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Journal of Biochemistry

Biji Chatterjee, Krishna Ghosh, Nitin Yadav, Santosh R Kanade
Lectins are omnipresent in almost all life forms, being the proteins which specifically bind to carbohydrate moieties on the cell surface; they have been explored for their anti-tumour activities. In this study, we purified a fucose specific-lectin (IFL) from Fenneropenaeus indicus hemolymph using fucose-affinity column and characterized for its hemagglutination activity, carbohydrate specificity, dependency on cations and cytotoxicity against cancer cells. The lectin showed non-specificity against human erythrocytes...
October 13, 2016: Journal of Biochemistry
Yan Zhang, Chunyu Yang, Andrew Dancis, Eiko Nakamaru-Ogiso
Yeast Dre2 (anamorsin or CIAPIN1) is an essential component for cytosolic Fe/S cluster biosynthesis. The C-terminal domain contains eight evolutionarily conserved cysteine residues, and we previously demonstrated that the yeast Dre2 overexpressed in Escherichia coli contains one binuclear ([2Fe-2S]) cluster and one tetranuclear ([4Fe-4S]) cluster. In this study, we replaced each conserved cysteine with alanine and analyzed the effects by Electron Paramagnetic Resonance. Although the C311A mutant lacked both signals, our data clearly suggest that the [2Fe-2S] cluster is ligated to Cys252, Cys263, Cys266 and Cys268, whereas the [4Fe-4S] cluster is ligated to Cys311, Cys314, Cys322 and Cys325...
September 26, 2016: Journal of Biochemistry
Yuki Kawakami, Mai Kinoshita, Yoshiko Mori, Shuji Okochi, Shiori Hirano, Ichika Shimoda, Keita Kanzaki, Toshiko Suzuki-Yamamoto, Masumi Kimoto, Mitsuaki Sugahara, Tetsuya Hori, Hiromichi Saino, Masashi Miyano, Shozo Yamamoto, Yoshitaka Takahashi
The X-ray crystal structure of an anti-leukotriene (LT) C4 monoclonal antibody (mAbLTC) in complex with LTC4 was determined, however, crystallographic studies alone are not enough to fully understand the structures of the antigen-binding site. To elucidate the individual contribution of Tyr-54 and Asn-58 in the light chain of mAbLTC, both of which formed a hydrogen bond with glutamic acid of LTC4, we examined whether substitution of the residues affects the antigen binding affinity and specificity using an anti-LTC4 single chain variable fragment (scFvLTC)...
September 20, 2016: Journal of Biochemistry
Ami Sotokawauchi, Miyuki Kato-Murayama, Kazutaka Murayama, Toshiaki Hosaka, Iori Maeda, Michio Onjo, Noboru Ohsawa, Dai-Ichiro Kato, Kazunari Arima, Mikako Shirouzu
Cucumisin [EC], a subtilisin-like serine endopeptidase, was isolated from melon fruit, Cucumis melo L. Mature cucumisin (67 kDa, 621 residues) is produced by removal of the propeptide (10 kDa, 88 residues) from the cucumisin precursor by subsequence processing. It is reported that cucumisin is inhibited by its own propeptide. The crystal structure of mature cucumisin is reported to be composed of three domains: the subtilisin-like catalytic domain, the protease-associated domain, and the C-terminal fibronectin-III-like domain...
September 10, 2016: Journal of Biochemistry
Hiroshi Kameda, Sayaka Usugi, Mana Kobayashi, Naoya Fukui, Seki Lee, Kunihiro Hongo, Tomohiro Mizobata, Yuki Sekiguchi, Yu Masaki, Amane Kobayashi, Tomotaka Oroguchi, Masayoshi Nakasako, Yuki Takayama, Masaki Yamamoto, Yasushi Kawata
The aggregation and deposition of α-synuclein (αSyn) in neuronal cells is correlated to pathogenesis of Parkinson's disease. Although the mechanism of αSyn aggregation and fibril formation has been studied extensively, the structural hallmarks that are directly responsible for toxicity toward cells is still under debate. Here, we have compared the structural characteristics of the toxic intermediate molecular species of αSyn and similar toxic species of another protein, GroES, using coherent X-ray diffraction analysis...
August 18, 2016: Journal of Biochemistry
Taiji Imoto
To analyze enzymatic reactions energetically for comparison with non-enzymatic reactions (first order) under the same dimension, a method to derive valid momentary first order rate constants for enzymatic reactions was developed. The momentary first order rate constant, kenz0 = kcat[E'S']e,0/[S]0, was derived for an enzymatic reaction under a certain condition. It was shown that this rate constant is applicable for a wide range of enzymatic reactions. Utilizing this constant, one can conduct reliable kinetic and energetic analyses of enzymatic reactions...
