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Journal of Molecular Recognition: JMR

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https://www.readbyqxmd.com/read/29143447/investigation-of-the-interactions-between-aptamer-and-misfolded-proteins-from-monomer-and-oligomer-to-fibril-by-single-molecule-force-spectroscopy
#1
Yan Zheng, Qing Wang, Xiaohai Yang, Zhiping Li, Lei Gao, Hua Zhang, Wenyan Nie, Xiuhua Geng, Kemin Wang
Increasing knowledge on the understanding interactions of aptamer with misfolded proteins (including monomer, oligomer, and amyloid fibril) is crucial for development of aggregation inhibitors and diagnosis of amyloid diseases. Herein, the interactions of lysozyme monomer-, oligomer-, and amyloid fibril-aptamer were investigated using single-molecule force spectroscopy. The results revealed that the aptamer screened against lysozyme monomer could also bind to oligomer and amyloid fibril, in spite of the recognition at a lower binding probability...
November 16, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/29143375/an-immunoinformatics-approach-to-define-t-cell-epitopes-from-polyketide-and-non-ribosomal-peptide-synthesis-proteins-of-mycobacterium-tuberculosis-as-potential-vaccine-candidates
#2
S Dhivya, V Baskar, S R Kumar, R Sathishkumar
The role of polyketide and non-ribosomal proteins from the class of small molecule metabolism of Mycobacterium tuberculosis is well documented in envelope organization, virulence, and pathogenesis. Consequently, the identification of T cell epitopes from these proteins could serve to define potential antigens for the development of vaccines. Fourty-one proteins from polyketide and non-ribosomal peptide synthesis of small molecule metabolism proteins of M tuberculosis H37Rv were analyzed computationally for the presence of HLA class I binding nanomeric peptides...
November 16, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/29119617/computer-aided-design-of-human-sialyltransferase-inhibitors-of-hst8sia-iii
#3
Christopher Dobie, Andrew P Montgomery, Rémi Szabo, Danielle Skropeta, Haibo Yu
Sialyltransferase (ST) upregulation and the resultant hypersialylation of tumour cell surfaces is an established hallmark of many cancers including lung, breast, ovarian, pancreatic and prostate cancer. The role of ST enzymes in tumour cell growth and metastasis, as well as links to multi-drug resistance, has seen ST inhibition emerge as a target for potential antimetastatic cancer treatments. The most potent of these reported inhibitors are transition-state analogues. Although there are several examples of these in the literature, many have suspected poor pharmacokinetic properties and are not readily synthetically accessible...
November 9, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/29115701/multispecificity-of-a-recombinant-anti-ras-monoclonal-antibody
#4
John W Schrader, Gary R McLean
Recombinant monoclonal antibodies (Ab's) have widespread application as research tools, diagnostic reagents and as biotherapeutics. Whilst studying the cellular molecular switch protein m-ras, a recombinant monoclonal antibody to m-ras was generated for use as a research tool. Antibody genes from a single rabbit B cell secreting IgG to an m-ras specific peptide sequence were expressed in mammalian cells, and monoclonal rabbit IgG binding was characterized by ELISA and peptide array blotting. Although the monoclonal Ab was selected for specificity to m-ras peptide, it also bound to both recombinant full-length m-ras and h-ras proteins...
November 8, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/29067762/study-on-the-interaction-between-cannabinol-and-dna-using-acridine-orange-as-a-fluorescence-probe
#5
Zhengshan Tian, Zechun Wang, Xinxin Han, Ning Wang, Ruiyong Wang
The interaction between cannabinol (CBN) and herring-sperm deoxyribonucleic acid was investigated by using acridine orange as a fluorescence probe in this work. UV-Vis spectroscopy, fluorescence spectroscopy, and DNA melting techniques were used. The fluorescence of DNA acridine orange was quenched by CBN. The results indicated that CBN can bind to DNA. The binding constant for the CBN and herring-sperm deoxyribonucleic acid was obtained at 3 temperatures, respectively. Results of molecular docking corroborated the experimental results obtained from spectroscopic investigations...
