Isoproterenol-induced beta-2 adrenergic receptor activation negatively regulates interleukin-2 signaling
Regulation of intracellular signaling pathways in lymphocytes is critical for cell homeostasis and immune response. Interleukin-2 (IL-2), a key regulator of lymphocytes, signals following receptor-ligand engagement and subsequent recruitment and activation of effector proteins including JAKs and STATs. Lymphocytes can also be regulated by the central nervous system through the β2 adrenergic receptor (β2AR) pathway which can affect cell trafficking, proliferation, differentiation, and cytokine production. The cross-talk between these two signaling pathways represents an important mechanism that has yet to be fully...
Source: Biochemical Journal - September 18, 2018 Category: Biochemistry Authors: Ruiz-Medina, B. E., Cadena-Medina, D. A., Esparza, E., Arrieta, A. J., Kirken, R. A. Tags: Research Articles Source Type: research

Gibberellin application ameliorates the adverse impact of short-term flooding on Glycine max L.
Flooding is an abiotic stress that creates hypoxic conditions triggered by redox potential leading to restricted growth and grain yield in plants. In the current study, we have investigated the effect of exogenous gibberellins (GA4+7) on soybean under flooding stress. A regulatory role of GAs on biochemical changes in soybean plants [including chlorophyll contents, endogenous bioactive GA1 and GA4, endogenous jasmonic acid (JA) and abscisic acid (ABA)] has been elucidated after 3 and 6 h of flooding stress. The modulation of stress-related bio-chemicals and their genetic determinants [for instance, ABA (Timing of CAB ...
Source: Biochemical Journal - September 18, 2018 Category: Biochemistry Authors: Khan, M. A., Hamayun, M., Iqbal, A., Khan, S. A., Hussain, A., Asaf, S., Khan, A. L., Yun, B.-W., Lee, I.-J. Tags: Research Articles Source Type: research

Biochemical characterization of Plasmodium complement factors binding protein for its role in immune modulation
Complement system is the first line of human defence against intruding pathogens and is recognized as a potentially useful therapeutic target. Human malaria parasite Plasmodium employs a series of intricate mechanisms that enables it to evade different arms of immune system, including the complement system. Here, we show the expression of a multi-domain Plasmodium Complement Control Protein 1, PfCCp1 at asexual blood stages and its binding affinity with C3b as well as C4b proteins of human complement cascade. Using a biochemical assay, we demonstrate that PfCCp1 binds with complement factors and inhibits complement activat...
Source: Biochemical Journal - September 14, 2018 Category: Biochemistry Authors: Sharma, S., Kumar, G., Vashishta, M., Pandey, R., Rathore, S., Chourasia, B. K., Singhal, J., Deshmukh, A., Kalamuddin, M., Paul, G., Panda, A., Tatiya, S., Rawat, K., Gupta, D., Mohmmed, A., Natarajan, K., Malhotra, P. Tags: Research Articles Source Type: research

Thermodynamic and functional characterization of the periplasmic triheme cytochrome PpcA from Geobacter metallireducens
The Geobacter metallireducens bacterium can couple the oxidation of a wide range of compounds to the reduction of several extracellular electron acceptors, including pollutants or electrode surfaces for current production in microbial fuel cells. For these reasons, G. metallireducens are of interest for practical biotechnological applications. The use of such electron acceptors relies on a mechanism that permits electrons to be transferred to the cell exterior. The cytochrome PpcA from G. metallireducens is a member of a family composed of five periplasmic triheme cytochromes, which are important to bridge the electron tra...
Source: Biochemical Journal - September 14, 2018 Category: Biochemistry Authors: Fernandes, T. M., Morgado, L., Salgueiro, C. A. Tags: Research Articles Source Type: research

Structure of ScpC, a virulence protease from Streptococcus pyogenes, reveals the functional domains and maturation mechanism
Group A Streptococcus (GAS; Streptococcus pyogenes) causes a wide range of infections, including pharyngitis, impetigo, and necrotizing fasciitis, and results in over half a million deaths annually. GAS ScpC (SpyCEP), a 180-kDa surface-exposed, subtilisin-like serine protease, acts as an essential virulence factor that helps S. pyogenes evade the innate immune response by cleaving and inactivating C-X-C chemokines. ScpC is thus a key candidate for the development of a vaccine against GAS and other pathogenic streptococcal species. Here, we report the crystal structures of full-length ScpC wild-type, the inactive mutant, an...
Source: Biochemical Journal - September 11, 2018 Category: Biochemistry Authors: Jobichen, C., Tan, Y. C., Prabhakar, M. T., Nayak, D., Biswas, D., Pannu, N. S., Hanski, E., Sivaraman, J. Tags: Research Articles Source Type: research

A copper transcription factor, AfMac1, regulates both iron and copper homeostasis in the opportunistic fungal pathogen Aspergillus fumigatus
Although iron and copper are co-ordinately regulated in living cells, the homeostatic effects of each of these metals on the other remain unknown. Here, we show the function of AfMac1, a transcriptional activator of the copper and iron regulons of Aspergillus fumigatus, on the interaction between iron and copper. In addition to the copper-specific AfMac1-binding motif 5'-TGTGCTCA-3' found in the promoter region of ctrC, the iron-specific AfMac1-binding motif 5'-AT(C/G)NN(A/T)T(A/C)-3' was identified in the iron regulon but not in the copper regulon by ChIP sequence analysis. Furthermore, mutation of the AfMac1-binding moti...
Source: Biochemical Journal - September 11, 2018 Category: Biochemistry Authors: Park, Y.-S., Kang, S., Seo, H., Yun, C.-W. Tags: Research Articles Source Type: research

