Mechanisms of Hsp90 regulation
Heat shock protein 90 (Hsp90) is a molecular chaperone that is involved in the activation of disparate client proteins. This implicates Hsp90 in diverse biological processes that require a variety of co-ordinated regulatory mechanisms to control its activity. Perhaps the most important regulator is heat shock factor 1 (HSF1), which is primarily responsible for upregulating Hsp90 by binding heat shock elements (HSEs) within Hsp90 promoters. HSF1 is itself subject to a variety of regulatory processes and can directly respond to stress. HSF1 also interacts with a variety of transcriptional factors that help integrate biologic...
Source: Biochemical Journal - August 11, 2016 Category: Biochemistry Authors: Prodromou, C. Tags: Review articles Source Type: research

Physiological and pathophysiological functions of Swiprosin-1/EFhd2 in the nervous system
Synaptic dysfunction and dysregulation of Ca2+ are linked to neurodegenerative processes and behavioural disorders. Our understanding of the causes and factors involved in behavioural disorders and neurodegeneration, especially Alzheimer's disease (AD), a tau-related disease, is on the one hand limited and on the other hand controversial. Here, we review recent data about the links between the Ca2+-binding EF-hand-containing cytoskeletal protein Swiprosin-1/EFhd2 and neurodegeneration. Specifically, we summarize the functional biochemical data obtained in vitro with the use of recombinant EFhd2 protein, and integrated...
Source: Biochemical Journal - August 11, 2016 Category: Biochemistry Authors: Mielenz, D., Gunn-Moore, F. Tags: Review articles Source Type: research

Prestin and the good vibrations
In a recent paper published in the Biochemical Journal, Lolli et al. presented evidence that the C-terminal STAS (sulfate transporter and anti-sigma factor antagonist) domain of the motor protein prestin possesses an anion-binding site. This discovery might shed light on an aspect of the function of this mysterious and fascinating protein that is crucial for the human hearing system. (Source: Biochemical Journal)
Source: Biochemical Journal - July 28, 2016 Category: Biochemistry Authors: Birke, A. S., Javelle, A. Tags: Commentaries Source Type: research

Development of a high-affinity peptide that prevents phospholemman (PLM) inhibition of the sodium/calcium exchanger 1 (NCX1)
NCX1 (Na+/Ca2+ exchanger 1) is an important regulator of intracellular Ca2+ and a potential therapeutic target for brain ischaemia and for diastolic heart failure with preserved ejection fraction. PLM (phospholemman), a substrate for protein kinases A and C, has been suggested to regulate NCX1 activity. However, although several studies have demonstrated that binding of phosphorylated PLM (pSer68-PLM) leads to NCX1 inhibition, other studies have failed to demonstrate a functional interaction of these proteins. In the present study, we aimed to analyse the biological function of the pSer68-PLM–NCX1 interaction by deve...
Source: Biochemical Journal - July 28, 2016 Category: Biochemistry Authors: Wanichawan, P., Hodne, K., Hafver, T. L., Lunde, M., Martinsen, M., Louch, W. E., Sejersted, O. M., Carlson, C. R. Tags: Research articles Source Type: research

Releasing the brakes in coagulation Factor IXa by co-operative maturation of the substrate-binding site
Coagulation Factor IX is positioned at the merging point of the intrinsic and extrinsic blood coagulation cascades. Factor IXa (activated Factor IX) serves as the trigger for amplification of coagulation through formation of the so-called Xase complex, which is a ternary complex of Factor IXa, its substrate Factor X and the cofactor Factor VIIIa on the surface of activated platelets. Within the Xase complex the substrate turnover by Factor IXa is enhanced 200000-fold; however, the mechanistic and structural basis for this dramatic enhancement remains only partly understood. A multifaceted approach using enzymatic, biophysi...
Source: Biochemical Journal - July 28, 2016 Category: Biochemistry Authors: Kristensen, L. H., Olsen, O. H., Blouse, G. E., Brandstetter, H. Tags: Research articles Source Type: research

New GroEL-like chaperonin of bacteriophage OBP Pseudomonas fluorescens suppresses thermal protein aggregation in an ATP-dependent manner
Recently, we discovered and studied the first virus-encoded chaperonin of bacteriophage EL Pseudomonas aeruginosa, gene product (gp) 146. In the present study, we performed bioinformatics analysis of currently predicted GroEL-like proteins encoded by phage genomes in comparison with cellular and mitochondrial chaperonins. Putative phage chaperonins share a low similarity and do not form a monophyletic group; nevertheless, they are closer to bacterial chaperonins in the phylogenetic tree. Experimental investigation of putative GroEL-like chaperonin proteins has been continued by physicochemical and functional characterizati...
Source: Biochemical Journal - July 28, 2016 Category: Biochemistry Authors: Semenyuk, P. I., Orlov, V. N., Sokolova, O. S., Kurochkina, L. P. Tags: Research articles Source Type: research

Substrate specificity and mapping of residues critical for transport in the high-affinity glutathione transporter Hgt1p
The high-affinity glutathione transporter Hgt1p of Saccharomyces cerevisiae belongs to a relatively new and structurally uncharacterized oligopeptide transporter (OPT) family. To understand the structural features required for interaction with Hgt1p, a quantitative investigation of substrate specificity of Hgt1p was carried out. Hgt1p showed a higher affinity for reduced glutathione (GSH), whereas it transported oxidized glutathione (GSSG) and other glutathione conjugates with lower affinity. To identify the residues of Hgt1p critical for substrate binding and translocation, all amino acid residues of the 13 predicted tran...
Source: Biochemical Journal - July 28, 2016 Category: Biochemistry Authors: Zulkifli, M., Yadav, S., Thakur, A., Singla, S., Sharma, M., Bachhawat, A. K. Tags: Research articles Source Type: research

