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Journal of Molecular Recognition: JMR

Nilkanta Chowdhury, Angshuman Bagchi
RhlR protein from opportunistic pathogen Pseudomonas aeruginosa is involved in the transcription of virulence genes of the organism. The RhlR protein functions as a dimer and binds to the cognate promoter DNA with the help of an autoinducer ligand BHL to initiate the transcription of the virulence genes. Till date, there are no reports that detail the mechanism of virulence gene expression by RhlR protein in P. aeruginosa. In this work, we tried to analyse the molecular aspects of the various binding interactions of the RhlR protein while formimg the dimmer as well as with the promoter DNA...
July 2, 2018: Journal of Molecular Recognition: JMR
Muntazir S Khan, Sourav Pal
We present a benchmark study of binding energies for dioxin-imprinted polymer complexes. A density functional theory approach was used for screening the polymerization precursors in the rational design of molecularly imprinted polymers (MIPs). Tetrachlorodibenzo-p-dioxin (TCDD) was taken as an imprinted molecule. The geometry optimization, natural bond orbital charge, and molecular electrostatic potential of TCDD and acrylamide (AM) were studied at the M062X level and 6-31G(d,p) belonging to one of the hybrid density functional theories...
July 1, 2018: Journal of Molecular Recognition: JMR
Mohammad Hasanzadeh, Elnaz Javidi, Abolghasem Jouyban, Ahad Mokhtarzadeh, Nasrin Shadjou, Soltanali Mahboob
The rapid and accurate determination of the level of taurine biomarker in various tissues and body fluids can be of great interest in the early diagnosis of several important pathologies and diseases. In the present study, an innovative electrochemical interface for quantitation of taurine based on ternary signal amplification strategy was fabricated. In this work, silver nanoparticles were electrodeposited onto green and biocompatible nanocomposite containing α-cyclodextrin as conductive matrix. Therefore, a double layer film based on α-cyclodextrin and silver nanoparticles was exploited to develop a highly sensitive electrochemical sensor for detection of taurine...
June 28, 2018: Journal of Molecular Recognition: JMR
Bushra Taj Muhammad, Azeem Ullah, Munira Taj Muhammad, Tanzila Arshad
Role of heterocyclic compounds with nitrogen substitution in therapeutic frontiers is well established. The efforts made in this study are directed to dissect the biological significance of benzimidazole-substituted zinc phthalocyanine derivative. Its capacity to act as an anticancer agent against the 2 B-lymphoma cell lines (low-grade and high-grade malignancy) was found out by recording florescence using Alamar blue dye. Further cytotoxic effect at the DNA level was analyzed by performing agarose gel electrophoresis...
June 27, 2018: Journal of Molecular Recognition: JMR
Khalid I Al Qumaizi, Razique Anwer, Nazia Ahmad, Saleh M Alosaimi, Tasneem Fatma
Pioglitazone is an antidiabetic drug used to treat type 2 diabetes mellitus. Interaction of Pioglitazone with calf thymus DNA was investigated using multispectroscopic techniques and molecular docking study. Quenching and binding constant was calculated at 3 different temperatures. The binding constant of Pioglitazone with calf thymus DNA was calculated to be 6.49 × 103 M-1 at 293 K. The quenching mechanism was found to be a static process, and thermodynamic parameters revealed van der Waals interactions and hydrogen bonds to be the major force working in Pioglitazone-DNA interaction...
June 25, 2018: Journal of Molecular Recognition: JMR
Nasrin Shadjou, Salar Alizadeh, Mohammad Hasanzadeh
The rapid and accurate determination of the level of taurine biomarker in various tissues and body fluids can be of great interest in the early diagnosis of several important pathologies and diseases. For the first time, this study reports on the electropolymerization of a low toxic and biocompatible nanocomposite "poly(aspartic acid)-graphene quantum dots (GQDs)" as a novel strategy for surface modification of glassy carbon electrode and preparation a new interface for measurement of taurine. Electrochemical deposition, as a well-controlled synthesis procedure, has been used for subsequently layer-by-layer preparation of GQDs nanostructures on poly(aspartic acid) using cyclic voltammetry techniques in the regime of -1...
June 25, 2018: Journal of Molecular Recognition: JMR
Rajan Patel, Neha Maurya, Mehraj Ud Din Parray, Nida Farooq, Abrar Siddique, Kanak Lata Verma, Neeraj Dohare
The present work is a brief overview of the effect of psychostimulant drug mephedrone hydrochloride (4MMC) on a transport protein, bovine serum albumin (BSA). The binding effect of 4MMC on BSA has been investigated by using UV-visible, steady-state fluorescence, time-resolved fluorescence, fluorescence resonance energy transfer, Fourier transform infrared, circular dichroism, and molecular docking method. 4-Methylmephedrone quenched the intrinsic fluorescence of BSA by static quenching mechanism, which was further confirmed by time-resolved fluorescence...
