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https://www.readbyqxmd.com/read/29793215/in-silico-insight-into-voltage-gated-sodium-channel-1-7-inhibition-for-anti-pain-drug-discovery
#1
Mingxing Wang, Wei Li, Ying Wang, Yongbo Song, Jian Wang, Maosheng Cheng
Studies on human genetics have implicated the voltage-gated sodium channel Nav1.7 as an appealing target for the treatment of pain. In this study, we put forward a ligand-based pharmacophore for the first time, which was generated by a set of multiple chemical scaffolds including sulfonamide and non-sulfonamide derivatives and consisted of four chemical features: an aromatic ring, a hydrophobic group and two hydrogen acceptors. The active cavity was divided into three regions according to the properties of the amino acids surrounded and was used for the docking of 16 known active inhibitors...
May 18, 2018: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/29793089/gold-and-gold-silver-alloy-nanoparticles-enhance-the-myogenic-differentiation-of-myoblasts-through-p38-mapk-signaling-pathway-and-promote-in-vivo-skeletal-muscle-regeneration
#2
Juan Ge, Kai Liu, Wen Niu, Mi Chen, Min Wang, Yumeng Xue, Chuanbo Gao, Peter X Ma, Bo Lei
Under the severe trauma condition, the skeletal muscles regeneration process is inhibited by forming fibrous scar tissues. Understanding the interaction between bioactive nanomaterials and myoblasts perhaps has important effect on the enhanced skeletal muscle tissue regeneration. Herein, we investigate the effect of monodispersed gold and gold-silver nanoparticles (AuNPs and Au-AgNPs) on the proliferation, myogenic differentiation and associated molecular mechanism of myoblasts (C2C12), as well as the in vivo skeletal muscle tissue regeneration...
May 18, 2018: Biomaterials
https://www.readbyqxmd.com/read/29793076/porcine-circovirus-type-2-inhibits-inter-%C3%AE-expression-by-targeting-karyopherin-alpha-3-in-pk-15-cells
#3
Jiansheng Li, Mingqing Lu, Bei Huang, Yingjun Lv
Interferon (IFN)-mediated antiviral response is an important part of host defense. Previous studies reported that porcine circovirus type 2 (PCV2) inhibits interferon production, but the mechanism is still poorly understood. In this study, PCV2 suppresses IFN-β and IRF3 promoters and mRNA level of IFN-β induced by ISD or Poly(I:C), but has no effect on the activation of AP-1 and NF-κB. Furthermore, PCV2 decreases the mRNA level of IFN-β and IFN-β promoter activity driven by STING, TBK1, IRF3, and IRF3/5D, and causes a reduction in the protein level of nuclear p-IRF3...
May 21, 2018: Virology
https://www.readbyqxmd.com/read/29793052/title-lhp1-interacts-with-atrx-through-plant-specific-domains-at-specific-loci-targeted-by-prc2
#4
Haifeng Wang, Danhua Jiang, Elin Axelsson, Zdravko J Lorković, Sean Montgomery, Sarah Holec, Bas J G E Pieters, Abbas H K Al Temimi, Jasmin Mecinović, Frédéric Berger
Heterochromatin Protein 1 (HP1) is a major regulator of chromatin structure and function. In animals, the network of proteins interacting with HP1 is mainly associated with constitutive heterochromatin marked by H3K9me3. HP1 physically interacts with the putative orthologue of the SNF2 chromatin remodeler ATRX, which controls deposition of the histone variant H3.3 in mammals. In Arabidopsis thaliana, we show that the orthologue of ATRX participates in H3.3 deposition and characterize the function of conserved domains of plant ATRX...
May 21, 2018: Molecular Plant
https://www.readbyqxmd.com/read/29793044/isolation-of-ferritin-and-its-interaction-with-bmnpv-in-the-silkworm-bombyx-mori
#5
Dong-Qiong Fei, Hai-Zhong Yu, Jia-Ping Xu, Shang-Zhi Zhang, Jie Wang, Bing Li, Li-Ang Yang, Pei Hu, Xin Xu, Kang Zhao, Toufeeq Shahzad
Ferritin is a ubiquitous iron storage protein that plays an important role in host defence against pathogen infections. In the present study, native ferritin was isolated from the hemolymph of Bombyx mori using native-polyacrylamide gel electrophoresis (native-PAGE) and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The results revealed that ferritin consisted of two subunits, designated as BmFerHCH and BmFerLCH. Previously integrated previous transcriptome and iTRAQ data showed that the two subunits were down-regulated in resistant silkworm strain BC9 and there was no obvious change in the expression levels of the subunits in susceptible silkworm strain P50 after BmNPV infection...