Crystal structures of the ligand-binding region of uPARAP: effect of calcium ion binding
We report the crystal structures of the first four domains of uPARAP (also named the ligand-binding region, LBR) at pH 7.4 in Ca2+-bound and Ca2+-free forms. The first domain (cysteine-rich or CysR domain) folds into a new and unique conformation different from the β-trefoil fold of typical CysR domains. The so-called long loop regions (LLRs) of the C-type lectin-like domain (CTLD) 1 and 2 (the third and fourth domain) mediate the direct contacts between these domains. These LLRs undergo a Ca2+-dependent conformational change, and this is likely to be the key structural determinant affecting the overall conformat...
Source: Biochemical Journal - July 28, 2016 Category: Biochemistry Authors: Yuan, C., Jurgensen, H. J., Engelholm, L. H., Li, R., Liu, M., Jiang, L., Luo, Z., Behrendt, N., Huang, M. Tags: Research articles Source Type: research

Discovery, characterization and in vivo activity of pyocin SD2, a protein antibiotic from Pseudomonas aeruginosa
Increasing rates of antibiotic resistance among Gram-negative pathogens such as Pseudomonas aeruginosa means alternative approaches to antibiotic development are urgently required. Pyocins, produced by P. aeruginosa for intraspecies competition, are highly potent protein antibiotics known to actively translocate across the outer membrane of P. aeruginosa. Understanding and exploiting the mechanisms by which pyocins target, penetrate and kill P. aeruginosa is a promising approach to antibiotic development. In this work we show the therapeutic potential of a newly identified tRNase pyocin, pyocin SD2, by demonstrating i...
Source: Biochemical Journal - July 28, 2016 Category: Biochemistry Authors: McCaughey, L. C., Josts, I., Grinter, R., White, P., Byron, O., Tucker, N. P., Matthews, J. M., Kleanthous, C., Whitchurch, C. B., Walker, D. Tags: Research articles Source Type: research

E2F and GATA switches turn off WD repeat domain 77 expression in differentiating cells
WDR77 (WD repeat domain 77) is expressed during earlier lung development when cells are rapidly proliferating, but is absent from adult lung. It is re-activated during lung tumorigenesis and is essential for lung cancer cell proliferation. Signalling pathways/molecules that control WDR77 gene expression are unknown. Promoter mapping, gel shift assay and ChIP revealed that the WDR77 promoter contains bona fide response elements for E2F and GATA transcriptional factors as demonstrated in prostate cancer, lung cancer and erythroid cells, as well as in mouse lung tissues. The WDR77 promoter is transactivated by E2F1, E2F3, GAT...
Source: Biochemical Journal - July 28, 2016 Category: Biochemistry Authors: Yu, M., Wang, U., Wang, Z. Tags: Research articles Source Type: research

Biosynthesis of polyamines and polyamine-containing molecules
Polyamines are evolutionarily ancient polycations derived from amino acids and are pervasive in all domains of life. They are essential for cell growth and proliferation in eukaryotes and are essential, important or dispensable for growth in bacteria. Polyamines present a useful scaffold to attach other moieties to, and are often incorporated into specialized metabolism. Life has evolved multiple pathways to synthesize polyamines, and structural variants of polyamines have evolved in bacteria, archaea and eukaryotes. Among the complex biosynthetic diversity, patterns of evolutionary reiteration can be distinguished, reveal...
Source: Biochemical Journal - July 28, 2016 Category: Biochemistry Authors: Michael, A. J. Tags: Review articles Source Type: research

Unravelling the mechanisms regulating muscle mitochondrial biogenesis
Skeletal muscle is a tissue with a low mitochondrial content under basal conditions, but it is responsive to acute increases in contractile activity patterns (i.e. exercise) which initiate the signalling of a compensatory response, leading to the biogenesis of mitochondria and improved organelle function. Exercise also promotes the degradation of poorly functioning mitochondria (i.e. mitophagy), thereby accelerating mitochondrial turnover, and preserving a pool of healthy organelles. In contrast, muscle disuse, as well as the aging process, are associated with reduced mitochondrial quality and quantity in muscle. This has ...
Source: Biochemical Journal - July 28, 2016 Category: Biochemistry Authors: Hood, D. A., Tryon, L. D., Carter, H. N., Kim, Y., Chen, C. C. W. Tags: Review articles Source Type: research

Inhibitory serpins. New insights into their folding, polymerization, regulation and clearance
Serpins are a widely distributed family of high molecular mass protein proteinase inhibitors that can inhibit both serine and cysteine proteinases by a remarkable mechanism-based kinetic trapping of an acyl or thioacyl enzyme intermediate that involves massive conformational transformation. The trapping is based on distortion of the proteinase in the complex, with energy derived from the unique metastability of the active serpin. Serpins are the favoured inhibitors for regulation of proteinases in complex proteolytic cascades, such as are involved in blood coagulation, fibrinolysis and complement activation, by virtue of t...
Source: Biochemical Journal - July 28, 2016 Category: Biochemistry Authors: Gettins, P. G. W., Olson, S. T. Tags: Review articles Source Type: research

The intricate regulation and complex functions of the Class III phosphoinositide 3-kinase Vps34
The Class III phosphoinositide 3-kinase Vps34 (vacuolar protein sorting 34) plays important roles in endocytic trafficking, macroautophagy, phagocytosis, cytokinesis and nutrient sensing. Recent studies have provided exciting new insights into the structure and regulation of this lipid kinase, and new cellular functions for Vps34 have emerged. This review critically examines the wealth of new data on this important enzyme, and attempts to integrate these findings with current models of Vps34 signalling. (Source: Biochemical Journal)
Source: Biochemical Journal - July 28, 2016 Category: Biochemistry Authors: Backer, J. M. Tags: Review articles Source Type: research

