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Journal of Molecular Recognition: JMR

Marta Spodzieja, Katarzyna Kalejta, Aleksandra S Kołodziejczyk, Martyna Maszota-Zieleniak, Sylwia Rodziewicz-Motowidło, Wioletta Żmudzińska, Paulina Czaplewska
Cystatin C originally identified as a cysteine proteases inhibitor has a broad spectrum of biological roles ranging from inhibition of extracellular cysteine protease activities, bone resorption, and modulation of inflammatory responses to stimulation of fibroblasts proliferation. There is an increasing number of evidence to suggest that human cystatin C (hCC) might play a protective role in the pathophysiology of sporadic Alzheimer's disease. In vivo and in vitro results well documented the association of hCC with Aβ and the hCC-induced inhibition of Aβ fibril formation...
October 7, 2016: Journal of Molecular Recognition: JMR
Ceren Bayraç, Hüseyin Avni Öktem
To monitor the specificity of Staphylococcus aureus aptamer (SA-31) against its target cell, we used enzyme-linked aptamer assay. In the presence of target cell, horseradish peroxidase-conjugated streptavidin bound to biotin-labeled SA-31 showed specific binding to S  aureus among 3 different bacteria with limit of detection of 10(3) colony-forming unit per milliliter. The apparent Ka was 1.39 μM(-1)  ± 0.3 μM(-1) . The binding of SA-31 to membrane proteins extracted from cell surface was characterized using isothermal titration calorimetry, and the effect of changes in binding temperature and salt concentrations of binding buffer was evaluated based on thermodynamic parameters (Ka , ΔH, and ΔG)...
October 3, 2016: Journal of Molecular Recognition: JMR
Manjanath Patgar, Amar Durgannavar, Sharanappa Nandibewoor, Shivamurti Chimatadar
The mechanism of the interaction between bovine serum albumin (BSA) and desvenlafaxine was studied using fluorescence, ultraviolet absorption, 3-dimensional fluorescence spectroscopy, circular dichroism, synchronous fluorescence spectroscopy, cyclic voltametry, differential scanning calorimetry, and attenuated total reflection-Fourier transform infrared spectroscopic techniques under physiological condition at pH 7.4. Stern-Volmer calculations authenticate the fluorescence of BSA that was quenched by desvenlafaxine in a collision quenching mode...
October 3, 2016: Journal of Molecular Recognition: JMR
Ketaki Apte, Reimer Stick, Manfred Radmacher
The lamina is a filamentous meshwork beneath the inner nuclear membrane that confers mechanical stability to nuclei. The E145K mutation in lamin A causes Hutchinson-Gilford progeria syndrome (HGPS). It affects lamin filament assembly and induces profound changes in the nuclear architecture. Expression of wild-type and E145K lamin A in Xenopus oocytes followed by atomic force microscopy (AFM) probing of isolated oocyte nuclei has shown significant changes in the mechanical properties of the lamina. Nuclei of oocytes expressing E145K lamin A are stiffer than those expressing wild-type lamin A...
September 28, 2016: Journal of Molecular Recognition: JMR
Maidul Beg, Anukul Maji, Amit Kumar Mandal, Somnath Das, Mt Nasima Aktara, Pradeep K Jha, Maidul Hossain
In recent years, green synthesized nanoparticles from plant extract have drawn a great interest due to their prospective nanomedicinal application. This study investigates a proficient, safer, and sustainable way for the preparation of AgNPs using medicinal plant Pongamia pinnata (family: Leguminoseae, species: Pinnata) seeds extract without using any external reducing and stabilizing agent. Both ultraviolet-visible spectrum at λmax  = 439 nm and energy dispersive X-ray spectra proof the formation of AgNPs...
September 28, 2016: Journal of Molecular Recognition: JMR
Hua-Jin Zeng, Min Miao, Ran Yang, Ling-Bo Qu
In this study, the fibrillation of hen egg-white lysozyme (HEWL) in the absence and presence of different concentrations of silybin was studied by thioflavin T spectroscopy, Congo red binding assays, 8-anilino-1-naphthalenesulfonic acid (ANS) fluorescence assay, circular dichroism, and transmission electron microscopy. The experimental results indicated that not only the fibrillation of HEWL at high temperature (65°C) and low pH (pH = 2.0) could be inhibited effectively by silybin but also the inhibition of HEWL by silybin followed a dose-dependent manner...
September 27, 2016: Journal of Molecular Recognition: JMR
B van Grinsven, K Betlem, T J Cleij, C E Banks, M Peeters
In recent years, there has been a tremendous increase in the papers published on synthetic recognition elements. Molecularly imprinted polymers (MIPs), also referred to as "man-made mimics" of antibodies, are able to rebind their template molecules with high affinity. Advantages compared with those of natural receptors include their excellent thermal and chemical stability, low cost, and ease of the production process. However, their use in commercial biosensors is limited owing to the difficulty to incorporate MIPs into suitable sensing platforms and traditional detection techniques, such as chromatography, that require bulky and sophisticated equipment...
