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Biochemical Journal

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https://www.readbyqxmd.com/read/28646128/%C3%AE-copi-mediates-the-retention-of-kae1-g701d-protein-in-golgi-apparatus-a-mechanistic-explanation-of-drta-associated-g701d-mutation
#1
Natapol Duangtum, Mutita Junking, Suratchanee Phadngam, Nunghathai Sawasdee, Andrea Castiglioni, Komgrid Charngkaew, Thawornchai Limjindaporn, Ciro Isidoro, Pa-Thai Yenchitsomanus
Mutations of solute carrier family 4 member 1 ( SLC4A1 ) gene encoding kidney anion (chloride/bicarbonate ion) exchanger 1 (kAE1) can cause genetic distal renal tubular acidosis (dRTA). Different SLC4A1 mutations give rise to mutant kAE1 proteins with distinct defects in protein trafficking. The mutant kAE1 protein may be retained in endoplasmic reticulum (ER), Golgi apparatus, or mis-targeted to the apical membrane, failing to display its function at the baso-lateral membrane. The ER-retained mutant kAE1 interacts with calnexin chaperone protein; disruption of this interaction permits the mutant kAE1 to reach the cell surface and display anion exchange activity...
June 23, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28642254/redox-regulation-of-a-guard-cellsnf1-relatedprotein-kinase-in-brassica-napus-%C3%A2-an-oilseed-crop
#2
Menmeng Zhu, Tong Zhang, Wei Ji, Cecilia Silva-Sanchez, Wenyuan Song, Sarah M Assmann, Alice C Harmon, Sixue Chen
Kinase-mediated phosphorylation is a pivotal regulatory process in stomatal responses to stresses. Through a redox proteomics study, a sucrose non-fermenting 1-related protein kinase (SnRK2.4) was identified to be redox regulated in Brassica napus guard cells upon abscisic acid (ABA) treatment. There are six genes encoding SnRK2.4 paralogs in B. napus Here we show that recombinant BnSnRK2.4-1C exhibited autophosphorylation activity and preferentially phosphorylated the N-terminal region of B. napus slow anion channel (BnSLAC1-NT) over generic substrates...
June 22, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28637792/reactive-sulfur-species-inactivate-ca-2-calmodulin-dependent-protein-kinase-iv-via-s-polysulfidation-of-its-active-site-cysteine-residue
#3
Tsuyoshi Takata, Hideshi Ihara, Naoya Hatano, Yukihiro Tsuchiya, Takaaki Akaike, Yasuo Watanabe
Reactive sulfur species (RSS) modulate protein functions via S- polysulfidation of reactive Cys residues. Here, we report that Ca(2+)/calmodulin (CaM)-dependent protein kinase IV (CaMKIV) was reversibly inactivated by RSS via polysulfidation of the active site Cys residue. CaMKIV is phosphorylated at Thr(196) by its upstream CaMK kinase (CaMKK), resulting in the induction of its full activity. In vitro incubation of CaMKIV with the exogenous RSS donors Na2Sn ( n = 2-4) resulted in dose-dependent inhibition of the CaMKK-induced phospho-Thr(196) and consequent inactivation of the enzyme activity...
June 21, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28634178/ascorbate-protects-the-di-heme-enzyme-maug-against-self-inflicted-oxidative-damage-by-an-unusual-antioxidant-mechanism
#4
Zhongxin Ma, Victor L Davidson
Ascorbate protects MauG from self-inactivation that occurs during the autoreduction of the reactive bis -Fe(IV) state of its diheme cofactor. The mechanism of protection does not involve direct reaction with reactive oxygen species in solution. Instead it binds to MauG and mitigates oxidative damage that occurs via internal transfer of electrons from amino acid residues within the protein to the high-valent hemes. The presence of ascorbate does not inhibit the natural catalytic reaction of MauG which catalyzes oxidative posttranslational modifications of a substrate protein that binds to the surface of MauG, and is oxidized by the high-valent hemes via long range electron transfer...