Correction: Chemical ubiquitination for decrypting a cellular code
(Source: Biochemical Journal)
Source: Biochemical Journal - July 12, 2016 Category: Biochemistry Authors: Stanley, M., Virdee, S. Tags: Corrections Source Type: research

Structural basis of the signalling through a bacterial membrane receptor HasR deciphered by an integrative approach
Bacteria use diverse signalling pathways to adapt gene expression to external stimuli. In Gram-negative bacteria, the binding of scarce nutrients to membrane transporters triggers a signalling process that up-regulates the expression of genes of various functions, from uptake of nutrient to production of virulence factors. Although proteins involved in this process have been identified, signal transduction through this family of transporters is not well understood. In the present study, using an integrative approach (EM, SAXS, X-ray crystallography and NMR), we have studied the structure of the haem transporter HasR captur...
Source: Biochemical Journal - July 12, 2016 Category: Biochemistry Authors: Wojtowicz, H., Prochnicka-Chalufour, A., de Amorim, G. C., Roudenko, O., Simenel, C., Malki, I., Pehau-Arnaudet, G., Gubellini, F., Koutsioubas, A., Perez, J., Delepelaire, P., Delepierre, M., Fronzes, R., Izadi-Pruneyre, N. Tags: Research articles Source Type: research

The role of fibrinogen glycation in ATTR: evidence for chaperone activity loss in disease
Transthyretin amyloidosis (ATTR) belongs to a class of disorders caused by protein misfolding and aggregation. ATTR is a disabling disorder of autosomal dominant trait, where transthyretin (TTR) forms amyloid deposits in different organs, causing dysfunction of the peripheral nervous system. We previously discovered that amyloid fibrils from ATTR patients are glycated by methylglyoxal. Even though no consensus has been reached about the actual role of methylglyoxal-derived advanced glycation end-products in amyloid diseases, evidence collected so far points to a role for protein glycation in conformational abnormalities, b...
Source: Biochemical Journal - July 12, 2016 Category: Biochemistry Authors: Fonseca, D., Gilberto, S., Ribeiro-Silva, C., Ribeiro, R., Guinote, I. B., Saraiva, S., Gomes, R. A., Mateus, E., Viana, A., Barroso, E., Freire, A. P., Freire, P., Cordeiro, C., da Costa, G. Tags: Research articles Source Type: research

Complexin splits the membrane-proximal region of a single SNAREpin
Complexin (Cpx) is thought to be a major regulator of soluble N-ethylmaleimide-sensitive factor-attachment protein receptor (SNARE)-dependent membrane fusion. Although the inhibition of membrane fusion by Cpx has been frequently reported, its structural basis has been elusive and an anticipated disruption of the SNARE core has never been observed. In the present study, to mimic the natural environment, we assembled a single SNAREpin between two nanodisc membrane patches. Single-molecule FRET (smFRET) detects a large conformational change, specifically at the C-terminal half, whereas no conformational change is observed at ...
Source: Biochemical Journal - July 12, 2016 Category: Biochemistry Authors: Yin, L., Kim, J., Shin, Y.-K. Tags: Research articles Source Type: research

Foxa2 and Hif1ab regulate maturation of intestinal goblet cells by modulating agr2 expression in zebrafish embryos
Mammalian anterior gradient 2 (AGR2), an endoplasmic reticulum (ER) protein disulfide-isomerase (PDI), is involved in cancer cell growth and metastasis, asthma and inflammatory bowel disease (IBD). Mice lacking Agr2 exhibit decreased Muc2 protein in intestinal goblet cells, abnormal Paneth cell development, ileitis and colitis. Despite its importance in cancer biology and inflammatory diseases, the mechanisms regulating agr2 expression in the gastrointestinal tract remain unclear. In the present study, we investigated the mechanisms that control agr2 expression in the pharynx and intestine of zebrafish by transient/stable ...
Source: Biochemical Journal - July 12, 2016 Category: Biochemistry Authors: Lai, Y.-R., Lu, Y.-F., Lien, H.-W., Huang, C.-J., Hwang, S.-P. L. Tags: Research articles Source Type: research

New insight on obesity and adipose-derived stem cells using comprehensive metabolomics
Obesity affects the functional capability of adipose-derived stem cells (ASCs) and their effective use in regenerative medicine through mechanisms that are still poorly understood. In the present study we used a multiplatform [LC/MS, GC/MS and capillary electrophoresis/MS (CE/MS)], metabolomics, untargeted approach to investigate the metabolic alteration underlying the inequalities observed in obesity-derived ASCs. The metabolic fingerprint (metabolites within the cells) and footprint (metabolites secreted in the culture medium), from obesity- and non-obesity-derived ASCs of humans or mice, were characterized to provide va...
Source: Biochemical Journal - July 12, 2016 Category: Biochemistry Authors: Mastrangelo, A., Panadero, M. I., Perez, L. M., Galvez, B. G., Garcia, A., Barbas, C., Ruperez, F. J. Tags: Research articles Source Type: research

