damage products to infiltrate the thiamin biosynthesis pathway. Comparative analysis of bacterial genomes uncovered a gene, thiD2, that is often fused to the thiamin synthesis gene thiE and could potentially encode a replacement for ThiD. Standalone ThiD2 proteins a...
Source: Biochemical Journal - August 10, 2017 Category: Biochemistry Authors: Thamm, A. M., Li, G., Taja-Moreno, M., Gerdes, S. Y., de Crecy-Lagard, V., Bruner, S. D., Hanson, A. D. Tags: Research Articles Source Type: research

As-CATH1-6, novel cathelicidins with potent antimicrobial and immunomodulatory properties from Alligator sinensis, play pivotal roles in host antimicrobial immune responses
Crocodilians are regarded as possessing a powerful immune system. However, the composition and action of the crocodilian immune system have remained unclear until now. Cathelicidins, the principal family of host defense peptides, play pivotal roles in vertebrate immune defense against microbial invasions. However, cathelicidins from crocodilians have not been extensively studied to date. In the present study, six novel cathelicidins (As-CATH1–6) were identified and characterized from the endangered Chinese alligator (Alligator sinensis). As-CATH1–6 exhibit no sequence similarity with any of the known cathelicid...
Source: Biochemical Journal - August 10, 2017 Category: Biochemistry Authors: Chen, Y., Cai, S., Qiao, X., Wu, M., Guo, Z., Wang, R., Kuang, Y.-Q., Yu, H., Wang, Y. Tags: Research Articles Source Type: research

A centrosomal protein FOR20 regulates microtubule assembly dynamics and plays a role in cell migration
Here, we report that a centrosomal protein FOR20 [FOP (FGFR1 (fibroblast growth factor receptor 1) oncogene protein)-like protein of molecular mass of 20 kDa; also named as C16orf63, FLJ31153 or PHSECRG2] can regulate the assembly and stability of microtubules. Both FOR20 IgG antibody and GST (glutathione S-transferase)-tagged FOR20 could precipitate tubulin from the HeLa cell extract, indicating a possible interaction between FOR20 and tubulin. FOR20 was also detected in goat brain tissue extract and it cycled with microtubule-associated proteins. Furthermore, FOR20 bound to purified tubulin and inhibited the assembl...
Source: Biochemical Journal - August 10, 2017 Category: Biochemistry Authors: Srivastava, S., Panda, D. Tags: Research Articles Source Type: research

Potential mechanisms linking SIRT activity and hypoxic 2-hydroxyglutarate generation: no role for direct enzyme (de)acetylation
2-Hydroxyglutarate (2-HG) is a hypoxic metabolite with potentially important epigenetic signaling roles. The mechanisms underlying 2-HG generation are poorly understood, but evidence suggests a potential regulatory role for the sirtuin family of lysine deacetylases. Thus, we hypothesized that the acetylation status of the major 2-HG-generating enzymes [lactate dehydrogenase (LDH), isocitrate dehydrogenase (IDH) and malate dehydrogenase (MDH)] may govern their 2-HG-generating activity. In vitro acetylation of these enzymes, with confirmation by western blotting, mass spectrometry, reversibility by recombinant sirtuins and a...
Source: Biochemical Journal - August 10, 2017 Category: Biochemistry Authors: Nadtochiy, S. M., Wang, Y. T., Zhang, J., Nehrke, K., Schafer, X., Welle, K., Ghaemmaghami, S., Munger, J., Brookes, P. S. Tags: Research Articles Source Type: research

Structure of the PSD-95/MAP1A complex reveals a unique target recognition mode of the MAGUK GK domain
The PSD-95 family of membrane-associated guanylate kinases (MAGUKs) are major synaptic scaffold proteins and play crucial roles in the dynamic regulation of dendritic remodelling, which is understood to be the foundation of synaptogenesis and synaptic plasticity. The guanylate kinase (GK) domain of MAGUK family proteins functions as a phosphor-peptide binding module. However, the GK domain of PSD-95 has been found to directly bind to a peptide sequence within the C-terminal region of neuronal-specific microtubule-associated protein 1A (MAP1A), although the detailed molecular mechanism governing this phosphorylation-indepen...
Source: Biochemical Journal - August 10, 2017 Category: Biochemistry Authors: Xia, Y., Shang, Y., Zhang, R., Zhu, J. Tags: Research Articles Source Type: research