June 20, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28592683/molecular-basis-of-function-and-the-unusual-antioxidant-activity-of-a-cyanobacterial-cysteine-desulfurase
#5
Manisha Banerjee, Dhiman Chakravarty, Anand Ballal
Cysteine desulfurases, which supply sulfur for iron-sulfur cluster biogenesis, are broadly distributed in all phyla including cyanobacteria, the progenitors of plant chloroplasts. The SUF (sulfur utilization factor) system is responsible for Fe-S cluster biosynthesis under stress. The suf operon from cyanobacterium, Anabaena PCC 7120, showed the presence of a cysteine desulfurase, sufS ( alr2495 ) but not the accessory sulfur accepting protein (SufE). However, an ORF ( alr3513 ) encoding a SufE-like protein (termed as AsaE, Anabaena sulfur acceptor E) was found at a location distinct from the suf operon...
June 7, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28592682/hotspots-of-age-related-protein-degradation-the-importance-of-neighbouring-residues-for-the-formation-of-non-disulfide-crosslinks-derived-from-cysteine
#6
Michael Gavin Friedrich, Zhen Wang, Aaron J Oakley, Kevin L Schey, Roger J W Truscott
Over time, the long-lived proteins that are present throughout the human body deteriorate. Typically, they become racemised, truncated and covalently crosslinked. One reaction responsible for age-related protein crosslinking in the lens was elucidated recently and shown to involve spontaneous formation of dehydroalanine (DHA) intermediates from phosphoserine. Cys residues are another potential source of DHA, and evidence was found for this in a number of lens crystallins. In the human lens, some sites were more prone to forming non-disulfide covalent crosslinks than others...
June 7, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28588043/heme-a-synthesis-and-c-c-o-activity-are-essential-for-trypanosoma-cruzi-infectivity-and-replication
#7
Marcelo Luciano Merli, Brenda Analía Cirulli, Simón Matías Menéndez-Bravo, Julia Alejandra Cricco
Trypanosoma cruzi , the causative agent of Chagas disease, presents a complex life cycle and adapts its metabolism to nutrients availability. Although T. cruzi is an aerobic organism, it does not produce heme. This cofactor is acquired from the host, and is distributed and inserted into different heme-proteins such as respiratory complexes in the parasite mitochondrion. It has been proposed that T. cruzi's energy metabolism relies on a branched respiratory chain with a cytochrome c oxidase type aa 3 (C c O) as the main terminal oxidase...
June 6, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28583991/mutations-of-pka-cyclic-nucleotide-binding-domains-reveal-novel-aspects-of-cyclic-nucleotide-selectivity
#8
Robin Lorenz, Eui-Whan Moon, Jeong Joo Kim, Sven H Schmidt, Banumathi Sankaran, Ioannis V Pavlidis, Choel Kim, Friedrich W Herberg
Cyclic AMP and cyclic GMP are ubiquitous second messengers that regulate the activity of effector proteins in all forms of life. The main effector proteins, the cAMP-dependent protein kinase (PKA) and the cGMP-dependent protein kinase (PKG), are preferentially activated by cAMP and cGMP, respectively. However, the molecular basis of this cyclic nucleotide is still not fully understood. Analysis of isolated cyclic nucleotide binding (CNB) domains of PKA RIα reveals that the C-terminal CNB-B has a higher cAMP affinity and selectivity than the N-terminal CNB-A...
June 5, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28572157/characterization-of-the-oligomeric-states-of-the-ck2-%C3%AE-2%C3%AE-2-holoenzyme-in-solution
#9
Graziano Lolli, Denise Naressi, Stefania Sarno, Roberto Battistutta
The regulatory mechanism of protein kinase CK2 has still to be fully clarified. The prevailing hypothesis is that CK2 is controlled by a self-polymerisation mechanism leading to inactive supramolecular assemblies that, when needed, can be disassembled into the α2β2 monomer, the active form of the holoenzyme. In vitro , monomeric α2β2 seems present only at high ionic strengths, typically 0.35-0.50 M NaCl, while at lower salt concentrations oligomers are formed. Here Size Exclusion Chromatography (SEC), Dynamic Light Scattering (DLS), Small Angle X-ray Scattering (SAXS) and mutagenesis have been employed for the characterization of the oligomeric states of CK2 in solution...
June 1, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28572156/g-protein-coupled-receptor-kinase-2-is-a-critical-regulator-of-tnf%C3%AE-signaling-in-colon-epithelial-cells
#10
Michael Steury, Peter C Lucas, Laura R McCabe, Narayanan Parameswaran
G protein-coupled receptor kinase-2 (GRK2) belongs to the GRK family of serine/threonine protein kinases critical in the regulation of GPCRs. Apart from this canonical role, GRK2 is also involved in several signaling pathways via distinct intracellular interactomes. In this study, we examined the role of GRK2 in TNFα signaling in colon epithelial cell-biological processes including wound healing, proliferation, apoptosis, and gene expression. Knockdown of GRK2 in the SW480 human colonic cells significantly enhanced TNFα-induced epithelial cell wound healing without any effect on apoptosis/proliferation...