Actinin-1 binds to the C-terminus of A2B adenosine receptor (A2BAR) and enhances A2BAR cell-surface expression
A2BAR (A2B adenosine receptor) has been implicated in several physiological conditions, such as allergic or inflammatory disorders, vasodilation, cell growth and epithelial electrolyte secretion. For mediating the protein–protein interactions of A2BAR, the receptor's C-terminus is recognized to be crucial. In the present study, we unexpectedly found that two point mutations in the A2BAR C-terminus (F297A and R298A) drastically impaired the expression of A2BAR protein by accelerating its degradation. Thus we tested the hypothesis that these two point mutations disrupt A2BAR's interaction with a protein essential for A...
Source: Biochemical Journal - July 12, 2016 Category: Biochemistry Authors: Sun, Y., Hu, W., Yu, X., Liu, Z., Tarran, R., Ravid, K., Huang, P. Tags: Research articles Source Type: research

Catalytic and substrate promiscuity: distinct multiple chemistries catalysed by the phosphatase domain of receptor protein tyrosine phosphatase
The presence of latent activities in enzymes is posited to underlie the natural evolution of new catalytic functions. However, the prevalence and extent of such substrate and catalytic ambiguity in evolved enzymes is difficult to address experimentally given the order-of-magnitude difference in the activities for native and, sometimes, promiscuous substrate/s. Further, such latent functions are of special interest when the activities concerned do not fall into the domain of substrate promiscuity. In the present study, we show a special case of such latent enzyme activity by demonstrating the presence of two mechanistically...
Source: Biochemical Journal - July 12, 2016 Category: Biochemistry Authors: Srinivasan, B., Marks, H., Mitra, S., Smalley, D. M., Skolnick, J. Tags: Research articles Source Type: research

Nuclear localizations of phosphatidylinositol 5-phosphate 4-kinases {alpha} and {beta} are dynamic and independently regulated during starvation-induced stress
The chicken B-cell line DT40 has two isoforms of phosphatidylinositol 5-phosphate 4-kinase (PI5P4K), α and β, which are likely to exist as a mixture of obligate homo- and hetero-dimers. Previous work has led us to speculate that an important role of the β isoform may be to target the more active PI5P4Kα isoform to the nucleus. In the present study we expand upon that work by genomically tagging the PI5P4Ks with fluorochromes in the presence or absence of stable or acute depletions of PI5P4Kβ. Consistent with our original hypothesis we find that PI5P4Kα is predominantly (possible entirely) c...
Source: Biochemical Journal - July 12, 2016 Category: Biochemistry Authors: Droubi, A., Bulley, S. J., Clarke, J. H., Irvine, R. F. Tags: Research articles Source Type: research

Selenophosphate synthetase 1 is an essential protein with roles in regulation of redox homoeostasis in mammals
Selenophosphate synthetase (SPS) was initially detected in bacteria and was shown to synthesize selenophosphate, the active selenium donor. However, mammals have two SPS paralogues, which are designated SPS1 and SPS2. Although it is known that SPS2 catalyses the synthesis of selenophosphate, the function of SPS1 remains largely unclear. To examine the role of SPS1 in mammals, we generated a Sps1-knockout mouse and found that systemic SPS1 deficiency led to embryos that were clearly underdeveloped by embryonic day (E)8.5 and virtually resorbed by E14.5. The knockout of Sps1 in the liver preserved viability, but significantl...
Source: Biochemical Journal - July 12, 2016 Category: Biochemistry Authors: Tobe, R., Carlson, B. A., Huh, J. H., Castro, N. P., Xu, X.-M., Tsuji, P. A., Lee, S.-G., Bang, J., Na, J.-W., Kong, Y.-Y., Beaglehole, D., Southon, E., Seifried, H., Tessarollo, L., Salomon, D. S., Schweizer, U., Gladyshev, V. N., Hatfield, D. L., Lee, B Tags: Research articles Source Type: research

miR-30a can inhibit DNA replication by targeting RPA1 thus slowing cancer cell proliferation
Cell proliferation was inhibited following forced over-expression of miR-30a in the ovary cancer cell line A2780DX5 and the gastric cancer cell line SGC7901R. Interestingly, miR-30a targets the DNA replication protein RPA1, hinders the replication of DNA and induces DNA fragmentation. Furthermore, ataxia telangiectasia mutated (ATM) and checkpoint kinase 2 (CHK2) were phosphorylated after DNA damage, which induced p53 expression, thus triggering the S-phase checkpoint, arresting cell cycle progression and ultimately initiating cancer cell apoptosis. Therefore, forced miR-30a over-expression in cancer cells can be a potenti...
Source: Biochemical Journal - July 12, 2016 Category: Biochemistry Authors: Zou, Z., Ni, M., Zhang, J., Chen, Y., Ma, H., Qian, S., Tang, L., Tang, J., Yao, H., Zhao, C., Lu, X., Sun, H., Qian, J., Mao, X., Lu, X., Liu, Q., Zen, J., Wu, H., Bao, Z., Lin, S., Sheng, H., Li, Y., Liang, Y., Chen, Z., Zong, D. Tags: Research articles Source Type: research

Domains of STIP1 responsible for regulating PrPC-dependent amyloid-{beta} oligomer toxicity
Soluble oligomers of amyloid-beta peptide (AβO) transmit neurotoxic signals through the cellular prion protein (PrPC) in Alzheimer's disease (AD). Secreted stress-inducible phosphoprotein 1 (STIP1), an Hsp70 and Hsp90 cochaperone, inhibits AβO binding to PrPC and protects neurons from AβO-induced cell death. Here, we investigated the molecular interactions between AβO and STIP1 binding to PrPC and their effect on neuronal cell death. We showed that residues located in a short region of PrP (90–110) mediate AβO binding and we narrowed the major interaction in this site to amino acids 91–...
Source: Biochemical Journal - July 12, 2016 Category: Biochemistry Authors: Maciejewski, A., Ostapchenko, V. G., Beraldo, F. H., Prado, V. F., Prado, M. A. M., Choy, W.-Y. Tags: Research articles Source Type: research

