Analysis of host protein interactions in plant viruses: an in silico study using Sesbania mosaic virus
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ORIGINAL PAPER
Analysis of host protein interactions in plant viruses: an in silico study using Sesbania mosaic virus Mariya Rashid1 · Shubham Mittal1 · Sangita Venkataraman2 Received: 6 July 2020 / Accepted: 8 September 2020 © Springer Science+Business Media, LLC, part of Springer Nature 2020
Abstract The dynamics of interactions of viral proteins with their host are pivotal in establishing a successful infection and ensuring systemic spread. To uncover these, an in silico analysis of the interactions between the coat protein (CP) of Sesbania mosaic virus (SeMV), a group IV virus with single-stranded positive-sense RNA genome was carried out with the known crystal structures of proteins belonging to the Fabaceae family, which is its natural host. SeMV is an isometric plant virus which infects Sesbania grandiflora, a member of Fabaceae, and causes mosaic symptoms. Earlier results have indicated that the assembly and disassembly events of SeMV favor the formation of CP dimers. Hence, the ability and strength of interactions of CP dimer with the host proteins were assessed using in silico protein–protein docking approaches. A set of 61 unique crystal structures of native proteins belonging to Fabaceae were downloaded from the Protein Data Bank (PDB) and docked with the CP dimer of SeMV. From the docking scores and interaction analysis, the host proteins were ranked according to their strength and significance of interactions with the CP dimers. The leads that were identified present themselves as strong candidates for developing antivirals against not only SeMV but also other related viruses that infect Fabaceae. The study is a prototype to understand host protein interactions in viruses and hosts. Keywords Sesbania mosaic virus · Coat protein · Host-virus interaction · Surface complementarity · Docking · Storage proteins
Introduction Protein–protein interactions are of prime importance at the cellular level; these are responsible for studying host–virus interactions and to gain useful insights into the strategies of detection and development of antivirals. According to the tenth International Committee on Taxonomy of Viruses (report 2018b.v1), plant viruses include 26 families, 118 genera, and 1516 species [1]. The yield loss that can be ascribed to plant viruses worldwide estimates to be more than 30 billion USD annually [2]. These viruses are especially devastating as most plants lack robust resistance to Edited by Karel Petrzik. * Sangita Venkataraman [email protected] 1
Department of Biotechnology, Amity University Haryana, Gurgaon 122413, India
Department of Biotechnology, Acharya Nagarjuna University, Nagarjuna Nagar, Guntur 522510, India
2
many of the viruses that infect them. Analysis of proteins involved in host–virus interactions may underpin the unique and unforeseen roles of these proteins in host infection. Thus, it is pivotal to study proteins in the context of their interacting partners to fully understand their function in infection [3]. A specific interaction between the
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