Ganglioside glycosyltransferases are S-acylated at conserved cysteine residues involved in homodimerisation
Ganglioside glycosyltransferases (GGTs) are type II membrane proteins bearing a short N-terminal cytoplasmic tail, a transmembrane domain (TMD), and a lumenal catalytic domain. The expression and activity of these enzymes largely determine the quality of the glycolipids that decorate mammalian cell membranes. Many glycosyltransferases (GTs) are themselves glycosylated, and this is important for their proper localisation, but few if any other post-translational modifications of these proteins have been reported. Here, we show that the GGTs, ST3Gal-V, ST8Sia-I, and β4GalNAcT-I are S-acylated at conserved cysteine residu...
Source: Biochemical Journal - August 7, 2017 Category: Biochemistry Authors: Chumpen Ramirez, S., Ruggiero, F. M., Daniotti, J. L., Valdez Taubas, J. Tags: Research Articles Source Type: research

Integration of flux measurements to resolve changes in anabolic and catabolic metabolism in cardiac myocytes
Although ancillary pathways of glucose metabolism are critical for synthesizing cellular building blocks and modulating stress responses, how they are regulated remains unclear. In the present study, we used radiometric glycolysis assays, [13C6]-glucose isotope tracing, and extracellular flux analysis to understand how phosphofructokinase (PFK)-mediated changes in glycolysis regulate glucose carbon partitioning into catabolic and anabolic pathways. Expression of kinase-deficient or phosphatase-deficient 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase in rat neonatal cardiomyocytes co-ordinately regulated glycolytic ra...
Source: Biochemical Journal - August 7, 2017 Category: Biochemistry Authors: Gibb, A. A., Lorkiewicz, P. K., Zheng, Y.-T., Zhang, X., Bhatnagar, A., Jones, S. P., Hill, B. G. Tags: Research Articles Source Type: research

The role of mass spectrometry analysis in bacterial effector characterization
Many secreted bacterial effector proteins play a critical role in host–pathogen interactions by mediating a variety of post-translational modifications, some of which do not occur natively within the eukaryotic proteome. The characterization of bacterial effector protein activity remains an important step to understanding the subversion of host cell biology during pathogen infection and although molecular biology and immunochemistry remain critical tools for gaining insights into bacterial effector functions, increasingly mass spectrometry (MS) and proteomic approaches are also playing an indispensable role. The focu...
Source: Biochemical Journal - August 7, 2017 Category: Biochemistry Authors: Scott, N. E., Hartland, E. L. Tags: Editorial Source Type: research

Carbohydrate-binding architecture of the multi-modular {alpha}-1,6-glucosyltransferase from Paenibacillus sp. 598K, which produces {alpha}-1,6-glucosyl-{alpha}-glucosaccharides from starch
Paenibacillus sp. 598K α-1,6-glucosyltransferase (Ps6TG31A), a member of glycoside hydrolase family 31, catalyzes exo-α-glucohydrolysis and transglucosylation and produces α-1,6-glucosyl-α-glucosaccharides from α-glucan via its disproportionation activity. The crystal structure of Ps6TG31A was determined by an anomalous dispersion method using a terbium derivative. The monomeric Ps6TG31A consisted of one catalytic (β/α)8-barrel domain and six small domains, one on the N-terminal and five on the C-terminal side. The structures of the enzyme complexed with maltohexaose, isomaltohexaos...
Source: Biochemical Journal - August 7, 2017 Category: Biochemistry Authors: Fujimoto, Z., Suzuki, N., Kishine, N., Ichinose, H., Momma, M., Kimura, A., Funane, K. Tags: Research Articles Source Type: research