Characterization of a high-affinity sialic acid-specific CBM40 from Clostridium perfringens and engineering of a divalent form
CBMs (carbohydrate-binding modules) are a class of polypeptides usually associated with carbohydrate-active enzymatic sites. We have characterized a new member of the CBM40 family, coded from a section of the gene NanI from Clostridium perfringens. Glycan arrays revealed its preference towards α(2,3)-linked sialosides, which was confirmed and quantified by calorimetric studies. The CBM40 binds to α(2,3)-sialyl-lactose with a Kd of ~30 μM, the highest affinity value for this class of proteins. Inspired by lectins' structure and their arrangement as multimeric proteins, we have engineered a dimeric form o...
Source: Biochemical Journal - July 12, 2016 Category: Biochemistry Authors: Ribeiro, J. P., Pau, W., Pifferi, C., Renaudet, O., Varrot, A., Mahal, L. K., Imberty, A. Tags: Research articles Source Type: research

An asparagine residue mediates intramolecular communication in nucleotide-regulated pyrophosphatase
We reported previously that CBS domains bind nucleotides co-operatively and induce positive kinetic co-operativity (non-Michaelian behaviour) in CBS-PPases (CBS domain-containing PPases). In the present study, we demonstrate that a homodimeric ehPPase (Ethanoligenens harbinense PPase) containing an inherent mutation in an otherwise conserved asparagine residue in a loop near the active site exhibits non-co-operative hydrolysis kinetics. A similar N312S substitution in ‘co-operative’ dhPPase (Desulfitobacterium hafniense PPase) abolished kinetic co-operativity while causing only minor effects on nucleotide-bindi...
Source: Biochemical Journal - July 12, 2016 Category: Biochemistry Authors: Anashkin, V. A., Salminen, A., Vorobjeva, N. N., Lahti, R., Baykov, A. A. Tags: Research articles Source Type: research

Congenital microcornea-cataract syndrome-causing mutation X253R increases {beta}B1-crystallin hydrophobicity to promote aggregate formation
The high solubility and lifelong stability of crystallins are crucial to the maintenance of lens transparency and optical properties. Numerous crystallin mutations have been linked to congenital cataract, which is one of the leading causes of newborn blindness. Besides cataract, several crystallin mutations have also been linked to syndromes such as congenital microcornea-cataract syndrome (CMCC). However, the molecular mechanism of CMCC caused by crystallin mutations remains elusive. In the present study, we investigated the mechanism of CMCC caused by the X253R mutation in βB1-crystallin. The exogenously expressed X...
Source: Biochemical Journal - July 12, 2016 Category: Biochemistry Authors: Leng, X.-Y., Li, H.-Y., Wang, J., Qi, L.-B., Xi, Y.-B., Yan, Y.-B. Tags: Research articles Source Type: research

The conserved protein Dre2 uses essential [2Fe-2S] and [4Fe-4S] clusters for its function in cytosolic iron-sulfur protein assembly
The cytosolic iron–sulfur (Fe–S) protein assembly (CIA) machinery comprises 11 essential components and matures Fe–S proteins involved in translation and genome maintenance. Maturation is initiated by the electron transfer chain NADPH–diflavin reductase Tah18–Fe–S protein Dre2 that facilitates the de novo assembly of a [4Fe–4S] cluster on the scaffold complex Cfd1-Nbp35. Tah18-Dre2 also play a critical role in the assembly of the diferric tyrosyl radical cofactor of ribonucleotide reductase. Dre2 contains eight conserved cysteine residues as potential co-ordinating ligands for Fe&n...
Source: Biochemical Journal - July 12, 2016 Category: Biochemistry Authors: Netz, D. J. A., Genau, H. M., Weiler, B. D., Bill, E., Pierik, A. J., Lill, R. Tags: Research articles Source Type: research

8,9-Dehydrohispanolone-15,16-lactol diterpene prevents LPS-triggered inflammatory responses by inhibiting endothelial activation
Endothelial activation contributes to lung inflammatory disorders by inducing leucocyte recruitment to pulmonary parenchyma. Consequently, vascular-targeted therapies constitute promising strategies for the treatment of inflammatory pathologies. In the present study, we evaluated the effect of 8,9-dehydrohispanolone-15,16-lactol diterpene (DT) on lung endothelium during inflammation. Lung endothelial cells pre-treated with DT and activated with lipopolysaccharide (LPS) or tumour necrosis factor-α (TNF-α) exhibited reduced expression of the pro-inflammatory cytokines Cxcl10, Ccl5 and Cxcl1, whereas the anti-infl...
Source: Biochemical Journal - July 12, 2016 Category: Biochemistry Authors: Jimenez-Garcia, L., Traves, P. G., Lopez-Fontal, R., Herranz, S., Higueras, M. A., de las Heras, B., Hortelano, S., Luque, A. Tags: Research articles Source Type: research

FKBPs facilitate the termination of spontaneous Ca2+ release in wild-type RyR2 but not CPVT mutant RyR2
FK506-binding proteins 12.6 (FKBP12.6) and 12 (FKBP12) tightly associate with the cardiac ryanodine receptor (RyR2). Studies suggest that dissociation of FKBP12.6 from mutant forms of RyR2 contributes to store overload-induced Ca2+ release (SOICR) and Ca2+-triggered arrhythmias. However, these findings are controversial. Previous studies focused on the effect of FKBP12.6 on the initiation of SOICR and did not explore changes in the termination of Ca2+ release. Less is known about FKBP12. We aimed to determine the effect of FKBP12.6 and FKBP12 on the termination of SOICR. Using single-cell imaging, in cells expressing wild-...
Source: Biochemical Journal - July 12, 2016 Category: Biochemistry Authors: Zhang, J. Z., Waddell, H. M. M., Wu, E., Dholakia, J., Okolo, C. A., McLay, J. C., Jones, P. P. Tags: Research articles Source Type: research