October 25, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/29024183/seventh-international-afmbiomed-conference-on-afm-in-life-sciences-and-medicine-april-11-to-15-2016-porto-portugal
#6
EDITORIAL
Susana R Sousa, Pierre Parot, Jean-Luc Pellequer
No abstract text is available yet for this article.
October 12, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/29024117/molecularly-imprinted-polymers-synthesized-via-template-immobilization-on-fumed-silica-nanoparticles-for-the-enrichment-of-phosphopeptides
#7
Mariana Duarte, Prabal Subedi, Ecevit Yilmaz, Katrin Marcus, Thomas Laurell, Simon Ekström
Phosphorylation is a protein post-translational modification (PTM) that plays an important role in cell signaling, cell differentiation, and metabolism. The hyper phosphorylated forms of certain proteins have been appointed as biomarkers for neurodegenerative diseases, and phosphorylation-related mutations are important for detecting cancer pathways. Due to the low abundance of phosphorylated proteins in biological fluids, sample enrichment is beneficial prior to detection. Thus, a need to find new strategies for enriching phosphopeptides has emerged...
October 12, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28994207/identification-of-peptide-binding-sites-within-bsa-using-rapid-laser-induced-covalent-cross-linking-combined-with-high-performance-mass-spectrometry
#8
Melinda Hauser, Chen Qian, Steven T King, Sarah Kauffman, Fred Naider, Robert L Hettich, Jeffrey M Becker
We are developing a rapid, time-resolved method using laser-activated cross-linking to capture protein-peptide interactions as a means to interrogate the interaction of serum proteins as delivery systems for peptides and other molecules. A model system was established to investigate the interactions between bovine serum albumin (BSA) and 2 peptides, the tridecapeptide budding-yeast mating pheromone (α-factor) and the decapeptide human gonadotropin-releasing hormone (GnRH). Cross-linking of α-factor, using a biotinylated, photoactivatable p-benzoyl-L-phenylalanine (Bpa)-modified analog, was energy-dependent and achieved within seconds of laser irradiation...
October 10, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28994156/synthesis-of-nano-sized-hydrogen-phosphate-imprinted-polymer-in-acetonitrile-water-mixture-and-its-use-as-a-recognition-element-of-hydrogen-phosphate-selective-all-solid-state-potentiometric-electrode
#9
Taher Alizadeh, Khalil Atayi
Herein, a new recipe is introduced for the preparation of hydrogen phosphate ion-imprinted polymer nanoparticles (nano-IIP) in acetonitrile/water (63.5:36.5) using phosphoric acid as the template. The nano-IIP obtained was used as the recognition element of a carbon paste potentiometric sensor. The IIP electrode showed a Nernstian response to hydrogen phosphate anion; whereas, the non-imprinted polymer (NIP)-based electrode had no considerable sensitivity to the anion. The presence of both methacrylic acid and vinyl pyridine in the IIP structure, as well as optimization of the functional monomers-template proportion, was found to be important to observe the sensing capability of the IIP electrode...
October 10, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28990233/molecular-dynamics-investigation-of-stereoselective-inhibition-mechanism-of-hif-2%C3%AE-arnt-heterodimer
#10
Dong-Ru Sun, Qing-Chuan Zheng, Hong-Xing Zhang
Hypoxia-inducible factors (HIFs) are heterodimeric transcription factors related with the onset and progression of solid tumors. Studies demonstrated a class of tetrazole containing chiral inhibitors could stereoselectively disrupt the HIF-2 dimerization and reduce the target gene expression. However, the dynamical features and structural motifs of the HIF-2 heterodimer caused by the binding of enantiomers have not been rationalized at the atomistic level. In this work, molecular dynamics (MD) simulations combined with adaptive steered MD (ASMD) simulations were used to investigate stereoselective interrupting mechanism of HIF-2...