The D' domain of von Willebrand factor requires the presence of the D3 domain for optimal factor VIII binding
The D'–D3 fragment of von Willebrand factor (VWF) can be divided into TIL'-E'-VWD3-C8_3-TIL3-E3 subdomains of which TIL'-E'-VWD3 comprises the main factor VIII (FVIII)-binding region. Yet, von Willebrand disease (VWD) Type 2 Normandy (2N) mutations, associated with impaired FVIII interaction, have been identified in C8_3-TIL3-E3. We now assessed the role of the VWF (sub)domains for FVIII binding using isolated D', D3 and monomeric C-terminal subdomain truncation variants of D'–D3. Competitive binding assays and surface plasmon resonance analysis revealed that D' requires the presence of D3 for effective interac...
Source: Biochemical Journal - September 11, 2018 Category: Biochemistry Authors: Przeradzka, M. A., Meems, H., van der Zwaan, C., Ebberink, E. H. T. M., van den Biggelaar, M., Mertens, K., Meijer, A. B. Tags: Research Articles Source Type: research

Structural insights into oxidation of medium-chain fatty acids and flavanone by myxobacterial cytochrome P450 CYP267B1
Oxidative biocatalytic reactions performed by cytochrome P450 enzymes (P450s) are of high interest for the chemical and pharmaceutical industries. CYP267B1 is a P450 enzyme from myxobacterium Sorangium cellulosum So ce56 displaying a broad substrate scope. In this work, a search for new substrates was performed, combined with product characterization and a structural analysis of substrate-bound complexes using X-ray crystallography and computational docking. The results demonstrate the ability of CYP267B1 to perform in-chain hydroxylations of medium-chain saturated fatty acids (decanoic acid, dodecanoic acid and tetradecan...
Source: Biochemical Journal - September 11, 2018 Category: Biochemistry Authors: Jozwik, I. K., Litzenburger, M., Khatri, Y., Schifrin, A., Girhard, M., Urlacher, V., Thunnissen, A.-M. W. H., Bernhardt, R. Tags: Research Articles Source Type: research

A frog cathelicidin peptide effectively promotes cutaneous wound healing in mice
Although cathelicidins in mammals have been well characterized, little is known about the function of cathelicidin in amphibians. In the present study, a novel 24-residue peptide (cathelicidin-NV, ARGKKECKDDRCRLLMKRGSFSYV) belonging to the cathelicidin family was identified from the skin of the plateau frog Nanorana ventripunctata. Cathelicidin-NV showed strong wound healing-promoting activity in a murine model with a full-thickness dermal wound. It directly enhanced the proliferation of keratinocyte cells, resulting in accelerated re-epithelialization of the wound site. Cathelicidin-NV also promoted the proliferation of f...
Source: Biochemical Journal - September 11, 2018 Category: Biochemistry Authors: Wu, J., Yang, J., Wang, X., Wei, L., Mi, K., Shen, Y., Liu, T., Yang, H., Mu, L. Tags: Research Articles Source Type: research

Y-box proteins combine versatile cold shock domains and arginine-rich motifs (ARMs) for pleiotropic functions in RNA biology
Y-box proteins are single-strand DNA- and RNA-binding proteins distinguished by a conserved cold shock domain (CSD) and a variable C-terminal domain organized into alternating short modules rich in basic or acidic amino acids. A huge literature depicts Y-box proteins as highly abundant, staggeringly versatile proteins that interact with all mRNAs and function in most forms of mRNA-specific regulation. The mechanisms by which Y-box proteins recognize mRNAs are unclear, because their CSDs bind a jumble of diverse elements, and the basic modules in the C-terminal domain are considered to bind nonspecifically to phosphates in ...
Source: Biochemical Journal - September 11, 2018 Category: Biochemistry Authors: Kleene, K. C. Tags: Review Articles Source Type: research

Characterizing the interaction between insulin-like growth factor 2 mRNA-binding protein 1 (IMP1) and KRAS expression
Insulin-like growth factor 2 mRNA-binding protein-1 (IMP1) has high affinity for KRAS mRNA, and it can regulate KRAS expression in cells. We first characterized the molecular interaction between IMP1 and KRAS mRNA. Using IMP1 variants with a point mutation in the GXXG motif at each KH domain, we showed that all KH domains play a critical role in the binding of KRAS RNA. We mapped the IMP1-binding sites on KRAS mRNA and show that IMP1 has the highest affinity for nts 1–185. Although it has lower affinity, IMP1 does bind to other coding regions and the 3'-UTR of KRAS mRNA. Eight antisense oligonucleotides (AONs) were d...
Source: Biochemical Journal - September 5, 2018 Category: Biochemistry Authors: Mackedenski, S., Wang, C., Li, W.-M., Lee, C. H. Tags: Research Articles Source Type: research

Prediction of secondary and tertiary structures of human BC200 RNA (BCYRN1) based on experimental and bioinformatic cross-validation
Based on experimental and bioinformatic approaches, we present the first empirically established complete secondary structure of human BC200 RNA. BC200 RNA is a brain-specific non-messenger RNA with a confirmed regulatory role in dendritic translation in neurons. Although the involvement of human BC200 RNA in various types of tumour and Alzheimer's disease has been repeatedly confirmed, the exact secondary structure remains not fully elucidated. To determine the secondary structure of BC200 RNA in vitro, we performed partial hydrolysis with sequence-specific nucleases and lead-induced cleavage. We also examined the availab...
Source: Biochemical Journal - September 5, 2018 Category: Biochemistry Authors: Sosinska-Zawierucha, P., Zawierucha, P., Breborowicz, A., Barciszewski, J. Tags: Research Articles Source Type: research