September 9, 2016: Journal of Molecular Recognition: JMR
Naiyf S Alharbi, Jamal M Khaled, Khalid E Alzaharni, Ramzi A Mothana, Mansour S Alsaid, Mansour Alhoshan, Lawrence Arockiasamy Dass, Shine Kadaikunnan, Ahmed S Alobaidi
The increasing prevalence of antibiotic-resistant bacteria is creating a real challenge for health care systems worldwide, making the development of novel antibiotics a necessity. In addition to the development of new antibiotics, there is an urgent need for in-depth characterization of the mechanisms of bacterial resistance toward new drugs. Here, we used essential oils extracted in our laboratory from Piper cubeba against methicillin-resistant Staphylococcus aureus ATCC 43300, one of the most prominent antibiotic-resistant bacteria...
September 5, 2016: Journal of Molecular Recognition: JMR
Eva Žerovnik
We describe studies performed thus far on stefin B from the family of cystatins as a model protein for folding and amyloid fibril formation studies. We also briefly mention our studies on aggregation of some of the missense EPM1 mutants of stefin B in cells, which mimic additional pathological traits (gain in toxic function) in selected patients with EPM1 disease. We collected data on the reported interactors of stefin B and discuss several hypotheses of possible cytosolic alternative functions.
August 31, 2016: Journal of Molecular Recognition: JMR
Sergey L Andreev, Valentina N Buneva, Georgy A Nevinsky
In the literature, there are no available data on how anti-DNA antibodies recognize DNA. In the present work, to study the molecular mechanism of DNA recognition by antibodies, we have used anti-DNA IgGs from blood sera of patients with multiple sclerosis. A stepwise increase in ligand complexity approach was used to estimate the relative contributions of virtually every nucleotide unit of different single- (ss) and double-stranded (ds) oligonucleotides to their affinity for IgG fraction having high affinity to DNA-cellulose...
August 25, 2016: Journal of Molecular Recognition: JMR
F Taghavi, M Habibi-Rezaei, M Bohlooli, M Farhadi, M Goodarzi, S Movaghati, P Maghami, C Taghibiglou, M Amanlou, T Haertlé, A A Moosavi-Movahedi
Oxidative stress has the main role in protein conformational changes and consequent direct involvement in different kind of diseases. Potassium sorbate as a widespread industrial preservative and glucose are two important oxidants that can be involved in oxidative stress. In this study the effect of ellagic acid as a phenolic antioxidant on amyloid fibril formation of human serum albumin upon incubation of potassium sorbate and glucose was studied using thioflavin T assay, surface tension, atomic force microscopy, Amadori product, and carbonyl content assays...
August 12, 2016: Journal of Molecular Recognition: JMR
Mohamed Boumaiza, Haifa Chahed, Aymen Ezzine, Maryse Jaouan, Alessandra Gianoncelli, Giovanna Longhi, Fernando Carmona, Paolo Arosio, Marie-Agnès Sari, Mohamed Nejib Marzouki
Hepcidin, a liver-expressed antimicrobial peptide, has been demonstrated to act as an iron regulatory hormone as well as to exert a wide spectrum of antimicrobial activity. The aim of this work was the expression, as secreted peptide, purification, and characterization of a new recombinant polyHis-tagged camel hepcidin (HepcD-His) in yeast Pichia pastoris. The use of this eukaryotic expression system, for the production of HepcD-His, having 6 histidine residues at its C terminus, was simpler and more efficient compared with the use of the prokaryotic system Escherichia coli...
August 10, 2016: Journal of Molecular Recognition: JMR
Neha Gupta, Kavita Shah, Meenakshi Singh
Neisseria meningitidis, a human-specific bacterial pathogen causes bacterial meningitis by invading the meninges (outer lining) of central nervous system. It is the polysaccharide present on the bacterial capsid that distinguishes various serogroups of N. meningitidis and can be utilized as antigens to elicit immune response. A computational approach identified candidate T-cell epitopes from outer membrane proteins Por B of N. meningitidis (MC58): ((273) KGLVDDADI(282) in loop VII and (170) GRHNSESYH(179) in loop IV) present on the exposed surface of immunogenic loops of class 3 outer membrane proteins allele of N...
