Oligomerized CARD16 promotes caspase-1 assembly and IL-1 β processing
Publication date: 2015 Source:FEBS Open Bio, Volume 5 Author(s): Tadayoshi Karasawa, Akira Kawashima, Fumitake Usui, Hiroaki Kimura, Koumei Shirasuna, Yoshiyuki Inoue, Takanori Komada, Motoi Kobayashi, Yoshiko Mizushina, Junji Sagara, Masafumi Takahashi Increasing evidence indicates that caspase recruitment domain (CARD)-mediated caspase-1 (CASP1) assembly is an essential process for its activation and subsequent interleukin (IL)-1β release, leading to the initiation of inflammation. Both CARD16 and CARD17 were previously reported as inhibitory homologs of CASP1; however, their molecular function...
Source: FEBS Open Bio - June 17, 2016 Category: Molecular Biology Source Type: research
Novel insights into structure –function mechanism and tissue-specific expression profiling of full-length dxr gene from Cymbopogon winterianus
In this study, full length DXR from citronella was characterized through in silico and tissue-specific expression studies to explain its structure–function mechanism, mode of cofactor recognition and differential expression. The modelled DXR has a three-domain architecture and its active site comprised of a cofactor (NADPH) binding pocket and the substrate-binding pocket. Molecular dynamics simulation studies indicated that DXR model retained most of its secondary structure during 10ns simulation in aqueous solution. The modelled DXR superimposes well with its closest structural homolog but subtle variations in the charg...
Source: FEBS Open Bio - June 17, 2016 Category: Molecular Biology Source Type: research
Mining disease genes using integrated protein –protein interaction and gene–gene co-regulation information
In this study, we constructed an eQTL-based gene–gene co-regulation network (GGCRN) and used it to mine for disease genes. We adopted the random walk with restart (RWR) algorithm to mine for genes associated with Alzheimer disease. Compared to the Human Protein Reference Database (HPRD) PPI network alone, the integrated HPRD PPI and GGCRN networks provided faster convergence and revealed new disease-related genes. Therefore, using the RWR algorithm for integrated PPI and GGCRN is an effective method for disease-associated gene mining. (Source: FEBS Open Bio)
Source: FEBS Open Bio - June 17, 2016 Category: Molecular Biology Source Type: research
Novel Cosic resonance (standing wave) solutions for components of the JAK –STAT cellular signaling pathway: A convergence of spectral density profiles
Publication date: 2015 Source:FEBS Open Bio, Volume 5 Author(s): Lukasz M. Karbowski, Nirosha J. Murugan, Michael A. Persinger Cosic discovered that spectral analyses of a protein sequence after each constituent amino acid had been transformed into an appropriate pseudopotential predicted a resonant energy between interacting molecules. Several experimental studies have verified the predicted peak wavelength of photons within the visible or near-visible light band for specific molecules. Here, this concept has been applied to a classic signaling pathway, JAK–STAT, traditionally composed of nine sequential prote...
Source: FEBS Open Bio - June 17, 2016 Category: Molecular Biology Source Type: research
Kr üppel-like factor 4 induces apoptosis and inhibits tumorigenic progression in SK-BR-3 breast cancer cells
Publication date: 2015 Source:FEBS Open Bio, Volume 5 Author(s): Bing Wang, Ming-zhi Zhao, Nai-peng Cui, Dan-dan Lin, An-yi Zhang, Yan Qin, Cai-yun Liu, Wei-tao Yan, Jian-hong Shi, Bao-ping Chen Krüppel-like factor 4 (KLF4) functions as either a tumor suppressor or an oncogene in different tissues by regulating the expression of various genes. The aim of this study was to reveal the functions of KLF4 in regulating breast cancer apoptosis, proliferation, and tumorigenic progression. KLF4 expression levels in breast cancer tissues and breast cancer cell lines were found to be much lower than those in...
Source: FEBS Open Bio - June 17, 2016 Category: Molecular Biology Source Type: research
Structure-based identification of functional residues in the nucleoside-2 ′-O-methylase domain of Bluetongue virus VP4 capping enzyme
In this study, we have exploited the structural information to identify the residues that are important for the catalytic activity of 2′-O MTase of VP4 and their influence on BTV replication. The effect of these mutations on GMP binding, guanylyltransferase (GTase) and methylase activities were analysed by a series of in vitro biochemical assays using recombinant mutant proteins; subsequently their effects on virus replication were assessed by introducing the same mutations in replicating viral genome using a reverse genetics system. Our data showed that single substitution mutations in the catalytic tetrad K-D-K-E were ...
Source: FEBS Open Bio - June 17, 2016 Category: Molecular Biology Source Type: research
Interaction of the dual targeting peptide of Thr-tRNA synthetase with the chloroplastic receptor Toc34 in Arabidopsis thaliana
In conclusion, we have demonstrated that the recognition of the dual targeting peptide of AtThr-tRNA synthetase is different for the mitochondrial and chloroplastic receptors. Graphical abstract (Source: FEBS Open Bio)
Source: FEBS Open Bio - December 8, 2015 Category: Molecular Biology Source Type: research
The cytotoxicity of BAMLET complexes is due to oleic acid and independent of the α-lactalbumin component
Publication date: 2015 Source:FEBS Open Bio, Volume 5 Author(s): Yamixa Delgado, Moraima Morales-Cruz, Cindy M. Figueroa, José Hernández-Román, Glinda Hernández, Kai Griebenow Lipid–protein complexes comprised of oleic acid (OA) non-covalently coupled to human/bovine α-lactalbumin, named HAMLET/BAMLET, display cytotoxic properties against cancer cells. However, there is still a substantial debate about the role of the protein in these complexes. To shed light into this, we obtained three different BAMLET complexes using varying synthesis conditions. Our data suggest that to form active BAMLET particl...