Reduced threshold for store overload-induced Ca2+ release is a common defect of RyR1 mutations associated with malignant hyperthermia and central core disease
Mutations in the skeletal muscle ryanodine receptor (RyR1) cause malignant hyperthermia (MH) and central core disease (CCD), whereas mutations in the cardiac ryanodine receptor (RyR2) lead to catecholaminergic polymorphic ventricular tachycardia (CPVT). Most disease-associated RyR1 and RyR2 mutations are located in the N-terminal, central, and C-terminal regions of the corresponding ryanodine receptor (RyR) isoform. An increasing body of evidence demonstrates that CPVT-associated RyR2 mutations enhance the propensity for spontaneous Ca2+ release during store Ca2+ overload, a process known as store overload-induced Ca2+ rel...
Source: Biochemical Journal - August 7, 2017 Category: Biochemistry Authors: Chen, W., Koop, A., Liu, Y., Guo, W., Wei, J., Wang, R., MacLennan, D. H., Dirksen, R. T., Chen, S. R. W. Tags: Research Articles Source Type: research

Protease-activated receptor-2 promotes kidney tubular epithelial inflammation by inhibiting autophagy via the PI3K/Akt/mTOR signalling pathway
Protease-activated receptor-2 (PAR2), which belongs to a specific class of the G-protein-coupled receptors, is central to several inflammation processes. However, the precise molecular mechanism involved remains undefined. Autophagy has been previously shown to affect inflammation. In the present study, we examine the effect of PAR2 on kidney tubular epithelial autophagy and on autophagy-related inflammation and reveal the underlying mechanism involved. Autophagic activity and levels of autophagic marker LC3 were examined in human kidney tubular epithelial cells with PAR2 knockdown or overexpression. We administered the ma...
Source: Biochemical Journal - August 2, 2017 Category: Biochemistry Authors: Du, C., Zhang, T., Xiao, X., Shi, Y., Duan, H., Ren, Y. Tags: Research Articles Source Type: research

A meta-analysis and review examining a possible role for oxidative stress and singlet oxygen in diverse diseases
From kinetic data (k, T) we calculated the thermodynamic parameters for various processes (nucleation, elongation, fibrillization, etc.) of proteinaceous diseases that are related to the β-amyloid protein (Alzheimer's), to tau protein (Alzheimer's, Pick's), to α-synuclein (Parkinson's), prion, amylin (type II diabetes), and to α-crystallin (cataract). Our calculations led to G= values that vary in the range 92.8–127 kJ mol–1 at 310 K. A value of ~10–30 kJ mol–1 is the activation energy for the diffusion of reactants, depending on the reaction and the medium....
Source: Biochemical Journal - August 2, 2017 Category: Biochemistry Authors: Petrou, A. L., Terzidaki, A. Tags: Hypotheses Source Type: research

Understanding the molecular differential recognition of muramyl peptide ligands by LRR domains of human NOD receptors
Human nucleotide-binding oligomerization domain proteins, hNOD1 and hNOD2, are host intracellular receptors with C-terminal leucine-rich repeat (LRR) domains, which recognize specific bacterial peptidoglycan (PG) fragments as their ligands. The specificity of this recognition is dependent on the third amino acid of the stem peptide of the PG ligand, which is usually meso-diaminopimelic acid (mesoDAP) or l-lysine (l-Lys). Since the LRR domains of hNOD receptors had been experimentally shown to confer the PG ligand-sensing specificity, we developed three-dimensional structures of hNOD1-LRR and the hNOD2-LRR to understand the...
Source: Biochemical Journal - July 27, 2017 Category: Biochemistry Authors: Vijayrajratnam, S., Pushkaran, A. C., Balakrishnan, A., Vasudevan, A. K., Biswas, R., Mohan, C. G. Tags: Research Articles Source Type: research