Eudesmane-type sesquiterpene diols directly synthesized by a sesquiterpene cyclase in Tripterygium wilfordii
Cryptomeridiol, a typical eudesmane diol, is the active principle component of the antispasmodic Proximol. Although it has been used for many years, the biosynthesis pathway of cryptomeridiol has remained blur. Among terpenoid natural products, terpenoid cyclases are responsible for cyclization and generation of hydrocarbon backbones. The cyclization is mediated by carbocationic cascades and ultimately terminated via deprotonation or nucleophilic capture. Isoprene precursors are, respectively, converted into hydrocarbons or hydroxylated backbones. A sesquiterpene cyclase in Tripterygium wilfordii (TwCS) was determined to d...
Source: Biochemical Journal - September 5, 2018 Category: Biochemistry Authors: Tong, Y.-r., Su, P., Guan, H.-y., Hu, T.-y., Chen, J.-l., Zhang, Y.-f., Zhao, Y.-j., Gao, L.-h., Zhang, X.-n., Huang, L.-q., Gao, W. Tags: Research Articles Source Type: research

PKA-site phosphorylation of importin13 regulates its subcellular localization and nuclear transport function
Importin 13 (IPO13) is a key member of the importin β superfamily, which can transport cargoes both into and out of the nucleus to contribute to a variety of important cellular processes. IPO13 is known to undergo phosphorylation, but the impact of this on function has not been investigated. Here, we show for the first time that IPO13 is phosphorylated by cAMP-dependent protein kinase A specifically at serine 193. Results from fluorescence recovery after photobleaching and fluorescence loss in photobleaching approaches establish that negative charge at serine 193 through phosphorylation or point mutation both reduces ...
Source: Biochemical Journal - August 31, 2018 Category: Biochemistry Authors: Liu, X., Lin, W., Shi, X., Davies, R. G., Wagstaff, K. M., Tao, T., Jans, D. A. Tags: Research Articles Source Type: research

Guarding the gateway to histidine biosynthesis in plants: Medicago truncatula ATP-phosphoribosyltransferase in relaxed and tense states
In the first committed step of histidine biosynthesis, adenosine 5'-triphosphate (ATP) and 5-phosphoribosyl-α1-pyrophosphate (PRPP), in the presence of ATP phosphoribosyltransferase (ATP-PRT, EC 2.4.2.17), yield phosphoribosyl-ATP. ATP-PRTs are subject to feedback inhibition by histidine that allosterically binds between the regulatory domains. Histidine biosynthetic pathways of bacteria, lower eukaryotes, and plants are considered promising targets for the design of antibiotics, antifungal agents, and herbicides because higher organisms are histidine heterotrophs. Plant ATP-PRTs are similar to one of the two types o...
Source: Biochemical Journal - August 31, 2018 Category: Biochemistry Authors: Ruszkowski, M. Tags: Research Articles Source Type: research

Structural and functional characterization of the RBBP4-ZNF827 interaction and its role in NuRD recruitment to telomeres
The nucleosome remodeling and histone deacetylase (NuRD) complex is an essential multi-subunit protein complex that regulates higher-order chromatin structure. Cancers that use the alternative lengthening of telomere (ALT) pathway of telomere maintenance recruit NuRD to their telomeres. This interaction is mediated by the N-terminal domain of the zinc-finger protein ZNF827. NuRD–ZNF827 plays a vital role in the ALT pathway by creating a molecular platform for recombination-mediated repair. Disruption of NuRD binding results in loss of ALT cell viability. Here, we present the crystal structure of the NuRD subunit RBBP...
Source: Biochemical Journal - August 31, 2018 Category: Biochemistry Authors: Yang, S. F., Sun, A.-a., Shi, Y., Li, F., Pickett, H. A. Tags: Research Articles Source Type: research

Lead induces the up-regulation of the protein arginine methyltransferase 5 possibly by its promoter demethylation
The studies on lead (Pb) exposure linking to epigenetic modulations are caused by its differential actions on global DNA methylation and histone modifications. These epigenetic changes may result in increased accessibility of the transcription factors to promoter DNA-binding elements leading to activation and expression of the gene. The protein arginine methyltransferase 5 (PRMT5) and its partner methylosome protein 50 (MEP50) together catalyze the mono- and symmetric dimethylation of arginine residues in many histone and non-histone protein substrates. Moreover, it is overexpressed in many forms of cancer. In the present ...
Source: Biochemical Journal - August 30, 2018 Category: Biochemistry Authors: Ghosh, K., Chatterjee, B., Kanade, S. R. Tags: Research Articles Source Type: research

Toxicity of dihydroxyacetone is exerted through the formation of methylglyoxal in Saccharomyces cerevisiae: effects on actin polarity and nuclear division
Dihydroxyacetone (DHA) is the smallest ketotriose, and it is utilized by many organisms as an energy source. However, at higher concentrations, DHA becomes toxic towards several organisms including the budding yeast Saccharomyces cerevisiae. In the present study, we show that DHA toxicity is due to its spontaneous conversion to methylglyoxal (MG) within yeast cells. A mutant defective in MG-metabolizing enzymes (glo1gre2gre3) exhibited higher susceptibility to DHA. Intracellular MG levels increased following the treatment of glo1gre2gre3 cells with DHA. We previously reported that MG depolarized the actin cytoskeleton and ...
Source: Biochemical Journal - August 30, 2018 Category: Biochemistry Authors: Nomura, W., Aoki, M., Inoue, Y. Tags: Research Articles Source Type: research

Arabidopsis calcineurin B-like proteins differentially regulate phosphorylation activity of CBL-interacting protein kinase 9
Calcium (Ca2+) is a versatile and ubiquitous second messenger in all eukaryotes including plants. In response to various stimuli, cytosolic calcium concentration ([Ca2+]cyt) is increased, leading to activation of Ca2+ sensors including Arabidopsis calcineurin B-like proteins (CBLs). CBLs interact with CBL-interacting protein kinases (CIPKs) to form CBL–CIPK complexes and transduce the signal downstream in the signalling pathway. Although there are many reports on the regulation of downstream targets by CBL–CIPK module, knowledge about the regulation of upstream components by individual CIPKs is inadequate. In t...
Source: Biochemical Journal - August 30, 2018 Category: Biochemistry Authors: Yadav, A. K., Jha, S. K., Sanyal, S. K., Luan, S., Pandey, G. K. Tags: Research Articles Source Type: research