Source: FEBS Open Bio - December 1, 2015 Category: Molecular Biology Source Type: research
Human, vector and parasite Hsp90 proteins: a comparative bioinformatics analysis
Publication date: Available online 14 November 2015 Source:FEBS Open Bio Author(s): Ngonidzashe Faya, David L. Penkler, Özlem Tastan Bishop The treatment of protozoan parasitic diseases is challenging, and thus identification and analysis of new drug targets is important. Parasites survive within host organisms, and some need intermediate hosts to complete their life cycle. Changing host environment puts stress on parasites, and often adaptation is accompanied by the expression of large amounts of heat shock proteins (Hsps). Among Hsps, Hsp90 proteins play an important role in stress environments. Yet, there has...
Source: FEBS Open Bio - November 17, 2015 Category: Molecular Biology Source Type: research
MicroRNA-431 inhibits migration and invasion of hepatocellular carcinoma cells by targeting the ZEB1-mediated epithelial–mensenchymal transition
In conclusion, miR-431 inhibits migration and invasion of HCC cells by suppressing ZEB1-mediated EMT. (Source: FEBS Open Bio)
Source: FEBS Open Bio - November 10, 2015 Category: Molecular Biology Source Type: research
Quantifying NAD(P)H production in the upper Entner–Doudoroff pathway from Pseudomonas putida KT2440
Publication date: Available online 10 November 2015 Source:FEBS Open Bio Author(s): Karel Olavarria, Marina Pupke Marone, Henrique da Costa Oliveira, Juan Camilo Roncallo, Fernanda Nogales da Costa Vasconcelos, Luiziana Ferreira da Silva, José Gregório Cabrera Gomez Despite the lack of biochemical information, all available in silico metabolic models of Pseudomonas putida KT2440 consider NADP as the only cofactor accepted by the glucose-6-phosphate dehydrogenases. Because the Entner–Doudoroff pathway is the main glycolytic route in this bacterium, determining how much NADH and NADPH are produced in th...
Source: FEBS Open Bio - November 10, 2015 Category: Molecular Biology Source Type: research
MicroRNA-519a promotes proliferation and inhibits apoptosis of hepatocellular carcinoma cells by targeting FOXF2
In conclusion, miR-519a is a novel prognostic predictor for HCC patients and it may potentiate proliferation and inhibits apoptosis of HCC cells by targeting FOXF2. (Source: FEBS Open Bio)
Source: FEBS Open Bio - November 8, 2015 Category: Molecular Biology Source Type: research
Prediction of microRNA target genes using an efficient genetic algorithm-based decision tree
Publication date: Available online 19 October 2015 Source:FEBS Open Bio Author(s): Behzad Rabiee-Ghahfarrokhi, Fariba Rafiei, Ali Akbar Niknafs, Behzad Zamani MicroRNAs (miRNAs) are small, non-coding RNA molecules that regulate gene expression in almost all plants and animals. They play an important role in key processes, such as proliferation, apoptosis, and pathogen–host interactions. Nevertheless, the mechanisms by which miRNAs act are not fully understood. The first step toward unraveling the function of a particular miRNA is the identification of its direct targets. This step has shown to be quite challe...
Source: FEBS Open Bio - November 3, 2015 Category: Molecular Biology Source Type: research
Production and characterization of neurosecretory protein GM using Escherichia coli and Chinese Hamster Ovary cells
In this study, we prepared rat NPGM to elucidate the structure of its mature form. We first expressed the predicted mature NPGM, containing an extra C-terminal Gly, in Escherichia coli SHuffle cells, which are engineered to promote the formation of native disulfide bridges in recombinant proteins. We observed the presence of a disulfide bond between the N-terminal Cys residue and the second Cys residue, while the C-terminal Cys residue was free. Secondly, we transfected a construct containing the entire NPGM open reading frame into Chinese Hamster Ovary cells, and observed that NPGM was cleaved immediately after the signal...
Source: FEBS Open Bio - November 3, 2015 Category: Molecular Biology Source Type: research
Homoiterons and expansion in ribosomal RNAs
Publication date: Available online 23 October 2015 Source:FEBS Open Bio Author(s): Michael S. Parker, Floyd R. Sallee, Edwards A. Park, Steven L. Parker Ribosomal RNAs in both prokaryotes and eukaryotes feature numerous repeats of three or more nucleotides with the same nucleobase (homoiterons). In prokaryotes these repeats are much more frequent in thermophile compared to mesophile or psychrophile species, and have similar frequency in both large RNAs. These features point to use of prokaryotic homoiterons in stabilization of both ribosomal subunits. The two large RNAs of eukaryotic cytoplasmic ribosomes have ...
Source: FEBS Open Bio - November 3, 2015 Category: Molecular Biology Source Type: research
