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Journal of Biochemistry

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https://www.readbyqxmd.com/read/28637331/antioxidants-as-stabilizers-for-his6-oph-is-this-an-unusual-or-regular-role-for-them-with-enzymes
#1
Elena N Efremenko, Ilya V Lyagin, Le Huu Cuong, Le Mai Huong
HASH(0x4802018)
June 16, 2017: Journal of Biochemistry
https://www.readbyqxmd.com/read/28637250/use-of-spytag-spycatcher-to-construct-bispecific-antibodies-that-target-two-epitopes-of-a-single-antigen
#2
Kyohei Yumura, Hiroki Akiba, Satoru Nagatoishi, Osamu Kusano-Arai, Hiroko Iwanari, Takao Hamakubo, Kouhei Tsumoto
Bispecific antibody targeting of two different antigens is promising, but when fragment-based antibodies are used, homogeneous production is difficult. To overcome this difficulty, we developed a method using the SpyTag/SpyCatcher system in which a covalent bond is formed between the two polypeptides. Using this method, we constructed a bispecific antibody that simultaneously interacted with two different epitopes of ROBO1, a membrane protein associated with cancer progression. A bispecific tetravalent antibody with an additional functional moiety was also constructed by using a dimeric biotin-binding protein...
June 16, 2017: Journal of Biochemistry
https://www.readbyqxmd.com/read/28575453/quantitative-analysis-of-phagosome-formation-and-maturation-using-an-escherichia-coli-probe-expressing-a-tandem-fluorescent-protein
#3
Maya Morita, Kazumasa Sawaki, Daiki Kinoshita, Chiye Sakurai, Naohiro Hori, Kiyotaka Hatsuzawa
Phagosome formation and maturation are essential innate immune mechanisms to engulf and digest foreign particles. To analyze these processes quantitatively, we established a specific Escherichia coli probe expressing a tandem fluorescent protein, comprising glutathione S-transferase fused with monomeric Cherry (mCherry) and monomeric Venus (mVenus). We demonstrated that mVenus was more susceptible to bleaching in an acidic environment than mCherry, and that the mVenus:mCherry fluorescence intensity ratio can be used to monitor phagosomal pH changes during maturation...
May 29, 2017: Journal of Biochemistry
https://www.readbyqxmd.com/read/28541399/assessment-of-direct-interaction-between-cd36-and-an-oxidized-glycerophospholipid-species
#4
Satoshi Tsuzuki, Masayuki Yamasaki, Yuki Kozai, Tatsuya Sugawara, Yuki Manabe, Kazuo Inoue, Tohru Fushiki
No abstract text is available yet for this article.
May 25, 2017: Journal of Biochemistry
https://www.readbyqxmd.com/read/28510655/mir-145-promoted-anoikis-resistance-in-tumor-endothelial-cells
#5
Kyoko Hida, Taisuke Kawamoto, Nako Maishi, Masahiro Morimoto, Kosuke Akiyama, Noritaka Ohga, Masanobu Shindoh, Nobuo Shinohara, Yasuhiro Hida
Tumor progression is dependent on tumor angiogenesis. We previously reported that the phenotype of tumor endothelial cells (TECs) is distinct from normal endothelial cells (NECs). Herein, we conducted a pathway analysis using a public TEC microarray database and identified several putative TEC-specific miRNAs. We found that miR-145 expression was upregulated in TECs and that miR-145 enhanced cell adhesion and anoikis resistance and upregulated Bcl-2 and Bcl-xl via ERK1/2in human microvascular endothelial cells...
May 16, 2017: Journal of Biochemistry
https://www.readbyqxmd.com/read/28486685/inhibition-of-ser-thr-phosphatase-ppm1d-induces-neutrophil-differentiation-in-hl-60-cells
#6
Rui Kamada, Fuki Kudoh, Fumihiko Yoshimura, Keiji Tanino, Kazuyasu Sakaguchi
Protein phosphatase Magnesium-dependent 1, Delta (PPM1D) is a wild-type p53-inducible Ser/Thr phosphatase that acts as a negative regulator of the p53 tumor suppressor. Gene amplification and overexpression of PPM1D have been reported in various cancers including leukemia and neuroblastoma. Therefore, PPM1D is a promising target in cancer therapy. It has been reported that PPM1D knockout mice exhibit neutrophilia in blood and show a defective immune response. Here, we found that inhibition of PPM1D induced neutrophil differentiation of human promyelocytic leukemia cell line HL-60...
