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Journal of Molecular Recognition: JMR

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https://www.readbyqxmd.com/read/28643851/fluorescent-competitive-aptasensor-for-detection-of-aflatoxin-b1
#1
Monali Mukherjee, Praveena Bhatt, Manonmani H K
Aflatoxin B1 (AFB1 ) is one of the most commonly found mycotoxins in food commodities, particularly cereals, oilseeds, spices and tree nuts. In the past decade, aptamers have come into limelight and emerged as a new biosensing element replacing antibodies in various detection formats. Herein we report a faster, more sensitive, high throughput method for the detection of AFB1 using AFB1 -specific aptamers. The assay format was based on a competitive reaction of the fluorescent tagged aptamer specific to AFB1 with the aflatoxin conjugate...
June 23, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28639323/molecular-interactions-of-dioxins-and-dlcs-with-the-xenosensors-pxr-and-car-an-in-silico-risk-assessment-approach
#2
Garima Verma, Mohemmed Faraz Khan, Mohammad Shaquiquzzaman, Wasim Akhtar, Mymoona Akhter, Syed Misbahul Hasan, Mohammad Mumtaz Alam
Dioxins and dioxin-like compounds (DLCs) are known to cause endocrine disruption in humans and animals. Being lipophilic xenobiotic chemicals, they can be easily absorbed into the biological system from the surrounding environments, thereby causing various health dysfunctions. In the present study, a total of 100 dioxins and DLCs were taken, and their binding pattern was assessed with the xenosensors pregnane X receptor (PXR) and constitutive androstane receptor (CAR) in comparison with the corresponding known inhibitors and a well-studied endocrine disrupting xenobiotic, bisphenol A (BPA)...
June 22, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28626866/activation-of-catalase-by-pioglitazone-multiple-spectroscopic-methods-combined-with-molecular-docking-studies
#3
Reza Yekta, Gholamreza Dehghan, Samaneh Rashtbari, Nader Sheibani, Ali Akbar Moosavi-Movahedi
Pioglitazone is an important prescription antidiabetic drug with positive roles in controlling high blood sugar in patients with type 2 diabetes. In the present study, we investigated the effects of pioglitazone on the structure and function of bovine liver catalase (BLC) using different spectroscopic and theoretical methods. UV-Vis absorption, fluorescence spectroscopy, synchronous fluorescence, and circular dichroism studies revealed conformational changes in the BLC structure and heme group in the presence of different concentrations of pioglitazone...
June 19, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28621027/aromatic-amino-acids-and-their-relevance-in-the-specificity-of-the-ph-domain
#4
Ja Morales, M Sobol, L C Rodriguez-Zapata, P Hozak, E Castano
Phosphoinositides are phosphatidylinositol derived, well known to be second messengers in various cell signaling pathways as well as in processes such as cell differentiation, cellular stress response, gene transcription, and chromatin remodeling. The pleckstrin homology domain of phospholipase C-delta 1 is responsible for recognizing and binding to PI(4,5)P2 and for this reason has been widely used to study this phosphoinositide as a biosensor when it is conjugated to a fluorescent tag. In this work, we modified the primary structure of pleckstrin homology domain by site-specific mutagenesis to change the specificity for phosphoinositides...
June 16, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28620979/an-application-of-cifap-for-predicting-the-binding-affinity-of-chk1-inhibitors-derived-from-2-aminothiazole-4-carboxamide
#5
Dilan Konyar, Ozlem Erdas, Ferda Nur Alpaslan, Erdem Buyukbingol
Investigation of protein-ligand interactions obtained from experiments has a crucial part in the design of newly discovered and effective drugs. Analyzing the data extracted from known interactions could help scientists to predict the binding affinities of promising ligands before conducting experiments. The objective of this study is to advance the CIFAP (compressed images for affinity prediction) method, which is relevant to a protein-ligand model, identifying 2D electrostatic potential images by separating the binding site of protein-ligand complexes and using the images for predicting the computational affinity information represented by pIC50 values...
