In-silico approach to characterize the structure and function of a hypothetical protein of Monkeypox virus exploring Chordopox-A20R domain-containing protein activity.

Background: Monkeypox has emerged as a noteworthy worldwide issue due to its daily escalating case count. This illness presents diverse symptoms, including skin manifestations, which have the potential to spread through contact. The transmission of this infectious agent is intricate and readily transfers between individuals.Methods: The hypothetical protein MPXV-SI-2022V502225_00135 strain of monkeypox underwent structural and functional analysis using NCBI-CD Search, Pfam, and InterProScan. Quality assessment utilized PROCHECK, QMEAN, Verify3D, and ERRAT, followed by protein-ligand docking, visualization, and a 100-nanosecond simulation on Schrodinger Maestro.Results: Different physicochemical properties were estimated, indicating a stable molecular weight (49147.14) and theoretical pI (5.62) with functional annotation tools predicting the target protein to contain the domain of Chordopox_A20R domain. In secondary structure analysis, the helix coil was found to be predominant. The three-dimensional (3D) structure of the protein was obtained using a template protein (PDB ID: 6zyc.1), which became more stable after YASARA energy minimization and was validated by quality assessment tools like PROCHECK, QMEAN, Verify3D, and ERRAT. Protein-ligand docking was conducted using PyRx 9.0 software to examine the binding and interactions between a ligand and a hypothetical protein, focusing on various amino acids. The model structure, active site, and binding site were visualized using the CASTp server, FTsite, and PyMOL. A 100 nanosecond simulation was performed with ligand CID_16124688 to evaluate the efficiency of this protein.Conclusion: The analysis revealed significant binding interactions and enhanced stability, aiding in drug or vaccine design for effective antiviral treatment and patient management.

Implementation of in silico methods to predict common epitopes for vaccine development against Chikungunya and Mayaro viruses.

Being a Positive sense RNA virus the recent reemergence of Chikungunya and Mayaro virus has taken the concern of the leading scientific communities of the world. Though the outbreak of Mayaro virus is limited to Neotropical region only, Chikungunya is already identified in over 60 countries around the world. Besides, the lack of a strong protective treatment, misdiagnosis issue and co-circulation of both the viruses calls for a new strategy which could potentially prevent these infections from spreading. In this study, we therefore, identified the peptide based vaccine candidates e.g. epitopes for B cell and T cell from Chikungunya virus which also showed to be homologous to the Mayaro virus through immuno-informatics and computational approaches. Final epitopes identified from the most antigenic structural polyprotein of both the viruses were 5 for CD8+ T cell Epitopes (209KPGDSGRPI217, 219TGTMGHFIL227, 239ALSVVTWNK247, 98KPGRRERMC106 and 100GRRERMCMK108), 2 epitopes for CD4+ T cell (105MCMKIENDCIFEVKH119 and 502DRTLLSQQSGNVKIT516) and a single epitope for B cell (504GGRFTIPTGAGKPGDSGRPI518). Analysis of our predicted epitopes for population coverage showed prominent population coverage (92.43%) around the world. Finally, molecular docking simulation of the foreseen T cell epitopes with respondent HLA alleles secured good HLA-epitope interaction. This study was directed towards the discovery of potential antigenic epitopes which can open up a new skyline to design novel vaccines for combating both of the diseases at the same time.

Mass-producible disposable needle-type ion-selective electrodes for plant research.

Easily mass-producible needle-type Na+ and K+ ion-selective electrodes (ISEs) were developed for the direct and indirect measurement of Na+ and K+ ion concentrations in live plants. A polyimide strip with a silver layer on one side and Ag/AgCl formed at one end was used to construct two types of ISEs. For the type I ISE, an electrolyte layer was formed on the layer of silver and Ag/AgCl, which was then covered with a protecting layer. Subsequently, an ion-selective membrane (ISM) was formed at the truncated end with Ag/AgCl. For the type II ISE, a syringe needle was used as a container and an ISM was formed at the sharp end. Then, the polyimide strip with Ag/AgCl at one end was inserted and an electrolyte solution was injected to complete the ISE. Reference electrodes (REs) with similar structures were fabricated by forming a liquid junction instead of the ISM. The electrode responses and the relationship between the ISE potential and the Na+/K+ ion concentration agreed with those predicted by the Nernst equation. The Na+ and K+ ion concentrations in different parts of the rice plant (Oryza sativa L.) were measured using the Na+ and K+ ISEs, respectively. The results obtained using these devices agreed well with those obtained using inductively coupled plasma atomic emission spectrometry, thus confirming the practical applicability of the developed ISEs.