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MicroScale Thermophoresis

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https://www.readbyqxmd.com/read/29160851/development-of-an-impedimetric-aptasensor-for-the-detection-of-staphylococcus-aureus
#1
Peggy Reich, Regina Stoltenburg, Beate Strehlitz, Dieter Frense, Dieter Beckmann
In combination with electrochemical impedance spectroscopy, aptamer-based biosensors are a powerful tool for fast analytical devices. Herein, we present an impedimetric aptasensor for the detection of the human pathogen Staphylococcus aureus. The used aptamer targets protein A, a surface bound virulence factor of S. aureus. The thiol-modified protein A-binding aptamer was co-immobilized with 6-mercapto-1-hexanol onto gold electrodes by self-assembly. Optimization of the ratio of aptamer to 6-mercapto-1-hexanol resulted in an average density of 1...
November 21, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29159976/design-and-study-of-lipopeptide-inhibitors-on-preventing-aggregation-of-human-islet-amyloid-polypeptide-residues-11-20
#2
Yexuan Mao, Lanlan Yu, Mengfan Mao, Chuanguo Ma, Lingbo Qu
Type 2 diabetes mellitus, a kind of conformational disease, has become an epidemic disease, which seriously endangers the quality of life and health of human beings. The deposition of human islet amyloid polypeptide (hIAPP) has been considered as one of the major pathological features of type 2 diabetes mellitus. As lipopeptides have some hydrophobic groups, which are similar to the reported aggregation inhibitors, and some lipopeptides could prevent cells from depositing of amyloid fibrils, several potential lipopeptide inhibitors have been engineered and synthesized, which have been assessed for their inhibitory effect in preventing amyloid fibrils formation of hIAPP11-20 by using the conventional thioflavin-T fluorescence assay and new technique microscale thermophoresis (MST)...
November 21, 2017: Journal of Peptide Science: An Official Publication of the European Peptide Society
https://www.readbyqxmd.com/read/29132826/use-of-chromatographic-and-electrophoretic-tools-for-assaying-elastase-collagenase-hyaluronidase-and-tyrosinase-activity
#3
REVIEW
Syntia Fayad, Philippe Morin, Reine Nehmé
Elastase, collagenase, hyaluronidase and tyrosinase, are very interesting enzymes due to their direct implication in skin aging and as therapeutic hits. Different techniques can be used to study these enzymes and to evaluate the influence of effectors on their kinetics. Nowadays, analytical techniques have become frequently used tools for miniaturizing enzyme assays. The main intention of this article is to review chromatographic and electrophoretic tools that study the four enzymes above mentioned. More specifically, the use of high-performance liquid chromatography and capillary electrophoresis and their derivative techniques for monitoring these enzymes will be investigated...
November 9, 2017: Journal of Chromatography. A
https://www.readbyqxmd.com/read/29123130/binding-of-mycotoxins-to-proteins-involved-in-neuronal-plasticity-a-combined-in-silico-wet-investigation
#4
Bernardina Scafuri, Antonio Varriale, Angelo Facchiano, Sabato D'Auria, Maria Elisabetta Raggi, Anna Marabotti
We have applied a combined computational procedure based on inverse and direct docking in order to identify putative protein targets of a panel of mycotoxins and xenobiotic compounds that can contaminate food and that are known to have several detrimental effects on human health. This procedure allowed us to identify a panel of human proteins as possible targets for aflatoxins, gliotoxin, ochratoxin A and deoxynivalenol. Steady-state fluorescence and microscale thermophoresis experiments allowed us to confirm the binding of some of these mycotoxins to acetylcholinesterase and X-linked neuroligin 4, two proteins involved in synapse activity and, particularly for the second protein, neuronal plasticity and development...
November 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29107641/genetic-coding-algorithm-for-sense-and-antisense-peptide-interactions
#5
Nikola Štambuk, Paško Konjevoda, Petra Turčić, Katalin Kövér, Renata Novak Kujundžić, Zoran Manojlović, Mario Gabričević
Sense and antisense peptides, i.e. peptides specified by complementary DNA and RNA sequences, interact with increased probability. Biro, Blalock, Mekler, Root-Bernstein and Siemion investigated the recognition rules of peptide-peptide interaction based on the complementary coding of DNA and RNA sequences in 3'→5' and 5'→3' directions. After more than three decades of theoretical and experimental investigations, the efficiency of this approach to predict peptide-peptide binding has been experimentally verified for more than 50 ligand-receptor systems, and represents a promising field of research...
