Derivation of a valid momentary first-order rate constant for kinetic and energetic analyses of enzymatic reactions
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, k enz0 = k cat[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. (Source: Journal of Biochemistry)
Source: Journal of Biochemistry - December 1, 2016 Category: Biochemistry Authors: Imoto, T. Tags: Regular Papers Source Type: research
Characterization of paramyosin and thin filaments in the smooth muscle of acorn worm, a member of hemichordates
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. We found a 100-kDa protein in the smooth muscle of acorn worm. This protein was identified with paramyosin, since the purified protein formed paracrystals with a constant axial periodicity in the presence of divalent cations as paramyosin of other animals, showed ability to interact with myosin and shared common antigenicity with echinoderm paramyosin. On the other hand, troponin band was not detected in isolated thin filaments, and the filaments increased myosin-AT...
Source: Journal of Biochemistry - December 1, 2016 Category: Biochemistry Authors: Sonobe, H., Obinata, T., Minokawa, T., Haruta, T., Kawamura, Y., Wakatsuki, S., Sato, N. Tags: Regular Papers Source Type: research
Characterization and redox regulation of Plasmodium falciparum methionine adenosyltransferase
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. falciparum methionine adenosyltransferase (PfalMAT). Notably, however, PfalMAT has been discussed as a target...
Source: Journal of Biochemistry - December 1, 2016 Category: Biochemistry Authors: Pretzel, J., Gehr, M., Eisenkolb, M., Wang, L., Fritz-Wolf, K., Rahlfs, S., Becker, K., Jortzik, E. Tags: Regular Papers Source Type: research
Serine racemase is involved in D-aspartate biosynthesis
d-Aspartate is found in the nervous and reproductive system and participates in various physiological roles. While several lines of evidence suggest that this amino acid has an endogenous origin, the enzyme responsible for mammalian d-Asp biosynthesis has not yet been identified. We show that mammalian serine racemase (SRR), the primary enzyme responsible for brain d-Ser production, catalyses Asp racemization via a two-base mechanism. We observed that overexpression of SRR in rat pheochromocytoma PC12 cells resulted in an increase in intracellular d-Asp compared with control cells, demonstrating that SRR functions as an As...
Source: Journal of Biochemistry - December 1, 2016 Category: Biochemistry Authors: Ito, T., Hayashida, M., Kobayashi, S., Muto, N., Hayashi, A., Yoshimura, T., Mori, H. Tags: Regular Papers Source Type: research
The double knockout of Bach1 and Bach2 in mice reveals shared compensatory mechanisms in regulating alveolar macrophage function and lung surfactant homeostasis
Pulmonary alveolar proteinosis (PAP) is a disease resulting from a dysfunction of the alveolar macrophages (AMs) where excess surfactant protein accumulates in the alveolar spaces. We previously reported that Bach2 KO mice developed PAP due to a defect in the handling of lipids by AMs. To investigate the functions of Bach1 and Bach2, which are regulated by oxidative stress, in the AMs and in lung homeostasis, we generated mice that lacked both Bach1 and Bach2 (Bach1/2 DKO mice). The Bach1/2 DKO mice showed more severe PAP phenotype than Bach2 KO mice with abnormal AMs, whereas the Bach1 KO mice did not develop any pulmonar...
Source: Journal of Biochemistry - December 1, 2016 Category: Biochemistry Authors: Ebina-Shibuya, R., Watanabe-Matsui, M., Matsumoto, M., Itoh-Nakadai, A., Funayama, R., Nakayama, K., Muto, A., Igarashi, K. Tags: Regular Papers Source Type: research
Toxicity of serum albumin on microglia upon seeding effect of amyloid peptide
We demonstrate in vitro cross-seeding of bovine serum albumin (BSA) in the presence of Aβ25-35 and their cytotoxic effects on microglial cells. To investigate the cross-seeding of BSA in the presence of Aβ25-35 fibrils, we examined how Aβ25-35 fibrils can function as seeds to trigger and accelerate BSA fibrillogenesis using ThT, intrinsic fluorescence, ANS fluorescence and transmission electron microscopy (TEM). Moreover, the effects of these fibrils on microglial viability were measured using MTT and Annexin V/propidium iodide (PI) staining. Although Aβ25-35 is toxic against microglia, it acted as seed...