June 19, 2018: Journal of Molecular Recognition: JMR
S Dinarelli, G Longo, S Krumova, S Todinova, A Danailova, S G Taneva, E Lenzi, V Mussi, M Girasole
Erythrocytes (RBCs) constitute a very interesting class of cells both for their physiological function and for a variety of peculiarities. Due to their exceptionally strong relationship with the environment, the morphology and nanoscale characteristics of these cells can reveal their biochemical status and structural integrity. Among the possible subjects of investigations, the RBCs' ageing is of the utmost importance. This is a fundamental phenomenon that, in physiological conditions, triggers the cell turnover and ensures the blood homeostasis...
June 6, 2018: Journal of Molecular Recognition: JMR
Samrat Dutta, Claudio Rivetti, Natalie R Gassman, Carl G Young, Bradley T Jones, Karin Scarpinato, Martin Guthold
Bent DNA, or DNA that is locally more flexible, is a recognition motif for many DNA binding proteins. These DNA conformational properties can thus influence many cellular processes, such as replication, transcription, and DNA repair. The importance of these DNA conformational properties is juxtaposed to the experimental difficulty to accurately determine small bends, locally more flexible DNA, or a combination of both (bends with increased flexibility). In essence, many current bulk methods use average quantities, such as the average end-to-end distance, to extract DNA conformational properties; they cannot access the additional information that is contained in the end-to-end distance distributions...
June 3, 2018: Journal of Molecular Recognition: JMR
Dong-Ru Sun, Zhi-Jun Wang, Qing-Chuan Zheng, Hong-Xing Zhang
Targeting transcription factors HIF-2 is currently considered to be the most direct way for the therapy of clear cell renal cell carcinoma. The preclinical inhibitor PT2399 and artificial inhibitor 0X3 have been identified as promising on-target inhibitors to inhibit the heterodimerization of HIF-2. However, the inhibition mechanism of PT2399 and 0X3 on HIF-2 remains unclear. To this end, molecular dynamics (MD) simulations and molecular docking were applied to investigate the effects of 2 inhibitors on structural motifs and heterodimerization of HIF-2...
May 23, 2018: Journal of Molecular Recognition: JMR
Pascale Milani, Julien Chlasta, Rawad Abdayem, Sanja Kezic, Marek Haftek
During formation of the stratum corneum (SC) barrier, terminally differentiated keratinocytes continue their maturation process within the dead superficial epidermal layer. Morphological studies of isolated human corneocytes have revealed differences between cornified envelopes purified from the deep and superficial SC. We used atomic force microscopy to measure the mechanical properties of native human corneocytes harvested by tape-stripping from different SC depths. Various conditions of data acquisition have been tested and optimized, in order to obtain exploitable and reproducible results...
May 22, 2018: Journal of Molecular Recognition: JMR
Birgit J Waldner, Johannes Kraml, Ursula Kahler, Alexander Spinn, Michael Schauperl, Maren Podewitz, Julian E Fuchs, Gabriele Cruciani, Klaus R Liedl
Serine proteases of the Chymotrypsin family are structurally very similar but have very different substrate preferences. This study investigates a set of 9 different proteases of this family comprising proteases that prefer substrates containing positively charged amino acids, negatively charged amino acids, and uncharged amino acids with varying degree of specificity. Here, we show that differences in electrostatic substrate preferences can be predicted reliably by electrostatic molecular interaction fields employing customized GRID probes...
May 22, 2018: Journal of Molecular Recognition: JMR
Anas Shamsi, Azaj Ahmed, Mohd Shahnawaz Khan, Fohad Mabood Husain, Samreen Amani, Bilqees Bano
In our present study, binding between an important anti renal cancer drug temsirolimus and human transferrin (hTF) was investigated employing spectroscopic and molecular docking approach. In the presence of temsirolimus, hyper chromaticity is observed in hTF in UV spectroscopy suggestive of complex formation between hTF and temsirolimus. Fluorescence spectroscopy revealed the occurrence of quenching in hTF in the presence of temsirolimus implying complex formation taking place between hTF and temsirolimus. Further, the mode of interaction between hTF and temsirolimus was revealed to be static by fluorescence quenching analysis at 3 different temperatures...
