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MicroScale Thermophoresis

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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
#1
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)...
September 21, 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
#2
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
#3
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...
September 11, 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
#4
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
#5
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
#6
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
#7
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 3, 2017: Future Medicinal Chemistry
https://www.readbyqxmd.com/read/28751219/structural-studies-with-bnsp-7-reveal-an-atypical-oligomeric-conformation-compared-to-phospholipases-a2-like-toxins
#8
Lino Fernando G de Lima, Rafael J Borges, Maria Alejandra Viviescas, Carlos A H Fernandes, Marcos R M Fontes
There are 2.5 million cases of snakebite per year and approximately 100,000 at 150,000 deaths. Thus, it is considered an important public health problem by the World Health Organization. Snakes from the Bothrops genus may cause severe local effects in the victims, so it is important to develop inhibitors to treat local effects in patients. In addition, approximately 30 different species of bothropic snakes have been described that may present differences in their venom composition. Small structural differences in the venom proteins may result in different ligands binding...
July 24, 2017: Biochimie
https://www.readbyqxmd.com/read/28721412/effect-of-ligand-binding-on-a-protein-with-a-complex-folding-landscape
#9
Hisham Mazal, Haim Aviram, Inbal Riven, Gilad Haran
Ligand binding to a protein can stabilize it significantly against unfolding. The variation of the folding free energy, ΔΔG(0), due to ligand binding can be derived from a simple reaction scheme involving exclusive binding to the native state. One obtains the following expression: , where Kd is the ligand dissociation constant and L is its concentration, R is the universal gas constant and T is the temperature. This expression has been shown to correctly describe experimental results on multiple proteins...
July 19, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28717148/human-ribosomal-p1-p2-heterodimer-represents-an-optimal-docking-site-for-ricin-a-chain-with-a-prominent-role-for-p1-c-terminus
#10
Przemysław Grela, Xiao-Ping Li, Patrycja Horbowicz, Monika Dźwierzyńska, Marek Tchórzewski, Nilgun E Tumer
The eukaryotic P-stalk contains two P1-P2 protein dimers with a conserved C- terminal domain (CTD) critical for the interaction with external factors. To understand the role of the individual CTD of human P1/P2 proteins, we examined the interaction of reconstituted human P-protein complexes and C-terminally truncated forms with ricin A chain (RTA), which binds to the stalk to depurinate the sarcin/ricin loop (SRL). The interaction between P-protein complexes and RTA was examined by surface plasmon resonance, isothermal titration calorimetry, microscale thermophoresis and bio-layer interferometry...
July 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28710278/phosphorylation-of-human-aquaporin-2-aqp2-allosterically-controls-its-interaction-with-the-lysosomal-trafficking-protein-lip5
#11
Jennifer Virginia Roche, Sabeen Survery, Stefan Kreida, Veronika Nesverova, Henry Ampah-Korsah, Maria Gourdon, Peter M T Deen, Susanna Törnroth-Horsefield
The interaction between the renal water channel aquaporin-2 (AQP2) and the lysosomal trafficking regulator-interacting protein LIP5 targets AQP2 to multivesicular bodies and facilitates lysosomal degradation. This interaction is part of a process that controls AQP2 apical membrane abundance in a vasopressin-dependent manner, allowing for urine volume adjustment. Vasopressin regulates phosphorylation at four sites within the AQP2 C terminus (Ser(256), Ser(261), Ser(264), and Thr(269)), of which Ser(256) is crucial and sufficient for AQP2 translocation from storage vesicles to the apical membrane...