Source: Journal of Biochemistry - December 1, 2016 Category: Biochemistry Authors: Ferdousi, M., Habibi-Rezaei, M., Balalaie, S., Ramezanpour, S., Sabouni, F., Poursasan, N., Sabokdast, M., Moosavi-Movahedi, A. A. Tags: Regular Papers Source Type: research
Role of reactive oxygen species-mediated MAPK and NF-{kappa}B activation in polygonatum cyrtonema lectin-induced apoptosis and autophagy in human lung adenocarcinoma A549 cells
Polygonatum cyrtonema lectin (PCL), a mannose/sialic acid-binding lectin isolated from the rhizomes of Polygonatum cyrtonema Hua, has been reported to possess remarkable anti-tumour effects via inducing apoptosis and autophagy. The aim of this study was to investigate the molecular mechanisms mediating PCL-induced apoptosis and autophagy in A549 cells. Herein, we found that the treatment of A549 cells with PCL caused a remarkable generation of reactive oxygen species (ROS) and ROS scavenger N-acetyl-cysteine (NAC) inhibited PCL-induced apoptosis and autophagy. In addition, PCL treatment activated mitogen-activated protein ...
Source: Journal of Biochemistry - December 1, 2016 Category: Biochemistry Authors: Liu, T., Wu, L., Wang, D., Wang, H., Chen, J., Yang, C., Bao, J., Wu, C. Tags: Regular Papers Source Type: research
Involvement of the NFX1-repressor complex in PKC-{delta}-induced repression of hTERT transcription
The human telomerase reverse transcriptase (hTERT) gene encodes an enzyme responsible for maintaining the integrity of chromosomal ends. hTERT plays a key role in cellular immortalization, tumorigenesis and the progression of cancer. Previously, we reported that hTERT repression is required for the induction of cellular senescence. Thus, transcriptional regulation mechanisms of the hTERT gene may be related to the mechanisms of cellular senescence. In the present study, we clarified the molecular mechanism of hTERT repression by protein kinase C (PKC)-, one of the cellular senescence-inducing factors. The results showed th...
Source: Journal of Biochemistry - October 30, 2016 Category: Biochemistry Authors: Yamashita, S., Fujii, K., Zhao, C., Takagi, H., Katakura, Y. Tags: Regular Papers Source Type: research
Conserved and unique thermodynamic properties of lactate dehydrogenases in an ectothermic organism, the teleost Microstomus achne, and an endothermic organism, bovine
It is widely believed that enzymatic activities in ectothermic organisms adapt to environmental temperatures. However, to date, no study has thoroughly compared multiple thermodynamic enzymatic characteristics across species living in dramatically different environments. To start to address this gap, we compared the characteristics of lactate dehydrogenase (LDH) purified from the muscles from slime flounder Microstomus achne white muscle and bovine skeletal muscle (bM4) and heart. The K m and V max for pyruvate reduction were about three times higher for M. achne LDH than bM4. Surprisingly, maximum LDH activity was obser...
Source: Journal of Biochemistry - October 30, 2016 Category: Biochemistry Authors: Yonezawa, M., Nakagawa, M., Nakamura, S., Goto, T., Sugawara, K., Kidokoro, S.-I., Wakui, H., Nunomura, W. Tags: Regular Papers Source Type: research
Charge-state-distribution analysis of Bach2 intrinsically disordered heme binding region
Bach2 is a transcriptional repressor that plays an important role in the differentiation of T-cells and B-cells. Bach2 is functionally regulated by heme binding, and possesses five Cys-Pro Cys-Pro (CP)-motifs as the heme binding site. To reveal the molecular mechanism of heme binding by Bach2, the intrinsically disordered heme binding region (a.a. 331-520; Bach2331–520) and its CP-motif mutant were prepared and characterized with and without heme, by UV-Vis spectroscopy and thermal profiles. In addition, the charge-state-distributions (CSDs) were assessed by electrospray ionization mass spectrometry. The UV-Vis spect...