A polybasic motif in ErbB3-binding protein 1 (EBP1) has key functions in nucleolar localization and polyphosphoinositide interaction
Polyphosphoinositides (PPIns) are present in the nucleus where they participate in crucial nuclear processes, such as chromatin remodelling, transcription and mRNA processing. In a previous interactomics study, aimed to gain further insight into nuclear PPIns functions, we identified ErbB3 binding protein 1 (EBP1) as a potential nuclear PPIn-binding protein in a lipid pull-down screen. EBP1 is a ubiquitous and conserved protein, located in both the cytoplasm and nucleolus, and associated with cell proliferation and survival. In the present study, we show that EBP1 binds directly to several PPIns via two distinct PPIn-bindi...
Source: Biochemical Journal - July 12, 2016 Category: Biochemistry Authors: Karlsson, T., Altankhuyag, A., Dobrovolska, O., Turcu, D. C., Lewis, A. E. Tags: Research articles Source Type: research

Structure and function of carbonic anhydrases
Carbonic anhydrases (CAs, EC 4.2.1.1) catalyse the interconversion between CO2 and bicarbonate as well as other hydrolytic reactions. Among the six genetic families known to date, the α-, β-, -, -, - and -CAs, detailed kinetic and X-ray crystallographic studies have allowed a deep understanding of the structure–function relationship in this superfamily of proteins. A metal hydroxide nucleophilic species of the enzyme, and a unique active site architecture, with half of it hydrophilic and the opposing part hydrophobic, allow these enzymes to act as some of the most effective catalysts known in Nature. The C...
Source: Biochemical Journal - July 12, 2016 Category: Biochemistry Authors: Supuran, C. T. Tags: Review articles Source Type: research

The ADAMTS hyalectanase family: biological insights from diverse species
The a disintegrin-like and metalloproteinase with thrombospondin type-1 motifs (ADAMTS) family of metzincins are complex secreted proteins that have diverse functions during development. The hyalectanases (ADAMTS1, 4, 5, 8, 9, 15 and 20) are a subset of this family that have enzymatic activity against hyalectan proteoglycans, the processing of which has important implications during development. This review explores the evolution, expression and developmental functions of the ADAMTS family, focusing on the ADAMTS hyalectanases and their substrates in diverse species. This review gives an overview of how the family and thei...
Source: Biochemical Journal - July 12, 2016 Category: Biochemistry Authors: Dancevic, C. M., McCulloch, D. R., Ward, A. C. Tags: Review articles Source Type: research

Protein lysine methylation by seven-{beta}-strand methyltransferases
Methylation of biomolecules is a frequent biochemical reaction within the cell, and a plethora of highly specific methyltransferases (MTases) catalyse the transfer of a methyl group from S-adenosylmethionine (AdoMet) to various substrates. The posttranslational methylation of lysine residues, catalysed by numerous lysine (K)-specific protein MTases (KMTs), is a very common and important protein modification, which recently has been subject to intense studies, particularly in the case of histone proteins. The majority of KMTs belong to a class of MTases that share a defining ‘SET domain’, and these enzymes mostl...
Source: Biochemical Journal - July 12, 2016 Category: Biochemistry Authors: Falnes, P. O., Jakobsson, M. E., Davydova, E., Ho, A., Małecki, J. Tags: Review articles Source Type: research

Dysregulation of intracellular trafficking and endosomal sorting in Alzheimer's disease: controversies and unanswered questions
Alzheimer's disease (AD) is characterized by the accumulation of amyloid plaques in the brain consisting of an aggregated form of amyloid β-peptide (Aβ) derived from sequential amyloidogenic processing of the amyloid precursor protein (APP) by membrane-bound proteases β-site APP-cleaving enzyme 1 (BACE1) and -secretase. The initial processing of APP by BACE1 is re-gulated by intracellular sorting events of the enzyme, which is a prime target for therapeutic intervention. GWAS (genome-wide sequencing studies) have identified several AD-susceptibility genes that are associated with the regulation of membrane t...
Source: Biochemical Journal - July 12, 2016 Category: Biochemistry Authors: Toh, W. H., Gleeson, P. A. Tags: Review articles Source Type: research

Transcription factors YY1, Sp1 and Sp3 modulate dystrophin Dp71 gene expression in hepatic cells
Dystrophin Dp71, the smallest product encoded by the Duchenne muscular dystrophy gene, is ubiquitously expressed in all non-muscle cells. Although Dp71 is involved in various cellular processes, the mechanisms underlying its expression have been little studied. In hepatic cells, Dp71 expression is down-regulated by the xenobiotic β-naphthoflavone. However, the effectors of this regulation remain unknown. In the present study we aimed at identifying DNA elements and transcription factors involved in Dp71 expression in hepatic cells. Relevant DNA elements on the Dp71 promoter were identified by comparing Dp71 5'-end fla...
Source: Biochemical Journal - June 28, 2016 Category: Biochemistry Authors: Penuelas-Urquides, K., Becerril-Esquivel, C., Mendoza-de-Leon, L. C., Silva-Ramirez, B., Davila-Velderrain, J., Cisneros, B., de Leon, M. B. Tags: Research articles Source Type: research