June 16, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28612997/a-structural-perspective-on-the-interactions-of-traf6-and-basigin-during-the-onset-of-melanoma-a-molecular-dynamics-simulation-study
#6
Ria Biswas, Semanti Ghosh, Angshuman Bagchi
Metastatic melanoma is the most fatal type of skin cancer. The roles of matrix metalloproteinases (MMPs) have well been established in the onset of melanoma. Basigin (BSG) belongs to the immunoglobulin superfamily and is critical for induction of extracellular MMPs during the onset of various cancers including melanoma. Tumor necrosis factor receptor-associated factor 6 (TRAF6) is an E3-ligase that interacts with BSG and mediates its membrane localization, which leads to MMP expression in melanoma cells. This makes TRAF6 a potential therapeutic target in melanoma...
June 14, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28608634/molecular-basis-for-the-recognition-of-ccn1-by-monoclonal-antibody-093g9
#7
Chen Zhong, Rongfen Huo, Kuan Hu, Jinlong Shen, Dangsheng Li, Ningli Li, Jianping Ding
CCN1, also named Cyr61 (cysteine-rich protein 61), is the first identified member of the CCN family that is composed of 6 secreted extracellular matrix-associated glycoproteins. CCN1 has been demonstrated to participate in pathogenesis of rheumatoid arthritis through various pathways. A monoclonal antibody, namely, 093G9, is effective to antagonize the effects of CCN1 and hence has potential therapeutic benefits against rheumatoid arthritis. Here, we show that the epitope recognized by 093G9 is mapped to residues 77 to 80 of CCN1, and a cyclic peptide encompassing residues 75 to 81 of CCN1 displays high binding affinity for 093G9...
June 13, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28608588/experimental-and-computational-characterization-on-the-binding-of-two-fluoroquinolones-to-bovine-hemoglobin
#8
Pengfei Qin, Xingren Pan, Rutao Liu, Jicai Qiu, Xiaoyan Fang
Ciprofloxacin (CPFX) and enrofloxacin (ENFX) are 2 representatives of widely used fluoroquinolones (FQs) with many human and veterinary applications. The residues of FQs in the environment are potentially harmful. Recently, great concern has been paid to their persistence and fate in the environment because of the potential adverse effects on humans and ecosystem functions. In the present study, we examined the interactions of bovine hemoglobin (BHb) with these 2 FQs by means of multiple spectroscopic and molecular docking methods under physiological conditions...
June 13, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28608578/cantharidin-inhibits-competitively-heme-fe-iii-binding-to-the-fa1-site-of-human-serum-albumin
#9
Fabio Polticelli, Loris Leboffe, Valentina Tortosa, Viviana Trezza, Gabriella Fanali, Mauro Fasano, Paolo Ascenzi
Cantharidin, a monoterpene isolated from the insect blister beetle, has long been used as a medicinal agent in the traditional Chinese medicine. Cantharidin inhibits a subgroup of serine/threonine phosphatases, thus inducing cell growth inhibition and cytotoxicity. Cantharidin has anticancer activity in vitro, since it is able of inducing p53-dependent apoptosis and double-strand breakage of DNA in cancer cells. Although the toxicity of cantharidin to the gastrointestinal and urinary tracts prevents its medical use, it is a promising lead compound for chemical modification to develop new anticancer therapeutics...
June 13, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28608547/computational-modeling-of-the-bat-hku4-coronavirus-3cl-pro-inhibitors-as-a-tool-for-the-development-of-antivirals-against-the-emerging-middle-east-respiratory-syndrome-mers-coronavirus
#10
Areej Abuhammad, Rua'a A Al-Aqtash, Brandon J Anson, Andrew D Mesecar, Mutasem O Taha
The Middle East respiratory syndrome coronavirus (MERS-CoV) is an emerging virus that poses a major challenge to clinical management. The 3C-like protease (3CL(pro) ) is essential for viral replication and thus represents a potential target for antiviral drug development. Presently, very few data are available on MERS-CoV 3CL(pro) inhibition by small molecules. We conducted extensive exploration of the pharmacophoric space of a recently identified set of peptidomimetic inhibitors of the bat HKU4-CoV 3CL(pro) ...
