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https://www.readbyqxmd.com/read/28092839/effect-and-mechanism-of-sorbus-pohuashanensis-hante-hedl-flavonoids-protect-against-arsenic-trioxide-induced-cardiotoxicity
#1
Xiaojin Yu, Zhenyu Wang, Zunpeng Shu, Zhengqing Li, Yuan Ning, Keli Yun, Haina Bai, Ruihai Liu, Wenli Liu
The cardiotoxicity of arsenic trioxide (ATO) limits its clinical application in cancer treatment. Evidences suggest that sorbus has antioxidant activity and its consumption has been linked with improved cardioprotection. In this study, we investigated the cardio-protective effect and mechanisms of Sorbus pohuashanensis (Hante) Hedl. flavonoids (SPF) against ATO in BALB/c mice and H9c2 cells. Eleven major flavonoids were confirmed by ultra-performance liquid chromatography electrospray ionization quadrupole time of flight mass spectrometry (UPLC-ESI-Q-TOF-MS)...
January 13, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28092832/sampling-conformational-space-of-intrinsically-disordered-proteins-in-explicit-solvent-comparison-between-well-tempered-ensemble-approach-and-solute-tempering-method
#2
Mengzhi Han, Ji Xu, Ying Ren
Intrinsically disordered proteins (IDPs) are a class of proteins that expected to be largely unstructured under physiological conditions. Due to their heterogeneous nature, experimental characterization of IDP is challenging. Temperature replica exchange molecular dynamics (T-REMD) is a widely used enhanced sampling method to probe structural characteristics of these proteins. However, its application has been hindered due to its tremendous computational cost, especially when simulating large systems in explicit solvent...
December 28, 2016: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28092811/towards-the-structure-of-the-tir-domain-signalosome
#3
REVIEW
Surekha Nimma, Thomas Ve, Simon J Williams, Bostjan Kobe
TIR (Toll/interleukin-1 receptor/resistance protein) domains feature in animal, plant and bacterial proteins involved in innate immunity pathways and associated processes. They function through protein:protein interactions, in particular self-association and homotypic association with other TIR domains. Structures of TIR domains from all phyla have been determined, but common association modes have only emerged for plant and bacterial TIR domains, and not for mammalian TIR domains. Numerous attempts involving hybrid approaches, which have combined structural, computational, mutagenesis and biophysical data, have failed to converge onto common models of how these domains associate and function...
January 13, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28092729/diverse-functions-for-different-forms-of-nuclear-actin
#4
REVIEW
Jori A Virtanen, Maria K Vartiainen
In addition to its essential roles as part of the cytoskeleton, actin has also been linked to many processes in the nucleus. Recent data has demonstrated the presence of both monomeric and polymeric actin in the nucleus, and implied distinct functional roles for these actin pools. Monomeric actin seems to be involved in regulation of gene expression through transcription factors, chromatin regulating complexes and RNA polymerases. In addition to cytoplasmic actin regulators, nuclear proteins, such as emerin, can regulate actin polymerization properties specifically in this compartment...
January 13, 2017: Current Opinion in Cell Biology
https://www.readbyqxmd.com/read/28092692/smile-seq-identifies-binding-motifs-of-single-and-dimeric-transcription-factors
#5
Alina Isakova, Romain Groux, Michael Imbeault, Pernille Rainer, Daniel Alpern, Riccardo Dainese, Giovanna Ambrosini, Didier Trono, Philipp Bucher, Bart Deplancke
Resolving the DNA-binding specificities of transcription factors (TFs) is of critical value for understanding gene regulation. Here, we present a novel, semiautomated protein-DNA interaction characterization technology, selective microfluidics-based ligand enrichment followed by sequencing (SMiLE-seq). SMiLE-seq is neither limited by DNA bait length nor biased toward strong affinity binders; it probes the DNA-binding properties of TFs over a wide affinity range in a fast and cost-effective fashion. We validated SMiLE-seq by analyzing 58 full-length human, mouse, and Drosophila TFs from distinct structural classes...