May 9, 2018: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/29793032/phosphorylated-and-non-phosphorylated-hck-kinase-domains-produced-by-cell-free-protein-expression
#6
Kazushige Katsura, Yuri Tomabechi, Takayoshi Matsuda, Mayumi Yonemochi, Junko Mikuni, Noboru Ohsawa, Takaho Terada, Shigeyuki Yokoyama, Mutsuko Kukimoto-Niino, Chie Takemoto, Mikako Shirouzu
Since phosphorylation is involved in various physiological events, kinases and interacting factors can be potential targets for drug discovery. For the development and improvement of inhibitors from the point of view of mechanistic enzymology, a cell-free protein synthesis system would be advantageous, since it could prepare mutant proteins easily. However, especially in the case of protein kinase, product solubility remains one of the major challenges. To overcome this problem, we prepared a chaperone-supplemented extract from Escherichia coli BL21 cells harboring a plasmid encoding a set of chaperone genes, dnaK, dnaJ, and grpE...
May 21, 2018: Protein Expression and Purification
https://www.readbyqxmd.com/read/29792904/monoclonal-antibody-dl11c8-identifies-adam23-as-a-component-of-lipid-raft-microdomains
#7
Zaine L M Borgonovo, Caroline F Ribeiro, Michele D M Costa, Ingrid L M Souza, Gustavo R Rossi, Monica V Alcantara, Max Ingberman, Luciano G Braga, Adriana F Mercadante, Lia S Nakao, Silvio M Zanata
A disintegrin and metalloprotease protein 23 (ADAM23) is a transmembrane type I glycoprotein involved with the development and maintenance of the nervous system, including neurite outgrowth, neuronal adhesion and differentiation and regulation of synaptic transmission. In addition, ADAM23 seems to participate in immune response and tumor establishment through interaction with different members of integrin receptors. Here, we describe a novel monoclonal antibody (DL11C8) that specifically recognizes the cysteine-rich domain of both pre-protein (100kDa) and mature (70 kDa) forms of ADAM23 from different species, including human, rodents and avian orthologs...
May 21, 2018: Neuroscience
https://www.readbyqxmd.com/read/29792880/molecular-alterations-during-larval-development-of-haemonchus-contortus-in-vitro-are-under-tight-post-transcriptional-control
#8
Guangxu Ma, Tao Wang, Pasi K Korhonen, Ching-Seng Ang, Nicholas A Williamson, Neil D Young, Andreas J Stroehlein, Ross S Hall, Anson V Koehler, Andreas Hofmann, Robin B Gasser
In this study, we explored the molecular alterations in the developmental switch from the L3 to the exsheathed L3 (×L3) and to the L4 stage of Haemonchus contortus in vitro using an integrated transcriptomic, proteomic and bioinformatic approach. Totals of 9,754 mRNAs, 88 microRNAs (miRNAs) and 1,591 proteins were identified, and 6,686 miRNA-mRNA pairs inferred in all larval stages studied. Approximately 16% of transcripts in the combined transcriptome (representing all three larval stages) were expressed as proteins, and there were positive correlations (r = 0...
May 22, 2018: International Journal for Parasitology
https://www.readbyqxmd.com/read/29792879/astragaloside-suppresses-apoptosis-of-the-podocytes-in-rats-with-diabetic-nephropathy-via-mir-378-traf5-signaling-pathway
#9
Xiao Lei, Bo-da Zhang, Ji-Gang Ren, Fang-Li Luo
AIMS: Apoptosis of podocytes plays a crucial role in diabetic nephropathy (DN) development, and astragaloside (AS-IV) has a significant impact on podocyte apoptosis. This study aims to explore the effect of AS-IV on diabetic nephropathy progression. MATERIALS AND METHODS: The diabetic nephropathy model was established in rats with streptozotocin (STZ) injection. The albuminuria was examined by using the enzyme linked immunosorbent assay (ELISA). The expression of miR-378, tumor-necrosis factor (TNF) receptor (TNFR)-associated factor 5 (TRAF5) mRNA and protein was analyzed by qRT-PCR and western blot, respectively...
May 21, 2018: Life Sciences
https://www.readbyqxmd.com/read/29792877/coordinating-multi-protein-mismatch-repair-by-managing-diffusion-mechanics-on-the-dna
#10
REVIEW
Daehyung Kim, Richard Fishel, Jong-Bong Lee
DNA mismatch repair (MMR) corrects DNA base pairing errors that occur during DNA replication. MMR catalyzes strand-specific DNA degradation and resynthesis by dynamic molecular coordination of sequential downstream pathways. The temporal and mechanistic order of molecular events is essential to insure interactions in MMR that occur over long distances on the DNA. Biophysical real-time studies of highly conserved components on mismatched DNA have shed light on the mechanics of MMR. Single-molecule imaging has visualized stochastically coordinated MMR interactions that are based on thermal fluctuation-driven motions...
