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Journal of Molecular Recognition: JMR

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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
#1
REVIEW
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
https://www.readbyqxmd.com/read/28370480/pop1-might-be-recruiting-its-type-ia-interface-for-nlrp3-mediated-pyd-pyd-interaction-insights-from-md-simulation
#11
Jitendra Maharana, Ashutosh Vats, Santwana Gautam, Bibhu Prasad Nayak, Sushil Kumar, Jasobanta Sendha, Sachinandan De
Inflammasomes are multiprotein caspase-activating complexes that enhance the maturation and release of proinflammatory cytokines (IL-1β and IL-18) in response to the invading pathogen and/or host-derived cellular stress. These are assembled by the sensory proteins (viz NLRC4, NLRP1, NLRP3, and AIM-2), adaptor protein (ASC), and effector molecule procaspase-1. In NLRP3-mediated inflammasome activation, ASC acts as a mediator between NLRP3 and procaspase-1 for the transmission of signals. A series of homotypic protein-protein interactions (NLRP3(PYD) :ASC(PYD) and ASC(CARD) :CASP1(CARD) ) propagates the downstream signaling for the production of proinflammatory cytokines...
April 3, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28349611/ion-cum-molecularly-dual-imprinted-polymer-for-simultaneous-removal-of-cadmium-and-salicylic-acid
#12
Deepali Rahangdale, Anupama Kumar, G Archana, Rita Sandip Dhodapkar
Ion cum molecularly dual imprinted polymer (DMIP) was synthesized for the simultaneous removal of salicylic acid (SA) and cadmium (Cd) by suspension polymerization method using chitosan (CTS) as functional polymer, epichlorohydrin as cross-linker, and 4-hydroxy benzoic acid (4HBA) as well as Cd as organic and inorganic templates, respectively. Use of the dummy template 4HBA during the synthesis of DMIP had the advantage of creating imprinted cavities in DMIP, which depicted good uptake for SA. Scanning electron microscopy and Fourier transform infrared spectroscopy indicated successful preparation of DMIP...
March 28, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28332252/functional-organic-material-for-roxarsone-and-its-derivatives-recognition-via-molecular-imprinting
#13
Weigang Fan, Xuemin Zhang, Yagang Zhang, Penglei Wang, Letao Zhang, Zhaoming Yin, Jun Yao, Wei Xiang
Roxarsone, one of feed add drugs containing arsenic, has been most widely used in poultry and swine industry. Roxarsone discharged into the environment has caused serious pollution problem. Herein, a reusable functional material for selective recognition and adsorption of roxarsone and its derivatives were designed and synthesized. The interaction mechanism is based on acid-base interaction and surface molecular imprinting. Dual functionalized core-shell structure with silica gel as the core was prepared to use as carrier for surface molecularly imprinted polymers...
March 22, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28326626/preparation-and-evaluation-of-molecularly-imprinted-polymer-for-selective-recognition-and-adsorption-of-gossypol
#14
Keke Zhi, Lulu Wang, Yagang Zhang, Xuemin Zhang, Letao Zhang, Li Liu, Jun Yao, Wei Xiang
Molecularly imprinted polymers (MIPs) were designed and prepared via bulk thermal polymerization with gossypol as the template molecule and dimethylaminoethyl methacrylate as the functional monomer. The morphology and microstructures of MIPs were characterized by scanning electron microscope and Brunauer-Emmett-Teller surface areas. Static adsorption tests were performed to evaluate adsorption behavior of gossypol by the MIPs. It was found that adsorption kinetics and adsorption isotherms data of MIPs for gossypol were fit well with the pseudo-second-order model and Freundlich model, respectively...
March 22, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28322473/synthesis-of-hydrophobic-nanoparticles-for-real-time-lysozyme-detection-using-surface-plasmon-resonance-sensor
#15
Yeşeren Saylan, Fatma Yılmaz, Ali Derazshamshir, Erkut Yılmaz, Adil Denizli
Diagnostic biomarkers such as proteins and enzymes are generally hard to detect because of the low abundance in biological fluids. To solve this problem, the advantages of surface plasmon resonance (SPR) and nanomaterial technologies have been combined. The SPR sensors are easy to prepare, no requirement of labelling and can be detected in real time. In addition, they have high specificity and sensitivity with low cost. The nanomaterials have also crucial functions such as efficiency improvement, selectivity, and sensitivity of the detection systems...
