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Ligands and binding

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https://www.readbyqxmd.com/read/28806774/fibroblast-growth-factor-receptor-1-mediates-internalization-of-pathogenic-spotted-fever-rickettsiae-into-host-endothelium
#1
Abha Sahni, Jignesh Patel, Hema P Narra, Casey L C Schroeder, David H Walker, Sanjeev K Sahni
Rickettsial infections continue to cause serious morbidity and mortality in severe human cases around the world. Host cell adhesion and invasion is an essential requisite for intracellular growth, replication, and subsequent dissemination of pathogenic rickettsiae. Heparan sulfate proteoglycans [HSPGs] facilitate the interactions between fibroblast growth factor(s) and their tyrosine kinase receptors resulting in receptor dimerization/activation and have been implicated in bacterial adhesion to target host cells...
2017: PloS One
https://www.readbyqxmd.com/read/28806750/characterization-of-novel-bangle-lectin-from-photorhabdus-asymbiotica-with-dual-sugar-binding-specificity-and-its-effect-on-host-immunity
#2
Gita Jančaříková, Josef Houser, Pavel Dobeš, Gabriel Demo, Pavel Hyršl, Michaela Wimmerová
Photorhabdus asymbiotica is one of the three recognized species of the Photorhabdus genus, which consists of gram-negative bioluminescent bacteria belonging to the family Morganellaceae. These bacteria live in a symbiotic relationship with nematodes from the genus Heterorhabditis, together forming a complex that is highly pathogenic for insects. Unlike other Photorhabdus species, which are strictly entomopathogenic, P. asymbiotica is unique in its ability to act as an emerging human pathogen. Analysis of the P...
August 14, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28806698/fluorescence-and-electron-paramagnetic-resonance-studies-of-norfloxacin-and-n-donor-mixed-ligand-ternary-copper-ii-complexes-stability-and-interaction-with-sds-micelles
#3
Gabriel S Vignoli Muniz, Jimmy Llontop Incio, Odivaldo C Alves, Klaus Krambrock, Letícia R Teixeira, Sonia R W Louro
The stability of ternary copper(II) complexes of a heterocyclic ligand, L (L being 2,2'-bipyridine (bipy) or 1,10-phenanthroline (phen)) and the fluorescent antibacterial agent norfloxacin (NFX) as the second ligand was studied at pH7.4 and different ionic strengths. Fluorescence quenching upon titration of NFX with the binary complexes allowed to obtain stability constants for NFX binding, Kb, as a function of ionic strength. The Kb values vary by more than two orders of magnitude when buffer concentration varies from 0...
August 5, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/28806645/evaluation-of-the-binding-of-four-anti-tumor-casiope%C3%A3-nas%C3%A2-to-human-serum-albumin
#4
Isabel Correia, Sladjana Borovic, Isabel Cavaco, Cristina P Matos, Somnath Roy, Hugo M Santos, Luz Fernandes, José L Capelo, Lena Ruiz-Azuara, João Costa Pessoa
The metal complexes designated by Casiopeínas® are mixed-ligand Cu(II)-compounds some of them having promising antineoplastic properties. We report studies of binding of Cu(glycinato)(4,7-dimethyl-1,10-phenanthroline) (Cas-II-Gly (1)), Cu(acetylacetonato)(4,7-dimethyl-1,10-phenanthroline) (Cas-III-Ea (2)), Cu(glycinato)(4,4'-dimethyl-2,2'-bipyridine) (Cas-IV-Gly (3)) and Cu(acetylacetonato)(4,4'-dimethyl-2,2'-bipyridine) (Cas-III-ia (4)) to human serum albumin (HSA) by circular dichroism (CD), Electron paramagnetic resonance (EPR) and fluorescence spectroscopy...
July 29, 2017: Journal of Inorganic Biochemistry
https://www.readbyqxmd.com/read/28806644/effects-of-the-fluorine-substituent-positions-of-the-intercalating-ligands-on-the-binding-behavior-and-third-strand-stabilization-of-two-ru-ii-complexes-toward-poly-u-%C3%A2-poly-a-poly-u-triplex-rna
#5
Mengna Peng, Wen Ni, Lifeng Tan
Two new Ru(II) polypyridyl complexes containing fluorine substituents, [Ru(bpy)2(o-fpip)](2+) (Ru1, bpy=2,2'-bipyridine, o-fpip=2-(2-fluorophenyl)imidazo[4,5-f] [1,10]phenanthroline) and [Ru(bpy)2(p-fpip)](2+) (Ru2, p-fpip=2-(4-fluorophenyl)imidazo[4,5-f] [1,10]phenanthroline) have been synthesized as binders for poly(U)•poly(A)∗poly(U) triplex RNA. The binding of the two complexes with the triplex RNA has been investigated by spectroscopic methods and viscosity measurements. Analysis of the electronic absorption spectra indicates that the association of intercalating Ru2 with the triplex RNA is greater than that of Ru1, which is also supported by spectroscopic titrations and viscosity measurements...