May 9, 2017: Journal of Biochemistry
https://www.readbyqxmd.com/read/28460043/cell-free-mitochondrial-fusion-assay-detected-by-specific-protease-reaction-revealed-ca2-as-regulator-of-mitofusin-dependent-mitochondrial-fusion
#7
Naotada Ishihara, Maki Maeda, Tadato Ban, Katsuyoshi Mihara
Mitochondrial dynamic by frequent fusion and fission have important roles in various cellular signaling processes and pathophysiology in vivo. However, the molecular mechanisms that regulate mitochondrial fusion, especially in mammalian cells, are not well understood. Accordingly, we developed a novel biochemical cell-free mitochondrial fusion assay system using isolated human mitochondria. We used a protease and its specific substrate that are essential for yeast autophagy; Atg4 protease is required for maturation and the de-conjugation of the ubiquitin-like modifier Atg8...
April 27, 2017: Journal of Biochemistry
https://www.readbyqxmd.com/read/28449070/in-situ-screening-for-postsynaptic-cell-adhesion-molecules-during-synapse-formation
#8
Takeshi Uemura, Tomoko Shiroshima, Asami Maeda, Misato Yasumura, Takashi Shimada, Yuko Fukata, Masaki Fukata, Tomoyuki Yoshida
Neuronal synapse formation is regulated by pre- and postsynaptic cell adhesion molecules. Presynaptic neurexins (NRXNs) and receptor protein tyrosine phosphatases (RPTPs; PTPδ, PTPσ, and LAR in mammals) can induce postsynaptic differentiation through the interaction with various postsynaptic cell adhesion molecules. Here, we developed a novel in situ screening method to identify postsynaptic membranous proteins involved in synaptogenesis. Magnetic beads coated with the extracellular domains of NRXN1β(-S4) and PTPδ-A6 variants preferentially induced excitatory postsynaptic differentiation on the beads' surface when co-cultured with cortical neurons...
April 25, 2017: Journal of Biochemistry
https://www.readbyqxmd.com/read/28444248/effects-of-various-spacers-between-biotin-and-the-phospholipid-headgroup-on-immobilization-and-sedimentation-of-biotinylated-phospholipid-containing-liposomes-facilitated-by-avidin-biotin-interactions
#9
Yasuhisa Sakamoto, Koji Kikuchi, Kazuaki Umeda, Hiroyuki Nakanishi
Immobilization and sedimentation of liposomes (lipid vesicles) are used in liposome-protein binding assays, facilitated by avidin/streptavidin/NeutrAvidin and biotinylated phospholipid-containing liposomes. Here, we examined the effects of three spacers [six-carbon (X), polyethylene glycol (PEG) 180 (molecular weight 180), and PEG2000 (molecular weight 2000)] between biotin and the phospholipid headgroup on the immobilization and sedimentation of small unilamellar liposomes/vesicles (SUVs). PEG180 and PEG2000 showed more efficient immobilization of biotinylated SUVs on NeutrAvidin-coated plates than X, but X and PEG180 showed more efficient sedimentation of biotinylated SUVs upon NeutrAvidin addition than PEG2000...
April 24, 2017: Journal of Biochemistry
https://www.readbyqxmd.com/read/28431120/solution-structure-of-a-reverse-transcriptase-recognition-site-of-a-line-rna-from-zebrafish
#10
Maina Otsu, Masaki Kajikawa, Norihiro Okada, Gota Kawai
Long interspersed nuclear element (LINE) is known to be transposed by reverse transcription using its RNA transcript. Recognition of the 3' stem-loop of LINE RNA by its reverse transcriptase (RT) is an important step of the retrotransposition. Our previous study revealed that the second G residue (G8) in the GGAUA loop of a 17mer LINE RNA from eel, UnaL2-17, is recognized by its RT and the U residue (U10) in the same loop is required to maintain the loop structure (Baba et al., 2004). ZfL2-2, a LINE from zebrafish, has the same 3' stem-loop with UnaL2 and ZfL2-1 has similar but distinct 3' stem-loop with an insertion which can form an additional stem-loop...
April 18, 2017: Journal of Biochemistry
https://www.readbyqxmd.com/read/28430987/rab32-subfamily-small-gtpases-pleiotropic-rabs-in-endosomal-trafficking
#11
Norihiko Ohbayashi, Mitsunori Fukuda, Yasunori Kanaho
Rab small GTPases, well-known regulators of membrane trafficking pathways in eukaryotic cells, comprise approximately 60 different members in mammals. During the past decade, our understanding of the functions of mammalian Rab32 subfamily members (Rab32 and Rab38) have deepened, especially on the biogenesis of lysosome-related organelles, such as melanosomes, and the protection mechanisms against several pathogenic microbial infections. Endosome-mediated membrane trafficking by Rab32 subfamily members plays pivotal roles in these events...
