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https://www.readbyqxmd.com/read/28107751/molecular-modeling-study-of-cp-690550-derivatives-as-jak3-kinase-inhibitors-through-combined-3d-qsar-molecular-docking-and-dynamics-simulation-techniques
#1
Jing Li Wang, Li Ping Cheng, Tian Chi Wang, Wei Deng, Fan Hong Wu
To develop more potent JAK3 kinase inhibitors, a series of CP-690550 derivatives were investigated using combined molecular modeling techniques, such as 3D-QSAR, molecular docking and molecular dynamics (MD). The leave-one-out correlation (q(2)) and non-cross-validated correlation coefficient (r(2)) of the best CoMFA model are 0.715 and 0.992, respectively. The q(2) and r(2) values of the best CoMSIA model are 0.739 and 0.995, respectively. The steric, electrostatic, and hydrophobic fields played important roles in determining the inhibitory activity of CP-690550 derivatives...
January 4, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28107648/parp-1-controls-the-adipogenic-transcriptional-program-by-parylating-c-ebp%C3%AE-and-modulating-its-transcriptional-activity
#2
Xin Luo, Keun Woo Ryu, Dae-Seok Kim, Tulip Nandu, Carlos J Medina, Rebecca Gupte, Bryan A Gibson, Raymond E Soccio, Yonghao Yu, Rana K Gupta, W Lee Kraus
Poly(ADP-ribosyl)ation (PARylation) is a post-translational modification of proteins mediated by PARP family members, such as PARP-1. Although PARylation has been studied extensively, few examples of definitive biological roles for site-specific PARylation have been reported. Here we show that C/EBPβ, a key pro-adipogenic transcription factor, is PARylated by PARP-1 on three amino acids in a conserved regulatory domain. PARylation at these sites inhibits C/EBPβ's DNA binding and transcriptional activities and attenuates adipogenesis in various genetic and cell-based models...
January 19, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28107609/carbon-nanodot-solar-cells-from-renewable-precursors
#3
Maria-Magdalena Titirici, Adam Marinovic, Steve Dunn, Lim Swee Kiat, Joe Briscoe
It has recently been shown that waste biomass can be converted into a wide range of functional materials, including those with desirable optical and electronic properties, offering the opportunity to find new uses for these renewable resources. Photovoltaics is one area where finding the combination of abundant, low-cost and non-toxic materials with the necessary functionality can be challenging. In this paper we compare the performance of carbon nanodots derived from a wide range of biomaterials obtained from different biomass sources as sensitizers for TiO2-based nanostructured solar cells; polysaccharides (chitosan and chitin), monosaccharide (D-glucose), amino acids (L-arginine and L-cysteine) and raw lobster shells are all used to produce carbon nanodots via hydrothermal carbonisation...
January 20, 2017: ChemSusChem
https://www.readbyqxmd.com/read/28107516/liver-amp-activated-protein-kinase-is-unnecessary-for-gluconeogenesis-but-protects-energy-state-during-nutrient-deprivation
#4
Clinton M Hasenour, D Emerson Ridley, Freyja D James, Curtis C Hughey, E Patrick Donahue, Benoit Viollet, Marc Foretz, Jamey D Young, David H Wasserman
AMPK is an energy sensor that protects cellular energy state by attenuating anabolic and promoting catabolic processes. AMPK signaling is purported to regulate hepatic gluconeogenesis and substrate oxidation; coordination of these processes is vital during nutrient deprivation or pathogenic during overnutrition. Here we directly test hepatic AMPK function in regulating metabolic fluxes that converge to produce glucose and energy in vivo. Flux analysis was applied in mice with a liver-specific deletion of AMPK (L-KO) or floxed control littermates to assess rates of hepatic glucose producing and citric acid cycle (CAC) fluxes...
2017: PloS One
https://www.readbyqxmd.com/read/28107470/development-of-a-blocking-elisa-using-a-monoclonal-antibody-to-a-dominant-epitope-in-non-structural-protein-3a-of-foot-and-mouth-disease-virus-as-a-matching-test-for-a-negative-marker-vaccine
#5
Yuanfang Fu, Pinghua Li, Yimei Cao, Na Wang, Pu Sun, Qian Shi, Xincheng Ji, Huifang Bao, Dong Li, Yingli Chen, Xingwen Bai, Xueqing Ma, Jing Zhang, Zengjun Lu, Zaixin Liu
Foot-and-mouth disease (FMD) is a devastating animal disease. Strategies for differentiation of infected from vaccinated animals (DIVA) remain very important for controlling disease. Development of an epitope-deleted marker vaccine and accompanying diagnostic method will improve the efficiency of DIVA. Here, a monoclonal antibody (Mab) was found to recognize a conserved "AEKNPLE" epitope spanning amino acids 109-115 of non-structural protein (NSP) 3A of foot-and-mouth disease virus (FMDV; O/Tibet/CHA/99 strain), which could be deleted by a reverse-genetic procedure...