June 13, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28513076/a-computational-assessment-of-the-predicted-structures-of-human-macrophage-migration-inhibitory-factor-1-orthologs-in-parasites-and-its-affinity-to-human-cd74-receptor
#11
Claudia Machicado, Luis A Marcos
The human macrophage migration inhibitory factor 1 (Hu-MIF-1) is a protein involved in the inflammatory and immunology response to parasite infection. In the present study, the existence of Hu-MIF-1 from parasites have been explored by mining WormBase. A total of 35 helminths were found to have Hu-MIF-1 homologs, including some parasites of importance for public health. Physicochemical, structural, and biological properties of Hu-MIF-1 were compared with its orthologs in parasites showing that most of these are secretory proteins, with positive net charge and presence of the Cys-Xaa-Xaa-Cys motif that is critical for its oxidoreductase activity...
May 17, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28503738/targeting-human-telomeric-g-quadruplex-dna-with-antitumour-natural-alkaloid-aristololactam-%C3%AE-d-glucoside-and-its-comparison-with-daunomycin
#12
Abhi Das, Sabyasachi Chatterjee, Gopinatha Suresh Kumar
Study on anticancer agents that act via stabilization of telomeric G-quadruplex DNA has emerged as novel and exciting field for anticancer drug discovery. The interaction of carbohydrate containing anticancer alkaloid aristololactam-β-D-glucoside (ADG) with human telomeric G-quadruplex DNA sequence was characterized by different biophysical techniques. The binding parameters were compared with daunomycin (DAN), a well-known chemotherapeutic drug. The Scatchard binding isotherms revealed noncooperative binding for both with the binding affinity values of (1...
May 15, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28470891/sequence-dependent-cleavage-of-mismatched-dna-by-ban-i-restriction-endonuclease
#13
Weimin Gao, Dan Zhu, Phouthone Keohavong
Restriction enzymes have previously shown the ability to cleave DNA substrates with mismatched base(s) in recognition sequences; in this study, Ban I endonuclease demonstrated this same ability. Single base substitutions were introduced, and fragments containing various types of unpaired base(s) (heteroduplex fragments) within the Ban I endonuclease recognition sequence, 5'-G|GPyPuCC-3', were generated. Each of the heteroduplex fragments was treated with Ban I endonuclease and analyzed by denaturing gradient gel electrophoresis...
May 4, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28470769/how-human-iggs-against-myelin-basic-protein-mbp-recognize-oligopeptides-and-mbp
#14
Sergey Belov, Valentina N Buneva, Georgy A Nevinsky
Myelin basic protein (MBP) is a major protein of myelin-proteolipid shell of axons, and it plays an important role in pathogenesis of multiple sclerosis. In the literature, there are no data on how antibodies recognize different protein antigens including MBP. A stepwise increase in ligand complexity was used to estimate the relative contributions of virtually every amino acid residue (AA) of a specific 12-mer LSRFSWGAEGQK oligopeptide corresponding to immunodominant sequence of MBP to the light chains and to intact anti-MBP IgGs from sera of patients with multiple sclerosis...
May 4, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28470740/structural-insights-of-mycobacterium-gtpase-obg-and-anti-sigma-f-factor-usfx-interaction
#15
Vikrant Kumar, Anil Kumar Tomar, Vishal Sahu, Sharmistha Dey, Savita Yadav
An essential protein for bacterial growth, GTPase-Obg (Obg), is known to play an unknown but crucial role in stress response as its expression increases in Mycobacterium under stress conditions. It is well reported that Obg interacts with anti-sigma-F factor Usfx; however, a detailed analysis and structural characterization of their physical interaction remain undone. In view of above-mentioned points, this study was conceptualized for performing binding analysis and structural characterization of Obg-Usfx interaction...