April 14, 2017: Journal of Biochemistry
https://www.readbyqxmd.com/read/28407125/cell-fate-modification-toward-the-hepatic-lineage-by-extrinsic-factors
#12
Masaki Kawamata, Atsushi Suzuki
The lineage of a somatic cell can be altered by targeting its signaling networks with small molecules and/or genetically altering the expression of key transcription factors. Depending on the combination of factors, fibroblasts can be fully reprogrammed into induced pluripotent stem (iPS) cells or directly converted into specific cell lineages, bypassing the pluripotent state. The generation of defined target cells will enormously benefit patients who require cell transplantation therapy. In the decade since iPS cells were first generated, many cell types have been induced from fibroblasts by direct conversion, including hepatocytes...
April 12, 2017: Journal of Biochemistry
https://www.readbyqxmd.com/read/28402412/effects-of-neutral-salts-and-ph-on-the-activity-and-stability-of-human-rnase-h2
#13
Misato Baba, Kenji Kojima, Rihoko Nakase, Shota Imai, Tomomi Yamasaki, Teisuke Takita, Robert J Crouch, Kiyoshi Yasukawa
Ribonuclease H (RNase H) specifically degrades the RNA of RNA/DNA hybrid. Recent study has shown that a single ribonucleotide is embedded in DNA double strand at every few thousand base pairs in human genome, and human RNase H2 is involved in its removal. Here, we examined the effects of neutral salts and pH on the activity and stability of human RNase H2. NaCl, KCl, RbCl, and NaBr increased the activity to 170-390% at 10-60 mM, while LiCl, LiBr, and CsCl inhibited it, suggesting that species of cation, but not anion, is responsible for the effect on activity...
April 11, 2017: Journal of Biochemistry
https://www.readbyqxmd.com/read/28398483/function-of-nuclear-membrane-proteins-in-shaping-the-nuclear-envelope-integrity-during-closed-mitosis
#14
Hui-Ju Yang, Masaaki Iwamoto, Yasushi Hiraoka, Tokuko Haraguchi
The nuclear envelope (NE) not only protects the genome from being directly accessed by detrimental agents but also regulates genome organization. Breaches in NE integrity threaten genome stability and impede cellular function. Nonetheless, the NE constantly remodels, and NE integrity is endangered in dividing or differentiating cells. Specifically, in unicellular eukaryotes undergoing closed mitosis, the NE expands instead of breaking down during chromosome segregation. The newly assembling nuclear pore complexes (NPCs) penetrate the existing NE in interphase...
June 1, 2017: Journal of Biochemistry
https://www.readbyqxmd.com/read/28338847/paradigm-shift-from-diagnosing-patients-based-on-common-symptoms-to-categorizing-patients-into-subtypes-with-different-pathogenic-mechanisms-to-guide-treatment-for-alzheimer-s-disease
#15
Keiro Shirotani, Masashi Asai, Nobuhisa Iwata
Alzheimer's disease (AD) is a major cause of dementia in the elderly, and the number of AD patients is rapidly growing as life expectancy increases. However, disease-modifying drugs are not yet available. According to the amyloid hypothesis, disease onset is triggered by aggregation and accumulation of amyloid-β peptide, followed by the formation of neurofibrillary tangles composed of hyperphosphorylated tau, and synaptic loss/neuronal cell death leading to dementia. Based on this hypothesis, various clinical trials for treatment of AD have been conducted, but most were discontinued due to failure to achieve cognitive improvement or appearance of adverse effects...
June 1, 2017: Journal of Biochemistry
https://www.readbyqxmd.com/read/28158808/simultaneous-ablation-of-prmt-1-and-prmt-5-abolishes-asymmetric-and-symmetric-arginine-dimethylations-in-caenorhabditis-elegans
#16
Keiko Hirota, Chihiro Shigekawa, Sho Araoi, Liang Sha, Takayuki Inagawa, Akihiko Kanou, Koichiro Kako, Hiroaki Daitoku, Akiyoshi Fukamizu
Protein arginine methyltransferases (PRMTs) catalyze the transfer of a methyl group from S-adenosylmethionine to arginine residues and are classified into two types: type I producing asymmetric dimethylarginine (ADMA) and type II producing symmetric dimethylarginine (SDMA). PRMTs have been shown to regulate many cellular processes, including signal transduction, transcriptional regulation and RNA processing. Since the loss-of-function mutation of PRMT1 and PRMT5, each of which is the predominant type I and II, respectively, causes embryonic lethality in mice, their physiological significance at the whole-body level remains largely unknown...