2017: PloS One
https://www.readbyqxmd.com/read/28107435/peptide-targeted-by-human-antibodies-associated-with-hiv-vaccine-associated-protection-assumes-a-dynamic-%C3%AE-helical-structure
#6
Mohammed S Aiyegbo, Evgeny Shmelkov, Lorenzo Dominguez, Michael Goger, Shibani Battacharya, Allan C deCamp, Peter B Gilbert, Phillip W Berman, Timothy Cardozo
The only evidence of vaccine-induced protection from HIV acquisition in humans was obtained in the RV144 HIV vaccine clinical trial. One immune correlate of risk in RV144 was observed to be higher titers of vaccine-induced antibodies (Abs) reacting with a 23-mer non-glycosylated peptide with the same amino acid sequence as a segment in the second variable (V2) loop of the MN strain of HIV. We used NMR to analyze the dynamic 3D structure of this peptide. Distance restraints between spatially proximate inter-residue protons were calculated from NOE cross peak intensities and used to constrain a thorough search of all possible conformations of the peptide...
2017: PloS One
https://www.readbyqxmd.com/read/28107387/neuronal-cell-death-and-degeneration-through-increased-nitroxidative-stress-and-tau-phosphorylation-in-hiv-1-transgenic-rats
#7
Young-Eun Cho, Myoung-Hwa Lee, Byoung-Joon Song
The underlying mechanisms for increased neurodegeneration and neurocognitive deficits in HIV-infected people are unclear. Therefore, this study was aimed to investigate the mechanisms of increased neurodegeneration in 5-month old male HIV-1 Transgenic (Tg) rats compared to the age- and gender-matched wild-type (WT) by evaluating histological changes and biochemical parameters of the key proteins involved in the cell death signaling and apoptosis. Histological and immunohistochemical analyses revealed decreased neuronal cells with elevated astrogliosis in HIV-1 Tg rats compared to WT...
2017: PloS One
https://www.readbyqxmd.com/read/28107009/nmr-and-computation-reveal-a-pressure-sensitive-folded-conformation-of-trp-cage
#8
Soichiro Kitazawa, Martin J Fossat, Scott A McCallum, Angel E Garcia, Catherine Ann Royer
Beyond defining the structure and stability of folded states of proteins, primary amino acid sequences determine all of the features of their conformational landscapes. Characterizing how sequence modulates the population of protein excited states or folding pathways requires atomic level detailed structural and energetic information. Such insight is essential for improving protein design strategies, as well as for interpreting protein evolution. Here, high pressure NMR and molecular dynamics simulations were combined to probe the conformational landscape of a small model protein, the tryptophan cage variant, Tc5b...
January 20, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28106998/identification-of-cyclic-depsipeptides-and-their-dedicated-synthetase-from-hapsidospora-irregularis
#9
Shuwei Zhang, Yixing Qiu, Thomas B Kakule, Zhenyu Lu, Fuchao Xu, John G Lamb, Christopher A Reilly, Yong Zheng, Shing Wo Simon Sham, Wei Wang, Lijiang Xuan, Eric W Schmidt, Jixun Zhan
Seven cyclic depsipeptides were isolated from Hapsidospora irregularis and structurally characterized as the calcium channel blocker leualacin and six new analogues based on the NMR and HRESIMS data. These new compounds were named leualacins B-G. The absolute configurations of the amino acids and 2-hydroxyisocaproic acids were determined by recording the optical rotation values. Biological studies showed that calcium influx elicited by leualacin F in primary human lobar bronchial epithelial cells involves the TRPA1 channel...
January 20, 2017: Journal of Natural Products
https://www.readbyqxmd.com/read/28106981/controlling-multi-cycle-replication-of-live-attenuated-hiv-1-using-an-unnatural-genetic-switch
#10
Zhe Yuan, Nanxi Wang, Guobin Kang, Wei Niu, Qingsheng Li, Jiantao Guo
A safe and effective human immunodeficiency virus type 1 (HIV-1) vaccine is urgently needed, but remains elusive. While HIV-1 live-attenuated vaccine can provide potent protection as demonstrated in rhesus macaque-simian immunodeficiency virus model, the potential pathogenic consequences associated with the uncontrolled virus replication preclude such vaccine from clinical applications. We investigated a novel approach to address this problem by controlling live-attenuated HIV-1 replication through an unnatural genetic switch that was based on the amber suppression strategy...