March 21, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28322471/synthesis-of-naproxen-imprinted-polymer-using-pickering-emulsion-polymerization
#16
Małgorzata Kujawska, Tongchang Zhou, Andrzej W Trochimczuk, Lei Ye
For the last decades, molecular imprinting is developing intensively, especially in the case of the application of new imprinting techniques. In this work, for the first time, a Pickering emulsion polymerization was used to synthesize the S-naproxen-imprinted polymer spheres following a noncovalent protocol. To enhance the knowledge about imprinting process using mentioned technique, thorough analysis of the synthesis process was performed. Optimization of polymerization conditions included the selection of functional monomer, cross-linking agent, type of porogen, surfactant, and the choice of appropriate amount of the template and porogen...
March 21, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28322467/a-new-strategy-for-accelerated-extraction-of-target-compounds-using-molecularly-imprinted-polymer-particles-embedded-in-a-paper-based-disk
#17
Mashaalah Zarejousheghani, Steffi Schrader, Monika Möder, Matthias Schmidt, Helko Borsdorf
In this study, a general simple and inexpensive method is introduced for the preparation of a paper-based selective disk-type solid phase extraction (SPE) technique, appropriate for fast and high throughput monitoring of target compounds. An ion exchange molecularly imprinted polymer (MIP) was synthesized for the extraction and analysis of acesulfame, an anthropogenic water quality marker. Acesulfame imprinting was used as an example for demonstrating the benefits of a nanosized, swellable MIP extraction sorbents integrated in an on-site compatible concept for water quality monitoring...
March 21, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28299833/unsupervised-pharmacophore-modeling-combined-with-qsar-analyses-revealed-novel-low-micromolar-sirt2-inhibitors
#18
Mohammad A Khanfar, Mutasem O Taha
Situin 2 (SIRT2) enzyme is a histone deacetylase that has important role in neuronal development. SIRT2 is clinically validated target for neurodegenerative diseases and some cancers. In this study, exhaustive unsupervised pharmacophore modeling was combined with quantitative structure-activity relationship (QSAR) analysis to explore the structural requirements for potent SIRT2 inhibitors using 146 known SIRT2 ligands. A computational workflow that combines genetic function algorithm with k-nearest neighbor or multiple linear regression was implemented to build self-consistent and predictive QSAR models based on combinations of pharmacophores and physicochemical descriptors...
March 15, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28295743/characterization-of-surface-binding-sites-in-glycoside-hydrolases-a-computational-study
#19
Samaneh Samaei-Daryan, Bahram Goliaei, Azadeh Ebrahim-Habibi
Structural properties of carbohydrate surface binding sites (SBSs) were investigated with computational methods. Eighty-five SBSs of 44 enzymes in 119 Protein Data Bank (PDB) files were collected as a dataset. On the basis of SBSs shape, they were divided into 3 categories: flat surfaces, clefts, and cavities (types A, B, and C, respectively). Ligand varieties showed the correlation between shape of SBSs and ligands size. To reduce cut-off differences in each SBSs with different ligand size, molecular docking were performed...
March 15, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28295815/elucidating-the-interaction-of-clofazimine-with-bovine-liver-catalase-a-comprehensive-spectroscopic-and-molecular-docking-approach
#20
Masihuz Zaman, Saima Nusrat, Syed Mohammad Zakariya, Mohsin Vahid Khan, Mohammad Rehan Ajmal, Rizwan Hasan Khan
Nowadays, understanding of interface between protein and drugs has become an active research area of interest. These types of interactions provide structural guidelines in drug design with greater clinical efficacy. Thus, structural changes in catalase induced by clofazimine were monitored by various biophysical techniques including UV-visible spectrometer, fluorescence spectroscopy, circular dichroism, and dynamic light scattering techniques. Increase in absorption spectra (UV-visible spectrum) confers the complex formation between drug and protein...
March 14, 2017: Journal of Molecular Recognition: JMR
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