Force-activated catalytic pathway accelerates bacterial adhesion against flow
Mechanical cues often influence the factors affecting the transition states of catalytic reactions and alter the activation pathway. However, tracking the real-time dynamics of such activation pathways is limited. Using single-molecule trapping of reaction intermediates, we developed a method that enabled us to perform one reaction at one site and simultaneously study the real-time dynamics of the catalytic pathway. Using this, we showed single-molecule calligraphy at nanometer resolution and deciphered the mechanism of the sortase A enzymatic reaction that, counter-intuitively, accelerates bacterial adhesion under shear t...
Source: Biochemical Journal - August 30, 2018 Category: Biochemistry Authors: Hazra, J. P., Arora, N., Sagar, A., Srinivasan, S., Chaudhuri, A., Rakshit, S. Tags: Research Articles Source Type: research

A role for trypanosomatid aldo-keto reductases in methylglyoxal, prostaglandin and isoprostane metabolism
Trypanosomatid parasites are the infectious agents causing Chagas disease, visceral and cutaneous leishmaniasis and human African trypanosomiasis. Recent work of others has implicated an aldo-keto reductase (AKR) in the susceptibility and resistance of Trypanosoma cruzi to benznidazole, a drug used to treat Chagas disease. Here, we show that TcAKR and homologues in the related parasites Trypanosoma brucei and Leishmania donovani do not reductively activate monocyclic (benznidazole, nifurtimox and fexinidazole) or bicyclic nitro-drugs such as PA-824. Rather, these enzymes metabolise a variety of toxic ketoaldehydes, such as...
Source: Biochemical Journal - August 30, 2018 Category: Biochemistry Authors: Roberts, A. J., Dunne, J., Scullion, P., Norval, S., Fairlamb, A. H. Tags: Research Articles Source Type: research

An appeal to magic? The discovery of a non-enzymatic metabolism and its role in the origins of life
Until recently, prebiotic precursors to metabolic pathways were not known. In parallel, chemistry achieved the synthesis of amino acids and nucleotides only in reaction sequences that do not resemble metabolic pathways, and by using condition step changes, incompatible with enzyme evolution. As a consequence, it was frequently assumed that the topological organisation of the metabolic pathway has formed in a Darwinian process. The situation changed with the discovery of a non-enzymatic glycolysis and pentose phosphate pathway. The suite of metabolism-like reactions is promoted by a metal cation, (Fe(II)), abundant in Arche...
Source: Biochemical Journal - August 30, 2018 Category: Biochemistry Authors: Ralser, M. Tags: Review Articles Source Type: research

Stimulation of the ATPase activity of Hsp90 by zerumbone modification of its cysteine residues destabilizes its clients and causes cytotoxicity
Hsp90 is an ATP-dependent molecular chaperone that assists folding and conformational maturation/maintenance of many proteins. It is a potential cancer drug target because it chaperones oncoproteins. A prokaryotic homolog of Hsp90 (HtpG) is essential for thermo-tolerance in some bacteria and virulence of zoonotic pathogens. To identify a new class of small molecules which target prokaryotic and eukaryotic Hsp90s, we studied the effects of a naturally occurring cyclic sesquiterpene, zerumbone, which inhibits proliferation of a wide variety of tumor cells, on the activity of Hsp90. Zerumbone enhanced the ATPase activity of c...
Source: Biochemical Journal - August 16, 2018 Category: Biochemistry Authors: Nakamoto, H., Amaya, Y., Komatsu, T., Suzuki, T., Dohmae, N., Nakamura, Y., Jantan, I., Miyata, Y. Tags: Research Articles Source Type: research

Evidence for substrate-assisted catalysis in N-acetylphosphoglucosamine mutase
N-acetylphosphoglucosamine mutase (AGM1) is a key component of the hexosamine biosynthetic pathway that produces UDP-GlcNAc, an essential precursor for a wide range of glycans in eukaryotes. AGM belongs to the α-d-phosphohexomutase metalloenzyme superfamily and catalyzes the interconversion of N-acetylglucosamine-6-phosphate (GlcNAc-6P) to N-acetylglucosamine-1-phosphate (GlcNAc-1P) through N-acetylglucosamine-1,6-bisphosphate (GlcNAc-1,6-bisP) as the catalytic intermediate. Although there is an understanding of the phosphoserine-dependent catalytic mechanism at enzymatic and structural level, the identity of the req...
Source: Biochemical Journal - August 16, 2018 Category: Biochemistry Authors: Raimi, O. G., Hurtado-Guerrero, R., van Aalten, D. M. F. Tags: Research Articles Source Type: research

Glycans and glycosaminoglycans in neurobiology: key regulators of neuronal cell function and fate
The aim of the present study was to examine the roles of l-fucose and the glycosaminoglycans (GAGs) keratan sulfate (KS) and chondroitin sulfate/dermatan sulfate (CS/DS) with selected functional molecules in neural tissues. Cell surface glycans and GAGs have evolved over millions of years to become cellular mediators which regulate fundamental aspects of cellular survival. The glycocalyx, which surrounds all cells, actuates responses to growth factors, cytokines and morphogens at the cellular boundary, silencing or activating downstream signaling pathways and gene expression. In this review, we have focused on interactions...
Source: Biochemical Journal - August 16, 2018 Category: Biochemistry Authors: Hayes, A. J., Melrose, J. Tags: Review Articles Source Type: research

