Browsing by Author "Arundhati Barik"

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Exploring the Function of Predicted T-Cell Epitopes in Enhancing Influenza Virus Vaccine Efficacy
(John Wiley and Sons Inc, 2024) Jitendra Malviya; Sawan Yadav; Priya Rathore; Arundhati Barik; Susnata Sovalin Mohapatra; Shweta Sareen; Brahmananda Sahoo; Suresh Chandra Singh; Nidhi Asthana
This study investigates the potential utility of predicted T-cell epitopes derived from the hemagglutinin (HA) sequences of the H1N1 and H5N1 serotypes of the influenza virus. The aim is to contribute to the improvement of a valuable influenza virus vaccine. The influenza virus, a member of the Orthomyxoviridae family, causes the contagious illness commonly known as the “flu.” It contains RNA and exhibits symptoms ranging from mild to severe, including fever, runny nose, sore throat, muscle aches, headaches, coughing, fatigue, and weakness. Each year, the flu epidemic results in a significant number of deaths and cases of severe illness worldwide. The study focuses on the HA protein, which is very useful for entry of virus and host cell strap, and the neuraminidase (NA) enzyme, which facilitates the free of the virus from the host cell. By utilizing computational tools such as Propred 1 and Propred, binding predictions for MHC class I and II are generated and conserved sequences are analyzed. The 3D structures of MHC class I and II human molecules are obtained from the Protein Data Bank (PDB) using the PATCH-DOCK server. Through patch docking of the analyzed conserved sequences with MHC I and II human molecules, conserved epitopes that hold potential for vaccine development are identified. This research highlights the importance of utilizing predicted T-cell epitopes in the design of effective influenza virus vaccines. By leveraging computational methods and structural analysis, this approach provides insights into the development of vaccines that target specific influenza virus serotypes. The identified conserved epitopes have the potential to enhance vaccine efficacy and contribute to the ongoing efforts to combat influenza virus infections. © 2024 Wiley-VCH GmbH.
In silico investigation on interaction of small Ag6 nano-particle cluster with tyramine neurotransmitter
(Nature Research, 2023) Subhendu Chakroborty; E. Shakerzadeh; T. Yadav; Nilima Priyadarsini Mishra; Arundhati Barik; Versha Upadhyay; Abhilasha; Siba Soren; Jitendra Malviya; Amiya Ranjan Panda; Kartik Uniyal; Narendra Kumar; Shradha Wagadre; F.P. Pandey
The interaction of tyramine neurotransmitter with silver nano-particle (Ag6) cluster is explored in terms of the molecular structure, electronic properties and NBO analysis of tyramine-AgNPs bio-molecular conjugate. The adsorption mechanism of tyramine onto the Ag6 cluster has been investigated through computing of the electronic and geometrical properties in addition to the adsorption energies in various possible configurations. The magnitude of adsorption energy corresponding to the most favorable tyramine-Ag6 bio-molecular conjugate has been computed to be − 14.36 kcal/mol in the gas phase, which infers a good adsorption of tyramine with AgNPs cluster suggesting the practical applications of tyramine-AgNPs bio-molecular conjugates in bio-sensing, drug delivery, bio-imaging and other applications. Different electronic properties such as the energy gap of HOMO–LUMO, Fermi level and work function have been investigated in detail. Moreover, the effect of aqueous media on adsorption energy and electronic properties of the most favorable tyramine-AgNPs bio-molecular conjugate is investigated in order to understand the impact of the real biological situation. © 2023, The Author(s).