January 16, 2017: Nature Methods
https://www.readbyqxmd.com/read/28092616/generation-and-characterization-of-a-monoclonal-antibody-against-duck-tembusu-virus-envelope-protein
#6
K Han, D Zhao, Y Liu, Q Liu, X Huang, J Yang, K Bi, T Xu, Y Li
Duck Tembusu virus (DTMUV) is a newly emerging pathogenic flavivirus that has caused massive economic losses to the duck industry in China. Envelope (E) protein of DTMUV is an important structural protein, which is able to induce protective immune response in target animals and can be used as specific serological diagnosis tool. In this study, a novel monoclonal antibody, designated mAb 3E9, was generated against DTMUV E protein. It is positive in indirect ELISA against both His-E protein and the purified whole viral antigen...
December 1, 2016: Polish Journal of Veterinary Sciences
https://www.readbyqxmd.com/read/28092615/immunoreactivity-of-arcuate-nucleus-astrocytes-in-rats-after-intragastric-administration-of-habanero-peppers-capsicum-chinese-jacq
#7
K Rycerz, A Krawczyk, J Jaworska-Adamu, M Gołyński, K Lutnicki, I Balicki
Habanero pepper fruits contain capsaicin (CAP) characterised by a spicy taste. Astrocytes express vanilloid receptor (TRPV1), which interacts with cannabinoids including CAP. Only a few studies revealed that CAP leads to alterations of the arcuate nucleus (ARC) structures. The aim of this study was to analyse the GFAP (GFAP-IR) and S100β (S100β-IR) immunoreactive astrocytes of ARC in adult rats after intragastric administration of habanero pepper fruits. Adult, Wistar rats received a peanut oil - control group (C) - and oil suspension of habanero pepper fruits at a dose of 0...
December 1, 2016: Polish Journal of Veterinary Sciences
https://www.readbyqxmd.com/read/28092572/pspel-in-silico-prediction-of-self-interacting-proteins-from-amino-acids-sequences-using-ensemble-learning
#8
Jian-Qiang Li, Zhu-Hong You, Xiao Li, Ming Zhong, Xing Chen
Self interacting proteins (SIPs) play an important role in various aspects of the structural and functional organization of the cell. Detecting SIPs is one of the most important issues in current molecular biology. Although a large number of SIPs data has been generated by experimental methods, wet laboratory approaches are both time-consuming and costly. In addition, they yield high false negative and positive rates. Thus, there is a great need for in silico methods to predict SIPs accurately and efficiently...
January 10, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28092474/novel-histone-deacetylase-6-hdac6-selective-inhibitors-a-patent-evaluation-wo2014181137
#9
Claudia A Simões-Pires, Philippe Bertrand, Muriel Cuendet
The invention described in this patent (WO2014181137) is related to hydroxamic acid derivatives with inhibitory activity towards histone deacetylases (HDACs), their synthetic process and pharmaceutical formulations, as well as a method for treating patients suffering from a list of selected tumoral, inflammatory, cardiac and chronic disorders. HDACs are known to deacetylate histones and other proteins, which makes HDAC inhibitors able to affect cell survival, cell signaling, transport, and gene expression. Those effects have been associated to the therapeutic success of HDAC inhibitors...
January 16, 2017: Expert Opinion on Therapeutic Patents
https://www.readbyqxmd.com/read/28092443/kinetics-and-structure-of-a-cold-adapted-hetero-octameric-atp-phosphoribosyltransferase
#10
Rozanne Stroek, Ying Ge, Paul D Talbot, Mateusz K Glok, Klaudia E Bernas, Catherine M Thomson, Eoin R Gould, Magnus S Alphey, Huanting Liu, Gordon J Florence, James H Naismith, Rafael Guimaraes da Silva
ATP-phosphoribosyltransferase (ATPPRT) catalyses the first step in histidine biosynthesis, the condensation of ATP and 5-phospho-α-D-ribosyl-1-pyrophosphate to generate N(1)-(5-phospho-β-D-ribosyl)-ATP and inorganic pyrophosphate. The enzyme is allosterically inhibited by histidine. Two forms of ATPPRT, encoded by the hisG gene, exist in nature, depending on the species. The long form, HisGL, is a single polypeptide chain with catalytic and regulatory domains. The short form, HisGS, lacks a regulatory domain, and cannot bind histidine...