January 20, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28106929/conformational-analysis-of-an-antibacterial-cyclodepsipeptide-active-against-m-tuberculosis-by-a-combined-roe-and-rdc-analysis
#11
Maic Fredersdorf, Michael Kurz, Armin Bauer, Marc-Olivier Ebert, Carla Rigling, Laurie Lannes, Christina Thiele
Griselimycin (GM) and methylgriselimycin (MGM), naturally produced by microorganisms of the genus Streptomyces, are cyclic depsipeptides composed of ten amino acids. They exhibit antibacterial activity against mycobacterium species by inhibiting the sliding clamp of prokaryotic DNA polymerase III and are therefore considered as potential anti-tuberculosis drugs. The difference between both peptides is the presence of L -(R)-4-methylproline in MGM instead of L -proline in GM at position 8 of the amino acid sequence...
January 20, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28106838/molecular-characterization-of-voltage-gated-sodium-channels-and-their-relations-with-paralytic-shellfish-toxin-bioaccumulation-in-the-pacific-oyster-crassostrea-gigas
#12
Floriane Boullot, Justine Castrec, Adeline Bidault, Natanael Dantas, Laura Payton, Mickael Perrigault, Damien Tran, Zouher Amzil, Pierre Boudry, Philippe Soudant, Hélène Hégaret, Caroline Fabioux
Paralytic shellfish toxins (PST) bind to voltage-gated sodium channels (Nav) and block conduction of action potential in excitable cells. This study aimed to (i) characterize Nav sequences in Crassostrea gigas and (ii) investigate a putative relation between Nav and PST-bioaccumulation in oysters. The phylogenetic analysis highlighted two types of Nav in C. gigas: a Nav1 (CgNav1) and a Nav2 (CgNav2) with sequence properties of sodium-selective and sodium/calcium-selective channels, respectively. Three alternative splice transcripts of CgNav1 named A, B and C, were characterized...
January 19, 2017: Marine Drugs
https://www.readbyqxmd.com/read/28106780/integrins-and-cell-metabolism-an-intimate-relationship-impacting-cancer
#13
REVIEW
Rehman Ata, Costin N Antonescu
Integrins are important regulators of cell survival, proliferation, adhesion and migration. Once activated, integrins establish a regulated link between the extracellular matrix and the cytoskeleton. Integrins have well-established functions in cancer, such as in controlling cell survival by engagement of many specific intracellular signaling pathways and in facilitating metastasis. Integrins and associated proteins are regulated by control of transcription, membrane traffic, and degradation, as well as by a number of post-translational modifications including glycosylation, allowing integrin function to be modulated to conform to various cellular needs and environmental conditions...
January 18, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28106766/the-anti-oxidant-defense-system-of-the-marine-polar-ciliate-euplotes-nobilii-characterization-of-the-msrb-gene-family
#14
Francesca Ricci, Federico M Lauro, Joseph J Grzymski, Robert Read, Rigers Bakiu, Gianfranco Santovito, Pierangelo Luporini, Adriana Vallesi
Organisms living in polar waters must cope with an extremely stressful environment dominated by freezing temperatures, high oxygen concentrations and UV radiation. To shed light on the genetic mechanisms on which the polar marine ciliate, Euplotes nobilii, relies to effectively cope with the oxidative stress, attention was focused on methionine sulfoxide reductases which repair proteins with oxidized methionines. A family of four structurally distinct MsrB genes, encoding enzymes specific for the reduction of the methionine-sulfoxide R-forms, were identified from a draft of the E...
January 18, 2017: Biology
https://www.readbyqxmd.com/read/28106735/mass-spectrometry-based-metabolomic-and-lipidomic-analyses-of-the-effects-of-dietary-platycodon-grandiflorum-on-liver-and-serum-of-obese-mice-under-a-high-fat-diet
#15
Hye Min Park, Kab-Tae Park, Edmond Changkyun Park, Seung Ii Kim, Myung Sook Choi, Kwang-Hyeon Liu, Choong Hwan Lee
We aimed to identify metabolites involved in the anti-obesity effects of Platycodon grandiflorum (PG) in high-fat diet (HFD)-fed mice using mass spectrometry (MS)-based metabolomic techniques. C57BL/6J mice were divided into four groups: normal diet (ND)-fed mice, HFD-fed mice, HFD with 1% PG extract-fed mice (HPGL), and HFD with 5% PG extract-fed mice (HPGH). After 8 weeks, the HFD group gained more weight than the ND group, while dietary 5% PG extract attenuated this change. The partial least squares discriminant analysis (PLS-DA) score plots showed a clear distinction between experimental groups in serum and liver markers...
