Current status of the development of Ras inhibitors
Despite the importance of ras as driver genes in many cancers, clinically effective anti-cancer drugs targeting their products, Ras, have been unavailable so far, which was in part ascribable to the apparently ‘undruggable’ nature of their tertiary structures. Nonetheless, recent studies in academia and industry have identified novel surface pockets accepting small-molecule ligands in both their active GTP-bound and inactive GDP-bound forms (Ras•GTP and Ras•GDP, respectively), which has led to a surge of investigations into the discovery of Ras-specific inhibitors particularly by utilizing their struc...
Source: Journal of Biochemistry - July 28, 2015 Category: Biochemistry Authors: Shima, F., Matsumoto, S., Yoshikawa, Y., Kawamura, T., Isa, M., Kataoka, T. Tags: JB Review Source Type: research
{beta}-Trefoil structure enables interactions between lectins and protease inhibitors that regulate their biological functions
Fungal ricin B-like lectins and protease inhibitors, mycocypins and mycospins, are important mediators in fungal defence against antagonists and all possess the β-trefoil fold. We demonstrate here that fungal β-trefoil proteins interact with each other, in addition to their apparent targets, and that these interactions modulate their biological activity. Such regulation of carbohydrate binding or inhibitory activity is observed for the first time in β-trefoil proteins and could constitute a mechanism for regulating their physiological functions. It could also have implications in molecular recognition of oth...
Source: Journal of Biochemistry - June 30, 2015 Category: Biochemistry Authors: Žurga, S., Pohleven, J., Kos, J., Sabotič, J. Tags: Regular Papers Source Type: research
Absence of lactobacilli containing glycolipids with the {alpha}-galactose epitope and the enhanced fucosylation of a receptor glycolipid GA1 in the digestive tracts of immune-deficient scid mice
The Lactobacillus species in the digestive tracts of immune-deficient scid mice was distinct from that in control mice, i.e. Lactobacillus murinus in scid and L. johnsonii in control mice, according to their 16S-rRNA, indicating that a symbiotic relationship between lactobacilli and a host is established under pressure from the immune system. The caecal and colonal contents rich in L. murinus of scid mice were loose with a strong sour smell, resulting in diarrhoea, and those with L. johnsonii in control mice included abundant solid materials. Lactobacillus glycolipids were revealed to be recognized by the immune system, an...
Source: Journal of Biochemistry - June 30, 2015 Category: Biochemistry Authors: Iwamori, M., Tanaka, K., Adachi, S., Aoki, D., Nomura, T. Tags: Regular Papers Source Type: research
Arkadia enhances BMP signalling through ubiquitylation and degradation of Smad6
In this study, we examined the effects of Arkadia on bone morphogenetic protein (BMP)-induced osteoblast differentiation. Knockdown of Arkadia reduced mineralization and expression of osteoblast differentiation markers. Furthermore, we showed that Smad6, a BMP-specific inhibitory Smad, is a target of Arkadia: wild-type (WT) Arkadia, but not the C937A (CA) mutant lacking E3 ubiquitin-ligase activity, induced ubiquitylation and proteasome-dependent degradation of Smad6. Accordingly, protein levels of Smad6, Smad7 and c-Ski were elevated in MEFs from Arkadia KO mice. Finally, expression of Arkadia attenuated blockade of BMP s...
Source: Journal of Biochemistry - June 30, 2015 Category: Biochemistry Authors: Tsubakihara, Y., Hikita, A., Yamamoto, S., Matsushita, S., Matsushita, N., Oshima, Y., Miyazawa, K., Imamura, T. Tags: Regular Papers Source Type: research
Identification and characterization of a cell division-regulating kinase AKB1 (associated kinase of Trypanosoma brucei 14-3-3) through proteomics study of the Tb14-3-3 binding proteins
We used a proteomics approach to identify the binding partners of Trypanosoma brucei 14-3-3 (Tb14-3-3) which led to the identification of a novel kinase, AKB1. The binding between these two proteins was mediated by an amphipathic groove structure in Tb14-3-3 and 1-438 amino acid sequence of AKB1. Recombinant AKB1 but not its ATP-binding-deficient mutant (DFG to NFG) possessed an auto-phosphorylation activity as well as a kinase activity towards a peptide substrate in vitro. However, the autophosphorylation was not required for the binding of AKB1 to Tb14-3-3. Interestingly, the kinase activity of AKB1 was inhibited by calc...