August 8, 2017: Journal of Inorganic Biochemistry
https://www.readbyqxmd.com/read/28806153/expression-purification-and-refolding-of-human-lipocalin-6-and-production-of-a-monoclonal-antibody-against-this-protein
#6
Jiong Chen, Wei Feng, Yue Zhao, Yaqin Li, Fei Zhan
Human lipocalin 6 (hLCN6) is a member of the lipocalin family, which is a group of structurally conserved hydrophobic ligand binding proteins, and widely distributed in animal, plant, and bacteria. Specific expression of hLCN6 in the epididymis and localization of this protein on the surface of spermatozoa suggest a role played by hLCN6, which may function as a transporter to carry ligands in the epididymal channel. However, the role of hLCN6 in sperm maturation has been largely unknown due to the lack of effective antibodies...
August 2017: Monoclonal Antibodies in Immunodiagnosis and Immunotherapy
https://www.readbyqxmd.com/read/28806087/size-dependent-relationships-between-protein-stability-and-thermal-unfolding-temperature-have-important-implications-for-analysis-of-protein-energetics-and-high-throughput-assays-of-protein-ligand-interactions
#7
Matthew Douglas Watson, Jeremy Monroe, Daniel P Raleigh
Changes in protein stability are commonly reported as changes in the melting temperature, ΔTM, or as changes in unfolding free energy at a particular temperature, ΔΔG°. Using data for 1124 mutants from 16 proteins we examine the relationship between ΔΔG° and ΔTM. A linear relationship is observed for each protein. The slopes of the plots of ΔTM vs ΔΔG° for different proteins scale as N(-1) where N is the number of residues in the protein. Thus, a given change in ΔG° causes a much larger change in TM for a small protein relative to the effect observed for a large protein...
August 14, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28806050/linking-high-throughput-screens-to-identify-moas-and-novel-inhibitors-of-mycobacterium-tuberculosis-dihydrofolate-reductase
#8
John P Santa Maria, Yumi Park, Lihu Yang, Nicholas Murgolo, Michael D Altman, Paul Zuck, Greg Adam, Chad Chamberlin, Peter Saradjian, Peter Dandliker, Helena I M Boshoff, Clifton E Barry, Charles Garlisi, David B Olsen, Katherine Young, Meir Glick, Elliott Nickbarg, Peter S Kutchukian
Though phenotypic and target-based high-throughput screening approaches have been employed to discover new antibiotics, the identification of promising therapeutic candidates remains challenging. Each approach provides different information, and understanding their results can provide hypotheses for mechanism of action (MoA) and reveal actionable chemical matter. Here we describe a framework for identifying efficacy targets of bioactive compounds. High throughput biophysical profiling against a broad range of targets coupled with machine learning is employed to identify chemical features with predicted efficacy targets for a given phenotypic screen...
August 14, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28805972/in-vitro-pharmacological-characterization-of-a-novel-unbiased-nop-receptor-selective-nonpeptide-agonist-at-403
#9
Federica Ferrari, Davide Malfacini, Blair V Journigan, Mark F Bird, Claudio Trapella, Remo Guerrini, David G Lambert, Girolamo Calo', Nurulain T Zaveri
Nociceptin/orphanin FQ (N/OFQ) regulates several biological functions via selective activation of the N/OFQ receptor (NOP), a member of the opioid receptor family. We recently identified a new high affinity and highly selective NOP agonist AT-403. In this study, we characterized the functional profile of AT-403 and compared it to other known nonpeptide NOP agonists Ro 65-6570, Ro 2q, SCH-221510, MCOPPB, AT-202 and SCH-486757, using the following assays: GTPγ[(35) S] stimulated binding, calcium mobilization assay in cells-expressing human NOP or classical opioid receptors and chimeric G proteins, bioluminescence resonance energy transfer (BRET) based assay for studying NOP receptor interaction with G protein and arrestin, and the electrically stimulated mouse vas deferens bioassay...
August 2017: Pharmacology Research & Perspectives
https://www.readbyqxmd.com/read/28805744/aptamer-cell-based-selection-overview-and-advances
#10
REVIEW
Silvia Catuogno, Carla Lucia Esposito
Aptamers are high affinity single-stranded DNA/RNA molecules, produced by a combinatorial procedure named SELEX (Systematic Evolution of Ligands by Exponential enrichment), that are emerging as promising diagnostic and therapeutic tools. Among selection strategies, procedures using living cells as complex targets (referred as "cell-SELEX") have been developed as an effective mean to generate aptamers for heavily modified cell surface proteins, assuring the binding of the target in its native conformation. Here we give an up-to-date overview on cell-SELEX technology, discussing the most recent advances with a particular focus on cancer cell targeting...
