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Molecular receptor affinity

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https://www.readbyqxmd.com/read/29149637/antiviral-potential-of-natural-compounds-against-influenza-virus-hemagglutinin
#1
S Kannan, P Kolandaivel
Influenza virus of different subtypes H1N1, H2N2, H3N2 and H5N1 cause many human pandemic deaths and threatening the people worldwide. The Hemagglutinin (HA) protein mediates viral attachment to host receptors act as an attractive target. The sixteen natural compounds have been chosen to target the HA protein. Molecular docking studies have been performed to find binding affinity of the compounds. Out of the sixteen, three compounds CI, CII and CIII found to posses a higher binding affinity. The molecular dynamics (MD) simulation has been performed to study the structural, dynamical properties for the nine different complexes CI, CII, CIII bound with H1, H2, H3 proteins and the results were compared...
November 4, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29149173/trade-off-and-flexibility-in-the-dynamic-regulation-of-the-cullin-ring-ubiquitin-ligase-repertoire
#2
Ronny Straube, Meera Shah, Dietrich Flockerzi, Dieter A Wolf
Cullin-RING ubiquitin ligases (CRLs) catalyze the ubiquitylation of substrates many of which are degraded by the 26S proteasome. Their modular architecture enables recognition of numerous substrates via exchangeable substrate receptors that competitively bind to a cullin scaffold with high affinity. Due to the plasticity of these interactions there is ongoing uncertainty how cells maintain a flexible CRL repertoire in view of changing substrate loads. Based on a series of in vivo and in vitro studies, different groups proposed that the exchange of substrate receptors is mediated by a protein exchange factor named Cand1...
November 17, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29147513/sortase-mediated-chemical-protein-synthesis-reveals-the-bidentate-binding-of-bisphosphorylated-p62-with-k63-diubiquitin
#3
Xiang-Long Tan, Man Pan, Yong Zheng, Shuai Gao, Lu-Jun Liang, Yi-Ming Li
Phosphorylation of S403 or S407 of the autophagic receptor protein p62 has recently been discovered to enhance the binding of p62 with ubiquitinated protein substrates to upregulate selective autophagy. To elucidate the molecular mechanism of how phosphorylation regulates the recruitment of ubiquitinated proteins, we report the first chemical synthesis of homogeneously phosphorylated p62, which enables the setting up of accurate in vitro systems for biochemical studies. Our synthesis employs the technology of sortase A-mediated protein hydrazide ligation, which successfully affords three types of phosphorylated p62 at the multi-milligram scale...
October 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/29146181/proximity-labeling-of-cis-ligands-of-cd22-siglec-2-reveals-stepwise-%C3%AE-2-6-sialic-acid-dependent-and-independent-interactions
#4
Amin Alborzian Deh Sheikh, Chizuru Akatsu, Akihiro Imamura, Hajjaj H M Abdu-Allah, Hiromu Takematsu, Hiromune Ando, Hideharu Ishida, Takeshi Tsubata
Lectins expressed on the cell surface are often bound and regulated by the membrane molecules containing the glycan ligands on the same cell (cis-ligands). However, molecular nature and function of cis-ligands are generally poorly understood partly because of weak interaction between lectins and glycan ligands. Cis-ligands are most extensively studied in CD22 (also known as Siglec-2), an inhibitory B lymphocyte receptor specifically recognizing α2,6 sialic acids. CD22, CD45 and IgM are suggested to be ligands of CD22...
November 13, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29144123/the-sign-of-nmr-chemical-shift-difference-as-a-determinant-of-the-origin-of-binding-selectivity-elucidation-of-the-position-dependence-of-phosphorylation-in-ligands-binding-to-scribble-pdz1
#5
Gustav Sundell, Beat Vögeli, Ylva Ivarsson, Celestine Chi
The use of NMR chemical shift perturbation to monitor changes taking place around the binding site of a ligand-protein interaction is a routine and widely applied methodology in the field of protein biochemistry. Shifts are often acquired by titrating various concentrations of ligand to a fixed concentration of the receptor and may serve the purposes, amongst others, to determine affinity constants, locate binding surfaces, or differentiate between binding mechanisms. Shifts are quantified by the so-called combined chemical shift difference...