Source: Journal of Biochemistry - June 30, 2015 Category: Biochemistry Authors: Inoue, M., Okamoto, K., Uemura, H., Yasuda, K., Motohara, Y., Morita, K., Hiromura, M., Reddy, E. P., Fukuma, T., Horikoshi, N. Tags: Regular Papers Source Type: research
Flavorase, a novel non-haemorrhagic metalloproteinase in Protobothrops flavoviridis venom, is a target molecule of small serum protein-3
Some venomous snakes possess anti-toxic proteins in their sera that may play a role in neutralizing the haemorrhagic factors or toxins in their own venom. Five small serum proteins (SSP-1–SSP-5) were isolated from the serum of Japanese viper (Protobothrops flavoviridis), and were found to act as self-defence proteins against the viper’s own toxic components. However, the physiological function of SSP-3 has not been completely elucidated. Affinity chromatography of the venom on an SSP-3-immobilized column identified a novel 55-kDa protein as the target molecule of SSP-3. Sequences of internal fragments of this S...
Source: Journal of Biochemistry - June 30, 2015 Category: Biochemistry Authors: Shioi, N., Nishijima, A., Terada, S. Tags: Regular Papers Source Type: research
A protective effect of milk fat globule EGF factor VIII (MFG-E8) on the spontaneous fusion of milk fat globules in breast milk
We report here that the MFGs in the milk of MFG-E8-deficient mice fused each other and turned into abnormally large size of lipid droplets within ~48 h after being secreted into mammary alveolar lumen in situ or being incubated at 37°C in vitro. This biophysical degeneration of MFGs in the MFG-E8-deficient milk was efficiently rescued in vitro by adding the milk serum of wild-type mice, isolated MFG-E8 or annexin V. Moreover, addition of ethylenediaminetetraacetic acid (30 mM) also protected the MFG fusion remarkably in vitro. In addition, bovine MFGs also fused each other when isolated from milk serum, and the fusion ...
Source: Journal of Biochemistry - June 30, 2015 Category: Biochemistry Authors: Yasueda, T., Oshima, K., Nakatani, H., Tabuchi, K., Nadano, D., Matsuda, T. Tags: Regular Papers Source Type: research
EDAC: Epithelial defence against cancer--cell competition between normal and transformed epithelial cells in mammals
During embryonic development or under certain pathological conditions, viable but suboptimal cells are often eliminated from the cellular society through a process termed cell competition. Cell competition was originally identified in Drosophila where cells with different properties compete for survival; ‘loser’ cells are eliminated from tissues and consequently ‘winner’ cells become dominant. Recent studies have shown that cell competition also occurs in mammals. While apoptotic cell death is the major fate for losers in Drosophila, outcompeted cells show more variable phenotypes in mammals, such a...
Source: Journal of Biochemistry - June 30, 2015 Category: Biochemistry Authors: Kajita, M., Fujita, Y. Tags: JB Reviews Source Type: research
Thermodynamics of antibody-antigen interaction revealed by mutation analysis of antibody variable regions
Antibodies (immunoglobulins) bind specific molecules (i.e. antigens) with high affinity and specificity. In order to understand their mechanisms of recognition, interaction analysis based on thermodynamic and kinetic parameters, as well as structure determination is crucial. In this review, we focus on mutational analysis which gives information about the role of each amino acid residue in antibody–antigen interaction. Taking anti-hen egg lysozyme antibodies and several anti-small molecule antibodies, the energetic contribution of hot-spot and non-hot-spot residues is discussed in terms of thermodynamics. Here, therm...
Source: Journal of Biochemistry - June 30, 2015 Category: Biochemistry Authors: Akiba, H., Tsumoto, K. Tags: JB Reviews Source Type: research
G364R mutation of MCM4 detected in human skin cancer cells affects DNA helicase activity of MCM4/6/7 complex
We examined G364R mutation of MCM4 detected in human skin cancer cells. Formation of MCM4/6/7 complex is not affected by the mutation. Consistent with this notion, the binding to MCM6 is comparable between the mutant MCM4 and wild-type MCM4. Nuclear localization of this mutant MCM4 expressed in HeLa cells supports this conclusion. Purified MCM4/6/7 complex containing the G364R MCM4 exhibited similar levels of single-stranded DNA binding and ATPase activities to the complex containing wild-type MCM4. However, the mutant complex showed only 30–50% of DNA helicase activity of the wild-type complex. When G364R MCM4 was e...
Source: Journal of Biochemistry - May 27, 2015 Category: Biochemistry Authors: Ishimi, Y., Irie, D. Tags: Regular Papers Source Type: research
Recombinant expression, molecular characterization and crystal structure of antitumor enzyme, L-lysine {alpha}-oxidase from Trichoderma viride
L-Lysine α-oxidase (LysOX) from Trichoderma viride is a homodimeric 112 kDa flavoenzyme that catalyzes the oxidative deamination of L-lysine to form α-keto--aminocaproate. LysOX severely inhibited growth of cancer cells but showed relatively low cytotoxicity for normal cells. We have determined the cDNA nucleotide sequence encoding LysOX from T. viride. The full-length cDNA consists of 2,119 bp and encodes a possible signal peptide (Met1-Arg77) and the mature protein (Ala78-Ile617). The LysOX gene have been cloned and heterologously expressed in Streptomyces lividans TK24 with the enzyme activity up to 9.8 U/ml...
