A peptide derived from the rotavirus outer capsid protein VP7 permeabilizes artificial membranes

Exploring rotavirus proteome to identify potential B- and T-cell epitope using computational immunoinformatics

Rotavirus is the most common cause of acute gastroenteritis in infants and children worldwide. The functional correlation of B- and T-cells to long-lasting immunity against rotavirus infection in the literature is limited. In this work, a series of computational immuno-informatics approaches were applied and identified 28 linear B-cells, 26 conformational B-cell, 44 T_C cell and 40 T_H cell binding epitopes for structural and non-structural proteins of rotavirus. Further selection of putative B and T cell epitopes in the multi-epitope vaccine construct was carried out based on immunogenicity, conservancy, allergenicity and the helical content of predicted epitopes. An in-silico vaccine constructs was developed using an N-terminal adjuvant (RGD motif) followed by T_C and T_H cell epitopes and B-cell epitope with an appropriate linker. Multi-threading models of multi-epitope vaccine construct with B- and T-cell epitopes were generated and molecular dynamics simulation was performed to determine the stability of designed vaccine. Codon optimized multi-epitope vaccine antigens was expressed and affinity purified using the E. coli expression system. Further the T cell epitope presentation assay using the recombinant multi-epitope constructs and the T cell epitope predicted and identified in this study have not been investigated. Multi-epitope vaccine construct encompassing predicted B- and T-cell epitopes may help to generate long-term immune responses against rotavirus. The computational findings reported in this study may provide information in developing epitope-based vaccine and diagnostic assay for rotavirus-led diarrhea in children's.

Isolation and characterization of Wad Medani virus obtained in the tuva Republic of Russia

Wad Medani virus (WMV) belongs to the genus Orbivirus and is a poorly studied arbovirus with unclear medical significance. Presently, a limited number of WMV strains are characterized and available in NCBI GenBank, some isolated many years ago. A new WMV strain was isolated in 2012 from Dermacentor nuttalli ticks collected from sheep in the Tuva Republic, Russia, and sequenced using high-throughput methods. Complete coding sequences were obtained revealing signs of multiple intersegment reassortments. These point to a high variability potential in WMV that may lead to the formation of strains with novel properties. These new data on WMV can promote better understanding of: ecological features of its circulation; relationships within the genus Orbivirus; and the medical significance of the virus.

Prediction of Amphiphilic Cell-Penetrating Peptide Building Blocks from Protein-Derived Amino Acid Sequences for Engineering of Drug Delivery Nanoassemblies

Amphiphilic molecules, forming self-assembled nanoarchitectures, are typically composed of hydrophobic and hydrophilic domains. Peptide amphiphiles can be designed from two, three, or four building blocks imparting novel structural and functional properties and affinities for interaction with cellular membranes or intracellular organelles. Here we present a combined numerical approach to design amphiphilic peptide scaffolds that are derived from the human nuclear K_i-67 protein. K_i-67 acts, like a biosurfactant, as a steric and electrostatic charge barrier against the collapse of mitotic chromosomes. The proposed predictive design of new K_i-67 protein-derived amphiphilic amino acid sequences exploits the computational outcomes of a set of web-accessible predictors, which are based on machine learning methods. The ensemble of such artificial intelligence algorithms, involving support vector machine (SVM), random forest (RF) classifiers, and neural networks (NN), enables the nanoengineering of a broad range of innovative peptide materials for therapeutic delivery in various applications. Amphiphilic cell-penetrating peptides (CPP), derived from natural protein sequences, may spontaneously form self-assembled nanocarriers characterized by enhanced cellular uptake. Thanks to their inherent low immunogenicity, they may enable the safe delivery of therapeutic molecules across the biological barriers.

Improved Detection of Plasmon Waveguide Resonance Using Diverging Beam, Liquid Crystal Retarder, and Application to Lipid Orientation Determination

Plasmon waveguide resonance (PWR) sensors exhibit narrow resonances at the two orthogonal polarizations, transverse electric (TE) and transverse magnetic (TM), which are narrower by almost an order of a magnitude than the standard surface plasmon resonance (SPR), and thus the figure of merit is enhanced. This fact is useful for measuring optical anisotropy of materials on the surface and determining the orientation of molecules with high resolution. Using the diverging beam approach and a liquid crystal retarder, we present experimental results by simultaneous detection of TE and TM polarized resonances as well as using fast higher contrast serial detection with a variable liquid crystal retarder. While simultaneous detection makes the system simpler, a serial one has the advantage of obtaining a larger contrast of the resonances and thus an improved signal-to-noise ratio. Although the sensitivity of the PWR resonances is smaller than the standard SPR, the angular width is much smaller, and thus the figure of merit is improved. When the measurement methodology has a high enough angular resolution, as is the one presented here, the PWR becomes advantageous over other SPR modes. The possibility of carrying out exact numerical simulations for anisotropic molecules using the 4 × 4 matrix approach brings another advantage of the PWR over SPR on the possibility of extracting the orientation of molecules adsorbed to the surface. High sensitivity of the TE and TM signals to the anisotropic molecules orientation is found here, and comparison to the experimental data allowed detection of the orientation of lipids on the sensor surface. The molecular orientations cannot be fully determined from the TM polarization alone as in standard SPR, which underlines the additional advantage of the PWR technique.

Atomic model of a nonenveloped virus reveals pH sensors for a coordinated process of cell entry

Viruses sense environmental cues (such as pH) to engage in membrane interactions for cell entry during infection but how non-enveloped viruses sense pH is largely undefined. Here, we report the structures — at high and low pH conditions — of bluetongue virus (BTV), which enters cells via a two-stage endosomal process. The receptor-binding protein VP2 possesses a zinc-finger and a conserved His866, which may function to maintain VP2 in a metastable state and to sense early-endosomal pH, respectively. The membrane penetration protein VP5 has three domains: dagger, unfurling, and anchoring. Notably, the β-meander motif of the anchoring domain contains a histidine cluster that could sense the late-endosomal pH and four putative membrane-interaction elements. Exposing BTV to low pH detaches VP2 and dramatically refolds the dagger and unfurling domains of VP5. Our biochemical and structure-guided mutagenesis studies support these coordinated pH-sensing mechanisms.