August 4, 2016: Journal of Molecular Recognition: JMR
Chunnian Song, Qing Wang, Tuo Xue, Yan Wang, Guangju Chen
We performed conventional and targeted molecular dynamics simulations to address the dynamic transition mechanisms of the conformational transitions from the GA 98 protein with only 1 mutation of Leu45Tyr to GB 98 and from the GA 88 protein with 7 mutations of Gly24Ala, Ile25Thr, Ile30Phe, Ile33Tyr, Leu45Tyr, Ile49Thr, and Leu50Lys to GB 88. The results show that the conformational transition mechanism from the mutated 3α GA 98 (GA 88) state to the α+4β GB 98 (GB 88) state via several intermediate conformations involves the bending of loops at the N and C termini firstly, the unfolding of αA and αC, then the traversing of αB, and the formation of the 4β layer with the conversion of the hydrophobic core...
August 2, 2016: Journal of Molecular Recognition: JMR
Mark Agostino, Ricardo L Mancera, Paul A Ramsland, Juan Fernández-Recio
The antibody crystallizable fragment (Fc) is recognized by effector proteins as part of the immune system. Pathogens produce proteins that bind Fc in order to subvert or evade the immune response. The structural characterization of the determinants of Fc-protein association is essential to improve our understanding of the immune system at the molecular level and to develop new therapeutic agents. Furthermore, Fc-binding peptides and proteins are frequently used to purify therapeutic antibodies. Although several structures of Fc-protein complexes are available, numerous others have not yet been determined...
November 2016: Journal of Molecular Recognition: JMR
Robert J Falconer
Isothermal titration calorimetry is a widely used biophysical technique for studying the formation or dissociation of molecular complexes. Over the last 5 years, much work has been published on the interpretation of isothermal titration calorimetry (ITC) data for single binding and multiple binding sites. As over 80% of ITC papers are on macromolecules of biological origin, this interpretation is challenging. Some researchers have attempted to link the thermodynamics constants to events at the molecular level...
October 2016: Journal of Molecular Recognition: JMR
Xianwei Zhu, Hiroaki Shinohara, Ryuta Miyatake, Takahiro Hohsaka
In the present study, a novel molecular biosensor system model was designed by using a couple of the fluorescent unnatural mutant streptavidin and the carbazole-labeled biotin. BODIPY-FL-aminophenylalanine (BFLAF), a fluorescent unnatural amino acid was position-specifically incorporated into Trp120 position of streptavidin by four-base codon method. On the other hand, carbazole-labeled biotin was synthesized as a quencher for the fluorescent Trp120BFLAF mutant streptavidin. The fluorescence of fluorescent Trp120BFLAF mutant streptavidin was decreased as we expected when carbazole-labeled biotin was added into the mutant streptavidin solution...
October 2016: Journal of Molecular Recognition: JMR
Yajun Zhang, Kaizhu Zeng, Jing Wang, Haiyang Gao, Yefei Nan, Xiaohui Zheng
As a xanthine derivative, doxofylline is believed to be dominant for fighting against asthma in practice. Unlike other xanthines, the antiasthmatic effects of doxofylline lack any definite proof of target and mediating mechanism according to previous reports. In this work, the interaction between doxofylline and β2 -AR was investigated by high performance affinity chromatography using frontal analysis and nonlinear model. The methodology involved the immobilization of β2 -AR on the silica gel by a random linking method, the determination of the binding parameters by frontal analysis and nonlinear chromatography and the exploration of the binding mechanism by site-directed molecular docking...
October 2016: Journal of Molecular Recognition: JMR
Hua-Jin Zeng, Dan Yang, Gui-Zhou Hu, Ran Yang, Ling-Bo Qu
In this study, the molecular interactions between pepsin and three pyrethroid insecticides, including fenvalerate, cyhalothrin and deltamethrin, were investigated by multi-spectroscopic and molecular docking methods under mimic physiological pH conditions. The results indicated that all of these insecticides could interact with pepsin to form insecticide-pepsin complexes. The binding constants, number of binding sites and thermodynamic parameters measured at different temperatures indicated that these three pyrethroid insecticides could spontaneously bind with pepsin mainly through electrostatic forces and hydrophobic interactions with one binding site...
October 2016: Journal of Molecular Recognition: JMR
Mahima Kaushik, Prashant Sinha, Pragya Jaiswal, Swati Mahendru, Kapil Roy, Shrikant Kukreti
Proteins as a biomolecule have been recognized as a "molecule with manifold biological functions". The functions not only include the structural, regulatory and transportation processes inside the body but also its capacity as an extremely specific catalyst for various biochemical reactions. Nature has been quite admirably using proteins as biocatalysts which are known as enzymes. Properties like higher reaction rate, good specificity, faster kinetics, production of lesser by-products and their non-hazardous nature make enzymes the most suitable targets for a process chemist to exploit...
October 2016: Journal of Molecular Recognition: JMR
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