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Molecular receptor affinity

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https://www.readbyqxmd.com/read/28437098/interaction-of-fibrin-with-the-very-low-density-lipoprotein-receptor-further-characterization-and-localization-of-the-vldl-receptor-binding-site-in-fibrin-%C3%AE-n-domains
#1
Sergiy Yakovlev, Leonid Medved
Our recent study revealed that fibrin and the VLDL receptor (VLDLR) interact with each other through a pair of fibrin βN-domains and CR domains of the receptor and this interaction promotes transendothelial migration of leukocytes and thereby inflammation. The major objectives of the present study were to further clarify the molecular mechanism of fibrin-VLDLR interaction and to identify amino acid residues in the βN-domains involved in this interaction. Our binding experiments with the (β15-66)2 fragment, which corresponds to a pair of fibrin βN-domains, and the VLDLR(1-8) fragment consisting of eight CR domains of VLDLR, revealed that interaction between them strongly depends on ionic strength and chemical modification of all Lys or Arg residues in (β15-66)2 results in abrogation of this interaction...
April 24, 2017: Biochemistry
https://www.readbyqxmd.com/read/28437008/effects-from-metal-ion-in-tumor-endothelial-marker-8-and-anthrax-protective-antigen-biolayer-interferometry-experiment-and-molecular-dynamics-simulation-study
#2
Zhe Jia, Christine Ackroyd, Tingting Han, Vibhor Agrawal, Yinling Liu, Kenneth Christensen, Brian Dominy
One of the anthrax receptors, tumor endothelial marker 8 (TEM8), is reported to be a potential anticancer target due to its over-expression during tumor angiogenesis. To extend our BioLayer Interferometry study in PA-TEM8 binding, we present a computational approach to reveal the role of an integral metal ion on receptor structure and binding thermodynamics. We estimated the interaction energy between PA and TEM8 using computer simulation. Consistent with experimental study, computational results indicate the metal ion in TEM8 contributes significantly to the binding affinity, and PA-TEM8 binding is more favorable in the presence of Mg(2+) than Ca(2+) ...
June 5, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28432336/structure-function-analysis-of-the-dna-binding-domain-of-a-transmembrane-transcriptional-activator
#3
Andreas Schlundt, Sophie Buchner, Robert Janowski, Thomas Heydenreich, Ralf Heermann, Jürgen Lassak, Arie Geerlof, Ralf Stehle, Dierk Niessing, Kirsten Jung, Michael Sattler
The transmembrane DNA-binding protein CadC of E. coli, a representative of the ToxR-like receptor family, combines input and effector domains for signal sensing and transcriptional activation, respectively, in a single protein, thus representing one of the simplest signalling systems. At acidic pH in a lysine-rich environment, CadC activates the transcription of the cadBA operon through recruitment of the RNA polymerase (RNAP) to the two cadBA promoter sites, Cad1 and Cad2, which are directly bound by CadC...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28432329/affinity-biosensors-using-recombinant-native-membrane-proteins-displayed-on-exosomes-application-to-botulinum-neurotoxin-b-receptor
#4
Richard Desplantes, Christian Lévêque, Benjamin Muller, Manuela Lotierzo, Géraldine Ferracci, Michel Popoff, Michael Seagar, Robert Mamoun, Oussama El Far
The development of simple molecular assays with membrane protein receptors in a native conformation still represents a challenging task. Exosomes are extracellular vesicles which, due to their stability and small size, are suited for analysis in various assay formats. Here, we describe a novel approach to sort recombinant fully native and functional membrane proteins to exosomes using a targeting peptide. Specific binding of high affinity ligands to the potassium channel Kv1.2, the G-protein coupled receptor CXCR4, and the botulinum neurotoxin type B (BoNT/B) receptor, indicated their correct assembly and outside out orientation in exosomes...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28429411/nanodiscs-for-inpharma-nmr-characterization-of-gpcrs-ligand-binding-to-the-human-a2a-adenosine-receptor
#5
Kai Fredriksson, Philip Lottmann, Sonja Hinz, Iounut Onila, Aliaksei Shymanets, Christian Harteneck, Christa E Müller, Christian Griesinger, Thomas E Exner
G-protein-coupled-receptors (GPCRs) are of fundamental importance for signal transduction through cell membranes. This makes them important drug targets, but structure-based drug design (SBDD) is still hampered by the limitations for structure determination of unmodified GPCRs. We show that the interligand NOEs for pharmacophore mapping (INPHARMA) method can provide valuable information on ligand poses inside the binding site of the unmodified human A2A adenosine receptor reconstituted in nanodiscs. By comparing experimental INPHARMA spectra with back-calculated spectra based on ligand poses obtained from molecular dynamics simulations, a complex structure for A2A R with the low-affinity ligand 3-pyrrolidin-1-ylquinoxalin-2-amine was determined based on the X-ray structure of ligand ZM-241,358 in complex with a modified A2A R...