August 9, 2016: Journal of Biochemistry
Natsuki Fukuda, Yoshiaki Suwa, Makiyo Uchida, Yoshihiro Kobashigawa, Hideshi Yokoyama, Hiroshi Morioka
Antibody is known to exhibit conformational change in the antigen recognition site after forming the initial complex. This structural change, which is widely known as "induced fit", is believed to be critical for high affinity (Kd of nM range) of antigen-antibody interaction. Elucidation of this "induced fit" process is essential for rational design of high affinity antibody, while it is prevented by limitation of the available biophysical and biochemical data of the initial complex. Here, we performed kinetic and thermodynamic analysis of the interaction between single-chain variable fragment (denoted as scFv) of 64M5 antibody and a (6-4) photoproduct by using surface plasmon resonance (denoted as SPR)...
August 9, 2016: Journal of Biochemistry
Hideaki Ogata, Wolfgang Lubitz, Yoshiki Higuchi
Hydrogenases catalyze the reversible conversion of molecular hydrogen to protons and electrons via a heterolytic splitting mechanism. The active sites of [NiFe] hydrogenases comprise a dinuclear Ni-Fe center carrying CO and CN(-) ligands. The catalytic activity of the standard (O2-sensitive) [NiFe] hydrogenases vanishes under aerobic conditions. The O2-tolerant [NiFe] hydrogenases can sustain H2 oxidation activity under atmospheric conditions. These hydrogenases have very similar active site structures that change the ligand sphere during the activation/catalytic process...
August 4, 2016: Journal of Biochemistry
Hiroki Sonobe, Takashi Obinata, Takuya Minokawa, Tomohiro Haruta, Yuuki Kawamura, Shinryu Wakatsuki, Naruki Sato
Paramyosin is a myosin-binding protein characteristic of invertebrate animals, while troponin is a Ca(2+)-dependent regulator of muscle contraction. Both proteins are widely distributed in protostomes, while in deuterostomes, their distribution is limited; namely, presence of paramyosin and absence of troponin are common features in echinoderm muscles, while muscles of chordates contain troponin but lack paramyosin. In this study, we examined the muscle of a hemichordate, acorn worm, to clarify whether this animal is like echinoderms or like the other deuterostome animals...
August 4, 2016: Journal of Biochemistry
Jette Pretzel, Marina Gehr, Maike Eisenkolb, Lihui Wang, Karin Fritz-Wolf, Stefan Rahlfs, Katja Becker, Esther Jortzik
As a methyl group donor for biochemical reactions, S-adenosylmethionine plays a central metabolic role in most organisms. Depletion of S-adenosylmethionine has downstream effects on polyamine metabolism and methylation reactions, and is an effective way to combat pathogenic microorganisms such as malaria parasites. Inhibition of both the methylation cycle and polyamine synthesis strongly affects Plasmodium falciparum growth. Despite its central position in the methylation cycle, not much is currently known about P...
July 27, 2016: Journal of Biochemistry
Masayasu Kojima, Akie Hamamoto, Takahiro Sato
In the gastric peptide hormone ghrelin, serine 3 (threonine 3 in frogs) is modified, primarily by n-octanoic acid; this modification is essential for ghrelin's activity. The enzyme that transfers n-octanoic acid to Ser3 of ghrelin is ghrelin O-acyltransferase (GOAT). GOAT, the only enzyme known to catalyze acyl modification of ghrelin, specifically modifies serine (or threonine) at the third position and does not modify other serine residues in ghrelin peptides. GOAT prefers n-hexanoyl-CoA over n-octanoyl-CoA as the acyl donor, although in the stomach the n-octanoyl form is the predominant form of acyl-modified ghrelin...
October 2016: Journal of Biochemistry
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No abstract text is available yet for this article.
September 2016: Journal of Biochemistry
Takashi Aoi
In 2006, induced pluripotent stem (iPS) cells were generated by Yamanaka and Takahashi for the first time from a mouse fibroblast culture by introducing four factors. In the 10 years since then, this breakthrough discovery has been making waves in the fields of biology and medical science. For example, various technologies for generating iPS cells have been developed, and we have cultivated a better understanding of the mechanisms involved in reprogramming. In addition, many researchers have explored the applications of iPS cells, such as drug discovery, the study of disease mechanisms and regenerative medicine, and the development of advanced technologies for the differentiation and qualification of the cells...