May 21, 2018: Journal of Molecular Biology
https://www.readbyqxmd.com/read/29792810/optogenetic-inhibition-of-g%C3%AE-q-protein-signaling-reduces-calcium-oscillation-stochasticity
#11
Pimkhuan Hannanta-Anan, Brian Y Chow
As fast terminators of G-protein coupled receptor (GPCR) signaling, regulators of G-protein signaling (RGS) serve critical roles in fine-tuning second messenger levels and, consequently, cellular responses to external stimuli. Here, we report the creation of an optogenetic RGS2 (opto-RGS2) that suppresses agonist-evoked calcium oscillations by the inactivation of Gαq protein. In this system, cryptochrome-mediated hetero-dimerization of the catalytic RGS2-box with its N-terminal amphipathic helix reconstitutes a functional membrane-localized complex that can dynamically suppress store-operated release of calcium...
May 24, 2018: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29792801/developing-a-novel-sulfoxide-containing-ms-cleavable-homobifunctional-cysteine-reactive-cross-linker-for-studying-protein-protein-interactions
#12
Craig B Gutierrez, Sarah A Block, Clinton Yu, Stephanie M Soohoo, Alexander S Huszagh, Scott D Rychnovsky, Lan Huang
Cross-linking mass spectrometry (XL-MS) has become an emerging technology for defining protein-protein interactions (PPIs) and elucidating architectures of large protein complexes. Up to now, the mostly widely used cross-linking reagents are targeting lysines. While such reagents have been successfully applied to map PPIs at the proteome-wide scale, comprehensive PPI profiling would require additional cross-linking chemistries. Cysteine is one of the most reactive amino acids and an attractive target for cross-linking owing to its unique role in protein structures...
May 24, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29792731/apr3-modulates-oxidative-stress-and-mitochondrial-function-in-arpe-19-cells
#13
Yuan Li, Xuan Zou, Jing Gao, Ke Cao, Zhihui Feng, Jiankang Liu
Impairment of retinal pigment epithelial (RPE) cells is considered a key contributor to the development of age-related macular degeneration. Apoptosis-related protein 3 (APR3) was recently discovered after treatment with all- trans retinoic acid, a pivotal molecule in RPE cells. However, the function of APR3 remains poorly understood. In the present study, we found that APR3 could interact with nuclear factor (erythroid-derived 2)-like 2, which is a regulator of phase II enzymes, and that knockdown of APR3 promoted nuclear factor (erythroid-derived 2)-like 2 nuclear translocation and activated expression of phase II enzymes, which was accompanied by improved redox status and mitochondrial activity...
May 24, 2018: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/29792724/a-systematic-understanding-of-signaling-by-erbb2-in-cancer-using-phosphoproteomics
#14
C Sidhanth, P Manasa, S Krishnapriya, S Sneha, S Bindhya, R P Nagare, M Garg, T S Ganesan
ErbB2 is an important receptor tyrosine kinase and a member of the ErbB family. Although it does not have a specific ligand, it transmits signals downstream by heterodimerization with other receptors in the family. It plays a major role in a variety of cellular responses like proliferation, differentiation, and adhesion. ErbB2 is amplified at the DNA level in breast cancer (20%-30%) and gastric cancer (10%-20%), and trastuzumab is effective as a therapeutic antibody. This review is a critical analysis of the currently published data on the signaling pathways of ErbB2 and the interacting proteins...
May 24, 2018: Biochemistry and Cell Biology, Biochimie et Biologie Cellulaire
https://www.readbyqxmd.com/read/29792714/docking-screens-for-dual-inhibitors-of-disparate-drug-targets-for-parkinson-s-disease
#15
Mariama Jaiteh, Alexey Zeifman, Marcus Saarinen, Per Svenningsson, José M Brea, Maria Isabel Loza, Jens Carlsson
Modulation of multiple biological targets with a single drug can lead to synergistic therapeutic effects and has been demonstrated to be essential for efficient treatment of CNS disorders. However, rational design of compounds that interact with several targets is very challenging. Here, we demonstrate that structure-based virtual screening can guide the discovery of multi-target ligands of unrelated proteins relevant for Parkinson's disease. A library with 5.4 million molecules was docked to crystal structures of the A2A adenosine receptor (A2AAR) and monoamine oxidase B (MAO-B)...