November 16, 2017: Biochemistry
https://www.readbyqxmd.com/read/29143175/vectors-for-expression-of-signal-peptide-dependent-proteins-in-baculovirus-insect-cell-systems-and-their-application-to-expression-and-purification-of-the-high-affinity-immunoglobulin-gamma-fc-receptor-i-in-complex-with-its-gamma-chain
#6
Le T M Le, Jens R Nyengaard, Monika M Golas, Bjoern Sander
Integral membrane proteins play a central role in various cellular functions and are important therapeutic targets. However, technical challenges in the overexpression and purification of membrane proteins often represent a limiting factor for biochemical and structural studies. Here, we constructed a set of vectors, derivatives of MultiBac vectors that can be used to express proteins with a cleavable N-terminal signal peptide in insect cells. We propose these vectors for expression of type I membrane proteins and other secretory pathway proteins that require the signal recognition particle for translocation to the endoplasmic reticulum (ER)...
November 15, 2017: Molecular Biotechnology
https://www.readbyqxmd.com/read/29142437/docking-based-screening-of-ficus-religiosa-phytochemicals-as-inhibitors-of-human-histamine-h2-receptor
#7
Amit Chaudhary, Birendra Singh Yadav, Swati Singh, Pramod Kumar Maurya, Alok Mishra, Shweta Srivastva, Pritish Kumar Varadwaj, Nand Kumar Singh, Ashutosh Mani
Background: Ficus religiosa L. is generally known as Peepal and belongs to family Moraceae. The tree is a source of many compounds having high medicinal value. In gastrointestinal tract, histamine H2 receptors have key role in histamine-stimulated gastric acid secretion. Their over stimulation causes its excessive production which is responsible for gastric ulcer. Objective: This study aims to screen the range of phytochemicals present in F. religiosa for binding with human histamine H2 and identify therapeutics for a gastric ulcer from the plant...
October 2017: Pharmacognosy Magazine
https://www.readbyqxmd.com/read/29135238/elucidating-protein-ligand-recognition-with-combined-surface-plasmon-resonance-and-surface-enhanced-raman-spectroscopy
#8
Ju-Young Kim, Zhi-Cong Zeng, Lifu Xiao, Zachary D Schultz
The ability to distinguish between specific and non-specific binding is important for assessing the interactions between protein receptors and ligands. Surface plasmon resonance (SPR) spectroscopy is an advanced tool to measure the binding events, yet the ability to distinguish between specific and non-specific binding remains a limitation. To address this problem, we use SPR spectroscopy correlated with surface enhanced Raman scattering (SERS). The chemical information present in SERS spectra provides insight into the molecular interactions between functionalized nanoparticles and proteins, which are not detectable by SPR alone...
November 14, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29131383/rational-optimization-of-tumor-suppressor-derived-peptide-inhibitor-selectivity-between-oncogene-tyrosine-kinases-erbb1-and-erbb2
#9
Yilin Deng, Jian Li
The tumor-suppressor protein Mig-6 has been found to directly target and inhibit the human ErbB receptor tyrosine kinases ErbB1 and ErbB2. Despite their highly homologous nature, these two kinases are separately involved in the development of different types of human cancer. Here, we utilized a rational strategy to iteratively optimize the interaction specificity of the two kinases with a Mig-6 derived peptide by exploiting structural diversity space. Instead of traditionally improving the peptide binding potency, the optimization attempts to maximize the affinity difference between peptides binding to ErbB1 and ErbB2...
November 13, 2017: Archiv der Pharmazie
https://www.readbyqxmd.com/read/29128640/binding-interactions-of-halogenated-bisphenol-a-with-mouse-ppar%C3%AE-in-vitro-investigation-and-molecular-dynamics-simulation
#10
Jie Zhang, Tiezhu Li, Tuoyi Wang, Tianzhu Guan, Hansong Yu, Zhuolin Li, Yongzhi Wang, Yongjun Wang, Tiehua Zhang
The binding of bisphenol A (BPA) and its halogenated derivatives (halogenated BPAs) to mouse peroxisome proliferator-activated receptor α ligand binding domain (mPPARα-LBD) was examined by a combination of in vitro investigation and in silico simulation. Fluorescence polarization (FP) assay showed that halogenated BPAs could bind to mPPARα-LBD* as the affinity ligands. The calculated electrostatic potential (ESP) illustrated the different charge distributions of halogenated BPAs with altered halogenation patterns...
November 8, 2017: Toxicology Letters
https://www.readbyqxmd.com/read/29127702/towards-functional-selectivity-for-%C3%AE-6%C3%A2-3%C3%AE-2-gabaa-receptors-a-series-of-novel-pyrazoloquinolinones
#11
Marco Treven, David C B Siebert, Raphael Holzinger, Konstantina Bampali, Jure Fabjan, Zdravko Varagic, Laurin Wimmer, Friederike Steudle, Petra Scholze, Michael Schnürch, Marko D Mihovilovic, Margot Ernst
BACKGROUND AND PURPOSE: The γ - aminobutyric acid type A (GABAA ) receptors are ligand-gated ion channels which play an important role in neurotransmission. Their variety of binding sites serves as an appealing target for many clinically relevant drugs. Here, we explored the functional selectivity of modulatory effects at specific extracellular α+/®- interfaces, using a systematically varied series of pyrazoloquinolinones. EXPERIMENTAL APPROACH: Recombinant GABAA receptors were expressed in Xenopus laevis oocytes and modulatory effects on GABA elicited currents by the newly synthesized and the reference compounds were investigated by the two-electrode voltage clamp method...