pVHL suppresses Akt/{beta}-catenin-mediated cell proliferation by inhibiting 14-3-3{zeta} expression
The mechanisms controlling degradation of cytosolic β-catenin are important for regulating β-catenin co-transcriptional activity. Loss of von Hippel–Lindau protein (pVHL) has been shown to stabilize β-catenin, increasing β-catenin transactivation and β-catenin-mediated cell proliferation. However, the role of phosphoinositide 3-kinase (PI3K)/Akt in the regulation of β-catenin signaling downstream from pVHL has never been addressed. Here, we report that hyperactivation of PI3K/Akt in cells lacking pVHL contributes to the stabilization and nuclear accumulation of active β-catenin. PI3...
Source: Biochemical Journal - July 27, 2017 Category: Biochemistry Authors: Castaneda, A., Serrano, C., Hernandez-Trejo, J. A., Gutierrez-Martinez, I. Z., Montejo-Lopez, W., Gomez-Suarez, M., Hernandez-Ruiz, M., Betanzos, A., Candelario-Martinez, A., Romo-Parra, H., Arias-Montano, J. A., Schnoor, M., Meraz Rios, M. A., Gutierrez- Tags: Research Articles Source Type: research

Novel targeted therapies for cancer cachexia
Anorexia and metabolic alterations are the main components of the cachectic syndrome. Glucose intolerance, fat depletion, muscle protein catabolism and other alterations are involved in the development of cancer cachexia, a multi-organ syndrome. Nutritional approach strategies are not satisfactory in reversing the cachectic syndrome. The aim of the present review is to deal with the recent therapeutic targeted approaches that have been designed to fight and counteract wasting in cancer patients. Indeed, some promising targeted therapeutic approaches include ghrelin agonists, selective androgen receptor agonists, β-blo...
Source: Biochemical Journal - July 27, 2017 Category: Biochemistry Authors: Argiles, J. M., Lopez-Soriano, F. J., Stemmler, B., Busquets, S. Tags: Review Articles Source Type: research

Cross-talk of Brassinosteroid signaling in controlling growth and stress responses
Plants are faced with a barrage of stresses in their environment and must constantly balance their growth and survival. As such, plants have evolved complex control systems that perceive and respond to external and internal stimuli in order to optimize these responses, many of which are mediated by signaling molecules such as phytohormones. One such class of molecules called Brassinosteroids (BRs) are an important group of plant steroid hormones involved in numerous aspects of plant life including growth, development and response to various stresses. The molecular determinants of the BR signaling pathway have been extensiv...
Source: Biochemical Journal - July 27, 2017 Category: Biochemistry Authors: Nolan, T., Chen, J., Yin, Y. Tags: Review Articles Source Type: research

Agmatine: multifunctional arginine metabolite and magic bullet in clinical neuroscience?
Agmatine, the decarboxylation product of arginine, was largely neglected as an important player in mammalian metabolism until the mid-1990s, when it was re-discovered as an endogenous ligand of imidazoline and α2-adrenergic receptors. Since then, a wide variety of agmatine-mediated effects have been observed, and consequently agmatine has moved from a wallflower existence into the limelight of clinical neuroscience research. Despite this quantum jump in scientific interest, the understanding of the anabolism and catabolism of this amine is still vague. The purification and biochemical characterization of natural mamm...
Source: Biochemical Journal - July 26, 2017 Category: Biochemistry Authors: Laube, G., Bernstein, H.-G. Tags: Review Articles Source Type: research

Engineering a monomeric variant of macrophage colony-stimulating factor (M-CSF) that antagonizes the c-FMS receptor
Enhanced activation of the signaling pathways that mediate the differentiation of mononuclear monocytes into osteoclasts is an underlying cause of several bone diseases and bone metastasis. In particular, dysregulation and overexpression of macrophage colony-stimulating factor (M-CSF) and its c-FMS tyrosine kinase receptor, proteins that are essential for osteoclast differentiation, are known to promote bone metastasis and osteoporosis, making both the ligand and its receptor attractive targets for therapeutic intervention. With this aim in mind, our starting point was the previously held concept that the potential of the ...
Source: Biochemical Journal - July 20, 2017 Category: Biochemistry Authors: Zur, Y., Rosenfeld, L., Bakhman, A., Ilic, S., Hayun, H., Shahar, A., Akabayov, B., Kosloff, M., Levaot, N., Papo, N. Tags: Research Articles Source Type: research