The cloak, dagger, and shield: proteases in plant-pathogen interactions
Plants sense the presence of pathogens or pests through the recognition of evolutionarily conserved microbe- or herbivore-associated molecular patterns or specific pathogen effectors, as well as plant endogenous danger-associated molecular patterns. This sensory capacity is largely mediated through plasma membrane and cytosol-localized receptors which trigger complex downstream immune signaling cascades. As immune signaling outputs are often associated with a high fitness cost, precise regulation of this signaling is critical. Protease-mediated proteolysis represents an important form of pathway regulation in this context....
Source: Biochemical Journal - August 16, 2018 Category: Biochemistry Authors: Hou, S., Jamieson, P., He, P. Tags: Review Articles Source Type: research

Mutation of G51 in SepF impairs FtsZ assembly promoting ability of SepF and retards the division of Mycobacterium smegmatis cells
The role of FtsZ-associated proteins in the regulation of the assembly dynamics of Mycobacterium smegmatis FtsZ is not clear. In this work, we examined the effect of M. smegmatis SepF on the assembly and stability of M. smegmatis FtsZ polymers. We discovered a single dominant point mutation in SepF (G51D or G51R) that renders the protein inactive. SepF promoted the polymerization of FtsZ, induced the bundling of FtsZ filaments, stabilized FtsZ filaments and reduced the GTPase activity of FtsZ. Surprisingly, both G51D-SepF and G51R-SepF neither stabilized FtsZ filaments nor showed a discernable effect on the GTPase activity...
Source: Biochemical Journal - August 14, 2018 Category: Biochemistry Authors: Bhattacharya, D., Sinha, K., Panda, D. Tags: Research Articles Source Type: research

Structure, interactions and action of Mycobacterium tuberculosis 3-hydroxyisobutyric acid dehydrogenase
Biochemical and crystallographic studies on Mycobacterium tuberculosis 3-hydroxyisobutyric acid dehydrogenase (MtHIBADH), a member of the 3-hydroxyacid dehydrogenase superfamily, have been carried out. Gel filtration and blue native PAGE of MtHIBADH show that the enzyme is a dimer. The enzyme preferentially uses NAD+ as the cofactor and is specific to S-hydroxyisobutyric acid (HIBA). It can also use R-HIBA, l-serine and 3-hydroxypropanoic acid (3-HP) as substrates, but with much less efficiency. The pH optimum for activity is ~11. Structures of the native enzyme, the holoenzyme, binary complexes with NAD+, S-HIBA, R-HIBA, ...
Source: Biochemical Journal - August 14, 2018 Category: Biochemistry Authors: Srikalaivani, R., Singh, A., Vijayan, M., Surolia, A. Tags: Research Articles Source Type: research

New tools for evaluating protein tyrosine sulfation: tyrosylprotein sulfotransferases (TPSTs) are novel targets for RAF protein kinase inhibitors
Protein tyrosine sulfation is a post-translational modification best known for regulating extracellular protein–protein interactions. Tyrosine sulfation is catalysed by two Golgi-resident enzymes termed tyrosylprotein sulfotransferases (TPSTs) 1 and 2, which transfer sulfate from the cofactor PAPS (3'-phosphoadenosine 5'-phosphosulfate) to a context-dependent tyrosine in a protein substrate. A lack of quantitative tyrosine sulfation assays has hampered the development of chemical biology approaches for the identification of small-molecule inhibitors of tyrosine sulfation. In the present paper, we describe the develop...
Source: Biochemical Journal - August 14, 2018 Category: Biochemistry Authors: Byrne, D. P., Li, Y., Ngamlert, P., Ramakrishnan, K., Eyers, C. E., Wells, C., Drewry, D. H., Zuercher, W. J., Berry, N. G., Fernig, D. G., Eyers, P. A. Tags: Research Articles Source Type: research

New tools for carbohydrate sulfation analysis: heparan sulfate 2-O-sulfotransferase (HS2ST) is a target for small-molecule protein kinase inhibitors
We report the susceptibility of HS2ST to a variety of cell-permeable compounds in vitro, including polyanionic polar molecules, the protein kinase inhibitor rottlerin and oxindole-based RAF kinase inhibitors. In a related study, published back-to-back with the present study, we demonstrated that tyrosyl protein sulfotranferases are also inhibited by a variety of protein kinase inhibitors. We propose that appropriately validated small-molecule compounds could become new tools for rapid inhibition of glycan (and protein) sulfation in cells, and that protein kinase inhibitors might be repurposed or redesigned for the specific...
Source: Biochemical Journal - August 14, 2018 Category: Biochemistry Authors: Byrne, D. P., Li, Y., Ramakrishnan, K., Barsukov, I. L., Yates, E. A., Eyers, C. E., Papy-Garcia, D., Chantepie, S., Pagadala, V., Liu, J., Wells, C., Drewry, D. H., Zuercher, W. J., Berry, N. G., Fernig, D. G., Eyers, P. A. Tags: Research Articles Source Type: research

Crystal structure and pH-dependent allosteric regulation of human {beta}-ureidopropionase, an enzyme involved in anticancer drug metabolism
β-Ureidopropionase (βUP) catalyzes the third step of the reductive pyrimidine catabolic pathway responsible for breakdown of uracil-, thymine- and pyrimidine-based antimetabolites such as 5-fluorouracil. Nitrilase-like βUPs use a tetrad of conserved residues (Cys233, Lys196, Glu119 and Glu207) for catalysis and occur in a variety of oligomeric states. Positive co-operativity toward the substrate N-carbamoyl-β-alanine and an oligomerization-dependent mechanism of substrate activation and product inhibition have been reported for the enzymes from some species but not others. Here, the activity of recombin...
Source: Biochemical Journal - July 31, 2018 Category: Biochemistry Authors: Maurer, D., Lohkamp, B., Krumpel, M., Widersten, M., Dobritzsch, D. Tags: Research Articles Source Type: research

