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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
Rahul Mishra, Xing Yu, Chandan Kishor, Gavan Holloway, Kam Lau, Mark von Itzstein, Barbara S Coulson, Helen Blanchard
The outer capsid spike protein VP4 of rotaviruses is a major determinant of infectivity and serotype specificity. Proteolytic cleavage of VP4 into 2 domains, VP8* and VP5*, enhances rotaviral infectivity. Interactions between the VP4 carbohydrate-binding domain (VP8*) and cell surface glycoconjugates facilitate initial virus-cell attachment and subsequent cell entry. Our saturation transfer difference nuclear magnetic resonance (STD NMR) and isothermal titration calorimetry (ITC) studies demonstrated that VP8*64-224 of canine rotavirus strain K9 interacts with N-acetylneuraminic and N-glycolylneuraminic acid derivatives, exhibiting comparable binding epitopes to VP8* from other neuraminidase-sensitive animal rotaviruses from pigs (CRW-8), cattle (bovine Nebraska calf diarrhoea virus, NCDV), and Rhesus monkeys (Simian rhesus rotavirus, RRV)...
April 23, 2018: Journal of Molecular Recognition: JMR
Lasse Thomsen, Leonid Gurevich
The incretin hormone glucagon-like peptide-1 (GLP-1) has been subject to substantial pharmaceutical research regarding the treatment of type 2 diabetes mellitus. However, quantification of GLP-1 levels remains complicated due to the low circulation concentration and concurrent existence of numerous metabolites, homologous peptides, and potentially introduced GLP-1 receptor agonists. Surface plasmon resonance (SPR) facilitates real-time monitoring allowing a more detailed characterisation of the interaction compared with conventional enzyme-linked immunosorbent assays (ELISA)...
April 19, 2018: Journal of Molecular Recognition: JMR
Kai-Li Zhou, Dong-Qi Pan, Yan-Yue Lou, Jie-Hua Shi
The intermolecular interaction of fosinopril, an angiotensin converting enzyme inhibitor with bovine serum albumin (BSA), has been investigated in physiological buffer (pH 7.4) by multi-spectroscopic methods and molecular docking technique. The results obtained from fluorescence and UV absorption spectroscopy revealed that the fluorescence quenching mechanism of BSA induced by fosinopril was mediated by the combined dynamic and static quenching, and the static quenching was dominant in this system. The binding constant, Kb , value was found to lie between 2...
April 16, 2018: Journal of Molecular Recognition: JMR
Mohammad Hasanzadeh, Fozieh Mokhtari, Vahid Jouyban-Gharamaleki, Ahad Mokhtarzadeh, Nasrin Shadjou
This study reports on the electropolymerization of a low toxic and biocompatible nanopolymer with entitle poly arginine-graphene quantum dots-chitosan (PARG-GQDs-CS) as a novel strategy for surface modification of glassy carbon surface and preparation of a new interface for measurement of malondialdehyde (MDA) in exhaled breath condensate. Electrochemical deposition, as a well-controlled synthesis procedure, has been used for subsequently layer-by-layer preparation of GQDs-CS nanostructures on a PARG prepolymerized on the surface of glassy carbon electrode using cyclic voltammetry techniques in the regime of -1...
April 15, 2018: Journal of Molecular Recognition: JMR
Paolo Ascenzi, Loris Leboffe, Daniele Toti, Fabio Polticelli, Viviana Trezza
Fipronil is a broad-spectrum pesticide widely used in agriculture, horticulture, and forestry. Because fipronil can cause a variety of toxic effects in animals and humans, its use is authorized as a pesticide in veterinary medicinal products for pets, but not for the treatment of livestock animals whose products are intended for consumption. Recently, however, the presence of fipronil residues has been detected in the eggs and meat of layer hens from farms located in different European countries. Given the relevance of fipronil toxicity for human health, it is important to gain information concerning its fate in the human body, including its binding mode to human serum albumin (HSA), the most abundant protein in plasma...
April 15, 2018: Journal of Molecular Recognition: JMR
Juxin Yin, Jianjian Zhuang, Shaowu Lv, Ying Mu
Excessive reactive oxygen species (ROS) levels are harmful to the body. The peroxidase, GPx, and the superoxide dismutase, SOD, are important antioxidant enzymes for preventing ROS-induced damage. Se-CuZn-65P is an enzyme mimetic with dual GPx and SOD antioxidant function. However, currently, its production is mainly based on the cysteine auxotrophic expression technique, which is inefficient, expensive, and time consuming. In this study, we combined protein engineering and the chemical mutation method to synthesize Se-CuZn-65P...