August 14, 2017: Biomedicines
https://www.readbyqxmd.com/read/28805386/solvation-effect-on-complexation-of-alkali-metal-cations-by-a-calix-4-arene-ketone-derivative
#11
Josip Pozar, Ivana Niksic-Franjic, Marija Cvetnic, Katarina Leko, Nikola Cindro, Katarina Piculjan, Ivana Borilovic, Leo Frkanec, Vladislav Tomisic
The medium effect on the complexation of alkali metal cations with a calix[4]arene ketone derivative (L) was systematically examined in methanol, ethanol, N-methylformamide, N,N-dimethylformamide, dimethyl sulfoxide, and acetonitrile. In all solvents the binding of Na+ cation by L was rather efficient, whereas the complexation of other alkali metal cations was observed only in methanol and acetonitrile. Complexation reactions were enthalpically controlled, while ligand dissolution was endothermic in all cases...
August 14, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28805376/discovery-and-biosensing-applications-of-diverse-rna-cleaving-dnazymes
#12
Meng Liu, Dingran Chang, Yingfu Li
DNA-based enzymes, or DNAzymes, are not known to exist in Nature but can be isolated from random-sequence DNA pools using test tube selection techniques. Since the report of the first DNAzyme in 1994, many catalytic DNA molecules for catalyzing wide-ranging chemical transformations have been isolated and studied. Our laboratory has a keen interest in searching for diverse DNAzymes capable of cleaving RNA-containing substrates, determining their sequence requirements and structural properties, and examining their potential as biosensors...
August 14, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28805355/sensing-mg-2-contributes-to-the-resistance-of-pseudomonas-aeruginosa-to-complement-mediated-opsonophagocytosis
#13
Mohammad Qadi, Sofía Izquierdo-Rabassa, Margalida Mateu Borrás, Antonio Doménech-Sánchez, Carlos Juan, Joanna B Goldberg, Robert E W Hancock, Sebastián Albertí
Pseudomonas aeruginosa adaptation to survive in the host hinges on its ability to probe the environment and respond appropriately. Rapid adaptation is often mediated by two-component regulatory systems, such as the PhoP/PhoQ system that responds to Mg(2+) ion concentration. However, there is limited information about the role of PhoQ in P. aeruginosa bloodstream infections. We used a murine model of systemic infection to test the virulence of a PhoQ-deficient mutant. Mutation of PhoQ impaired the virulence and the ability to cause bacteremia of P...
August 14, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28805144/a-qm-protein-ligand-investigation-of-anti-psychotic-drugs-with-the-dopamine-d2-receptor-d2r
#14
Ramin Ekhteiari Salmas, Yusuf Serhat Is, Serdar Durdagi, Matthias Stein, Mine Yurtsever
The dopamine D2 Receptor (D2R) is a member of the G-Protein Coupled Receptor (GPCR) family and plays a critical role in neurotransmission activities in the human brain. Dysfunction in dopamine receptor signaling may lead to mental health illnesses such as schizophrenia and Parkinson's disease. D2R is the target protein of the commonly used anti-psychotic drugs such as risperidone, clozapine, aripiprazole, olanzapine, ziprasidone and quetiapine. Due to their significant side effects and nonselective profiles, the discovery of novel drugs has become a challenge for researchers working in this field...
August 14, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28805060/substrate-induced-facilitated-dissociation-of-competitive-inhibitor-from-the-active-site-of-o-acetyl-serine-sulfhydrylase-reveal-a-competitive-allostery-mechanism
#15
Appu Kumar Singh, Mary Krishna Ekka, Abhishek Kaushik, Vaibhav Kumar Pandya, Ravi Pratap Singh, Srijita Banerjee, Monica Mittal, Vijay Singh, Sangaralingam Kumaran
By classical competitive-antagonism, substrate and competitive-inhibitor must bind mutually exclusively to the active site. The competitive inhibition of O-acetyl serine sulfhydrylase (OASS) by C-terminal of serine acetyltransferase (SAT) presents a paradox, because the C-terminal of SAT binds to the active site of OASS with 4-6 log fold (104 -106) more affinity than that of the substrate. Therefore, we employed multiple approaches to understand how substrate gains access to OASS active site under physiological conditions...