June 1, 2017: Journal of Biochemistry
https://www.readbyqxmd.com/read/28130416/crystal-structure-of-the-solute-binding-protein-bxle-from-streptomyces-thermoviolaceus-opc-520-complexed-with-xylobiose
#17
Koji Tomoo, Yasuhiro Miki, Hideaki Morioka, Kiho Seike, Toshimasa Ishida, Sadao Ikenishi, Katsushiro Miyamoto, Tomokazu Hasegawa, Akihito Yamano, Kensaku Hamada, Hiroshi Tsujibo
BxlE from Streptomyces thermoviolaceus OPC-520 is a xylo-oligosaccharide (mainly xylobiose)-binding protein that serves as the initial receptor for the bacterial ABC-type xylo-oligosaccharide transport system. To determine the ligand-binding mechanism of BxlE, X-ray structures of ligand-free (open form) and ligand (xylobiose)-bound (closed form) BxlE were determined at 1.85 Å resolution. BxlE consists of two globular domains that are linked by two β-strands, with the cleft at the interface of the two domains creating the ligand-binding pocket...
June 1, 2017: Journal of Biochemistry
https://www.readbyqxmd.com/read/28096454/mitochondrial-function-is-required-for-extracellular-atp-induced-nlrp3-inflammasome-activation
#18
Daichi Sadatomi, Kazutaka Nakashioya, Sayaka Mamiya, Shino Honda, Yuka Kameyama, Yasuo Yamamura, Susumu Tanimura, Kohsuke Takeda
The NLRP3 inflammasome plays a critical role in the processing and release of inflammatory cytokines, such as interleukin-1β (IL-1β) and IL-18. Accumulating evidence suggests that mitochondria are common mediators of NLRP3 inflammasome activation induced by a wide range of inflammatory stimuli; however, the precise role of mitochondria is still not fully understood. Here, we show that mitochondrial function is required for extracellular ATP-induced NLRP3 inflammasome activation. Extracellular ATP induced the loss of mitochondrial membrane potential and mitochondrial fragmentation in a different manner than other stimuli in primary mouse macrophages...
June 1, 2017: Journal of Biochemistry
https://www.readbyqxmd.com/read/28082720/enzymatic-kinetics-of-the-quinol-peroxidase-of-an-aggressive-periodontopathic-bacterium
#19
Tasuku Abe, Taketo Kawarai, Yukihiro Takahashi, Kiyoshi Konishi
Aggregatibacter actinomycetemcomitans is an oral pathogen for aggressive periodontitis, and encodes a triheme c-containing membrane-bound enzyme, quinol peroxidase (QPO) that catalyzes peroxidase activity using quinol in the respiratory chain. In the previous work, we have characterized recombinant QPO purified from the membrane fraction of Escherichia coli harboring a plasmid containing QPO gene. Irreversible inactivation of QPO by high concentration of H2O2 exhibited pseudo-first order kinetics. Analysis of initial-rate kinetics of QPO may suggest that enzyme catalytic mechanism is explained by a Ping Pong Bi Bi system rather than sequential systems...
June 1, 2017: Journal of Biochemistry
https://www.readbyqxmd.com/read/28011817/a-mechanism-for-evasion-of-ctl-immunity-by-altered-o-glycosylation-of-hla-class-i
#20
Mihoko Sutoh Yoneyama, Yuki Tobisawa, Shingo Hatakeyama, Misaki Sato, Kiyoshi Tone, Yota Tatara, Ikuko Kakizaki, Tomihisa Funyu, Minoru Fukuda, Senji Hoshi, Chikara Ohyama, Shigeru Tsuboi
Anti-tumour immunity by cytotoxic T-lymphocytes (CTLs) is essential to suppress tumour progression. Cancer cells that evade CTL immunity proliferate in the host, promoting metastasis, but mechanisms underlying this capacity remain unknown. Here we report that bladder cancer cells metastasized to lymph nodes evade CTL immunity by a new mechanism via altered glycosylation. CTLs normally recognize and kill cancer cells presenting antigenic peptides on human leukocyte antigen (HLA) class I. We show bladder cancer cells expressing the O-glycan processing enzyme, core2 β-1,6-N-acetylglucosaminyltransferase (C2GnT) exhibit HLA class I O-glycan modified with poly-N-acetyllactosamine and are highly susceptible to CTL...
June 1, 2017: Journal of Biochemistry
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