September 2016: Journal of Biochemistry
Saki Inuzuka, Kei-Ichiro Nishimura, Hitoshi Kakizawa, Yuki Fujita, Hiroyuki Furuta, Shigeyoshi Matsumura, Yoshiya Ikawa
The Vc2 riboswitch possesses an aptamer domain belonging to the class-I c-di-GMP riboswitch family. This domain has been analysed and the molecular mechanism by which it recognizes the c-di-GMP ligand has been elucidated. On the other hand, the regulatory mechanism of the full-length Vc2 riboswitch to control its downstream open reading frame (ORF) remains largely unknown. In this study, we performed in vivo reporter assays and in vitro biochemical analyses of the full-length riboswitch and its aptamer domain...
September 2016: Journal of Biochemistry
Rupali Yadav, Kuldeep Verma, Mintu Chandra, Madhumita Mukherjee, Sunando Datta
Entamoeba histolytica, an enteric parasite expresses a Gal/GalNAc-specific lectin that contributes to its virulence by establishing adhesion to host cell. In this study, carbohydrate recognition domain of Hgl (EhCRD) was purified and biophysical studies were conducted to understand the thermodynamic basis of its binding to carbohydrate and Ca(++) Here, we show that carbohydrate recognition domain (CRD) of the lectin binds to calcium through DPN motif. To decipher the role of calcium in carbohydrate binding and host cell adhesion, biophysical and cell-based studies were carried out...
September 2016: Journal of Biochemistry
Priyabrata Das, Soma Mukhopadhyay, Nirmal Kumar Sarkar, Suvra Mandal, Manoj Kar, Ashis Mukhopadhyay
Iron chelation therapies are required for the treatment of iron overloaded patients; nonetheless, their side effects are also well known. We have evaluated iron-chelating activity of wheat grass extract (WHE) and its purified compound, mugineic acid in murine model with phenylhydrazine (PHZ) and dextran induced acute and chronic iron overload conditions. PHZ and dextran treatment induced acute and chronic iron overload condition in mice, respectively, as indicated by increased serum and tissue iron in both cases...
September 2016: Journal of Biochemistry
Rubi Figueroa-Teran, Heidi Pak, Gary J Blomquist, Claus Tittiger
Ips spp. bark beetles use ipsdienol, ipsenol, ipsdienone and ipsenone as aggregation pheromone components and pheromone precursors. For Ips pini, the short-chain oxidoreductase ipsdienol dehydrogenase (IDOLDH) converts (-)-ipsdienol to ipsdienone, and thus likely plays a role in determining pheromone composition. In order to further understand the role of IDOLDH in pheromone biosynthesis, we compared IDOLDH to its nearest functionally characterized ortholog with a solved structure: human L-3-hydroxyacyl-CoA dehydrogenase type II/ amyloid-β binding alcohol dehydrogenase (hHADH II/ABAD), and conducted functional assays of recombinant IDOLDH to determine substrate and product ranges and structural characteristics...
September 2016: Journal of Biochemistry
Naomi Motoyoshi, Hiroko Kobayashi, Tadashi Itagaki, Norio Inokuchi
The aim of this study was to phylogenetically characterize the location of the RNase T2 enzyme in the starfish (Asterias amurensis). We isolated an RNase T2 ribonuclease (RNase Aa) from the ovaries of starfish and determined its amino acid sequence by protein chemistry and cloning cDNA encoding RNase Aa. The isolated protein had 231 amino acid residues, a predicted molecular mass of 25,906 Da, and an optimal pH of 5.0. RNase Aa preferentially released guanylic acid from the RNA. The catalytic sites of the RNase T2 family are conserved in RNase Aa; furthermore, the distribution of the cysteine residues in RNase Aa is similar to that in other animal and plant T2 RNases...
September 2016: Journal of Biochemistry
Keisuke Ito, Hideki Enomoto
Neurotrophic factors and their receptors play a central role in neuronal survival. Since neurons have a highly polarized morphology, target-derived neurotrophic factor signaling is transported retrogradely along the axon to the cell body. A body of evidence suggests that retrograde transport of the neurotrophic factors and their receptors is required for signal propagation. Retrograde transport of neurotrophic factor signaling is crucial not only for neuronal development, but also for preventing neuronal degeneration...
August 2016: Journal of Biochemistry
Yoichi Miyamoto, Kohji Yamada, Yoshihiro Yoneda
Importin α performs the indispensable role of ferrying proteins from the cytoplasm into the nucleus with a transport carrier, importin β1. Mammalian cells from mouse or human contain either six or seven importin α subtypes, respectively, each with a tightly regulated expression. Therefore, the combination of subtype expression in a cell defines distinct signaling pathways to achieve progressive changes in gene expression essential for cellular events, such as differentiation. Recent studies reveal that, in addition to nucleocytoplasmic transport, importin αs also serve non-transport functions...
August 2016: Journal of Biochemistry
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