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Journal of Molecular Recognition: JMR

Hua-Xin Zhang, Dan Zhou, Qing-Hua Xia
In this work, the interaction of an anti-HIV drug lamivudine and human serum albumin (HSA) was studied by multispectroscopic and molecular modeling methods. The fluorescence emission spectra showed that the fluorescence of HSA was quenched by lamivudine through static mechanism with HSA-lamivudine complex produced at ground state. According to the binding equilibriums observed at 4 different temperatures, the number of binding site, binding constant, enthalpy change, entropy change, and Gibbs free energy change of the interaction were calculated...
March 7, 2018: Journal of Molecular Recognition: JMR
Donald J Winzor
Rigorous consideration of the consequences of antibody bivalence in the published competitive kinetic procedure for quantifying the solution characteristics of an antigen-antibody interaction in solution has rendered redundant the practice of substituting the Fab fragment for the antibody to ensure validity of the analysis of results in terms of theory developed for a univalent analyte. Although the quantitative expressions differ for univalent and bivalent analytes, the additional contribution arising from bivalence is likely to be well within the limits of experimental uncertainty in the measured binding constant...
February 27, 2018: Journal of Molecular Recognition: JMR
Svetlana V Baranova, Pavel S Dmitrenok, Anastasiya D Zubkova, Nikita V Ivanisenko, Elena S Odintsova, Valentina N Buneva, Georgy A Nevinsky
Histones and their posttranslational modified forms play pivotal roles in chromatin functioning and gene transcription. Also, histones are harmful when they enter the intercellular space; their administration to animals results in systemic inflammatory and toxic responses. Autoantibodies having enzymatic activities (abzymes) are the specific feature of several autoimmune and viral diseases. Electrophoretically homogeneous IgGs containing no canonical proteases were purified from sera of HIV-infected patients by using several affinity chromatographies...
February 19, 2018: Journal of Molecular Recognition: JMR
Liu Yang, Man Zhu, Yuan Kang, Tianfeng Yang, Weina Ma
The binding property between a ligand and its receptor is very important for numerous biological processes. In this study, we developed a high epidermal growth factor receptor (EGFR)-expression cell membrane chromatography (CMC) method to investigate the binding characteristics between EGFR and the ligands gefitinib, erlotinib, canertinib, afatinib, and vandetanib. Competitive binding analysis using gefitinib as the marker was used to investigate the interactions that occurred at specific binding sites on EGFR...
January 24, 2018: Journal of Molecular Recognition: JMR
Rana Shadjou, Mohammad Hasanzadeh, Mohammad Heidar-Poor, Nasrin Shadjou
Aflatoxins are potential food pollutants produced by fungi. One of important toxins is aflatoxin M1 (AFM1). A great deal of concern is associated with AFM1 toxicity. In the present study, an innovative electrochemical interface for quantitation of AFM1 based on ternary signal amplification strategy was fabricated. In this work, silver nanoparticles was electrodeposited onto green and biocompatible nanocomposite containing α-cyclodextrin as conductive matrix and graphene quantum dots as amplification element...
January 17, 2018: Journal of Molecular Recognition: JMR
Huan Zhang, Chong Zhang, Xiao-Yan Dong, Jie Zheng, Yan Sun
Dysfunctional accumulation of amyloid β-protein (Aβ) mediated by Cu2+ exhibits higher neurotoxicity and accelerates the progress of Alzheimer's disease, so inhibition of Cu2+ -mediated Aβ aggregation and cytotoxicity has been considered as a therapeutic strategy for the disease. Herein, a nonapeptide was designed by linking HH to the C-terminus of a peptide inhibitor of Aβ aggregation, LVFFARK (LK7). We found that the nonapeptide, LK7-HH, possessed dual functionality, including enhanced inhibition capability on Aβ aggregation as compared to LK7, and chelating Cu2+ with a dissociation constant of 5...
January 10, 2018: Journal of Molecular Recognition: JMR
David A Spivak
No abstract text is available yet for this article.
January 9, 2018: Journal of Molecular Recognition: JMR
Hongping Wu, Hai Wang, Wuqi Jiang, Zhengxing Lian
Toll-like receptors (TLRs) are an important part of the innate immune system, acting as a first line of defense against many invading pathogens. The ligand known to bind Gallus toll-like receptor 21 (gTLR21) is the unmethylated cytosine phosphate guanine dideoxy nucleotide motif; however, the evolutionary characteristics and structural biology of gTLR21 are poorly elaborated. Our results suggest that gTLR21 is phylogenetically and evolutionarily related to the TLR11 family and is perhaps a close ortholog of the Mus TLR13...
December 27, 2017: Journal of Molecular Recognition: JMR
Mei-Ling Sun, Li-Mei Sun, Yong-Qing Wang
The human HtrA family of serine proteases (HtrA1, HtrA2, HtrA3, and HtrA4) are the key enzymes associated with pregnancy and closely related to the development and progression of many pathological events. Previously, it was found that halogen substitution at the indole moiety of peptide Trp-1 residue can form a geometrically satisfactory halogen bond with the Drosophila discs large, zona occludens-1 (PDZ) domain of HtrA proteases. Here, we attempt to systematically investigate the effect of substitution with 4 halogen types and 2 indole positions on the binding affinity and specificity of peptide ligands to the 4 HtrA PDZ domains...
December 20, 2017: Journal of Molecular Recognition: JMR
A Kulandaisamy, Ambuj Srivastava, R Nagarajan, M Michael Gromiha
Protein-DNA interactions are involved in various fundamental biological processes such as replication, transcription, DNA repair, and gene regulation. To understand the interaction in protein-DNA complexes, the integrative study of binding and stabilizing residues is important. In the present study, we have identified key residues that play a dual role in both binding and stability from a nonredundant dataset of 319 protein-DNA complexes. We observed that key residues are identified in very less number of complexes (29%) and only about 4% of stabilizing/binding residues are identified as key residues...
April 2018: Journal of Molecular Recognition: JMR
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...
February 2018: Journal of Molecular Recognition: JMR
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...
February 2018: Journal of Molecular Recognition: JMR
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...
January 2018: Journal of Molecular Recognition: JMR
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)...
January 2018: Journal of Molecular Recognition: JMR
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...
January 2018: Journal of Molecular Recognition: JMR
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...
January 2018: Journal of Molecular Recognition: JMR
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)...
January 2018: Journal of Molecular Recognition: JMR
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...
January 2018: Journal of Molecular Recognition: JMR
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)...
January 2018: Journal of Molecular Recognition: JMR
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...
January 2018: Journal of Molecular Recognition: JMR
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