October 9, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28983989/detailed-positron-annihilation-lifetime-spectroscopic-investigation-of-atrazine-imprinted-polymers-grafted-onto-pe-pp-non-woven-fabrics
#11
Meshude Akbulut Söylemez, Olgun Güven
This study presents the preparation of molecularly imprinted matrices by using radiation-induced grafting technique onto polyethylene/polypropylene (PE/PP) non-woven fabrics. Atrazine imprinted polymers were grafted onto PE/PP non-woven fabrics through the use of methacrylic acid (MAA) and ethylene glycol dimethylacrylate (EGDMA) as the functional monomer and crosslinking agent, respectively. Grafted MIPs were characterized by attenuated total reflectance Fourier transform infra-red spectroscopy (ATR-FTIR), X-ray photoelectron spectroscopy (XPS), elemental analysis, scanning electron microscopy (SEM), and positron annihilation lifetime spectroscopy (PALS)...
October 6, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28983974/molecular-design-of-stat3-derived-peptide-selectivity-between-bet-proteins-brd2-and-brd4-in-ovarian-cancer
#12
Lixia Zhu, Xi Ding
Stat3 signaling has been recognized as a potential therapeutic target of human ovarian cancer. The signaling is transducted through the peptide-medicated interaction of Stat3 with BET family members Brd2 and Brd4 -- 2 highly homologous proteins involved in differential downstream pathways. Here, we reported a successful design of peptide selectivity between the Brd2 and Brd4. The design resulted in 3 linear peptides SMSLQCXYLGVA, QSKVLTXSYWGA, and RQCNLGXLYMNY with high or moderate selectivity for Brd2 over Brd4 (S = 3...
October 6, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28961341/biophysical-insight-into-the-heparin-peptide-interaction-and-its-modulation-by-a-small-molecule
#13
Neha Tiwari, Ankit Srivastava, Bishwajit Kundu, Manoj Munde
The heparin-protein interaction plays a vital role in numerous physiological and pathological processes. Not only is the binding mechanism of these interactions poorly understood, studies concerning their therapeutic targeting are also limited. Here, we have studied the interaction of the heparin interacting peptide (HIP) from Tat (which plays important role in HIV infections) with heparin. Isothermal titration calorimetry binding exhibits distinct biphasic isotherm with two different affinities in the HIP-heparin complex formation...
September 29, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28895236/protein-surface-roughness-accounts-for-binding-free-energy-of-plasmepsin-ii-ligand-complexes
#14
Mario E Valdés-Tresanco, Mario S Valdés-Tresanco, Pedro A Valiente, Germinal Cocho, Ricardo Mansilla, J M Nieto-Villar
The calculation of absolute binding affinities for protein-inhibitor complexes remains as one of the main challenges in computational structure-based ligand design. The present work explored the calculations of surface fractal dimension (as a measure of surface roughness) and the relationship with experimental binding free energies of Plasmepsin II complexes. Plasmepsin II is an attractive target for novel therapeutic compounds to treat malaria. However, the structural flexibility of this enzyme is a drawback when searching for specific inhibitors...
September 12, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28872251/room-temperature-synthesis-and-binding-studies-of-solution-processable-histamine-imprinted-microspheres
#15
Edwin F Romano, Clovia I Holdsworth, Joselito P Quirino, Regina C So
Accurate quantification of histamine levels in food and in biological samples is important for monitoring the quality of food products and for the detection of pathophysiological conditions. In this study, solution processable histamine-imprinted microspheres were synthesized at 30°C via dilute free radical phototochemical polymerization technique using ethylene glycol dimethacrylate (EGDMA) as the crosslinker and methacrylic acid (MAA) as the monomer. The processability of the resulting polymer is dictated by the monomer feed concentration (eg, 4 wt% 80:20 EGDMA:MAA formulation) and solvent (acetonitrile)...
September 5, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28856782/activity-of-zn-and-mg-phthalocyanines-and-porphyrazines-in-amyloid-aggregation-of-insulin
#16
V Kovalska, S Chernii, M Losytskyy, J Ostapko, I Tretyakova, A Gorski, V Chernii, S Yarmoluk
Formation of the deposits of protein aggregates-amyloid fibrils in an intracellular and intercellular space-is common to a large group of amyloid-associated disorders. Among the approaches to develop of therapy of such disorders is the use of agents preventing protein fibrillization. Polyaromatic complexes-porphyrins and phthalocyanines-are known as compounds possessing anti-fibrillogenic activity. Here, we explore the impact of related macrocyclic complexes-phthalocyanines (Pc) and octaphenyl porphyrazines (Pz) of Mg and Zn-on aggregation of amyloidogenic protein insulin...
