Epitope-Based Immunoinformatics and Molecular Docking Studies of Nucleocapsid Protein and Ovarian Tumor Domain of Crimean–Congo Hemorrhagic Fever Virus

Crimean–Congo hemorrhagic fever virus (CCHFV), the fatal human pathogen is transmitted to humans by tick bite, or exposure to infected blood or tissues of infected livestock. The CCHFV genome consists of three RNA segments namely, S, M, and L. The unusual large viral L protein has an ovarian tumor (OTU) protease domain located in the N terminus. It is likely that the protein may be autoproteolytically cleaved to generate the active virus L polymerase with additional functions. Identification of the epitope regions of the virus is important for the diagnosis, phylogeny studies, and drug discovery. Early diagnosis and treatment of CCHF infection is critical to the survival of patients and the control of the disease. In this study, we undertook different in silico approaches using molecular docking and immunoinformatics tools to predict epitopes which can be helpful for vaccine designing. Small molecule ligands against OTU domain and protein–protein interaction between a viral and a host protein have been studied using docking tools

NFATc1 affects mouse splenic B cell function by controlling the calcineurin–NFAT signaling network

Mouse B cells lacking NFATc1 exhibit defective proliferation, survival, isotype class switching, cytokine production, and T cell help

Assignment of PolyProline II Conformation and Analysis of Sequence – Structure Relationship

International audienceBACKGROUND: Secondary structures are elements of great importance in structural biology, biochemistry and bioinformatics. They are broadly composed of two repetitive structures namely α-helices and β-sheets, apart from turns, and the rest is associated to coil. These repetitive secondary structures have specific and conserved biophysical and geometric properties. PolyProline II (PPII) helix is yet another interesting repetitive structure which is less frequent and not usually associated with stabilizing interactions. Recent studies have shown that PPII frequency is higher than expected, and they could have an important role in protein - protein interactions. METHODOLOGY/PRINCIPAL FINDINGS: A major factor that limits the study of PPII is that its assignment cannot be carried out with the most commonly used secondary structure assignment methods (SSAMs). The purpose of this work is to propose a PPII assignment methodology that can be defined in the frame of DSSP secondary structure assignment. Considering the ambiguity in PPII assignments by different methods, a consensus assignment strategy was utilized. To define the most consensual rule of PPII assignment, three SSAMs that can assign PPII, were compared and analyzed. The assignment rule was defined to have a maximum coverage of all assignments made by these SSAMs. Not many constraints were added to the assignment and only PPII helices of at least 2 residues length are defined. CONCLUSIONS/SIGNIFICANCE: The simple rules designed in this study for characterizing PPII conformation, lead to the assignment of 5% of all amino as PPII. Sequence - structure relationships associated with PPII, defined by the different SSAMs, underline few striking differences. A specific study of amino acid preferences in their N and C-cap regions was carried out as their solvent accessibility and contact patterns. Thus the assignment of PPII can be coupled with DSSP and thus opens a simple way for further analysis in this field

Adsorption of Methylene Blue, Bromophenol Blue, and Coomassie Brilliant Blue by α-chitin nanoparticles

Expelling of dyestuff into water resource system causes major thread to the environment. Adsorption is the cost effective and potential method to remove the dyes from the effluents. Therefore, an attempt was made to study the adsorption of dyestuff (Methylene Blue (MB), Bromophenol Blue (BPB) and Coomassie Brilliant Blue (CBB)) by α-chitin nanoparticles (CNP) prepared from Penaeus monodon (Fabricius, 1798) shell waste. On contrary to the most recognizable adsorption studies using chitin, this is the first study using unique nanoparticles of ⩽50 nm used for the dye adsorption process. The results showed that the adsorption process increased with increase in the concentration of CNP, contact time and temperature with the dyestuff, whereas the adsorption process decreased with increase in the initial dye concentration and strong acidic pH. The results from Fourier transform infrared (FTIR) spectroscopy confirmed that the interaction between dyestuff and CNP involved physical adsorption. The adsorption process obeys Langmuir isotherm (R2 values were 0.992, 0.999 and 0.992 for MB, BPB and CBB, and RL value lies between 0 and 1 for all the three dyes) and pseudo second order kinetics (R2 values were 0.996, 0.999 and 0.996 for MB, BPB and CBB) more effectively. The isotherm and kinetic models confirmed that CNP can be used as a suitable adsorbent material for the removal of dyestuff from effluents