September 1, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28698641/a-transcription-activator-like-effector-tal7-of-xanthomonas-oryzae-pv-oryzicola-activates-rice-gene-os09g29100-to-suppress-rice-immunity
#12
Lulu Cai, Yanyan Cao, Zhengyin Xu, Wenxiu Ma, Muhammad Zakria, Lifang Zou, Zaiquan Cheng, Gongyou Chen
Xanthomonas oryzae pv. oryzicola (Xoc) and X. oryzae pv. oryzae (Xoo) cause bacterial leaf streak (BLS) and bacterial leaf blight (BLB) in rice, respectively. Unlike Xoo, endogenous avirulence-resistance (avr-R) gene interactions have not been identified in the Xoc-rice pathosystem; however, both pathogens possess transcription activator-like effectors (TALEs) that are known to modulate R or S genes in rice. The transfer of individual tal genes from Xoc RS105 (hypervirulent) into Xoc YNB0-17 (hypovirulent) led to the identification of tal7, which suppressed avrXa7-Xa7 mediated defense in rice containing an Xa7 R gene...
July 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28681565/tubulin-acetylation-a-novel-functional-avenue-for-cdyl-in-sperm
#13
Sweta Parab, Veena Dalvi, Sushma Mylavaram, Abhipriya Kishore, Susan Idicula-Thomas, Shobha Sonawane, Priyanka Parte
Motility in sperm is driven by the flagella, the principal component of which is the axoneme. The microtubules which make up the 9 + 2 axoneme are composed of heterodimers of alpha and beta tubulins and undergo several post-translational modifications. We have earlier reported that HDAC6 functions as tubulin deacetylase in sperm and has a role in sperm movement. While exploring the specific tubulin acetyltransferase (TAT) in sperm, we observed the presence of Chromodomain Y-Like (CDYL), on the principal piece of rat spermatozoa which compelled us to explore its function in sperm...
July 6, 2017: Cytoskeleton
https://www.readbyqxmd.com/read/28674022/fsip1-binds-her2-directly-to-regulate-breast-cancer-growth-and-invasiveness
#14
Tong Liu, Hao Zhang, Li Sun, Danyu Zhao, Peng Liu, Meisi Yan, Neeha Zaidi, Sudeh Izadmehr, Animesh Gupta, Wahid Abu-Amer, Minna Luo, Jie Yang, Xunyan Ou, Yining Wang, Xuefeng Bai, Yan Wang, Maria I New, Mone Zaidi, Tony Yuen, Caigang Liu
Fibrous sheath interacting protein 1 (FSIP1), a spermatogenesis-related testicular antigen, is expressed in abundance in breast cancers, particularly in those overexpressing human epidermal growth factor receptor 2 (HER2); however, little is known about its role in regulating the growth and metastasis of breast cancer cells. We and others have shown previously that FSIP1 expression in breast cancer correlates positively with HER2-positivity, recurrence, and metastases and negatively with survival. Here, using coimmunoprecipitation and microscale thermophoresis, we find that FSIP1 binds to the intracellular domain of HER2 directly...
July 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28640595/detection-and-characterization-of-small-molecule-interactions-with-fibrillar-protein-aggregates-using-microscale-thermophoresis
#15
Emily Fisher, Yanyan Zhao, Robert Richardson, Malgorzata Janik, Alexander K Buell, Franklin I Aigbirhio, Gergely Tóth
Neurodegenerative diseases such as Parkinson's and Alzheimer's disease share the pathological hallmark of fibrillar protein aggregates. The specific detection of these protein aggregates by positron emission tomography (PET) in the patient brain can yield valuable information for diagnosis and disease progression. However, the identification of novel small compounds that bind fibrillar protein aggregates has been a challenge. In this study, microscale thermophoresis (MST) was applied to assess the binding affinity of known small molecule ligands of α-synuclein fibrils, which were also tested in parallel in a thioflavin T fluorescence competition assay for further validation...