May 16, 2018: Journal of Molecular Recognition: JMR
Van-Chien Bui, Thi-Huong Nguyen
Cations-induced DNA aggregation can modify the local structure of oligonucleotides and has potential applications in medicine and biotechnology. Here, we used atomic force microscopy to investigate λ-DNA aggregation on Mg2+ -treated glass (Mg2+ /glass) and in Mg2+ solution. Atomic force microscopy topography images showed that some DNA fragments were slightly stacked together on 10 mM Mg2+ /glass and stacked stronger on ≥50 mM Mg2+ /glass. They also showed that DNA aggregated stronger in Mg2+ solution than on Mg2+ /glass, ie, DNAs are strongly stacked and twisted at 10 mM Mg2+ , rolled together at 50 mM Mg2+ , and slightly aggregated to form small particles at 100 mM Mg2+ ...
May 15, 2018: Journal of Molecular Recognition: JMR
Agnieszka Kolodziejczyk, Aleksandra Jakubowska, Magdalena Kucinska, Tomasz Wasiak, Piotr Komorowski, Krzysztof Makowski, Bogdan Walkowiak
Endothelial cells, due to their location, are interesting objects for atomic force spectroscopy study. They constitute a barrier between blood and vessel tissues located deeper, and therefore they are the first line of contact with various substances present in blood, eg, drugs or nanoparticles. This work intends to verify whether the mechanical response of immortalized human umbilical vein endothelial cells (EA.hy926), when exposed to silver nanoparticles, as measured using force spectroscopy, could be effectively used as a bio-indicator of the physiological state of the cells...
May 10, 2018: Journal of Molecular Recognition: JMR
S Dinarelli, M Girasole, P Spitalieri, R V Talarico, M Murdocca, A Botta, G Novelli, R Mango, F Sangiuolo, G Longo
Myotonic Dystrophy type 1 (DM1) is the most common form of muscular dystrophy in adults, characterized by a variety of multisystemic features and associated with cardiac anomalies. Among cardiac phenomena, conduction defects, ventricular arrhythmias, and dilated cardiomyopathy represent the main cause of sudden death in DM1 patients. Patient-specific induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) represent a powerful in vitro model for molecular, biochemical, and physiological studies of disease in the target cells...
May 10, 2018: Journal of Molecular Recognition: JMR
Rasha M Bashatwah, Mohammad A Khanfar, Sanaa K Bardaweel
Inorganic polyphosphate (polyP) is present in all living forms of life. Studied mainly in prokaryotes, polyP and its associated enzymes are vital in diverse metabolic activities, in some structural functions, and most importantly in stress responses. Bacterial species, including many pathogens, encode a homolog of a major polyP synthesis enzyme, Poly Phosphate Kinase (PPK) with 2 different genes coding for PPK1 and PPK2. Genetic deletion of the ppk1 gene leads to reduced polyP levels and the consequent loss of virulence and stress adaptation responses...
May 8, 2018: Journal of Molecular Recognition: JMR
E Kozlova, A Chernysh, V Sergunova, O Gudkova, E Manchenko, A Kozlov
The morphology and functional state of red blood cells (RBCs) mainly depends on the configuration of the spectrin network, which can be broken under the influence of intoxication because of oxidation processes in the cells. Measurement of these processes is a complex problem. The most suitable and prospective method that resolves this problem is atomic force microscopy (AFM). We used AFM to study the changes in the spectrin matrix and RBC morphology during oxidation processes caused by ultraviolet (UV) irradiation in RBC suspension...
May 8, 2018: Journal of Molecular Recognition: JMR
Prem Kumar Viji Babu, Carmela Rianna, Gazanfer Belge, Ursula Mirastschijski, Manfred Radmacher
Mechanical properties of myofibroblasts play a key role in Dupuytren's disease. Here, we used atomic force microscopy to measure the viscoelastic properties of 3 different types of human primary fibroblasts derived from a same patient: normal and scar dermal fibroblasts and palmar fascial fibroblasts from Dupuytren's nodules. Different stiffness hydrogels (soft ~1 kPa and stiff ~ 50 kPa) were used as cell culture matrix to mimic the mechanical properties of the natural tissues, and atomic force microscopy step response force curves were used to discriminate between elastic and viscous properties of cells...
April 27, 2018: Journal of Molecular Recognition: JMR
Haresh Ajani, Josef Jansa, Cemal Köprülüoğlu, Pavel Hobza, Vladimír Kryštof, Antonín Lyčka, Martin Lepsik
We report on the synthesis, activity testing, docking, and quantum mechanical scoring of novel imidazo[1,2-c]pyrimidin-5(6H)-one scaffold for cyclin-dependent kinase 2 (CDK2) inhibition. A series of 26 compounds substituted with aromatic moieties at position 8 has been tested in in vitro enzyme assays and shown to inhibit CDK2. 2D structure-activity relationships have ascertained that small substituents at position 8 (up to the size of naphtyl or methoxyphenyl) generally lead to single-digit micromolar IC50 values, whereas bigger substituents (substituted biphenyls) decreased the compounds' activities...
April 23, 2018: Journal of Molecular Recognition: JMR
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