Binding mode of AIF(370-394) peptide to CypA: insights from NMR, label-free and molecular docking studies
The complex formation between the proteins apoptosis-inducing factor (AIF) and cyclophilin A (CypA) following oxidative stress in neuronal cells has been suggested as a main target for reverting ischemia-stroke damage. Recently, a peptide encompassing AIF residues 370–394 has been developed to target the AIF-binding site on CypA, to prevent the association between the two proteins and suppress glutamate-induced cell death in neuronal cells. Using a combined approach based on NMR spectroscopy, synthesis and in vitro testing of all Ala-scan mutants of the peptide and molecular docking/molecular dynamics, we have genera...
Source: Biochemical Journal - July 31, 2018 Category: Biochemistry Authors: Farina, B., Sturlese, M., Mascanzoni, F., Caporale, A., Monti, A., Di Sorbo, G., Fattorusso, R., Ruvo, M., Doti, N. Tags: Research Articles Source Type: research

Interaction of the cryptic fragment of myelin basic protein with mitochondrial voltage-dependent anion-selective channel-1 affects cell energy metabolism
In demyelinating nervous system disorders, myelin basic protein (MBP), a major component of the myelin sheath, is proteolyzed and its fragments are released in the neural environment. Here, we demonstrated that, in contrast with MBP, the cellular uptake of the cryptic 84–104 epitope (MBP84-104) did not involve the low-density lipoprotein receptor-related protein-1, a scavenger receptor. Our pull-down assay, mass spectrometry and molecular modeling studies suggested that, similar with many other unfolded and aberrant proteins and peptides, the internalized MBP84-104 was capable of binding to the voltage-dependent anio...
Source: Biochemical Journal - July 31, 2018 Category: Biochemistry Authors: Remacle, A. G., Hullugundi, S. K., Dolkas, J., Angert, M., Cieplak, P., Scott, D., Chernov, A. V., Shubayev, V. I., Strongin, A. Y. Tags: Research Articles Source Type: research

Cilium structure, assembly, and disassembly regulated by the cytoskeleton
The cilium, once considered a vestigial structure, is a conserved, microtubule-based organelle critical for transducing extracellular chemical and mechanical signals that control cell polarity, differentiation, and proliferation. The cilium undergoes cycles of assembly and disassembly that are controlled by complex inter-relationships with the cytoskeleton. Microtubules form the core of the cilium, the axoneme, and are regulated by post-translational modifications, associated proteins, and microtubule dynamics. Although actin and septin cytoskeletons are not major components of the axoneme, they also regulate cilium organi...
Source: Biochemical Journal - July 31, 2018 Category: Biochemistry Authors: Mirvis, M., Stearns, T., James Nelson, W. Tags: Review Articles Source Type: research

The role of metabolism and tunneling nanotube-mediated intercellular mitochondria exchange in cancer drug resistance
Intercellular communications play a major role in tissue homeostasis. In pathologies such as cancer, cellular interactions within the tumor microenvironment (TME) contribute to tumor progression and resistance to therapy. Tunneling nanotubes (TNTs) are newly discovered long-range intercellular connections that allow the exchange between cells of various cargos, ranging from ions to whole organelles such as mitochondria. TNT-transferred mitochondria were shown to change the metabolism and functional properties of recipient cells as reported for both normal and cancer cells. Metabolic plasticity is now considered a hallmark ...
Source: Biochemical Journal - July 31, 2018 Category: Biochemistry Authors: Hekmatshoar, Y., Nakhle, J., Galloni, M., Vignais, M.-L. Tags: Review Articles Source Type: research

Interplay between negative and positive design elements in G{alpha} helical domains of G proteins determines interaction specificity toward RGS2
Regulators of G protein signaling (RGS) proteins inactivate Gα subunits, thereby controlling G protein-coupled signaling networks. Among all RGS proteins, RGS2 is unique in interacting only with the Gαq but not with the Gαi subfamily. Previous studies suggested that this specificity is determined by the RGS domain and, in particular, by three RGS2-specific residues that lead to a unique mode of interaction with Gαq. This interaction was further proposed to act through contacts with the Gα GTPase domain. Here, we combined energy calculations and GTPase activity measurements to determine which G...
Source: Biochemical Journal - July 26, 2018 Category: Biochemistry Authors: Kasom, M., Gharra, S., Sadiya, I., Avital-Shacham, M., Kosloff, M. Tags: Research Articles Source Type: research

The chromatin nuclear protein NUPR1L is intrinsically disordered and binds to the same proteins as its paralogue
NUPR1 is a protumoral multifunctional intrinsically disordered protein (IDP), which is activated during the acute phases of pancreatitis. It interacts with other IDPs such as prothymosin α, as well as with folded proteins such as the C-terminal region of RING1-B (C-RING1B) of the Polycomb complex; in all those interactions, residues around Ala33 and Thr68 (the ‘hot-spot’ region) of NUPR1 intervene. Its paralogue, NUPR1L, is also expressed in response to DNA damage, it is p53-regulated, and its expression down-regulates that of the NUPR1 gene. In this work, we characterized the conformational preferences o...
Source: Biochemical Journal - July 26, 2018 Category: Biochemistry Authors: Neira, J. L., Lopez, M. B., Sevilla, P., Rizzuti, B., Camara-Artigas, A., Vidal, M., Iovanna, J. L. Tags: Research Articles Source Type: research