November 11, 2017: British Journal of Pharmacology
https://www.readbyqxmd.com/read/29126515/endocrine-disruptors-eds-and-hormone-dependent-cancers-correlation-or-causal-relationship
#12
Henri Rochefort
The selective increase in the incidence of hormone-dependent cancers (breast, prostate, testicular) in industrialized countries is associated with the increasing number of endocrine disruptors (EDs) in the environment and raises questions about the role of EDs in mammary carcinogenesis. Answering these questions is difficult because the number of EDs is large and varies with time. Moreover hormonal carcinogenesis is multifactorial and progresses slowly and in stages. This discussion will be limited to breast cancer and three EDs: distilbene, bisphenol A (BPA), and dichlorodiphenyltrichloroethane (DDT)...
September 2017: Comptes Rendus Biologies
https://www.readbyqxmd.com/read/29125553/structure-based-design-of-potent-and-selective-ligands-at-the-four-adenosine-receptors
#13
Willem Jespers, Ana Oliveira, Rubén Prieto-Díaz, María Majellaro, Johan Åqvist, Eddy Sotelo, Hugo Gutiérrez-de-Terán
The four receptors that signal for adenosine, A₁, A2A, A2B and A₃ ARs, belong to the superfamily of G protein-coupled receptors (GPCRs). They mediate a number of (patho)physiological functions and have attracted the interest of the biopharmaceutical sector for decades as potential drug targets. The many crystal structures of the A2A, and lately the A₁ ARs, allow for the use of advanced computational, structure-based ligand design methodologies. Over the last decade, we have assessed the efficient synthesis of novel ligands specifically addressed to each of the four ARs...
November 10, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29125295/structure-activity-relationships-and-biological-characterization-of-a-novel-potent-and-serum-stable-c-x-c-chemokine-receptor-type-4-cxcr4-antagonist
#14
Salvatore Di Maro, Francesco Saverio Di Leva, Anna Maria Trotta, Diego Brancaccio, Luigi Portella, Michela Aurilio, Stefano Tomassi, Anna Messere, Deborah Sementa, Secondo Lastoria, Alfonso Carotenuto, Ettore Novellino, Stefania Scala, Luciana Marinelli
In our ongoing pursuit of CXCR4 antagonists as potential anticancer agents, we recently developed a potent, selective and plasma stable peptide, Ac-Arg-Ala-[D-Cys-Arg-Phe-Phe-Cys]-COOH (3). Nevertheless, this compound was still not enough potent (IC50 ≈ 53 nM) to enter preclinical studies. Thus, a lead-optimization campaign was here undertaken to further improve the binding affinity of 3 while preserving its selectivity and proteolytic stability. Specifically, extensive structure-activity relationships (SARs) investigations were carried out on both its aromatic and disulfide forming amino acids...
November 10, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29123220/significance-of-dopamine-d1-receptor-signalling-for-steroidogenic-differentiation-of-human-induced-pluripotent-stem-cells
#15
Koji Matsuo, Masakatsu Sone, Kyoko Honda-Kohmo, Takafumi Toyohara, Takuhiro Sonoyama, Daisuke Taura, Katsutoshi Kojima, Yorihide Fukuda, Youichi Ohno, Mayumi Inoue, Akira Ohta, Kenji Osafune, Kazuwa Nakao, Nobuya Inagaki
Human induced pluripotent stem cells (hiPSCs) are expected to be both a revolutionary cell source for regenerative medicine and a powerful tool to investigate the molecular mechanisms underlying human cell development in vitro. In the present study, we tried to elucidate the steroidogenic differentiation processes using hiPSC-derived intermediate mesoderm (IM) that is known to be the origin of the human adrenal cortex and gonads. We first performed chemical screening to identify small molecules that induce steroidogenic differentiation of IM cells expressing Odd-skipped related 1 (OSR1), an early IM marker...