August 14, 2017: Biochemistry
https://www.readbyqxmd.com/read/28805059/probing-membrane-receptor-ligand-specificity-with-surface-and-tip-enhanced-raman-scattering
#16
Lifu Xiao, Karen A Bailey, Hao Wang, Zachary D Schultz
The specific interaction between a ligand and a protein is a key component in minimizing off-target effects in drug discovery. Investigating these interactions with membrane protein receptors can be quite challenging. In this report, we show how spectral variance observed in surface-enhanced Raman scattering (SERS) and tip-enhanced Raman scattering (TERS) can be correlated with ligand specificity in affinity-based assays. Variations in the enhanced Raman spectra of three peptide ligands (i.e. cyclic-RGDFC, cyclic-isoDGRFC, and CisoDGRC), which have different binding affinity to αvβ3 integrin, are reported from isolated proteins and from receptors in intact cancer cell membranes...
August 14, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28804547/epha2-targeted-intratumoral-therapy-for-non-small-cell-lung-cancer-using-albumin-mesospheres
#17
Hung-Yen Lee, Kamal A Mohammed, Fredric Kaye, Brij M Moudgil, Najmunnisa Nasreen
Lung cancer, primarily non-small cell lung cancer (NSCLC), is the leading cause of cancer mortality and the prognosis of patients with advanced or metastatic NSCLC is poor. Despite significant advances in diagnosis and treatment, little improvement has been seen in NSCLC mortality. Recently, Intratumoral Chemotherapy, a direct local delivery of chemotherapeutic drugs, has shown promise in clinical studies. However, toxicity and high dosage of chemotherapeutic agents used for treatment are a limitation. Moreover, these drugs damage indiscriminately, cancerous as well as normal tissues...
2017: American Journal of Translational Research
https://www.readbyqxmd.com/read/28804489/normalized-synergy-predicts-that-cd8-co-receptor-contribution-to-t-cell-receptor-tcr-and-pmhc-binding-decreases-as-tcr-affinity-increases-in-human-viral-specific-t-cells
#18
Chad M Williams, Alexandra A Schonnesen, Shu-Qi Zhang, Ke-Yue Ma, Chenfeng He, Tori Yamamoto, S Gail Eckhardt, Christopher A Klebanoff, Ning Jiang
The discovery of naturally occurring T cell receptors (TCRs) that confer specific, high-affinity recognition of pathogen and cancer-associated antigens remains a major goal in cellular immunotherapies. The contribution of the CD8 co-receptor to the interaction between the TCR and peptide-bound major histocompatibility complex (pMHC) has previously been correlated with the activation and responsiveness of CD8(+) T cells. However, these studies have been limited to model systems of genetically engineered hybridoma TCRs or transgenic mouse TCRs against either a single epitope or an array of altered peptide ligands...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28803976/canavalia-bonariensis-lectin-molecular-bases-of-glycoconjugates-interaction-and-antiglioma-potential
#19
Benildo Sousa Cavada, Mayara Torquato Lima Silva, Vinicius Jose Silva Osterne, Vanir Reis Pinto-Junior, Ana Paula Machado do Nascimento, Ingrid Alessandra Victoria Wolin, Isabella Aparecida Heinrich, Clareane Avelino Simplicio Nobre, Cleane Gomes Moreira, Claudia Figueiredo Lossio, Cintia Renata Costa Rocha, Jorge Luiz Martins, Kyria Santiago Nascimento, Rodrigo Bainy Leal
CaBo is a mannose/glucose-specific lectin purified from seeds of Canavalia bonariensis. In the present work, we report the CaBo crystal structure determined to atomic resolution in the presence of X-man, a specific ligand. Similar to the structural characteristics of other legume lectins, CaBo presented the jellyroll motif, a metal binding site occupied by calcium and manganese ions close to the carbohydrate-recognition domain (CRD). In vitro test of CaBo cytotoxicity against glioma cells demonstrated its ability to decrease the cellular viability and migration by induction of autophagy and cell death...
August 10, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28803967/igdb-2-an-ig-fniii-protein-binds-the-ion-channel-lgc-34-and-controls-sensory-compartment-morphogenesis-in-c-elegans
#20
Wendy Wang, Elliot A Perens, Grigorios Oikonomou, Yun Lu, Shai Shaham
Sensory organ glia surround neuronal receptive endings (NREs), forming a specialized compartment important for neuronal activity, and reminiscent of glia-ensheathed synapses in the central nervous system. We previously showed that DAF-6, a Patched-related protein, is required in glia of the C. elegans amphid sensory organ to restrict sensory compartment size. LIT-1, a Nemo-like kinase, and SNX-1, a retromer component, antagonize DAF-6 and promote compartment expansion. To further explore the machinery underlying compartment size control, we sought genes whose inactivation restores normal compartment size to daf-6 mutants...
August 10, 2017: Developmental Biology
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