October 28, 2017: Bio Systems
https://www.readbyqxmd.com/read/29072708/preparation-of-glycoconjugates-from-unprotected-carbohydrates-for-protein-binding-studies
#6
Christian T Hjuler, Nicolai N Maolanon, Jørgen Sauer, Jens Stougaard, Mikkel B Thygesen, Knud J Jensen
Glycobiology, in particular the study of carbohydrate-protein interactions and the events that follow, has become an important research focus in recent decades. To study these interactions, many assays require homogeneous glycoconjugates in suitable amounts. Their synthesis is one of the methodological challenges of glycobiology. Here, we describe a versatile, three-stage protocol for the formation of glycoconjugates from unprotected carbohydrates, including those purified from natural sources, as exemplified here by rhizobial Nod factors and exopolysaccharide fragments...
November 2017: Nature Protocols
https://www.readbyqxmd.com/read/29054528/using-two-site-binding-models-to-analyze-microscale-thermophoresis-data
#7
Shih-Chia Tso, Qiuyan Chen, Sergey A Vishnivetskiy, Vsevolod V Gurevich, T M Iverson, Chad A Brautigam
The emergence of microscale thermophoresis (MST) as a technique for determining the dissociation constants for bimolecular interactions has enabled these quantities to be measured in systems that were previously difficult or impracticable. However, most models for analyses of these data featured the assumption of a simple 1:1 binding interaction. The only model widely used for multiple binding sites was the Hill equation. Here, we describe two new MST analytic models that assume a 1:2 binding scheme: the first features two microscopic binding constants (KD(1) and KD(2)), while the other assumes symmetry in the bivalent molecule, culminating in a model with a single macroscopic dissociation constant (KD,M) and a single factor (α) that accounts for apparent cooperativity in the binding...
October 17, 2017: Analytical Biochemistry
https://www.readbyqxmd.com/read/29052990/spatial-screening-of-hemagglutinin-on-influenza-a-virus-particles-sialyl-lacnac-displays-on-dna-and-peg-scaffolds-reveal-the-requirements-for-bivalency-enhanced-interactions-with-weak-monovalent-binders
#8
Victor Bandlow, Susanne Liese, Daniel Lauster, Kai Ludwig, Roland R Netz, Andreas Herrmann, Oliver Seitz
Attachment of the Influenza A virus onto host cells involves multivalent interactions between virus surface hemagglutinin (HA) and sialoside-containing glyco ligands. Despite the development of extremely powerful multivalent binders of the Influenza virus and other viruses, comparably little is known about the optimal spacing of HA ligands, which ought to bridge binding sites within or across the trimeric HA molecules. To explore the criteria for ligand economical high affinity binding, we systematically probed distance-affinity relationships by means of two differently behaving scaffold types based on (i) flexible polyethylene glycol (PEG) conjugates and (ii) rigid self-assembled DNA·PNA complexes...
November 15, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29048271/microscale-thermophoresis-mst-for-studying-actin-polymerization-kinetics
#9
Andrea Topf, Peter Franz, Georgios Tsiavaliaris
Here, we present a MicroScale Thermophoresis (MST)-based assay for in vitro assessment of actin polymerization. By monitoring the thermophoretic behavior of ATTO488-labeled actin in a temperature gradient over time, we could follow polymerization in real time and resolve its three characteristic phases: nucleation, elongation, and steady-state equilibration. Titration experiments allowed us to evaluate the effects of actin-binding proteins (ABPs) on polymerization, including DNase I-induced inhibition and mDia2FH1FH2 (mDia2)-assisted acceleration of nucleation...
October 1, 2017: BioTechniques
https://www.readbyqxmd.com/read/29031064/fragment-based-approach-to-identify-ido1-inhibitor-building-blocks
#10
Alice Coletti, Francesca Camponeschi, Elisa Albini, Francesco Antonio Greco, Vincenzo Maione, Chiara Custodi, Federica Ianni, Ursula Grohmann, Ciriana Orabona, Francesca Cantini, Antonio Macchiarulo
Indoleamine 2,3-dioxygenase 1 (IDO1) is attracting a great deal of interest as drug target in immune-oncology being highly expressed in cancer cells and participating to the tumor immune-editing process. Although several classes of IDO1 inhibitors have been reported in literature and patent applications, only few compounds have proved optimal pharmacological profile in preclinical studies to be advanced in clinical trials. Accordingly, the quest for novel structural classes of IDO1 inhibitors is still open...