January 17, 2017: Nutrients
https://www.readbyqxmd.com/read/28106726/discrepancy-between-hepatitis-c-virus-genotypes-and-ns4-based-serotypes-association-with-their-subgenomic-sequences
#16
Nan Nwe Win, Shingo Nakamoto, Tatsuo Kanda, Hiroki Takahashi, Azusa Takahashi-Nakaguchi, Shin Yasui, Masato Nakamura, Shuang Wu, Fumio Imazeki, Shigeru Mikami, Osamu Yokosuka, Tohru Gonoi, Hiroshi Shirasawa
Determination of hepatitis C virus (HCV) genotypes plays an important role in the direct-acting agent era. Discrepancies between HCV genotyping and serotyping assays are occasionally observed. Eighteen samples with discrepant results between genotyping and serotyping methods were analyzed. HCV serotyping and genotyping were based on the HCV nonstructural 4 (NS4) region and 5'-untranslated region (5'-UTR), respectively. HCV core and NS4 regions were chosen to be sequenced and were compared with the genotyping and serotyping results...
January 17, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28106620/effects-of-histidine-and-%C3%AE-alanine-supplementation-on-human-muscle-carnosine-storage
#17
Laura Blancquaert, Inge Everaert, Maarten Missinne, Audrey Baguet, Sanne Stegen, Anneke Volkaert, Mirko Petrovic, Chris Vervaet, Eric Achten, Mieke De Maeyer, Stefaan De Henauw, Wim Derave
PURPOSE: Carnosine is a dipeptide composed of β-alanine and L-histidine and is present in skeletal muscle. Chronic oral β-alanine supplementation can induce muscle carnosine loading and is therefore seen as the rate-limiting factor for carnosine synthesis. However, the effect of L-histidine supplementation on carnosine levels in humans is never established. This study aims to investigate whether 1) L-histidine supplementation can induce muscle carnosine loading and 2) combined supplementation of both amino acids is more efficient than β-alanine supplementation alone...
January 19, 2017: Medicine and Science in Sports and Exercise
https://www.readbyqxmd.com/read/28106476/quantification-of-hepcidin-25-in-human-cerebrospinal-fluid-using-lc-ms-ms
#18
Constance Delaby, Pauline Bros, Jérôme Vialaret, Amandine Moulinier, Vincent Delatour, Audrey Gabelle, Sylvain Lehmann, Christophe Hirtz
AIM: Hepcidin, the main iron metabolism regulator, can be detected in various biological fluids. Here, we describe a quantitative method of LC-MS/MS to quantify the 25 amino acid isoform of hepcidin (hepcidin-25) in human cerebrospinal fluid (CSF). Results & methodology: Samples were prepared through protein precipitation followed by solid phase extraction (SPE) and injected into a triple-quadrupole mass spectrometer. Validation of our method included determination of LOQ (0.1 ng/ml), repeatability, intermediate precision, recovery and linearity (up to 25 ng/ml)...
January 20, 2017: Bioanalysis
https://www.readbyqxmd.com/read/28106337/in-vivo-metabolomic-interpretation-of-the-anti-obesity-effects-of-hyacinth-bean-dolichos-lablab-l-administration-in-high-fat-diet-mice
#19
Dong Ho Suh, Hye Won Lee, Eun Sung Jung, Digar Singh, Seung-Hyung Kim, Choong Hwan Lee
SCOPE: The esoteric anti-obesity effects of hyacinth bean (Dolichos lablab L) have largely remained unexplored. Herein, we investigated the anti-obesity mechanisms of hyacinth bean compared to milk thistle, a natural herb employed for ameliorating obesity-related diseases, using high fat-diet (HFD) fed mice towards unfolding the perplexing mechanisms. METHODS AND RESULTS: C57BL/6J mice were orally administered hyacinth bean (25 mg/kg/day) and milk thistle (100 mg/kg/day) for 9 weeks along with HFD...
January 20, 2017: Molecular Nutrition & Food Research
https://www.readbyqxmd.com/read/28106305/diversity-oriented-peptide-stapling-a-third-generation-cuaac-stapling-and-functionalisation-strategy
#20
Thu Tran Phuong, Christian Ørnbøl Larsen, Tobias Røndbjerg, Martina De Foresta, Micha Ben Achim Kunze, Ales Marek, Jacob Hartvig Løper, Lotte-Emilie Boyhus, Astrid Knuhtsen, Kresten Lindorff-Larsen, Daniel Sejer Pedersen
The introduction of macrocyclic constraints in peptides (peptide stapling) is an important tool within peptide medicinal chemistry for stabilising and pre-organising peptides in a desired conformation. In recent years, the copper-catalysed azide-alkyne cycloaddition (CuAAC) has emerged as a powerful method for peptide stapling. However, to date CuAAC stapling has not provided a simple method for obtaining peptides that are easily diversified further. In the present study, we report a new diversity-oriented peptide stapling (DOPS) methodology based on CuAAC chemistry...
January 20, 2017: Chemistry: a European Journal
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