Elucidating the Interacting Domains ofChandipuraVirus Nucleocapsid Protein

Kapila Kumar,Sreejith Rajasekharan,Sahil Gulati,Jyoti Rana,Amita Gupta,Reema Gabrani,Vijay K Chaudhary,Chakresh K Jain,Sanjay Gupta

doi:10.1155/2013/594319

Kapila Kumar, Sreejith Rajasekharan + Show 7 more

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https://doi.org/10.1155/2013/594319

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Abstract

The nucleocapsid (N) protein of Chandipura virus (CHPV) plays a crucial role in viral life cycle, besides being an important structural component of the virion through proper organization of its interactions with other viral proteins. In a recent study, the authors had mapped the associations among CHPV proteins and shown that N protein interacts with four of the viral proteins: N, phosphoprotein (P), matrix protein (M), and glycoprotein (G). The present study aimed to distinguish the regions of CHPV N protein responsible for its interactions with other viral proteins. In this direction, we have generated the structure of CHPV N protein by homology modeling using SWISS-MODEL workspace and Accelrys Discovery Studio client 2.55 and mapped the domains of N protein using PiSQRD. The interactions of N protein fragments with other proteins were determined by ZDOCK rigid-body docking method and validated by yeast two-hybrid and ELISA. The study revealed a unique binding site, comprising of amino acids 1–30 at the N terminus of the nucleocapsid protein (N1) that is instrumental in its interactions with N, P, M, and G proteins. It was also observed that N2 associates with N and G proteins while N3 interacts with N, P, and M proteins.

Highlights

Chandipura virus (CHPV) is a recently recognized emerging human pathogen [1,2,3] of the genus Vesiculovirus and family Rhabdoviridae [4]
The transcription of the genome by viral encoded RNA-dependent RNA polymerase (RdRp; L protein) produces five capped and polyadenylated mRNAs which code for five proteins nucleocapsid protein (N), phosphoprotein (P), matrix protein (M), glycoprotein (G), and large protein (L) in sequential order and in decreasing amounts [6]
Vesicular stomatitis virus (VSV), Indiana strain N protein complex (PDB ID: 3HHW), and M protein (PDB ID: 1LG7) were used as templates for homology modeling of CHPV proteins as both these viruses belong to the same genus and their N and M proteins shares 71.3% and 28% sequence similarity, respectively

Summary

Introduction

Chandipura virus (CHPV) is a recently recognized emerging human pathogen [1,2,3] of the genus Vesiculovirus and family Rhabdoviridae [4]. The transcription of the genome by viral encoded RNA-dependent RNA polymerase (RdRp; L protein) produces five capped and polyadenylated mRNAs which code for five proteins nucleocapsid protein (N), phosphoprotein (P), matrix protein (M), glycoprotein (G), and large protein (L) in sequential order and in decreasing amounts [6] Interactions among these proteins are essential for functioning of key processes during virus replication and pathogenesis. In its active form, N protein tightly wraps the RNA genome and maintains the structural integrity along with the template function of the negative strand genome RNA Within the virion, this encapsidated RNA (N-RNA) template is associated with the transcription factor (P protein) of the RNA polymerase complex to form the transcribing ribonucleoprotein (RNP) particle [9]. With the elucidation of interactions of N protein with M and G proteins [14], there arises a need to further map the specific regions of CHPV N protein involved in mediating its interactions

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