November 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29119352/using-physics-based-pose-predictions-and-free-energy-perturbation-calculations-to-predict-binding-poses-and-relative-binding-affinities-for-fxr-ligands-in-the-d3r-grand-challenge-2
#16
Christina Athanasiou, Sofia Vasilakaki, Dimitris Dellis, Zoe Cournia
Computer-aided drug design has become an integral part of drug discovery and development in the pharmaceutical and biotechnology industry, and is nowadays extensively used in the lead identification and lead optimization phases. The drug design data resource (D3R) organizes challenges against blinded experimental data to prospectively test computational methodologies as an opportunity for improved methods and algorithms to emerge. We participated in Grand Challenge 2 to predict the crystallographic poses of 36 Farnesoid X Receptor (FXR)-bound ligands and the relative binding affinities for two designated subsets of 18 and 15 FXR-bound ligands...
November 8, 2017: Journal of Computer-aided Molecular Design
https://www.readbyqxmd.com/read/29118117/a-y161f-hemagglutinin-substitution-increases-thermostability-and-improves-yields-of-2009-h1n1-influenza-a-virus-in-cells
#17
Feng Wen, Lei Li, Nan Zhao, Meng-Jung Chiang, Hang Xie, Jim Cooley, Richard Webby, Peng George Wang, Xiu-Feng Wan
Vaccination is the primary strategy for influenza prevention and control. Yet egg-based vaccines, the predominant production platform, have several disadvantages including the emergence of viral antigenic variants that can be induced during egg passage. These limitations have prompted development of cell-based vaccines which themselves are not without issue. Most importantly, vaccine seed viruses often do not grow efficiently in mammalian cell lines. Here we aimed to identify novel high-yield signatures for influenza viruses in continuous Madin-Darby canine kidney (MDCK) and Vero cells...
November 8, 2017: Journal of Virology
https://www.readbyqxmd.com/read/29114668/an-integrative-omics-perspective-for-the-analysis-of-chemical-signals-in-ecological-interactions
#18
A E Brunetti, F Carnevale Neto, M C Vera, C Taboada, D P Pavarini, A Bauermeister, N P Lopes
All living organisms emit, detect, and respond to chemical stimuli, thus creating an almost limitless number of interactions by means of chemical signals. Technological and intellectual advances in the last two decades have enabled chemical signals analyses at several molecular levels, including gene expression, molecular diversity, and receptor affinity. These advances have also deepened our understanding of nature to encompass interactions at multiple organism levels across different taxa. This tutorial review describes the most recent analytical developments in 'omics' technologies (i...
November 8, 2017: Chemical Society Reviews
https://www.readbyqxmd.com/read/29109273/blockade-of-activin-type-ii-receptors-with-a-dual-anti-actriia-iib-antibody-is-critical-to-promote-maximal-skeletal-muscle-hypertrophy
#19
Frederic Morvan, Jean-Michel Rondeau, Chao Zou, Giulia Minetti, Clemens Scheufler, Meike Scharenberg, Carsten Jacobi, Pascale Brebbia, Veronique Ritter, Gauthier Toussaint, Claudia Koelbing, Xavier Leber, Alain Schilb, Florian Witte, Sylvie Lehmann, Elke Koch, Sabine Geisse, David J Glass, Estelle Lach-Trifilieff
The TGF-β family ligands myostatin, GDF11, and activins are negative regulators of skeletal muscle mass, which have been reported to primarily signal via the ActRIIB receptor on skeletal muscle and thereby induce muscle wasting described as cachexia. Use of a soluble ActRIIB-Fc "trap," to block myostatin pathway signaling in normal or cachectic mice leads to hypertrophy or prevention of muscle loss, perhaps suggesting that the ActRIIB receptor is primarily responsible for muscle growth regulation. Genetic evidence demonstrates however that both ActRIIB- and ActRIIA-deficient mice display a hypertrophic phenotype...
November 6, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29109154/hierarchical-protein-targeting-and-secretion-is-controlled-by-an-affinity-switch-in-the-type-iii-secretion-system-of-enteropathogenic-escherichia-coli
#20
Athina G Portaliou, Konstantinos C Tsolis, Maria S Loos, Vassileia Balabanidou, Josep Rayo, Alexandra Tsirigotaki, Valerie F Crepin, Gad Frankel, Charalampos G Kalodimos, Spyridoula Karamanou, Anastassios Economou
Type III secretion (T3S), a protein export pathway common to Gram-negative pathogens, comprises a trans-envelope syringe, the injectisome, with a cytoplasm-facing translocase channel. Exported substrates are chaperone-delivered to the translocase, EscV in enteropathogenic Escherichia coli, and cross it in strict hierarchical manner, for example, first "translocators", then "effectors". We dissected T3S substrate targeting and hierarchical switching by reconstituting them in vitro using inverted inner membrane vesicles...
November 6, 2017: EMBO Journal
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