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Journal of Molecular Recognition: JMR

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https://www.readbyqxmd.com/read/28417509/a-biomolecular-recognition-approach-for-the-functionalization-of-cellulose-with-gold-nanoparticles
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
https://www.readbyqxmd.com/read/28295715/grb7-protein-ra-domain-oligomerization
#14
Malika P Godamudunage, Albert Foster, Darius Warren, Barbara A Lyons
The growth factor receptor bound protein 7 (Grb7) is an adaptor protein that is often coamplified with the erythroblastosis oncogene B 2 receptor in 20% to 30% of breast cancer patients. Grb7 overexpression has been linked to increased cell migration and cancer metastasis. The ras associating and pleckstrin homology domain region of Grb7 has been reported to interact with various other downstream signaling proteins such as four and half Lin11, Isl-1, Mec-3 (LIM) domains isoform 2 and filamin α. These interactions are believed to play a role in regulating Grb7-mediated cell migration function...
March 14, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28295701/the-impact-of-binding-of-macrocyclic-metal-complexes-on-amyloid-fibrillization-of-insulin-and-lysozyme
#15
Vladyslava Kovalska, Svitlana Chernii, Vsevolod Cherepanov, Mykhaylo Losytskyy, Victor Chernii, Oleg Varzatskii, Anton Naumovets, Sergiy Yarmoluk
Amyloid fibrils are insoluble protein aggregates whose accumulation in cells and tissues is connected with a range of pathological diseases. We studied the impact of 2 metal complexes (axially coordinated Hf phthalocyanine and iron (II) clathrochelate) on aggregation of insulin and lysozyme. For both proteins, the host-guest interaction with these compounds changes the kinetics of fibrillization and affects the morphology of final aggregates. The Hf phthalocyanine is a very efficient inhibitor of insulin fibrillization; in its presence, only very low amounts of fibrils with the diameters of 0...
March 14, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28256775/enhanced-adhesion-of-streptococcus-mutans-to-hydroxyapatite-after-exposure-to-saliva
#16
Christian Spengler, Nicolas Thewes, Friederike Nolle, Thomas Faidt, Natalia Umanskaya, Matthias Hannig, Markus Bischoff, Karin Jacobs
Streptococcus mutans cells form robust biofilms on human teeth and are strongly related to caries incidents. Hence, understanding the adhesion of S. mutans in the human oral cavity is of major interest for preventive dentistry. In this study, we report on atomic force microscopy-based single-cell force spectroscopy measurements of S. mutans cells to hydroxyapatite surfaces. We observe for almost all measurements a significant difference in adhesion strength for S. mutans as well as for Staphylococcus carnosus cells...
March 3, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28247484/the-involvement-of-coordinative-interactions-in-the-binding-of-dihydrolipoamide-dehydrogenase-to-titanium-dioxide-localization-of-a-putative-binding-site
#17
Avraham Dayan, Gilad Babin, Assaf Ganoth, Nivin Samir Kayouf, Neta Nitoker Eliaz, Srijana Mukkala, Yossi Tsfadia, Gideon Fleminger
Titanium (Ti) and its alloys are widely used in orthodontic and orthopedic implants by virtue to their high biocompatibility, mechanical strength, and high resistance to corrosion. Biointegration of the implants with the tissue requires strong interactions, which involve biological molecules, proteins in particular, with metal oxide surfaces. An exocellular high-affinity titanium dioxide (TiO2 )-binding protein (TiBP), purified from Rhodococcus ruber, has been previously studied in our lab. This protein was shown to be homologous with the orthologous cytoplasmic rhodococcal dihydrolipoamide dehydrogenase (rhDLDH)...
February 28, 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
#18
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...
February 24, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28233349/inhibitory-effect-of-2-4-dichlorophenoxyacetic-acid-on-ros-autophagy-formation-and-mrna-replication-for-influenza-virus-infection
#19
Gansukh Enkhtaivan, Pandurangan Muthuraman, Doo Hwan Kim
Influenza virus has had a high rate of antigenic shift and drift that causes significant morbidity and mortality in humans and animals. The lack of excellent pharmacological treatment underlines the importance of the development of the novel antiviral drugs. We investigated the anti-influenza A and B viruses of 2,4-dichlorophenoxyacetic acid (2,4-D), which is the synthetic analog to auxin and is used as a popular herbicide in the agricultural practices. 2,4-D was evaluated using a cytopathic effect reduction method; assay results showed that 2,4-D possessed strong anti-influenza A and B viruses inhibiting the formation of a visible cytopathic effect...
February 24, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28156029/cationic-imprinting-of-pb-ii-within-composite-networks-based-on-bovine-or-fish-chondroitin-sulfate
#20
Vanessa R A Ferreira, Manuel A Azenha, M Teresa Mêna, Cosme Moura, Carlos M Pereira, Ricardo I Pérez-Martín, José A Vázquez, A Fernando Silva
Imprinting chondroitin sulfate (CS)/silica composites with Pb(II) and Cu(II) cations was explored with CS of bovine and different fish species origin. The process was based on the assumption that particular arrangements of the linear CS chains in aqueous solution, induced so as to accommodate cross complexation with the cations, would be embodied into a tridimensional matrix created through an organoalkoxysilane sol-gel scheme. The presence of Cu(II) in the synthesis of the composites did not result in the production of significantly stronger Cu(II)-oriented binding arrangements, and therefore, the imprinting was not successful...
February 3, 2017: Journal of Molecular Recognition: JMR
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