Physical and functional interactions between the serotonin transporter and the neutral amino acid transporter ASCT2
The activity of serotonergic systems depends on the reuptake of extracellular serotonin via its plasma membrane serotonin [5-HT (5-hydroxytryptamine)] transporter (SERT), a member of the Na+/Cl–-dependent solute carrier 6 family. SERT is finely regulated by multiple molecular mechanisms including its physical interaction with intracellular proteins. The majority of previously identified SERT partners that control its functional activity are soluble proteins, which bind to its intracellular domains. SERT also interacts with transmembrane proteins, but its association with other plasma membrane transporters remains to ...
Source: Biochemical Journal - June 28, 2016 Category: Biochemistry Authors: Seyer, P., Vandermoere, F., Cassier, E., Bockaert, J., Marin, P. Tags: Research articles Source Type: research

EssC: domain structures inform on the elusive translocation channel in the Type VII secretion system
We present crystal structures of the N-terminal FHA domains (EssC-N) and a C-terminal fragment EssC-C from Geobacillus thermodenitrificans, encompassing two of the ATPase-type modules, D2 and D3. Module D2 binds ATP with high affinity whereas D3 does not. The EssC-N and EssC-C constructs are monomeric in solution, but the full-length recombinant protein, with a molecular mass of approximately 169 kDa, forms a multimer of approximately 1 MDa. The observation of protomer contacts in the crystal structure of EssC-C together with similarity to the DNA translocase FtsK, suggests a model for a hexameric EssC assembly. Such ...
Source: Biochemical Journal - June 28, 2016 Category: Biochemistry Authors: Zoltner, M., Ng, W. M. A. V., Money, J. J., Fyfe, P. K., Kneuper, H., Palmer, T., Hunter, W. N. Tags: Research articles Source Type: research

Dissecting the role of ADAM10 as a mediator of Staphylococcus aureus {alpha}-toxin action
Staphylococcus aureus is a leading cause of bacterial infections in humans, including life-threatening diseases such as pneumonia and sepsis. Its small membrane-pore-forming α-toxin is considered an important virulence factor. By destroying cell–cell contacts through cleavage of cadherins, the metalloproteinase ADAM10 (a disintegrin and metalloproteinase 10) critically contributes to α-toxin-dependent pathology of experimental S. aureus infections in mice. Moreover, ADAM10 was proposed to be a receptor for α-toxin. However, it is unclear whether the catalytic activity or specific domains of ADAM10 a...
Source: Biochemical Journal - June 28, 2016 Category: Biochemistry Authors: von Hoven, G., Rivas, A. J., Neukirch, C., Klein, S., Hamm, C., Qin, Q., Meyenburg, M., Fuser, S., Saftig, P., Hellmann, N., Postina, R., Husmann, M. Tags: Research articles Source Type: research

Unveiling the basis of alkaline stability of an evolved versatile peroxidase
A variant of high biotechnological interest (called 2-1B) was obtained by directed evolution of the Pleurotus eryngii VP (versatile peroxidase) expressed in Saccharomyces cerevisiae [García-Ruiz, González-Pérez, Ruiz-Dueñas, Martínez and Alcalde (2012) Biochem. J. 441, 487–498]. 2-1B shows seven mutations in the mature protein that resulted in improved functional expression, activity and thermostability, along with a remarkable stronger alkaline stability (it retains 60% of the initial activity after 120 h of incubation at pH 9 compared with complete inactivation of the na...
Source: Biochemical Journal - June 28, 2016 Category: Biochemistry Authors: Saez-Jimenez, V., Acebes, S., Garcia-Ruiz, E., Romero, A., Guallar, V., Alcalde, M., Medrano, F. J., Martinez, A. T., Ruiz-Duenas, F. J. Tags: Research articles Source Type: research

Characterization of Drosophila CMP-sialic acid synthetase activity reveals unusual enzymatic properties
CMP-sialic acid synthetase (CSAS) is a key enzyme of the sialylation pathway. CSAS produces the activated sugar donor, CMP-sialic acid, which serves as a substrate for sialyltransferases to modify glycan termini with sialic acid. Unlike other animal CSASs that normally localize in the nucleus, Drosophila melanogaster CSAS (DmCSAS) localizes in the cell secretory compartment, predominantly in the Golgi, which suggests that this enzyme has properties distinct from those of its vertebrate counterparts. To test this hypothesis, we purified recombinant DmCSAS and characterized its activity in vitro. Our experiments reveale...
Source: Biochemical Journal - June 28, 2016 Category: Biochemistry Authors: Mertsalov, I. B., Novikov, B. N., Scott, H., Dangott, L., Panin, V. M. Tags: Research articles Source Type: research

GDF-15 enhances intracellular Ca2+ by increasing Cav1.3 expression in rat cerebellar granule neurons
We reported previously that GDF-15 increased delayed rectifier outward K+ currents and Kv2.1 α subunit expression through TβRII (TGF-β receptor II) to activate Src kinase and Akt/mTOR (mammalian target of rapamycin) signalling in rat CGNs (cerebellar granule neurons). In the present study, we found that treatment of CGNs with GDF-15 for 24 h increased the intracellular Ca2+ concentration ([Ca2+]i) in response to membrane depolarization, as determined by Ca2+ imaging. Whole-cell current recordings indicated that GDF-15 increased the inward Ca2+ current (ICa) without altering steady-state activation of C...
Source: Biochemical Journal - June 28, 2016 Category: Biochemistry Authors: Lu, J.-M., Wang, C.-Y., Hu, C., Fang, Y.-J., Mei, Y.-A. Tags: Research articles Source Type: research

