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Journal of Molecular Recognition: JMR

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https://www.readbyqxmd.com/read/28895236/protein-surface-roughness-accounts-for-binding-free-energy-of-plasmepsin-ii-ligand-complexes
#1
Mario E Valdés-Tresanco, Mario S Valdés-Tresanco, Pedro A Valiente, Germinal Cocho, Ricardo Mansilla, J M Nieto-Villar
The calculation of absolute binding affinities for protein-inhibitor complexes remains as one of the main challenges in computational structure-based ligand design. The present work explored the calculations of surface fractal dimension (as a measure of surface roughness) and the relationship with experimental binding free energies of Plasmepsin II complexes. Plasmepsin II is an attractive target for novel therapeutic compounds to treat malaria. However, the structural flexibility of this enzyme is a drawback when searching for specific inhibitors...
September 12, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28872251/room-temperature-synthesis-and-binding-studies-of-solution-processable-histamine-imprinted-microspheres
#2
Edwin F Romano, Clovia I Holdsworth, Joselito P Quirino, Regina C So
Accurate quantification of histamine levels in food and in biological samples is important for monitoring the quality of food products and for the detection of pathophysiological conditions. In this study, solution processable histamine-imprinted microspheres were synthesized at 30°C via dilute free radical phototochemical polymerization technique using ethylene glycol dimethacrylate (EGDMA) as the crosslinker and methacrylic acid (MAA) as the monomer. The processability of the resulting polymer is dictated by the monomer feed concentration (eg, 4 wt% 80:20 EGDMA:MAA formulation) and solvent (acetonitrile)...
September 5, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28856782/activity-of-zn-and-mg-phthalocyanines-and-porphyrazines-in-amyloid-aggregation-of-insulin
#3
V Kovalska, S Chernii, M Losytskyy, J Ostapko, I Tretyakova, A Gorski, V Chernii, S Yarmoluk
Formation of the deposits of protein aggregates-amyloid fibrils in an intracellular and intercellular space-is common to a large group of amyloid-associated disorders. Among the approaches to develop of therapy of such disorders is the use of agents preventing protein fibrillization. Polyaromatic complexes-porphyrins and phthalocyanines-are known as compounds possessing anti-fibrillogenic activity. Here, we explore the impact of related macrocyclic complexes-phthalocyanines (Pc) and octaphenyl porphyrazines (Pz) of Mg and Zn-on aggregation of amyloidogenic protein insulin...
August 30, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28850770/molecular-insights-into-a%C3%AE-42-protofibril-destabilization-with-a-fluorinated-compound-d744-a-molecular-dynamics-simulation-study
#4
Rajneet Kaur Saini, Suniba Shuaib, Bhupesh Goyal
The aggregation of amyloid β-peptide (Aβ42 ) into toxic oligomers, fibrils, has been identified as a key process in Alzheimer's disease (AD) progression. The role of halogen-substituted compounds have been highlighted in the disassembly of Aβ protofibril. However, the underlying inhibitory mechanism of Aβ42 protofibril destabilization remains elusive. In this regard, a combined molecular docking and molecular dynamics (MD) simulations were performed to elucidate the inhibitory mechanism of a fluorinated compound, D744, which has been reported previously for potential in vitro and in vivo inhibitory activity against Aβ42 aggregation and reduction in the Aβ-induced cytotoxicity...
August 29, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28836695/synthesis-binding-ability-and-cell-cytotoxicity-of-fluorescent-probes-for-l-arginine-detection-based-on-naphthalene-derivatives-experiment-and-theory
#5
Jie Li, Yang Zhang, Yanmei Chen, Xuefang Shang, Tongyu Ti, Hongli Chen, Tianyun Wang, Jinlian Zhang, Xiufang Xu
Inspired by biological related parts, Schiff base derivatives and functional groups of chemical modification can provide efficient detection method of amino acids. Therefore, we have designed and prepared 4 compounds based on Schiff base derivatives involving ─NO2 , ─OH, and naphthyl group. Results indicated that compound 4 containing 2 nitro groups showed strong sensitivity and high selectivity for arginine (Arg) among normal 18 kinds of standard amino acids (alanine, valine, leucine, isoleucine, methionine, aspartic acid, glutamic acid, arginine, glycine, serine, asparagine, phenylalanine, histidine, tryptophan, proline, lysine, glutamine, and cysteine)...
August 24, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28833724/construction-and-characterization-of-mutated-lea-peptides-in-escherichia-coli-to-develop-an-efficient-protein-expression-system
#6
Nishit Pathak, Hiro Hamada, Shinya Ikeno
To develop an efficient protein expression system, we designed a late embryogenesis abundant (LEA) peptide by mutating the LEA peptide constructed in our previous study (LEA-I). The peptide is based on the repeating units of an 11mer motif characteristic of LEA proteins from Polypedilum vanderplanki larvae. In the amino acid sequence of the 13mer LEA peptide, glycine at the 6th and 12th positions was replaced with other amino acids via point mutations. Glutamic acid, lysine, leucine, and asparagine in the LEA peptide at the 6th and 12th positions increased green fluorescence protein (GFP) expression...