July 6, 2017: ACS Chemical Neuroscience
https://www.readbyqxmd.com/read/28616954/surface-charge-and-particle-size-determine-the-metabolic-fate-of-dendritic-polyglycerols
#16
Kritee Pant, Johanna Pufe, Kristof Zarschler, Ralf Bergmann, Jörg Steinbach, Sabine Reimann, Rainer Haag, Jens Pietzsch, Holger Stephan
Dendritic polyglycerols (dPG) are water soluble, polyether-based nanomaterials which hold great potential in diagnostic as well as therapeutic applications. In order to translate them for in vivo applications, a systematic assessment regarding their cell and tissue interactions as well as their metabolic fate in vivo is a crucial step. Herein, we explore the structure-activity relationship of three different sizes (ca. 3, 5, and 10 nm) of neutral dendritic polyglycerol (dPG) and their corresponding negatively charged sulfate analogs (dPGS) on their in vitro and in vivo characteristics...
June 29, 2017: Nanoscale
https://www.readbyqxmd.com/read/28594954/the-monoclonal-s9-6-antibody-exhibits-highly-variable-binding-affinities-towards-different-r-loop-sequences
#17
Fabian König, Thomas Schubert, Gernot Längst
The monoclonal antibody S9.6 is a widely-used tool to purify, analyse and quantify R-loop structures in cells. A previous study using the surface plasmon resonance technology and a single-chain variable fragment (scFv) of S9.6 showed high affinity (0.6 nM) for DNA-RNA and also a high affinity (2.7 nM) for RNA-RNA hybrids. We used the microscale thermophoresis method allowing surface independent interaction studies and electromobility shift assays to evaluate additional RNA-DNA hybrid sequences and to quantify the binding affinities of the S9...
2017: PloS One
https://www.readbyqxmd.com/read/28580714/marine-alkaloid-oroidin-analogues-with-antiviral-potential-a-novel-class-of-synthetic-compounds-targeting-the-cellular-chaperone-hsp90
#18
Katja-Emilia Lillsunde, Tihomir Tomašič, Danijel Kikelj, Päivi Tammela
Marine organisms and their metabolites are a diverse source of scaffolds for potential pharmacological molecular probes and, less frequently, for pharmaceutical lead compounds. In this study, 157 synthetic analogues of marine sponge-derived alkaloids clathrodin and oroidin were screened against replicon models of two RNA viruses, hepatitis C (HCV) and Chikungunya virus (CHIKV) as part of a larger screening project. Four compounds were found to selectively inhibit the HCV replicon (IC50 1.6-4.6 μM). These belong to the 4,5,6,7-tetrahydrobenzo[1,2-d]thiazole class of compounds originally designed to target the ATP-binding site of bacterial DNA gyrase...
June 5, 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/28522394/interaction-research-on-an-antiviral-molecule-that-targets-the-coat-protein-of-southern-rice-black-streaked-dwarf-virus
#19
Longlu Ran, Yan Ding, Liangzhi Luo, Xiuhai Gan, Xiangyang Li, Yongzhong Chen, Deyu Hu, Baoan Song
Southern rice black-streaked dwarf virus (SRBSDV) coat protein (P10) is the key protein required for viral transmission and host plant infection and is thus a promising target for anti-SRBSDV agent screening. In this study, P10 was obtained from Escherichia coli through cloning, expression, and purification. The antiviral agent Ningnanmycin was selected as control, and a series of antiviral compounds based on the structural scaffold of ferulic acid were analyzed. Size-exclusion chromatography analysis results showed that compound F27 can alter the aggregation of P10 proteins...
October 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28499498/aptatope-mapping-of-the-binding-site-of-a-progesterone-aptamer-on-the-steroid-ring-structure
#20
Vasso Skouridou, Thomas Schubert, Abdulaziz S Bashammakh, Mohammad S El-Shahawi, Abdulrahman O Alyoubi, Ciara K O'Sullivan
In this work we report the mapping of the binding site of the only progesterone aptamer published to date, in an approach referred to as aptatope mapping. By linking the binding data obtained from microscale thermophoresis analysis to the structural differences on the ring structure of a range of steroids, we elucidated the moieties involved in aptamer-progesterone binding. This approach can be further exploited for the characterization of aptamer specificity and ultimately facilitate the development of aptamer-based assays depending on the desired specificity...
August 15, 2017: Analytical Biochemistry
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