May 24, 2018: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29792687/co-mobility-of-gabarap-and-phosphatidylinositol-4-kinase-2a-on-cytoplasmic-vesicles
#16
Yan Chen, Hui-Qiao Sun, John P Eichorst, Joseph P Albanesi, Helen Yin, Joachim D Mueller
We previously reported that recruitment of the Type IIA phosphatidylinositol 4-kinase (PI4K2A) to autophagosomes by GABARAP, a member of the Atg8 family of autophagy-related proteins, is important for autophagosome-lysosome fusion. Because both PI4K2A and GABARAP have also been implicated in the intracellular trafficking of plasma membrane receptors in the secretory/endocytic pathway, we characterized their interaction in cells under non-autophagic conditions. Fluorescence fluctuation spectroscopy measurements revealed that GABARAP exists predominantly as a cytosolic monomer in live cells, but is recruited to small cytoplasmic vesicles upon overexpression of PI4K2A...
May 24, 2018: Biochemistry
https://www.readbyqxmd.com/read/29792674/partial-intrinsic-disorder-governs-the-dengue-capsid-protein-conformational-ensemble
#17
Priscilla L S Boon, Wuan Geok Saw, Xin Xiang Lim, Palur Venkata Raghuvamsi, Roland G Huber, Jan K Marzinek, Daniel A Holdbrook, Ganesh S Anand, Gerhard Grüber, Peter J Bond
The 11 kDa, positively charged dengue capsid protein (C protein) exists stably as a homodimer and co-localizes with the viral genome within mature viral particles. Its core is composed of four alpha helices encompassing a small hydrophobic patch that may interact with lipids, but approximately 20% of the protein at the N-terminus is intrinsically disordered, making it challenging to elucidate its conformational landscape. Here, we combine small-angle X-ray scattering (SAXS), amide hydrogen-deuterium exchange mass spectrometry (HDXMS), and atomic-resolution molecular dynamics (MD) simulations to probe the dynamics of dengue C proteins...
May 24, 2018: ACS Chemical Biology
https://www.readbyqxmd.com/read/29792672/biosynthesis-of-lincosamide-antibiotics-reactions-associated-with-degradation-and-detoxification-pathways-play-a-constructive-role
#18
Daozhong Zhang, Zhijun Tang, Wen Liu
Natural products typically are small molecules produced by living organisms. These products possess a wide variety of biological activities and thus have historically played a critical role in medicinal chemistry and chemical biology either as chemotherapeutic agents or as useful tools. Natural products are not synthesized for use by human beings; rather, living organisms produce them in response to various biochemical processes and environmental concerns, both internal and external. These processes/concerns are often dynamic and thus motivate the diversification, optimization, and selection of small molecules in line with changes in biological function...
May 24, 2018: Accounts of Chemical Research
https://www.readbyqxmd.com/read/29792552/immobilization-rapidly-induces-thioredoxin-interacting-protein-txnip-gene-expression-together-with-insulin-resistance-in-rat-skeletal-muscle
#19
Emi Kawamoto, Keigo Tamakoshi, Song-Gyu Ra, Hiroyuki Masuda, Kentaro Kawanaka
Acute short-duration of disuse induces the development of insulin resistance for glucose uptake in rodent skeletal muscle. Since thioredoxin-interacting protein (TXNIP) has been implicated in the downregulation of insulin signaling and glucose uptake, we examined the possibility that muscle disuse rapidly induces insulin resistance via increased TXNIP mRNA and protein expression. Male Wistar rats were subjected to unilateral 6-hr hindlimb immobilization by plaster cast. At the end of this period, the soleus muscles from both immobilized and contralateral non-immobilized hindlimbs were excised and examined...
May 24, 2018: Journal of Applied Physiology
https://www.readbyqxmd.com/read/29792377/comparative-analysis-of-probiotic-bacteria-based-on-a-new-definition-of-core-genome
#20
Maria Satti, Yasuhiro Tanizawa, Akihito Endo, Masanori Arita
The commensal genus Bifidobacterium has probiotic properties. We prepared a public library of the gene functions of the genus Bifidobacterium for its online annotation. Orthologous gene cluster analysis showed that the pan genomes of Bifidobacterium and Lactobacillus exhibit striking similarities when mapped to the Clusters of Orthologous Group (COG) database of proteins. When the core genes in each genus were selected based on our statistical definition of "core genome", core genes were present in at least 92% of 52 Bifidobacterium and in 97% of 178 Lactobacillus genomes...
March 26, 2018: Journal of Bioinformatics and Computational Biology
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