August 23, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28791744/assessment-of-the-imprinting-efficiency-of-an-imide-with-a-stoichiometric-pyridine-based-functional-monomer-in-precipitation-polymerisation
#7
K Fremielle Lim, Andrew J Hall, Stefania Lettieri, Clovia I Holdsworth
The efficiency of the stoichiometric non-covalent imprinting of the imide 2,3,5-tri-O-acetyluridine (TAU) with 2,6-bis(acrylamido)pyridine (BAAPy) as functional monomer due to their strong donor-acceptor-donor/acceptor-donor-acceptor (DAD/ADA) hydrogen bond array interaction has been evaluated by bulk imprinting. This study is the first to investigate the imprinting and template rebinding efficiencies of the TAU/BAAPy molecularly imprinted polymeric (MIP) system prepared by precipitation polymerisation. We found that the stoichiometric 1:1 T:FM ratio has not been maintained in precipitation polymerisation and an optimal TAU:BAAPy ratio of 1:2...
August 9, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28707399/neuroglobin-and-friends
#8
REVIEW
Marco Fiocchetti, Manuela Cipolletti, Valentina Brandi, Fabio Polticelli, Paolo Ascenzi
In the year 2000, the third member of the globin family was discovered in human and mouse brain and named neuroglobin (Ngb). Neuroglobin overexpression significantly protects both heart and brain from hypoxic/ischemic and oxidative stress-related insults, whereas decreased Ngb levels lead to an exacerbation of tissue injuries. Moreover, Ngb overexpression protects neurons from mitochondrial dysfunctions and neurodegenerative disorders such as Alzheimer disease; however, it facilitates the survival of cancer cells...
July 14, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28675615/betamethasone-based-chiral-electrochemical-sensor-coupled-to-chemometric-methods-for-determination-of-mandelic-acid-enantiomers
#9
Marjan Borazjani, Ali Mehdinia, Ali Jabbari
A chiral biosensing platform was developed using betamethasone (BMZ) as chiral recognition element through multilayered electrochemical deposition of BMZ, overoxidized polypyrrole, and nanosheets of graphene (OPPy-BMZ/GR), for enantio-recognition of mandelic acid (MA) enantiomers. The deposited film was characterized by scanning electron microscopy, differential pulse voltammetry, cyclic voltammetry, and electrochemical impedance spectroscopy. It was shown that the chiral sensing platform can discriminate R- and S-MA differential pulse voltammetry signals, at the voltages of 1...
July 4, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28675505/supramolecular-interactions-between-%C3%AE-lapachone-with-cyclodextrins-studied-using-isothermal-titration-calorimetry-and-molecular-modeling
#10
Francisco H Xavier-Junior, Marcelo M Rabello, Marcelo Z Hernandes, Marília E S Dias, Otoni H M S Andrada, Beatriz P Bezerra, Alejandro P Ayala, Nereide S Santos-Magalhães
Supramolecular interactions between β-lapachone (β-lap) and cyclodextrins (CDs) were investigated by isothermal titration calorimetry. The most favorable host: guest interaction was characterized using X-ray powder diffraction (XRD), differential scanning calorimetry and thermogravimetry (DSC/TG), spectroscopy (FT-IR), spectroscopy (2D ROESY) nuclear magnetic resonance (NMR), and molecular modeling. Phase solubility diagrams showed β-, HP-β-, SBE-β-, γ-, and HP-γ-CDs at 1.5% (w/w) allowed an increase in apparent solubility of β-lap with enhancement factors of 12...
July 4, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28449373/biophysical-analysis-of-the-dynamics-of-calmodulin-interactions-with-neurogranin-and-ca-2-calmodulin-dependent-kinase-ii
#11
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)...
August 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28233410/conformational-energy-range-of-ligands-in-protein-crystal-structures-the-difficult-quest-for-accurate-understanding
#12
REVIEW
Megan L Peach, Raul E Cachau, Marc C Nicklaus
In this review, we address a fundamental question: What is the range of conformational energies seen in ligands in protein-ligand crystal structures? This value is important biophysically, for better understanding the protein-ligand binding process; and practically, for providing a parameter to be used in many computational drug design methods such as docking and pharmacophore searches. We synthesize a selection of previously reported conflicting results from computational studies of this issue and conclude that high ligand conformational energies really are present in some crystal structures...
August 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28643851/fluorescent-competitive-aptasensor-for-detection-of-aflatoxin-b1
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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