December 1, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29024298/detailed-evidence-for-an-unparalleled-interaction-mode-between-calmodulin-and-orai-proteins
#11
Lukas Traxler, Petr Rathner, Marc Fahrner, Michael Stadlbauer, Felix Faschinger, Tatsiana Charnavets, Norbert Müller, Christoph Romanin, Peter Hinterdorfer, Hermann J Gruber
Calmodulin (CaM) binds most of its targets by wrapping around an amphipathic α-helix. The N-terminus of Orai proteins contains a conserved CaM-binding segment but the binding mechanism has been only partially characterized. Here, microscale thermophoresis (MST), surface plasmon resonance (SPR), and atomic force microscopy (AFM) were employed to study the binding equilibria, the kinetics, and the single-molecule interaction forces involved in the binding of CaM to the conserved helical segments of Orai1 and Orai3...
October 11, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28986788/microscale-thermophoresis-a-rapid-and-precise-method-to-quantify-protein-nucleic-acid-interactions-in-solution
#12
Adrian Michael Mueller, Dennis Breitsprecher, Stefan Duhr, Philipp Baaske, Thomas Schubert, Gernot Längst
Interactions between nucleic acids and proteins are driving gene expression programs and regulating the development of organisms. The binding affinities of transcription factors to their target sites are essential parameters to reveal their binding site occupancy and function in vivo. Microscale Thermophoresis (MST) is a rapid and precise method allowing for quantitative analysis of molecular interactions in solution on a microliter scale. The technique is based on the movement of molecules in temperature gradients, which is referred to as thermophoresis, and depends on molecule size, charge, and hydration shell...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28956389/-identification-of-cyclic-di-gmp-protein-receptors-high-throughput-screening-strategies-and-experimental-verification
#13
Shouting Cheng, Fangfang Wang, Wei Qian
cyclic di-GMP (c-di-GMP) is a universal second messenger in bacterial cells. It regulates various biological processes such as biofilm development, pathogenicity, motility, exopolysaccharide (EPS) production and cell cycle. The second messenger exerts its function by binding to effectors, such as riboswitches and proteins. However, due to the diverse conformations of c-di-GMP, its effectors are hardly to be predicted by homology search. Identification of c-di-GMP effectors is the initial step to investigate its regulatory function in bacterial signal transduction, however, it remains to be a technically difficult task...
September 25, 2017: Sheng Wu Gong Cheng Xue Bao, Chinese Journal of Biotechnology
https://www.readbyqxmd.com/read/28943299/interaction-of-quindoline-derivative-with-telomeric-repeat-containing-rna-induces-telomeric-dna-damage-response-in-cancer-cells-through-inhibition-of-telomeric-repeat-factor-2
#14
Yan Zhang, Deying Zeng, Jiaojiao Cao, Mingxue Wang, Bing Shu, Guotao Kuang, Tian-Miao Ou, Jia-Heng Tan, Lian-Quan Gu, Zhi-Shu Huang, Ding Li
BACKGROUND: Telomeric repeat-containing RNA (TERRA) is a large non-coding RNA in mammalian cells, which forms an integral component of telomeric heterochromatin. TERRA can bind to an allosteric site of telomeric repeat factor 2 (TRF2), a key component of Shelterin that protect chromosome termini. Both TERRA and TRF2 have been recognized as promising new therapeutic targets for cancer treatment. METHODS: Our methods include FRET assay, SPR, CD, microscale thermophoresis (MST), enzyme-linked immunosorbent assay (ELISA), chromatin immunoprecipitation (ChIP), colony formation assays, Western blot, immunofluorescence, cell cycle arrest and apoptosis detection, and xCELLigence real-time cell analysis (RTCA)...
December 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28924040/a-b-z-junction-induced-by-an-a-a-mismatch-in-gac-repeats-in-the-gene-for-cartilage-oligomeric-matrix-protein-promotes-binding-with-the-hz%C3%AE-adar1-protein
#15
Narendar Kolimi, Yogeeshwar Ajjugal, Thenmalarchelvi Rathinavelan
GAC repeat expansion from five to seven in the exonic region of the gene for cartilage oligomeric matrix protein (COMP) leads to pseudoachondroplasia, a skeletal abnormality. However, the molecular mechanism by which GAC expansions in the COMP gene lead to skeletal dysplasias is poorly understood. Here, we used MD simulations which indicate that an A...A mismatch in a d(GAC)6.d(GAC)6 duplex induces negative supercoiling, leading to a local B-to-Z DNA transition. This transition facilitates the binding of d(GAC)7...