April 21, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28428126/interactions-of-tetracyclines-with-ovalbumin-the-main-allergen-protein-from-egg-white-spectroscopic-and-electrophoretic-studies
#6
Maria Dayanne de A Dantas, Humberto de Araújo Tenório, Thiago Inácio B Lopes, Hugo Juarez V Pereira, Anita J Marsaioli, Isis M Figueiredo, Josué Carinhanha Caldas Santos
The interactions of tetracycline (TC), oxytetracycline (OTC) and chlortetracycline (CTC) with ovalbumin (OVA), the main allergen protein of egg white, were investigated by molecular spectroscopy and electrophoresis at three pH conditions (1.5, 4.6 and 7.4). Molecular and synchronous fluorescence, UV-vis spectroscopy, electrophoresis and (1)H NMR were used to study the interaction process. Tetracyclines interact with ovalbumin fluorescence by a static quenching mechanism with non-fluorescent complex formation changing the native protein structure...
April 17, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28426939/high-throughput-agonist-shift-assay-development-for-the-analysis-of-m1-positive-allosteric-modulators
#7
Michelle F Homsher, Douglas C Beshore, Jason Cassaday, Brian Squadroni, Elizabeth Mohammed, Michelle Hartnett, Stephen Day, Lei Ma, David Pechter, Michelle D Smith, Fredrick Monsma, Paul Zuck, Michael F Finley, Victor N Uebele, Jeffrey D Hermes
Agonist shift assays feature cross-titrations of allosteric modulators and orthosteric ligands. Information generated in agonist shift assays can include a modulator's effect on the orthosteric agonist's potency (alpha) and efficacy (beta), as well as direct agonist activity of the allosteric ligand (tauB) and the intrinsic binding affinity of the modulator to the unoccupied receptor (KB). Because of the heavy resource demand and complex data handling, these allosteric parameters are determined infrequently during the course of a drug discovery program and on a relatively small subset of compounds...
April 1, 2017: SLAS Discovery
https://www.readbyqxmd.com/read/28425855/tumor-targeting-peptides-ligands-for-molecular-imaging-and-therapy
#8
Ning Zhao, Yeshan Qin, Hongguang Liu, Z Cheng
The aberrant proliferation of tumor cells and abundant vasculature in tumor tissues are closely correlated with receptors that are specifically dysregulated in tumor cells. These tumor-associated targets are critical in early diagnosis and therapy selection. Ligands such as antibodies, proteins, polypeptides and polysaccharides that specifically bind to these targets can significantly improve the detection and cure rate when used as tumor imaging probes or anti-tumor agents. Compared to other targeting ligands, peptides have attracted increasingly more attention in tumor diagnostics and therapeutics because of their small sizes, high affinity, stability, ease of modification and low immunogenicity...
April 19, 2017: Anti-cancer Agents in Medicinal Chemistry
https://www.readbyqxmd.com/read/28422724/utilizing-combinatorial-engineering-to-develop-tie2-targeting-antagonistic-angiopoetin-2-ligands-as-candidates-for-anti-angiogenesis-therapy
#9
Tomer Shlamkovich, Lidan Aharon, William A Barton, Niv Papo
In many human cancers, the receptor tyrosine kinase (RTK) Tie2 plays important roles in mediating proliferation, survival, migration and angiogenesis. Thus, molecules that could potently inhibit activation of the Tie2 receptor would have a significant impact on cancer therapy. Nevertheless, attempts to develop Tie2-targeted inhibitors have met with little success, and there is currently no FDA-approved therapeutic selectively targeting Tie2. We used a combinatorial protein engineering approach to develop a new generation of angiopoietin (Ang) 2-derived Tie2 antagonists as potential cancer therapeutics and as tools to study angiogenesis...
April 4, 2017: Oncotarget
https://www.readbyqxmd.com/read/28421694/molecular-engineering-and-plant-expression-of-an-immunoglobulin-heavy-chain-scaffold-for-delivery-of-a-dengue-vaccine-candidate
#10
Mi-Young Kim, Craig Van Dolleweerd, Alastair Copland, Matthew John Paul, Sven Hofmann, Gina R Webster, Emily Julik, Ivonne Ceballos-Olvera, Jorge Reyes-Del Valle, Moon-Sik Yang, Yong-Suk Jang, Rajko Reljic, Julian K Ma
In order to enhance vaccine uptake by the immune cells in vivo, molecular engineering approach was employed to construct a Polymeric Immunoglobulin G Scaffold (PIGS) that incorporates multiple copies of an antigen and targets the Fc gamma receptors on antigen-presenting cells. These self-adjuvanting immunogens were tested in the context of dengue infection, for which there is currently no globally licensed vaccine yet. Thus, the consensus domain III sequence (cEDIII) of dengue glycoprotein E was incorporated into PIGS and expressed in both tobacco plants and Chinese Ovary Hamster cells...