Source: Journal of Biochemistry - May 27, 2015 Category: Biochemistry Authors: Amano, M., Mizuguchi, H., Sano, T., Kondo, H., Shinyashiki, K., Inagaki, J., Tamura, T., Kawaguchi, T., Kusakabe, H., Imada, K., Inagaki, K. Tags: Regular Papers Source Type: research
Preparation of monoPEGylated Cyanovirin-N's derivative and its anti-influenza A virus bioactivity in vitro and in vivo
Influenza A virus (IAV) has been raising public health and safety concerns worldwide. Cyanovirin-N (CVN) is a prominent anti-IAV candidate, but both cytotoxicity and immunogenicity have hindered the development of this protein as a viable therapy. In this article, linker-CVN (LCVN) with a flexible and hydrophilic polypeptide at the N-terminus was efficiently produced from the cytoplasm of Escherichia coli at a >15-l scale. PEGylation at the N-terminal α-amine of LCVN was also reformed as 20 kDa PEGylated linkered Cyanovirin-N (PEG20k–LCVN). The 50% effective concentrations of PEG20k–LCVN were 0.43 &plu...
Source: Journal of Biochemistry - May 27, 2015 Category: Biochemistry Authors: Wu, C., Chen, W., Chen, J., Han, B., Peng, Z., Ge, F., Wei, B., Liu, M., Zhang, M., Qian, C., Hou, Z., Liu, G., Guo, C., Wang, Y., Kitazato, K., Yu, G., Zou, C., Xiong, S. Tags: Regular Papers Source Type: research
Basic and aromatic residues in the C-terminal domain of PriC are involved in ssDNA and SSB binding
In this study, we prepared several PriC mutants in which basic and aromatic amino acid residues were mutated to alanine. Five of these residues, Arg107, Lys111, Phe118, Arg121 and Lys165 in the C-terminal domain, were shown to be involved in ssDNA binding. Moreover, we evaluated the binding of the PriC mutants to the ssDNA-binding protein (SSB) complex. Five residues, Phe118, Arg121, Arg129, Tyr152 and Arg155 in the C-terminal domain of PriC, were shown to be involved in SSB binding in the presence of ssDNA. On the basis of these results, we propose a structural model of the C-terminal domain of PriC and discuss how the in...
Source: Journal of Biochemistry - May 27, 2015 Category: Biochemistry Authors: Aramaki, T., Abe, Y., Furutani, K., Katayama, T., Ueda, T. Tags: Regular Papers Source Type: research
Overproduction and easy recovery of biofuels from engineered cyanobacteria, autolyzing multicellular cells
In this study, the overexpression and easy recovery of alkane (a saturated hydrocarbon, C17H36) as a biofuel were examined in recombinants of the cyanobacteria ABRG5-3 and Synechocystis sp. strain PCC6803. The results obtained indicated that the accumulated mass of alkane accounted for ~50 or 60% of the dry weight of ABRG5-3 or PCC6803 recombinant cells, respectively. Furthermore, cultivating cells in liquid medium BG11 in which the nitrogen resource had been depleted promoted the production of alkane and cell lysis, resulting in the easy recovery of target products from the supernatant. (Source: Journal of Biochemistry)
Source: Journal of Biochemistry - May 27, 2015 Category: Biochemistry Authors: Yoshida, S., Takahashi, M., Ikeda, A., Fukuda, H., Kitazaki, C., Asayama, M. Tags: Regular Papers Source Type: research
Peptidoglycan recognition protein-triggered induction of Escherichia coli gene in Drosophila melanogaster
Interaction between the host and pathogen determines the fate of both organisms during the infectious state. The host is equipped with a battery of immune reactions, while the pathogen displays a variety of mechanisms to compromise host immunity. Although bacteria alter their pattern of gene expression in host organisms, studies to elucidate the mechanism behind this are only in their infancy. We here examined the possibility that host immune proteins directly participate in the change of gene expression in bacteria. Escherichia coli was treated with a mixture of the extracellular region of peptidoglycan recognition protei...
Source: Journal of Biochemistry - May 27, 2015 Category: Biochemistry Authors: Kong, Q., Nakai, Y., Kuroda, N., Shiratsuchi, A., Nagaosa, K., Nakanishi, Y. Tags: Regular Papers Source Type: research