Source: Journal of Biochemistry - October 30, 2016 Category: Biochemistry Authors: Suenaga, T., Watanabe-Matsui, M., Uejima, T., Shima, H., Matsui, T., Ikeda-Saito, M., Shirouzu, M., Igarashi, K., Murayama, K. Tags: Regular Papers Source Type: research
A novel method to detect translation of membrane proteins following microvesicle intercellular transfer of nucleic acids
This study supports the significant role of MV’s in the transfer of deleterious traits in cancer populations and describes a new paradigm in mechanisms governing the acquisition of traits in cancer cell populations. (Source: Journal of Biochemistry)
Source: Journal of Biochemistry - October 30, 2016 Category: Biochemistry Authors: Lu, J. F., Pokharel, D., Padula, M. P., Bebawy, M. Tags: Regular Papers Source Type: research
Enzymatic characterization of recombinant rat DDHD2: a soluble diacylglycerol lipase
DDHD2 has been reported to exhibit phospholipase A1, triacylglycerol (TG) lipase and diacylglycerol (DG) lipase activities. However, the detailed enzymatic properties of DDHD2 have not yet been elucidated. In the current study, the substrate specificity of DDHD2 towards DG, TG and phosphatidic acid (PA) has been examined using highly purified recombinant rat DDHD2 (rDDHD2) with a liquid chromatography mass spectrometer. The k cat/Km value for DG (18:0/20:4) was much higher than those for TG (18:1/18:1/18:1), and PA (18:0/20:4) in the presence of sodium deoxycholate. The enzyme activity of rDDHD2 towards DG (18:0/20:4) wa...
Source: Journal of Biochemistry - October 30, 2016 Category: Biochemistry Authors: Araki, M., Ohshima, N., Aso, C., Konishi, A., Obinata, H., Tatei, K., Izumi, T. Tags: Regular Papers Source Type: research
Aptamers that bind specifically to human KPNA2 (importin-{alpha}1) and efficiently interfere with nuclear transport
In this study, we isolated aptamers 76 and 72, which bind specifically and efficiently to KPNA2, a member of a subfamily of importin-α1. Both of these aptamers bind to KPNA2 with an equilibrium dissociation constant (K d) of 150 nM and discriminate between KPNA2 and other sub-family members of importin-α, such as KPNA1 and KPNA3. These aptamers specifically interfere with the nuclear transport of cargo proteins mediated by KPNA2 but neither with KPNA1 nor KPNA3, which belongs to other subfamily of importins. These results suggest that the selected aptamers (76 and 72) warrant further study to explore not only ...
Source: Journal of Biochemistry - October 30, 2016 Category: Biochemistry Authors: Yasuhara, N., Kumar, P. K. R. Tags: Regular Papers Source Type: research
Structure and function of [NiFe] hydrogenases
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. An important structural difference between thes...
Source: Journal of Biochemistry - October 30, 2016 Category: Biochemistry Authors: Ogata, H., Lubitz, W., Higuchi, Y. Tags: JB Review Source Type: research
Phytochrome-interacting ankyrin repeat protein 2 modulates phytochrome A-mediated PIF3 phosphorylation in light signal transduction
Light signals recognized by phytochromes are transduced through interactions between down-stream signaling components. Phytochrome-interacting ankyrin repeat protein 2 (PIA2) was found to interact with phytochrome interacting factor 3 (PIF3), a well-known repressor of plant photomorphogenesis in response to phytochrome-mediated light signalling. Both PIA2 and PIF3 are known to be positive regulators of anthocyanin accumulation in Arabidopsis seedlings under far-red conditions. Thus, we investigated the functional relationship between PIA2 and PIF3 in light signalling. We found that PIA2 suppressed PIF3 phosphorylation by p...
Source: Journal of Biochemistry - October 2, 2016 Category: Biochemistry Authors: Yoo, J., Cho, M.-H., Lee, S.-W., Bhoo, S. H. Tags: Regular Papers Source Type: research