September 18, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28911862/fatty-acid-binding-protein-fabp-5-interacts-with-the-calnexin-cytoplasmic-domain-at-the-endoplasmic-reticulum
#16
Joanna Jung, Jessica Wang, Jody Groenendyk, Dukgyu Lee, Marek Michalak, Luis B Agellon
Calnexin is a type 1 integral endoplasmic reticulum membrane molecular chaperone with an endoplasmic reticulum luminal chaperone domain and a highly conserved C-terminal domain oriented to the cytoplasm. Fabp5 is a cytoplasmic protein that binds long-chain fatty acids and other lipophilic ligands. Using a yeast two-hybrid screen, immunoprecipitation, microscale thermophoresis analysis and cellular fractionation, we discovered that Fabp5 interacts with the calnexin cytoplasmic C-tail domain at the endoplasmic reticulum...
November 4, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28873526/characterization-and-effects-of-binding-of-food-derived-bioactive-phycocyanobilin-to-bovine-serum-albumin
#17
Simeon Minic, Dragana Stanic-Vucinic, Mirjana Radomirovic, Milica Radibratovic, Milos Milcic, Milan Nikolic, Tanja Cirkovic Velickovic
Phycocyanobilin (PCB) is a blue tetrapyrrole chromophore of C-phycocyanin, the main protein of the microalga Spirulina, with numerous proven health-related benefits. We examined binding of PCB to bovine serum albumin (BSA) and how it affects protein and ligand stability. Protein fluorescence quenching and microscale thermophoresis demonstrated high-affinity binding (Ka=2×10(6)M(-1)). Spectroscopic titration with molecular docking analysis revealed two binding sites on BSA, at the inter-domain cleft and at subdomain IB, while CD spectroscopy indicated stereo-selective binding of the P conformer of the pigment to the protein...
January 15, 2018: Food Chemistry
https://www.readbyqxmd.com/read/28838690/synthesis-and-antiviral-evaluation-of-novel-1-3-4-oxadiazole-thiadiazole-chalcone-conjugates
#18
Xiuhai Gan, Deyu Hu, Zhuo Chen, Yanjiao Wang, Baoan Song
A series of novel 1,3,4-oxadiazole/thiadiazole-chalcone conjugates were synthesized and their in vitro and in vivo antiviral activities were evaluated via microscale thermophoresis method and half-leaf method, respectively. The in vitro results indicated that compounds 7g, 7l, 8h, and 8l displayed good antiviral activity against TMV, with the binding constant values of 5.93, 6.15, 6.02, and 5.04μM, respectively, which were comparable to that of Ninnanmycin (6.78μM) and even better than that of Ribavirin (99...
September 15, 2017: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/28817778/the-oxidation-state-of-4fe4s-clusters-modulates-the-dna-binding-affinity-of-dna-repair-proteins
#19
Edmund C M Tse, Theodore J Zwang, Jacqueline K Barton
A central question important to understanding DNA repair is how certain proteins are able to search for, detect, and fix DNA damage on a biologically relevant time scale. A feature of many base excision repair proteins is that they contain [4Fe4S] clusters that may aid their search for lesions. In this paper, we establish the importance of the oxidation state of the redox-active [4Fe4S] cluster in the DNA damage detection process. We utilize DNA-modified electrodes to generate repair proteins with [4Fe4S] clusters in the 2+ and 3+ states by bulk electrolysis under an O2-free atmosphere...
August 29, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28771024/binding-properties-of-different-categories-of-ido1-inhibitors-a-microscale-thermophoresis-study
#20
Francesco Antonio Greco, Alice Coletti, Chiara Custodi, Daniela Dolciami, Alessandro Di Michele, Andrea Carotti, Maura Marinozzi, Nina Schlinck, Antonio Macchiarulo
AIM: Inhibition of IDO1 is a strategy pursued in the immune-oncology pipeline for the development of novel anticancer therapies. At odds with an ever-increasing number of inhibitors being disclosed in the literature and patent applications, only very few compounds have hitherto advanced in clinical settings. MATERIALS & METHODS: We have used MicroScale Thermophoresis analysis and docking calculations to assess on a quantitative basis the binding properties of distinct categories of inhibitors to IDO1...
August 2017: Future Medicinal Chemistry
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