January 16, 2017: Biochemistry
https://www.readbyqxmd.com/read/28092441/local-mode-analysis-decoding-ir-spectra-by-visualizing-molecular-details
#11
Matthias Massarczyk, Till Rudack, Jürgen Schlitter, Jens Kuhne, Carsten Kötting, Klaus Gerwert
Integration of experimental and computational approaches to investigate chemical reactions in proteins has proven to be very successful. Experimentally, time-resolved FTIR difference-spectroscopy monitors chemical reactions at atomic detail. To decode detailed structural information encoded in IR spectra, QM/MM calculations are performed. Here, we present a novel method which we call Local Mode Analysis (LMA) for calculating IR spectra and assigning spectral IR bands on the basis of movements of nuclei and partial charges from just a single QM/MM trajectory...
January 16, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28092440/molecular-interactions-between-graphene-and-biological-molecules
#12
Xingquan Zou, Shuai Wei, Joshua Jasensky, Minyu Xiao, Qiuming Wang, Charles L Brooks, Zhan Chen
Applications of graphene have extended into areas of nanobio-technology such as nanobio-medicine, nanobio-sensing, as well as nanoelectronics with biomolecules. These applications involve interactions between proteins, peptides, DNA, RNA etc. and graphene, therefore understanding such molecular interactions is essential. For example, many applications based on using graphene and peptides require peptides to interact with (e.g., noncovalently bind to) graphene at one end, while simultaneously exposing the other end to the surrounding medium (e...
January 16, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28092439/molecular-details-of-the-ph-domain-of-acap1-bar-ph-protein-binding-to-pip-containing-membrane
#13
Chun Chan, Lanyuan Lu, Fei Sun, Jun Fan
ACAP1 proteins were previously reported to specifically bind PIP2-containing cell membranes and form well-structured protein lattices in order to conduct membrane tubulation. We carried out molecular dynamics simulations to characterize orientation of the PH domains with respect to the BAR domains inside the protein dimer. Followed by molecular dynamics simulations, we present a comprehensive orientation analysis of PH domain under different states including unbound and bound with lipids. We have examined two binding pockets on the PH domain and present PMF profiles of the two pockets to account for their preference to PIP2 lipids...
January 16, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28092438/biofunctionalization-of-nerve-interface-via-biocompatible-polymer-roughened-pt-black-on-cuff-electrode-for-chronic-recording
#14
Yi Jae Lee, Han-Jun Kim, Ji Yoon Kang, Sun Hee Do, Soo Hyun Lee
Peripheral nerve cuff electrodes with roughened Pt black (BPt) are coated with polyethylene glycol (PEG) and Nafion (NF). Although the influence of coated PEG and Nafion on roughened BPt on the electrical properties is weak, the cuff electrode with BPt/PEG and BPt/Nafion exhibits some very important properties. For example, it markedly decreases interfacial impedance, increases charge storage capacity (CSC) due to retaining the BPt surface structure, good stability without exfoliation in repetitive cyclic voltammetry scanning because it is protected by PEG or Nafion coating...
January 16, 2017: Advanced Healthcare Materials
https://www.readbyqxmd.com/read/28092367/molecular-architecture-and-dynamics-of-ash1-mrna-recognition-by-its-mrna-transport-complex
#15
Franziska Theresia Edelmann, Andreas Schlundt, Roland Gerhard Heym, Andreas Jenner, Annika Niedner-Boblenz, Muhammad Ibrahim Syed, Jean-Christophe Paillart, Ralf Stehle, Robert Janowski, Michael Sattler, Ralf-Peter Jansen, Dierk Niessing
mRNA localization is an essential mechanism of gene regulation and is required for processes such as stem-cell division, embryogenesis and neuronal plasticity. It is not known which features in the cis-acting mRNA localization elements (LEs) are specifically recognized by motor-containing transport complexes. To the best of our knowledge, no high-resolution structure is available for any LE in complex with its cognate protein complex. Using X-ray crystallography and complementary techniques, we carried out a detailed assessment of an LE of the ASH1 mRNA from yeast, its complex with its shuttling RNA-binding protein She2p, and its highly specific, cytoplasmic complex with She3p...