June 1, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28559305/biochemical-and-functional-characterization-of-the-human-tissue-kallikrein-9
#11
Panagiota S Filippou, Sofia Farkona, Davor Brinc, Yijing Yu, Ioannis Prassas, Eleftherios P Diamandis
Human tissue kallikrein 9 (KLK9) is a member of the kallikrein-related family of proteases. Despite its known expression profile, much less is known about the functional roles of this protease and its implications in normal physiology and disease. We present here the first data on the biochemical characterization of KLK9, investigate parameters that affect its enzymatic activity (such as inhibitors) and provide preliminary insights into its putative substrates. We show that mature KLK9 (mat-KLK9) is a glycosylated chymotrypsin-like enzyme with strong preference for tyrosine over phenylalanine at the P1 cleavage position...
May 30, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28559304/the-transcription-regulation-mechanism-of-the-syntaxin-1a-gene-via-protein-kinase-a
#12
Takahiro Nakayama, Kimio Akagawa
Syntaxin 1A ( Stx1a ) is primarily involved in the docking of synaptic vesicles at active zones in neurons. Its gene is a TATA-less gene with several transcription initiation sites, which is activated by the binding of Sp1 and acetylated histone H3 (H3) in the core promoter region (CPR) through the derepression of class1-histone deacetylase (HDAC). In the present study, to clarify the factor characterizing Stx1a gene expression via the protein kinase A (PKA) pathway inducing the Stx1a mRNA, we investigated if the epigenetic process is involved in the Stx1a gene transcription induced by PKA signalling...
May 30, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28536157/identification-of-a-conformational-heparin-recognition-motif-on-the-peptide-hormone-secretin-key-role-for-cell-surface-binding
#13
Noe Quittot, Phuong Trang Nguyen, Armelle Tchoumi Nerée, Marc P Lussier, Steve Bourgault
Secretin is a peptide hormone that exerts pleiotropic physiological functions by specifically binding to its cognate membrane-bound receptor. The membrane catalysis model of peptide-receptor interactions states that soluble peptidic ligands initially interact with the plasma membrane. This interaction increases the local concentration and structures the peptide, enhancing the rate of receptor binding. However, this model does not consider the dense network of glycosaminoglycans (GAGs) at the surface of eukaryotic cells...
May 23, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28533266/non-linearity-of-the-collagen-triple-helix-in-solution-and-implications-for-collagen-function
#14
Kenneth T Walker, Ruodan Nan, David W Wright, Jayesh Gor, Anthony C Bishop, George I Makhatadze, Barbara Brodsky, Stephen J Perkins
Collagen adopts a characteristic supercoiled triple helical conformation which requires a repeating (Xaa-Yaa-Gly)n sequence. Despite the abundance of collagen, a combined experimental and atomistic modelling approach has not so far quantitated the degree of flexibility seen experimentally in the solution structures of collagen triple helices. To address this question, we report an experimental study on the flexibility of varying lengths of collagen triple helical peptides, composed of six, eight, ten and twelve repeats of the most stable Pro-Hyp-Gly (POG) units...
May 22, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28526744/combining-properties-of-different-classes-of-pi3k%C3%AE-inhibitors-to-understand-molecular-features-that-confer-selectivity
#15
Grace Q Gong, Jackie D Kendall, James Mj Dickson, Gordon W Rewcastle, Christina M Buchanan, William A Denny, Peter R Shepherd, Jack U Flanagan
Phosphoinositide 3-kinases (PI3K) are major regulators of many cellular functions, and hyperactivation of PI3K cell signalling pathways is a major target for anticancer drug discovery. PI3Kα is the isoform most implicated in cancer, and our aim is to selectively inhibit this isoform, which may be more beneficial than concurrent inhibition of all Class I PI3Ks. We have used structure-guided design to merge high selectivity and high affinity characteristics found in existing compounds. Molecular docking including the prediction of water-mediated interactions, was used to model interactions between the ligands and the PI3Kα affinity pocket...