AKAP18:PKA-RII{alpha} structure reveals crucial anchor points for recognition of regulatory subunits of PKA
A-kinase anchoring proteins (AKAPs) interact with the dimerization/docking (D/D) domains of regulatory subunits of the ubiquitous protein kinase A (PKA). AKAPs tether PKA to defined cellular compartments establishing distinct pools to increase the specificity of PKA signalling. Here, we elucidated the structure of an extended PKA-binding domain of AKAP18β bound to the D/D domain of the regulatory RIIα subunits of PKA. We identified three hydrophilic anchor points in AKAP18β outside the core PKA-binding domain, which mediate contacts with the D/D domain. Such anchor points are conserved within AKAPs that bin...
Source: Biochemical Journal - June 28, 2016 Category: Biochemistry Authors: Gotz, F., Roske, Y., Schulz, M. S., Autenrieth, K., Bertinetti, D., Faelber, K., Zuhlke, K., Kreuchwig, A., Kennedy, E. J., Krause, G., Daumke, O., Herberg, F. W., Heinemann, U., Klussmann, E. Tags: Research articles Source Type: research

Mode of action of DNA-competitive small molecule inhibitors of tyrosyl DNA phosphodiesterase 2
Tyrosyl-DNA phosphodiesterase 2 (TDP2) is a 5'-tyrosyl DNA phosphodiesterase important for the repair of DNA adducts generated by non-productive (abortive) activity of topoisomerase II (TOP2). TDP2 facilitates therapeutic resistance to topoisomerase poisons, which are widely used in the treatment of a range of cancer types. Consequently, TDP2 is an interesting target for the development of small molecule inhibitors that could restore sensitivity to topoisomerase-directed therapies. Previous studies identified a class of deazaflavin-based molecules that showed inhibitory activity against TDP2 at therapeutically useful conce...
Source: Biochemical Journal - June 28, 2016 Category: Biochemistry Authors: Hornyak, P., Askwith, T., Walker, S., Komulainen, E., Paradowski, M., Pennicott, L. E., Bartlett, E. J., Brissett, N. C., Raoof, A., Watson, M., Jordan, A. M., Ogilvie, D. J., Ward, S. E., Atack, J. R., Pearl, L. H., Caldecott, K. W., Oliver, A. W. Tags: Research articles Source Type: research

The growing landscape of tubulin acetylation: lysine 40 and many more
Tubulin heterodimers are the building block of microtubules, which are major elements of the cytoskeleton. Several types of post-translational modifications are found on tubulin subunits as well as on the microtubule polymer to regulate the multiple roles of microtubules. Acetylation of lysine 40 (K40) of the α-tubulin subunit is one of these post-translational modifications which has been extensively studied. We summarize the current knowledge about the structural aspects of K40 acetylation, the functional consequences, the enzymes involved and their regulation. Most importantly, we discuss the potential import...
Source: Biochemical Journal - June 28, 2016 Category: Biochemistry Authors: Sadoul, K., Khochbin, S. Tags: Review articles Source Type: research

Regulatory principles in metabolism-then and now
The importance of metabolic pathways for life and the nature of participating reactions have challenged physiologists and biochemists for over a hundred years. Eric Arthur Newsholme contributed many original hypotheses and concepts to the field of metabolic regulation, demonstrating that metabolic pathways have a fundamental thermodynamic structure and that near identical regulatory mechanisms exist in multiple species across the animal kingdom. His work at Oxford University from the 1970s to 1990s was groundbreaking and led to better understanding of development and demise across the lifespan as well as the basis of metab...
Source: Biochemical Journal - June 28, 2016 Category: Biochemistry Authors: Curi, R., Newsholme, P., Marzuca-Nassr, G. N., Takahashi, H. K., Hirabara, S. M., Cruzat, V., Krause, M., de Bittencourt, P. I. H. Tags: Review articles Source Type: research

Protein partners of the calcium channel {beta} subunit highlight new cellular functions
Calcium plays a key role in cell signalling by its intervention in a wide range of physiological processes. Its entry into cells occurs mainly via voltage-gated calcium channels (VGCC), which are found not only in the plasma membrane of excitable cells but also in cells insensitive to electrical signals. VGCC are composed of different subunits, α1, β, α2 and , among which the cytosolic β subunit (Cavβ) controls the trafficking of the channel to the plasma membrane, its regulation and its gating properties. For many years, these were the main functions associated with Cavβ. However, a growing...
Source: Biochemical Journal - June 28, 2016 Category: Biochemistry Authors: Rima, M., Daghsni, M., Fajloun, Z., M'rad, R., Bruses, J. L., Ronjat, M., De Waard, M. Tags: Review articles Source Type: research

{alpha}-Lipoic acid promotes {alpha}-tubulin hyperacetylation and blocks the turnover of mitochondria through mitophagy
Lysine acetylation is tightly coupled to the nutritional status of the cell, as the availability of its cofactor, acetyl-CoA, fluctuates with changing metabolic conditions. Recent studies have demonstrated that acetyl-CoA levels act as an indicator of cellular nourishment, and increased abundance of this metabolite can block the induction of cellular recycling programmes. In the present study we investigated the cross-talk between mitochondrial metabolic pathways, acetylation and autophagy, using chemical inducers of mitochondrial acetyl-CoA production. Treatment of cells with α-lipoic acid (αLA), a cofactor of...
Source: Biochemical Journal - June 10, 2016 Category: Biochemistry Authors: Stoner, M. W., Thapa, D., Zhang, M., Gibson, G. A., Calderon, M. J., St. Croix, C. M., Scott, I. Tags: Research articles Source Type: research