Green synthesis of silver nanoparticles using Lippia nodiflora aerial extract and evaluation of their antioxidant, antibacterial and cytotoxic effects

Silver nanoparticles biosynthesis has received increasing attention in the field of nanotechnology due to their antimicrobial and biomedical applications. Green synthesis of metal nanoparticles is anticipated as a cost effective and eco-friendly alternative in the current research scenario. With this aim, the aqueous extracts made from the aerial parts of Lippia nodiflora were used as the reducing agents to synthesize silver nanoparticles (AgNPs) and their antioxidant, antibacterial and cytotoxic properties have also been evaluated. The biosynthesized AgNPs were characterized by UVâVisible Spectroscopy, Fourier-Transform Infrared Spectroscopy (FTIR) and X-Ray Diffraction (XRD) analysis. The AgNPs were found to be stable at â25.2â¯mV through zeta potential study. The morphology and size of synthesized silver nanoparticles were confirmed by Scanning Electron Microscope with energy dispersive spectra (SEM-EDX) and Transmission Electron Microscopy (TEM) analysis with size range from 30 to 60â¯nm. Biosynthesized AgNPs exhibited strong antioxidant activity as well as showed potent antibacterial activity against human pathogenic bacteria. The cytotoxicity study of AgNPs was also revealed against MCF-7 breast cancer cell lines in a dose-dependent manner. The recognized bioactivity confirmed by the synthesized AgNPs directs towards the clinical use as an antioxidant, antibacterial and cytotoxic agent. Keywords: Lippia nodiflora, Silver nanoparticles, SEM, Antioxidant, Antibacterial, Cytotoxicit

Bioassay-guided isolation and identification of bioactive compound from aerial parts of <i>Luffa acutangula</i> against lung cancer cell line NCI-H460

<div><p></p><p><i>Luffa acutangula</i> (Cucurbitaceae) is widely used as a traditional medicine in India and was reported to possess various pharmacological activities including its anti-proliferative effects. In this study, the bioactive compound of ethanolic extract of <i>L. acutangula</i> (LA) was isolated using bioassay-guided approach. Five major fractions were collected and evaluated for their anti-proliferative activity against non-small cell lung cancer cells (NCI-H460). Among the test fractions, the fraction LA/FII effectively decreased the growth of cancer cells with IC₅₀ values of 10 µg/ml concentration. Furthermore, it significantly increased intracellular reactive oxygen species and decreased the mitochondrial membrane potential. The apoptogenic activity of fraction LA/FII was confirmed by cell shrinkage, membrane blebbing and formation of apoptotic bodies. A single bioactive compound was isolated from the active faction, LA/FII and subsequently identified as 1,8 dihydroxy-4-methylanthracene 9,10-dione (compound <b>1</b>) by comparing its spectral data [Ultraviolet (UV), Infrared (IR), Nuclear magnetic resonance (NMR) and Electrospray Ionization-Mass Spectroscopy (ESI-MS)] with literature values. This is the first report on the isolation of compound <b>1</b> from this plant.</p></div

Reassessing random-coil statistics in unfolded proteins

The Gaussian-distributed random coil has been the dominant model for denatured proteins since the 1950s, and it has long been interpreted to mean that proteins are featureless, statistical coils in 6 M guanidinium chloride. Here, we demonstrate that random-coil statistics are not a unique signature of featureless polymers. The random-coil model does predict the experimentally determined coil dimensions of denatured proteins successfully. Yet, other equally convincing experiments have shown that denatured proteins are biased toward specific conformations, in apparent conflict with the random-coil model. We seek to resolve this paradox by introducing a contrived counterexample in which largely native protein ensembles nevertheless exhibit random-coil characteristics. Specifically, proteins of known structure were used to generate disordered conformers by varying backbone torsion angles at random for ≈8% of the residues; the remaining ≈92% of the residues remained fixed in their native conformation. Ensembles of these disordered structures were generated for 33 proteins by using a torsion-angle Monte Carlo algorithm with hard-sphere sterics; bulk statistics were then calculated for each ensemble. Despite this extreme degree of imposed internal structure, these ensembles have end-to-end distances and mean radii of gyration that agree well with random-coil expectations in all but two cases