Structural insights into lethal contractural syndrome type 3 (LCCS3) caused by a missense mutation of PIP5K{gamma}
Signaling molecule phosphatidylinositol 4,5-bisphosphate is produced primarily by phosphatidylinositol 4-phosphate 5-kinase (PIP5K). PIP5K is essential for the development of the human neuronal system, which has been exemplified by a recessive genetic disorder, lethal congenital contractural syndrome type 3, caused by a single aspartate-to-asparagine mutation in the kinase domain of PIP5K. So far, the exact role of this aspartate residue has yet to be elucidated. In this work, we conducted structural, functional and computational studies on a zebrafish PIP5Kα variant with a mutation at the same site. Compared with th...
Source: Biochemical Journal - July 26, 2018 Category: Biochemistry Authors: Zeng, X., Uyar, A., Sui, D., Donyapour, N., Wu, D., Dickson, A., Hu, J. Tags: Research Articles Source Type: research

Characterization of the PLP-dependent transaminase initiating azasugar biosynthesis
Biosynthesis of the azasugar 1-deoxynojirimycin (DNJ) critically involves a transamination in the first committed step. Here, we identify the azasugar biosynthetic cluster signature in Paenibacillus polymyxa SC2 (Ppo), homologous to that reported in Bacillus amyloliquefaciens FZB42 (Bam), and report the characterization of the aminotransferase GabT1 (named from Bam). GabT1 from Ppo exhibits a specific activity of 4.9 nmol/min/mg at 30°C (pH 7.5), a somewhat promiscuous amino donor selectivity, and curvilinear steady-state kinetics that do not reflect the predicted ping-pong behavior typical of aminotransferases. A...
Source: Biochemical Journal - July 17, 2018 Category: Biochemistry Authors: Arciola, J. M., Horenstein, N. A. Tags: Research Articles Source Type: research

Systems analysis of metabolism in platelet concentrates during storage in platelet additive solution
Platelets (PLTs) deteriorate over time when stored within blood banks through a biological process known as PLT storage lesion (PSL). Here, we describe the refinement of the biochemical model of PLT metabolism, iAT-PLT-636, and its application to describe and investigate changes in metabolism during PLT storage. Changes in extracellular acetate and citrate were measured in buffy coat and apheresis PLT units over 10 days of storage in the PLT additive solution T-Sol. Metabolic network analysis of these data was performed alongside our prior metabolomics data to describe the metabolism of fresh (days 1–3), intermediate...
Source: Biochemical Journal - July 17, 2018 Category: Biochemistry Authors: Johannsson, F., Guthmundsson, S., Paglia, G., Guthmundsson, S., Palsson, B., Sigurjonsson, O. E., Rolfsson, O. Tags: Research Articles Source Type: research

Crystal structures of the kinase domain of PpkA, a key regulatory component of T6SS, reveal a general inhibitory mechanism
The type VI secretion system (T6SS) is a versatile and widespread export system found in many Gram-negative bacteria that delivers effector proteins into target cells. The functions of T6SSs are tightly regulated by diverse mechanisms at multiple levels, including post-translational modification through threonine phosphorylation via the Ser/Thr protein kinase (STPK) PpkA. Here, we identified that PpkA is essential for T6SS secretion in Serratia marcescens since its deletion eliminated the secretion of haemolysin co-regulated protein, while the periplasmic and transmembrane portion of PpkA was found to be disposable for T6S...
Source: Biochemical Journal - July 17, 2018 Category: Biochemistry Authors: Li, P., Xu, D., Ma, T., Wang, D., Li, W., He, J., Ran, T., Wang, W. Tags: Research Articles Source Type: research

Plant mitochondrial protein import: the ins and outs
The majority of the mitochondrial proteome, required to fulfil its diverse range of functions, is cytosolically synthesised and translocated via specialised machinery. The dedicated translocases, receptors, and associated proteins have been characterised in great detail in yeast over the last several decades, yet many of the mechanisms that regulate these processes in higher eukaryotes are still unknown. In this review, we highlight the current knowledge of mitochondrial protein import in plants. Despite the fact that the mechanisms of mitochondrial protein import have remained conserved across species, many unique feature...
Source: Biochemical Journal - July 17, 2018 Category: Biochemistry Authors: Ghifari, A. S., Gill-Hille, M., Murcha, M. W. Tags: Review Articles Source Type: research

Global conformational changes in IgG-Fc upon mutation of the FcRn-binding site are not associated with altered antibody-dependent effector functions
Antibody engineering is important for many diagnostic and clinical applications of monoclonal antibodies. We recently reported a series of fragment crystallizable (Fc) mutations targeting the neonatal Fc receptor (FcRn) site on a Lewis Y (Ley) binding IgG1, hu3S193. The hu3S193 variants displayed shortened in vivo half-lives and may have potential for radioimaging or radiotherapy of Ley-positive tumors. Here, we report Fc crystal structures of wild-type hu3S193, seven FcRn-binding site variants, and a variant lacking C1q binding or complement-dependent cytotoxicity (CDC) activity. The Fc conformation of the FcRn-binding si...
Source: Biochemical Journal - July 5, 2018 Category: Biochemistry Authors: Burvenich, I. J. G., Farrugia, W., Liu, Z., Makris, D., King, D., Gloria, B., Perani, A., Allan, L. C., Scott, A. M., Ramsland, P. A. Tags: Research Articles Source Type: research

Probing the specificity of CYP112 in bacterial gibberellin biosynthesis
Biosynthesis of the gibberellin A (GA) plant hormones evolved independently in plant-associated fungi and bacteria. While the relevant enzymes have distinct evolutionary origins, the pathways proceed via highly similar reactions. One particularly complex transformation involves combined demethylation and -lactone ring formation, catalyzed in bacteria by the cytochrome P450 CYP112 in three individual steps, which involves large structural changes in the transition from substrate to product, with further divergence in the recently demonstrated use of two separate mechanistic routes. Here, the substrate specificity of the iso...
Source: Biochemical Journal - July 5, 2018 Category: Biochemistry Authors: Nagel, R., Peters, R. J. Tags: Research Articles Source Type: research