May 19, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28526743/systematic-identification-of-functional-residues-of-artemisia-annua-amorpha-4-11-diene-synthase
#16
Xin Fang, Jian-Xu Li, Jin-Quan Huang, You-Li Xiao, Peng Zhang, Xiao-Ya Chen
Terpene synthases (TPSs) are responsible for the extremely diversified and complex structure of terpenoids. Amorpha-4,11-diene synthase (ADS) has a high (90%) fidelity in generating the sesquiterpene precursor for biosynthesis of artemisinin, an antimalarial drug, however, little is known about how active site residues of ADS involved in the carbocation rearrangement and cyclization reactions. Here, we identify seven residues that are key to most of the catalytic steps in ADS. By structural modeling and amino acid sequence alignments of ADS with two functionally relevant sesquiterpene synthases from Artemisia annua, we performed site-directed mutagenesis and found that a single substitution, T296V, impaired the ring closure activity almost completely, and tetra-substitutions (L374Y/L404V/L405I/G439S) led to an enzyme generating 80% monocyclic bisabolyl-type sesquiterpenes, whereas a double mutant (T399L/T447G) showed compromised activity in regioselective deprotonation to yield 34...
May 19, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28522638/a-self-consistent-structural-perturbation-approach-for-determining-the-magnitude-and-extent-of-allosteric-coupling-in-proteins
#17
Nandakumar Rajasekaran, Athi N Naganathan
Elucidating the extent of energetic coupling between residues in single-domain proteins, a fundamental determinant of allostery, information transfer and folding cooperativity, has remained a grand challenge. While several sequence- and structure-based approaches have been proposed, a self-consistent description that is simultaneously compatible with unfolding thermodynamics is lacking. We had recently developed a simple structural perturbation protocol that captures the changes in thermodynamic stabilities induced by point mutations within the protein interior...
May 18, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28515264/functional-characterization-of-the-copper-transcription-factor-mrpa%C3%A2-from-aspergillus-fumigatus
#18
Yong-Sung Park, Tae-Hyoung Kim, Cheol-Won Yun
Although copper functions as a cofactor in many physiological processes, copper overload leads to harmful effects in living cells. Thus, copper homeostasis is tightly regulated. However, detailed copper metabolic pathways have not yet been identified in filamentous fungi. In this report, we investigated the copper transcription factor AfMac1 (Aspergillus fumigatus Mac1 homologue), and identified its regulatory mechanism in A. fumigatus AfMac1 has domains homologous to the DNA- and copper-binding domains of Mac1 from Saccharomyces cerevisiae , and AfMac1 efficiently complemented Mac1 in S...
May 17, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28512205/phorbol-12-myristate-13-acetate-mediated-stabilization-of-leukemia-inhibitory-factor-lif-mrna-involvement-of-nucleolin-and-pcbp1
#19
Alina Chakraborty, Srimoyee Mukherjee, Sucharita Saha, Soumasree De, Sumita Sengupta Bandyopadhyay
LIF is a potent pleiotropic cytokine involved in diverse biological activities, thereby requiring precise spatial and temporal control of its expression. The present study reveals that enhanced expression of Leukemia Inhibitory Factor in response to PMA (phorbol-12-myristate-13-acetate) in human histiocytic lymphoma cell-line U937 largely happens through stabilization of its mRNA. Functional characterization of the long 3'-untranslated region (3'-UTR) of human lif -mRNA revealed several conserved sequences with conventional cis -acting elements...
May 16, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28507161/interleukin-1-and-traf6-dependent-activation-of-tak1-in-the-absence-of-tab2-and-tab3
#20
Jiazhen Zhang, Thomas Macartney, Mark Peggie, Philip Cohen
Interleukin-1 (IL-1) signaling induces the formation of Lys63-linked ubiquitin (K63-Ub) chains, which are thought to activate the "master" protein kinase TAK1 by interacting with its TAB2 and TAB3 subunits. Here, we report that IL-1b can also activate the TAB1-TAK1 heterodimer present in TAB2/TAB3 double knock-out (DKO) IL-1 receptor-expressing cells. The IL-1b-dependent activation of the TAB1-TAK1 heterodimer in TAB2/3 DKO cells required the expression and E3 ligase activity of TRAF6 and was reduced by the siRNA knock-down of Ubc13, an E2 conjugating enzyme that directs the formation of K63-Ub chains...
May 15, 2017: Biochemical Journal
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