April 19, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28421441/n-methyl-serotonin-analogues-from-the-bufo-bufo-toad-venom-interact-efficiently-with-the-%C3%AE-7-nicotinic-acetylcholine-receptors
#11
E V Kryukova, D S Lebedev, I A Ivanov, D A Ivanov, V G Starkov, V I Tsetlin, Yu N Utkin
Two low-molecular-weight compounds were isolated from the parotid gland secret of the toad Bufo bufo, which by absorption spectra and HPLC-MS/MS chromatography data correspond to di- and trimethyl derivatives of serotonin (5-hydorxytryptamine): bufotenine (confirmed by counter synthesis) and bufotenidine (5-HTQ). In experiments on competitive radioligand binding, these compounds showed a higher affinity and selectivity for neuronal α7 nicotinic acetylcholine receptors compared with the muscular cholinergic receptors...
January 2017: Doklady. Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28419241/central-hypothyroidism-due-to-a-trhr-mutation-causing-impaired-ligand-affinity-and-transactivation-of-gq
#12
Marta García, Jesús González de Buitrago, Mireia Jiménez-Rosés, Leonardo Pardo, Patricia M Hinkle, José C Moreno
Context: Central congenital hypothyroidism (CCH) is an underdiagnosed disorder characterized by deficient production and bioactivity of TSH leading to low thyroid hormone synthesis. TRH receptor (TRHR) defects are rare recessive disorders usually associated with incidentally identified CCH and short stature in childhood. Objectives: Clinical and genetic characterization of a consanguineous family of Roma origin with central hypothyroidism and identification of underlying molecular mechanisms...
April 17, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/28418199/evaluation-of-biological-activity-and-computer-aided-design-of-new-soft-glucocorticoids
#13
Vladimir Dobričić, Vesna Jaćević, Jelica Vučićević, Katarina Nikolic, Sote Vladimirov, Olivera Čudina
Soft glucocorticoids are compounds that are biotransformed to inactive and non-toxic metabolites and have fewer side effects than traditional glucocorticoids. A new class of 17β-carboxamide steroids has been recently introduced by our group. In this study, local anti-inflammatory activity of these derivatives was evaluated by use of the croton oil-induced ear edema test. Glucocorticoids with the highest maximal edema inhibition (MEI) were pointed out, and the systemic side effects of those with the lowest EC50 values were significantly lower in comparison to dexamethasone...
April 18, 2017: Archiv der Pharmazie
https://www.readbyqxmd.com/read/28414172/lccl-protein-complex-formation-in-plasmodium-is-critically-dependent-on-lap1
#14
Annie Z Tremp, Vikram Sharma, Victoria Carter, Edwin Lasonder, Johannes T Dessens
Successful sporogony of Plasmodium berghei in vector mosquitoes requires expression of a family of six modular proteins named LCCL lectin domain adhesive-like proteins (LAPs). The LAPs share a subcellular localization in the crystalloid, a unique parasite organelle that forms during ookinete development. Here, LAP interactions in P. berghei were studied using a series of parasite lines stably expressing reporter-tagged LAPs combined with affinity purification and high accuracy label free quantitative mass spectrometry...
April 13, 2017: Molecular and Biochemical Parasitology
https://www.readbyqxmd.com/read/28412198/potential-role-of-lycopene-in-targeting-proprotein-convertase-subtilisin-kexin-type-9-to-combat-hypercholesterolemia
#15
Sahir Sultan Alvi, Irfan A Ansari, Imran Khan, Johar Iqbal, M Salman Khan
Proprotein convertase subtilisin/kexin type 9 (PCSK-9) is a serine protease of the proprotien convertase (PC) family that has profound effects on plasma low density lipoprotein cholesterol (LDL-C) levels, the major risk factor for coronary heart disease (CHD), through its ability to mediate LDL receptor (LDL-R) protein degradation and reduced recycling to the surface of hepatocytes. Thus, the current study was premeditated not only to evaluate the role of lycopene in targeting the inhibition of PCSK-9 via modulation of genes involved in cholesterol homeostasis in HFD rats but also to examine a correlation between HFD induced inflammatory cascades and subsequent regulation of PCSK-9 expression...