May 4, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28449373/biophysical-analysis-of-the-dynamics-of-calmodulin-interactions-with-neurogranin-and-ca2-calmodulin-dependent-kinase-ii
#16
Christian Seeger, Vladimir O Talibov, U Helena Danielson
Calmodulin (CaM) functions depend on interactions with CaM-binding proteins, regulated by Ca2+. Induced structural changes influence the affinity, kinetics, and specificities of the interactions. The dynamics of CaM interactions with neurogranin (Ng) and the CaM-binding region of Ca2+/calmodulin-dependent kinase II (CaMKII290-309 ) have been studied using biophysical methods. These proteins have opposite Ca2+ dependencies for CaM binding. Surface plasmon resonance biosensor analysis confirmed that Ca2+ and CaM interact very rapidly, and with moderate affinity ( KDSPR=3μM)...
April 27, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28444792/a-computational-approach-to-study-functional-monomer-protein-molecular-interactions-to-optimize-protein-molecular-imprinting
#17
R Boroznjak, J Reut, A Tretjakov, A Lomaka, A Öpik, V Syritski
Molecular imprinting has become a promising approach for synthesis of polymeric materials having binding sites with a predetermined selectivity for a given analyte, the so-called molecularly imprinted polymers (MIPs), which can be used as artificial receptors in various application fields. Realization of binding sites in a MIP involves the formation of prepolymerization complexes between a template molecule and monomers, their subsequent polymerization, and the removal of the template. It is believed that the strength of the monomer-template interactions in the prepolymerization mixture influences directly on the quality of the binding sites in a MIP and consequently on its performance...
April 26, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28417509/a-biomolecular-recognition-approach-for-the-functionalization-of-cellulose-with-gold-nanoparticles
#18
A Almeida, A M M Rosa, A M Azevedo, D M F Prazeres
Materials with new and improved functionalities can be obtained by modifying cellulose with gold nanoparticles (AuNPs) via the in situ reduction of a gold precursor or the deposition or covalent immobilization of pre-synthesized AuNPs. Here, we present an alternative biomolecular recognition approach to functionalize cellulose with biotin-AuNPs that relies on a complex of 2 recognition elements: a ZZ-CBM3 fusion that combines a carbohydrate-binding module (CBM) with the ZZ fragment of the staphylococcal protein A and an anti-biotin antibody...
April 17, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28397380/regulation-of-protein-binding-activities-of-molecularly-imprinted-polymers-via-post-imprinting-modifications-to-exchange-functional-groups-within-the-imprinted-cavity
#19
Hirobumi Sunayama, Yukiya Kitayama, Toshifumi Takeuchi
We prepared lysozyme-imprinted polymers bearing modifiable sites within the imprinted cavity to introduce various functional groups via post-imprinting modifications. For this purpose, ({[2-(2-methacrylamido)-ethyldithio]-ethylcarbamoyl}-methoxy)acetic acid (MDTA), which has a carboxy group to interact with the target protein, lysozyme, and a disulfide linkage for post-imprinting modifications, was used as a functional monomer. A lysozyme-imprinted polymer film was prepared by copolymerization of MDTA with a cross-linker, N,N'-methylenebisacrylamide, in the presence of lysozyme...
April 11, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28374551/the-impact-of-hyperglycemia-on-adhesion-between-endothelial-and-cancer-cells-revealed-by-single-cell-force-spectroscopy
#20
Katarzyna E Malek-Zietek, Marta Targosz-Korecka, Marek Szymonski
The impact of hyperglycemia on adhesion between lung carcinoma cells (A549) and pulmonary human aorta endothelial cells (PHAEC) was studied using the single-cell force spectroscopy. Cancer cells were immobilized on a tipless Atomic Force Microscopy (AFM) cantilever and a single layer of endothelial cells was prepared on a glass slide. The measured force-distance curves provided information about the detachment force and about the frequency of specific ligand-receptor rupture events. Measurements were performed for different times of short term (up to 2 h) and prolonged hyperglycemia (3 h - 24 h)...
April 4, 2017: Journal of Molecular Recognition: JMR
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