April 15, 2018: Journal of Molecular Recognition: JMR
Lining Zhao, Shimeng Hu, Qiwei Meng, Mengchen Xu, Hao Zhang, Rutao Liu
As a promising biolabeling biomaterials, quantum dots (QDs) present a great potential. However, the toxicity of QDs to organisms has attracted wide attention. In our research, we introduced an in vitro method to study the molecular mechanisms for the structure and activity alterations of Candida rugosa lipase (CRL) with the binding of 3-mercaptopropionic acid-capped CdTe QDs. Multiple spectroscopic methods, isothermal titration calorimetry, and enzyme activity measurements were used in this paper. QDs statically quenched the intrinsic fluorescence of CRL with the quenching constant decreases from 2...
April 14, 2018: Journal of Molecular Recognition: JMR
Neha Gupta, Roop Shikha Singh, Kavita Shah, Rajniti Prasad, Meenakshi Singh
Epitope imprinting is a promising technique for fabrication of novel diagnostic tools. In this study, an epitope imprinted methodology for recognition of target epitope sequence as well as targeted protein infused by bacterial infection in blood samples of patients suffering from brain fever is developed. Template sequence chosen is a ferric iron binding fbp A protein present in Neisseria meningitidis bacteria. To orient the imprinting template peptide sequence on gold surface of electrochemical quartz crystal microbalance (EQCM), thiol chemistry was utilized to form the self-assembled monolayer on EQCM electrode...
April 6, 2018: Journal of Molecular Recognition: JMR
Navid Niaei, Mohammad Hasanzadeh, Nasrin Shadjou
In the present study, the interaction of human serum albumin (HSA) with some cardiovascular drugs (CARs) under physiological conditions was investigated via the fluorescence spectroscopic and Fourier transform infrared spectroscopy. The CAR included Captopril, Timolol, Propranolol, Atenolol, and Amiodarone. Cardiovascular drugs can effectively quench the endogenous fluorescence of HSA by static quenching mechanism. The fluorescence quenching of HSA is mainly caused by complex formation of HSA with CAR. The binding reaction of CAR with HSA can be concluded that hydrophobic and electrostatic interactions are the main binding forces in the CAR-HSA system...
April 6, 2018: Journal of Molecular Recognition: JMR
Ramakrishna Dumpati, Vishwanath Ramatenki, Rajender Vadija, Santhiprada Vellanki, Uma Vuruputuri
The study considers the Suppressor of cytokine signaling 1 (SOCS1) protein as a novel Type 2 diabetes mellitus (T2DM) drug target. T2DM in human beings is also triggered by the over expression of SOCS proteins. The SOCS1 acts as a ubiquitin ligase (E3), degrades Insulin Receptor Substrate 1 and 2 (IRS1 and IRS2) proteins, and causes insulin resistance. Therefore, the structure of the SOCS1 protein was evaluated using homology-modeling and molecular dynamics methods and validated using standard computational protocols...
April 6, 2018: Journal of Molecular Recognition: JMR
Lubna Maryam, Ashima Sharma, Mohd W Azam, Shahper N Khan, Asad U Khan
The infections caused by multidrug resistant bacteria are widely treated with carabapenem antibiotics as a drug of choice, and human serum albumin (HSA) plays a vital role in binding with drugs and affecting its rate of delivery and efficacy. So, we have initiated this study to characterize the mechanism of doripenem binding and to locate its site of binding on HSA by using spectroscopic and docking approaches. The binding of doripenem leads to alteration of the environment surrounding Trp-214 residue of HSA as observed by UV spectroscopic study...
March 30, 2018: Journal of Molecular Recognition: JMR
Leila Roufegarinejad, Ali Jahanban-Esfahlan, Sanaz Sajed-Amin, Vahid Panahi-Azar, Mahnaz Tabibiazar
Thymol is the main monoterpene phenol present in the essential oils which is used in the food industry as flavoring and preservative agent. In this study, the interaction of thymol with the concentration range of 1 to 6 μM and bovine serum albumin (BSA) at fixed concentration of 1 μM was investigated by fluorescence, UV-vis, and molecular docking methods under physiological-like condition. Fluorescence experiments were performed at 5 different temperatures, and the results showed that the fluorescence quenching of BSA by thymol was because of a static quenching mechanism...
March 30, 2018: Journal of Molecular Recognition: JMR
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