Molecular insights of inhibition in sickle hemoglobin polymerization upon glutathionylation: hydrogen/deuterium exchange mass spectrometry and molecular dynamics simulation-based approach
In sickle cell anemia, polymerization of hemoglobin in its deoxy state leads to the formation of insoluble fibers that result in sickling of red blood cells. Stereo-specific binding of isopropyl group of βVal6, the mutated amino-acid residue of a tetrameric sickle hemoglobin molecule (HbS), with hydrophobic groove of another HbS tetramer initiates the polymerization. Glutathionylation of βCys93 in HbS was reported to inhibit the polymerization. However, the mechanism of inhibition in polymerization is unknown to date. In our study, the molecular insights of inhibition in polymerization were investigated by monito...
Source: Biochemical Journal - July 5, 2018 Category: Biochemistry Authors: Das, R., Mitra, A., Mitra, G., Maity, D., Bhat, V., Pal, D., Ross, C., Kurpad, A. V., Mandal, A. K. Tags: Research Articles Source Type: research

Anti-{sigma} factor YlaD regulates transcriptional activity of {sigma} factor YlaC and sporulation via manganese-dependent redox-sensing molecular switch in Bacillus subtilis
YlaD, a membrane-anchored anti-sigma () factor of Bacillus subtilis, contains a HX3CXXC motif that functions as a redox-sensing domain and belongs to one of the zinc (Zn)-co-ordinated anti- factor families. Despite previously showing that the YlaC transcription is controlled by YlaD, experimental evidence of how the YlaC–YlaD interaction is affected by active cysteines and/or metal ions is lacking. Here, we showed that the Pyla promoter is autoregulated solely by YlaC. Moreover, reduced YlaD contained Zn and iron, while oxidized YlaD did not. Cysteine substitution in YlaD led to changes in its secondary structure; Cy...
Source: Biochemical Journal - July 5, 2018 Category: Biochemistry Authors: Kwak, M.-K., Ryu, H.-B., Song, S.-H., Lee, J.-W., Kang, S.-O. Tags: Research Articles Source Type: research

Trade-offs with stability modulate innate and mutationally acquired drug resistance in bacterial dihydrofolate reductase enzymes
Structural stability is a major constraint on the evolution of protein sequences. However, under strong directional selection, mutations that confer novel phenotypes but compromise structural stability of proteins may be permissible. During the evolution of antibiotic resistance, mutations that confer drug resistance often have pleiotropic effects on the structure and function of antibiotic-target proteins, usually essential metabolic enzymes. In the present study, we show that trimethoprim (TMP)-resistant alleles of dihydrofolate reductase from Escherichia coli (EcDHFR) harboring the Trp30Gly, Trp30Arg or Trp30Cys mutatio...
Source: Biochemical Journal - June 29, 2018 Category: Biochemistry Authors: Matange, N., Bodkhe, S., Patel, M., Shah, P. Tags: Research Articles Source Type: research

DIS3 isoforms vary in their endoribonuclease activity and are differentially expressed within haematological cancers
DIS3 (defective in sister chromatid joining) is the catalytic subunit of the exosome, a protein complex involved in the 3'–5' degradation of RNAs. DIS3 is a highly conserved exoribonuclease, also known as Rrp44. Global sequencing studies have identified DIS3 as being mutated in a range of cancers, with a considerable incidence in multiple myeloma. In this work, we have identified two protein-coding isoforms of DIS3. Both isoforms are functionally relevant and result from alternative splicing. They differ from each other in the size of their N-terminal PIN (PilT N-terminal) domain, which has been shown to have endorib...
Source: Biochemical Journal - June 29, 2018 Category: Biochemistry Authors: Robinson, S. R., Viegas, S. C., Matos, R. G., Domingues, S., Bedir, M., Stewart, H. J. S., Chevassut, T. J., Oliver, A. W., Arraiano, C. M., Newbury, S. F. Tags: Research Articles Source Type: research

SINHCAF/FAM60A and SIN3A specifically repress HIF-2{alpha} expression
The SIN3A–HDAC (histone deacetylase) complex is a master transcriptional repressor, required for development but often deregulated in disease. Here, we report that the recently identified new component of this complex, SINHCAF (SIN3A and HDAC-associated factor)/FAM60A (family of homology 60A), links the SIN3A–HDAC co-repressor complex function to the hypoxia response. We show that SINHCAF specifically represses HIF-2α mRNA and protein expression, via its interaction with the transcription factor SP1 (specificity protein 1) and recruitment of HDAC1 to the HIF-2α promoter. SINHCAF control over HIF-2&a...
Source: Biochemical Journal - June 29, 2018 Category: Biochemistry Authors: Biddlestone, J., Batie, M., Bandarra, D., Munoz, I., Rocha, S. Tags: Research Articles Source Type: research

Effect of the actin- and calcium-regulating activities of ITPKB on the metastatic potential of lung cancer cells
Inositol-1,4,5-trisphosphate 3-kinase-A (ITPKA) exhibits oncogenic activity in lung cancer cells by regulating Ins(1,4,5)P3-mediated calcium release and cytoskeletal dynamics. Since, in normal cells, ITPKA is mainly expressed in the brain, it is an excellent target for selected therapy of lung cancer. However, ITPKB is strongly expressed in normal lung tissues, but is down-regulated in lung cancer cells by miR-375, assuming that ITPKB might have tumor suppressor activity. In addition, ITPKB binds to F-actin making it likely that, similar to ITPKA, it controls actin dynamics. Thus, the treatment of ITPKA-expressing lung can...
Source: Biochemical Journal - June 26, 2018 Category: Biochemistry Authors: Bäder, S., Glaubke, E., Grüb, S., Muhs, S., Wellbrock, J., Nalaskowski, M., Lange, T., Windhorst, S. Tags: Research Articles Source Type: research