Redox regulation of a guard cell SNF1-related protein kinase in Brassica napus, an oilseed crop
Kinase-mediated phosphorylation is a pivotal regulatory process in stomatal responses to stresses. Through a redox proteomics study, a sucrose non-fermenting 1-related protein kinase (SnRK2.4) was identified to be redox-regulated in Brassica napus guard cells upon abscisic acid treatment. There are six genes encoding SnRK2.4 paralogs in B. napus. Here, we show that recombinant BnSnRK2.4-1C exhibited autophosphorylation activity and preferentially phosphorylated the N-terminal region of B. napus slow anion channel (BnSLAC1-NT) over generic substrates. The in vitro activity of BnSnRK2.4-1C requires the presence of manganese ...
Source: Biochemical Journal - July 17, 2017 Category: Biochemistry Authors: Zhu, M., Zhang, T., Ji, W., Silva-Sanchez, C., Song, W.-y., Assmann, S. M., Harmon, A. C., Chen, S. Tags: Research Articles Source Type: research

{gamma}-COPI mediates the retention of kAE1 G701D protein in Golgi apparatus - a mechanistic explanation of distal renal tubular acidosis associated with the G701D mutation
Mutations of the solute carrier family 4 member 1 (SLC4A1) gene encoding kidney anion (chloride/bicarbonate ion) exchanger 1 (kAE1) can cause genetic distal renal tubular acidosis (dRTA). Different SLC4A1 mutations give rise to mutant kAE1 proteins with distinct defects in protein trafficking. The mutant kAE1 protein may be retained in endoplasmic reticulum (ER) or Golgi apparatus, or mis-targeted to the apical membrane, failing to display its function at the baso-lateral membrane. The ER-retained mutant kAE1 interacts with calnexin chaperone protein; disruption of this interaction permits the mutant kAE1 to reach the cell...
Source: Biochemical Journal - July 17, 2017 Category: Biochemistry Authors: Duangtum, N., Junking, M., Phadngam, S., Sawasdee, N., Castiglioni, A., Charngkaew, K., Limjindaporn, T., Isidoro, C., Yenchitsomanus, P.-t. Tags: Research Articles Source Type: research

Ascorbate protects the diheme enzyme, MauG, against self-inflicted oxidative damage by an unusual antioxidant mechanism
Ascorbate protects MauG from self-inactivation that occurs during the autoreduction of the reactive bis-FeIV state of its diheme cofactor. The mechanism of protection does not involve direct reaction with reactive oxygen species in solution. Instead, it binds to MauG and mitigates oxidative damage that occurs via internal transfer of electrons from amino acid residues within the protein to the high-valent hemes. The presence of ascorbate does not inhibit the natural catalytic reaction of MauG, which catalyzes oxidative post-translational modifications of a substrate protein that binds to the surface of MauG and is oxidized...
Source: Biochemical Journal - July 17, 2017 Category: Biochemistry Authors: Ma, Z., Davidson, V. L. Tags: Research Articles Source Type: research

Reactive sulfur species inactivate Ca2+/calmodulin-dependent protein kinase IV via S-polysulfidation of its active-site cysteine residue
Reactive sulfur species (RSS) modulate protein functions via S-polysulfidation of reactive Cys residues. Here, we report that Ca2+/calmodulin (CaM)-dependent protein kinase IV (CaMKIV) was reversibly inactivated by RSS via polysulfidation of the active-site Cys residue. CaMKIV is phosphorylated at Thr196 by its upstream CaMK kinase (CaMKK), resulting in the induction of its full activity. In vitro incubation of CaMKIV with the exogenous RSS donors Na2Sn (n = 2–4) resulted in dose-dependent inhibition of the CaMKK-induced phospho-Thr196 and consequent inactivation of the enzyme activity. Conversely, mutated CaMKIV (C1...
Source: Biochemical Journal - July 17, 2017 Category: Biochemistry Authors: Takata, T., Ihara, H., Hatano, N., Tsuchiya, Y., Akaike, T., Watanabe, Y. Tags: Research Articles Source Type: research