January 16, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28092269/analysis-of-microtubule-growth-dynamics-arising-from-altered-actin-network-structure-and-contractility-in-breast-tumor-cells
#16
Eleanor Ory, Lekhana Bhandary, Amanda Boggs, Kristi Chakrabarti, Joshua Parker, Wolfgang Losert, Stuart S Martin
The periphery of epithelial cells is shaped by opposing cytoskeletal physical forces generated predominately by two dynamic force generating systems - growing microtubule ends push against the boundary from the cell center, and the actin cortex contracts the attached plasma membrane. Here we investigate how changes to the structure and dynamics of the actin cortex alter the dynamics of microtubules. Current drugs target actin polymerization and contraction to reduce cell division and invasiveness; however, the impacts on microtubule dynamics remain incompletely understood...
January 16, 2017: Physical Biology
https://www.readbyqxmd.com/read/28092121/hox-functional-diversity-novel-insights-from-flexible-motif-folding-and-plastic-protein-interaction
#17
Miguel Ortiz-Lombardia, Nicolas Foos, Corinne Maurel-Zaffran, Andrew J Saurin, Yacine Graba
How the formidable diversity of forms emerges from developmental and evolutionary processes is one of the most fascinating questions in biology. The homeodomain-containing Hox proteins were recognized early on as major actors in diversifying animal body plans. The molecular mechanisms underlying how this transcription factor family controls a large array of context- and cell-specific biological functions is, however, still poorly understood. Clues to functional diversity have emerged from studies exploring how Hox protein activity is controlled through interactions with PBC class proteins, also evolutionary conserved HD-containing proteins...
January 16, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28092049/rosette-assay-highly-customizable-dot-blot-for-sh2-domain-screening
#18
Khong Y Ng, Kazuya Machida
With a growing number of high-throughput studies, structural analyses, and availability of protein-protein interaction databases, it is now possible to apply web-based prediction tools to SH2 domain-interactions. However, in silico prediction is not always reliable and requires experimental validation. Rosette assay is a dot blot-based reverse-phase assay developed for the assessment of binding between SH2 domains and their ligands. It is conveniently customizable, allowing for low- to high-throughput analysis of interactions between various numbers of SH2 domains and their ligands, e...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28092038/nmr-chemical-shift-mapping-of-sh2-peptide-interactions
#19
Marissa A McKercher, Deborah S Wuttke
Heteronuclear single quantum coherence (HSQC) nuclear magnetic resonance (NMR) experiments offer a rapid and high resolution approach to gaining binding and conformational insights into a protein-peptide interaction. By tracking (1)H and (15)N chemical shift changes over the course of a peptide titration into isotopically labeled protein, amide NH pairs of amino acids whose chemical environment changes upon peptide binding can be identified. When mapped onto a structure of the protein, this approach can identify the peptide-binding interface or regions undergoing conformation changes within a protein upon ligand binding...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28092037/structural-characterization-of-monomeric-dimeric-state-of-p59-fyn-sh2-domain
#20
Radu Huculeci, Fabien Kieken, Abel Garcia-Pino, Lieven Buts, Nico van Nuland, Tom Lenaerts
Src homology 2 (SH2) domains are key modulators in various signaling pathways allowing the recognition of phosphotyrosine sites of different proteins. Despite the fact that SH2 domains acquire their biological functions in a monomeric state, a multitude of reports have shown their tendency to dimerize. Here, we provide a technical description on how to isolate and characterize by gel filtration, circular dichroism (CD), and nuclear magnetic resonance (NMR) each conformational state of p59(fyn) SH2 domain.
2017: Methods in Molecular Biology
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