August 30, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28850770/molecular-insights-into-a%C3%AE-42-protofibril-destabilization-with-a-fluorinated-compound-d744-a-molecular-dynamics-simulation-study
#17
Rajneet Kaur Saini, Suniba Shuaib, Bhupesh Goyal
The aggregation of amyloid β-peptide (Aβ42 ) into toxic oligomers, fibrils, has been identified as a key process in Alzheimer's disease (AD) progression. The role of halogen-substituted compounds have been highlighted in the disassembly of Aβ protofibril. However, the underlying inhibitory mechanism of Aβ42 protofibril destabilization remains elusive. In this regard, a combined molecular docking and molecular dynamics (MD) simulations were performed to elucidate the inhibitory mechanism of a fluorinated compound, D744, which has been reported previously for potential in vitro and in vivo inhibitory activity against Aβ42 aggregation and reduction in the Aβ-induced cytotoxicity...
August 29, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28836695/synthesis-binding-ability-and-cell-cytotoxicity-of-fluorescent-probes-for-l-arginine-detection-based-on-naphthalene-derivatives-experiment-and-theory
#18
Jie Li, Yang Zhang, Yanmei Chen, Xuefang Shang, Tongyu Ti, Hongli Chen, Tianyun Wang, Jinlian Zhang, Xiufang Xu
Inspired by biological related parts, Schiff base derivatives and functional groups of chemical modification can provide efficient detection method of amino acids. Therefore, we have designed and prepared 4 compounds based on Schiff base derivatives involving ─NO2 , ─OH, and naphthyl group. Results indicated that compound 4 containing 2 nitro groups showed strong sensitivity and high selectivity for arginine (Arg) among normal 18 kinds of standard amino acids (alanine, valine, leucine, isoleucine, methionine, aspartic acid, glutamic acid, arginine, glycine, serine, asparagine, phenylalanine, histidine, tryptophan, proline, lysine, glutamine, and cysteine)...
August 24, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28833724/construction-and-characterization-of-mutated-lea-peptides-in-escherichia-coli-to-develop-an-efficient-protein-expression-system
#19
Nishit Pathak, Hiro Hamada, Shinya Ikeno
To develop an efficient protein expression system, we designed a late embryogenesis abundant (LEA) peptide by mutating the LEA peptide constructed in our previous study (LEA-I). The peptide is based on the repeating units of an 11mer motif characteristic of LEA proteins from Polypedilum vanderplanki larvae. In the amino acid sequence of the 13mer LEA peptide, glycine at the 6th and 12th positions was replaced with other amino acids via point mutations. Glutamic acid, lysine, leucine, and asparagine in the LEA peptide at the 6th and 12th positions increased green fluorescence protein (GFP) expression...
August 23, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28791744/assessment-of-the-imprinting-efficiency-of-an-imide-with-a-stoichiometric-pyridine-based-functional-monomer-in-precipitation-polymerisation
#20
K Fremielle Lim, Andrew J Hall, Stefania Lettieri, Clovia I Holdsworth
The efficiency of the stoichiometric non-covalent imprinting of the imide 2,3,5-tri-O-acetyluridine (TAU) with 2,6-bis(acrylamido)pyridine (BAAPy) as functional monomer due to their strong donor-acceptor-donor/acceptor-donor-acceptor (DAD/ADA) hydrogen bond array interaction has been evaluated by bulk imprinting. This study is the first to investigate the imprinting and template rebinding efficiencies of the TAU/BAAPy molecularly imprinted polymeric (MIP) system prepared by precipitation polymerisation. We found that the stoichiometric 1:1 T:FM ratio has not been maintained in precipitation polymerisation and an optimal TAU:BAAPy ratio of 1:2...
August 9, 2017: Journal of Molecular Recognition: JMR
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