Protein trafficking in the mitochondrial intermembrane space: mechanisms and links to human disease
Mitochondria fulfill a diverse range of functions in cells including oxygen metabolism, homeostasis of inorganic ions and execution of apoptosis. Biogenesis of mitochondria relies on protein import pathways that are ensured by dedicated multiprotein translocase complexes localized in all sub-compartments of these organelles. The key components and pathways involved in protein targeting and assembly have been characterized in great detail over the last three decades. This includes the oxidative folding machinery in the intermembrane space, which contributes to the redox-dependent control of proteostasis. Here, we focus on s...
Source: Biochemical Journal - July 12, 2017 Category: Biochemistry Authors: MacPherson, L., Tokatlidis, K. Tags: Review Articles Source Type: research

Eukaryotic transcription factors: paradigms of protein intrinsic disorder
Gene-specific transcription factors (TFs) are key regulatory components of signaling pathways, controlling, for example, cell growth, development, and stress responses. Their biological functions are determined by their molecular structures, as exemplified by their structured DNA-binding domains targeting specific cis-acting elements in genes, and by the significant lack of fixed tertiary structure in their extensive intrinsically disordered regions. Recent research in protein intrinsic disorder (ID) has changed our understanding of transcriptional activation domains from ‘negative noodles’ to ID regions with f...
Source: Biochemical Journal - July 12, 2017 Category: Biochemistry Authors: Staby, L., O'Shea, C., Willemoës, M., Theisen, F., Kragelund, B. B., Skriver, K. Tags: Review Articles Source Type: research

Protein CoAlation: a redox-regulated protein modification by coenzyme A in mammalian cells
Coenzyme A (CoA) is an obligatory cofactor in all branches of life. CoA and its derivatives are involved in major metabolic pathways, allosteric interactions and the regulation of gene expression. Abnormal biosynthesis and homeostasis of CoA and its derivatives have been associated with various human pathologies, including cancer, diabetes and neurodegeneration. Using an anti-CoA monoclonal antibody and mass spectrometry, we identified a wide range of cellular proteins which are modified by covalent attachment of CoA to cysteine thiols (CoAlation). We show that protein CoAlation is a reversible post-translational modificat...
Source: Biochemical Journal - July 11, 2017 Category: Biochemistry Authors: Tsuchiya, Y., Peak-Chew, S. Y., Newell, C., Miller-Aidoo, S., Mangal, S., Zhyvoloup, A., Bakovic, J., Malanchuk, O., Pereira, G. C., Kotiadis, V., Szabadkai, G., Duchen, M. R., Campbell, M., Cuenca, S. R., Vidal-Puig, A., James, A. M., Murphy, M. P., Filo Tags: Research Articles Source Type: research

Hotspots of age-related protein degradation: the importance of neighboring residues for the formation of non-disulfide crosslinks derived from cysteine
Over time, the long-lived proteins that are present throughout the human body deteriorate. Typically, they become racemized, truncated, and covalently cross-linked. One reaction responsible for age-related protein cross-linking in the lens was elucidated recently and shown to involve spontaneous formation of dehydroalanine (DHA) intermediates from phosphoserine. Cys residues are another potential source of DHA, and evidence for this was found in many lens crystallins. In the human lens, some sites were more prone to forming non-disulfide covalent cross-links than others. Foremost among them was Cys5 in βA4 crystallin....
Source: Biochemical Journal - July 11, 2017 Category: Biochemistry Authors: Friedrich, M. G., Wang, Z., Oakley, A. J., Schey, K. L., Truscott, R. J. W. Tags: Research Articles Source Type: research

Transcription regulation mechanism of the syntaxin 1A gene via protein kinase A
Syntaxin 1A (Stx1a) is primarily involved in the docking of synaptic vesicles at active zones in neurons. Its gene is a TATA-less gene, with several transcription initiation sites, which is activated by the binding of Sp1 and acetylated histone H3 (H3) in the core promoter region (CPR) through the derepression of class I histone deacetylase (HDAC). In the present study, to clarify the factor characterizing Stx1a gene expression via the protein kinase A (PKA) pathway inducing the Stx1a mRNA, we investigated whether the epigenetic process is involved in the Stx1a gene transcription induced by PKA signaling. We found that the...
Source: Biochemical Journal - July 11, 2017 Category: Biochemistry Authors: Nakayama, T., Akagawa, K. Tags: Research Articles Source Type: research