April 12, 2017: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/28411541/spectroscopic-and-molecular-modeling-approaches-to-investigate-the-interaction-of-bisphenol-a-bisphenol-f-and-their-diglycidyl-ethers-with-ppar%C3%AE
#16
Jie Zhang, Tiehua Zhang, Tianzhu Guan, Ping Ruan, Dayong Ren, Weichang Dai, Hansong Yu, Tiezhu Li
A fluorescence polarization (FP) assay for the simultaneous determination of bisphenol A (BPA), bisphenol F (BPF), bisphenol A diglycidyl ether (BADGE) and bisphenol F diglycidyl ether (BFDGE) was developed. The method was based on the competition between bisphenols (BPs) and fluorescein-labeled dexamethasone derivative (Dex-fl) for mouse peroxisome proliferator-activated receptor α ligand binding domain (mPPARα-LBD). A recombinant soluble protein derivative mPPARα-LBD* was prepared, then in vitro binding of 4 BPs to mPPARα-LBD* was investigated...
April 9, 2017: Chemosphere
https://www.readbyqxmd.com/read/28409274/toward-molecular-imaging-of-the-free-fatty-acid-receptor-1
#17
Ewa Hellström-Lindahl, Ola Åberg, Cecilia Ericsson, Gavin O'Mahony, Peter Johnström, Stanko Skrtic, Olof Eriksson
AIMS: Molecular imaging of the free fatty acid receptor 1 (FFAR1) would be a valuable tool for drug development by enabling in vivo target engagement studies in human. It has also been suggested as a putative target for beta cell imaging, but the inherent lipophilicity of most FFAR1 binders produces high off-target binding, which has hampered progress in this area. The aim of this study was to generate a suitable lead compound for further PET labeling. METHODS: In order to identify a lead compound for future PET labeling for quantitative imaging of FFAR1 in human, we evaluated tritiated small molecule FFAR1 binding probes ([(3)H]AZ1, [(3)H]AZ2 and [(3)H]TAK-875) for their off-target binding, receptor density and affinity in human pancreatic tissue (islets and exocrine) and rodent insulinoma...
April 13, 2017: Acta Diabetologica
https://www.readbyqxmd.com/read/28405240/targeting-the-ubiquitin-conjugating-enzyme-e2d4-for-cancer-drug-discovery-a-structure-based-approach
#18
Vishwanath Ramatenki, Ramakrishna Dumpati, Rajender Vadija, Santhiprada Vellanki, Sarita Rajender Potlapally, Rohini Rondla, Uma Vuruputuri
Cancer progression is a global burden. The incidence and mortality now reach 30 million deaths per year. Several pathways of cancer are under investigation for the discovery of effective therapeutics. The present study highlights the structural details of the ubiquitin protein 'Ubiquitin-conjugating enzyme E2D4' (UBE2D4) for the novel lead structure identification in cancer drug discovery process. The evaluation of 3D structure of UBE2D4 was carried out using homology modelling techniques. The optimized structure was validated by standard computational protocols...
April 2017: Journal of Chemical Biology
https://www.readbyqxmd.com/read/28402272/ginkgolic-acids-inhibit-migration-in-breast-cancer-cells-by-inhibition-of-nemo-sumoylation-and-nf-%C3%AE%C2%BAb-activity
#19
Sami Hamdoun, Thomas Efferth
Ginkgolic acids (GA), a group of alkyl phenols found in crude extracts of Ginkgo biloba leaves, are known to have anticancer activity, but their mode of action is not well understood. Our aim in this study was to investigate the anti-migratory activity of seven GA against breast cancer cells and to determine the molecular mechanism behind this activity. All seven GA and their mixture inhibited wound healing in MCF-7 and MDA-MB 231 breast cancer cells. None of the compounds nor the mixture showed cytotoxicity towards the two cell lines, if tested by the resazurin assay...
March 28, 2017: Oncotarget
https://www.readbyqxmd.com/read/28401609/platinum-based-organometallic-folders-for-the-recognition-of-electron-deficient-aromatic-substrates
#20
Eduardo Victor Peris, Daniel Nuevo, Sergio Gonell, Macarena Poyatos
A series of platinum complexes with cis-oriented polyaromatic N-heterocyclic carbene ligands were prepared and characterized. The relative disposition of the polyaromatic ligands about the metal make these compounds to behave as a metallofolder, with a pocket defined by the void space between the polyaromatic functionalities. The complexes were used as receptors of organic molecules, where they showed selective affinity for binding electron-deficient aromatic substrates, such as 1,2,4,5-tetracyanobenzene (TCNB), 2,4,7-trinitro-9-fluorenone (NTFLU) and 1,4,5,8-naphtalenetetracarboxylic dianhydride (NTCDA)...
April 12, 2017: Chemistry: a European Journal
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