Japanese encephalitis virus – exploring the dark proteome and disorder–function paradigm

Abstract

Japanese encephalitis virus (JEV) is one of the major causes of viral encephalitis all around the globe. Approximately 3 billion people in endemic areas are at risk of Japanese encephalitis. To develop a wholistic understanding of the viral proteome, it is important to investigate both its ordered and disordered proteins. However, the functional and structural significance of disordered regions in the JEV proteome has not been systematically investigated as of yet. To fill this gap, we used here a set of bioinformatics tools to analyze the JEV proteome for the predisposition of its proteins for intrinsic disorder and for the presence of the disorder‐based binding regions (also known as molecular recognition features, MoRFs). We also analyzed all JEV proteins for the presence of the probable nucleic acid‐binding (DNA and RNA) sites. The results of these computational studies are experimentally validated using JEV capsid protein as an illustrative example. In agreement with bioinformatic analysis, we found that the N‐terminal region of the JEV capsid (residues 1–30) is intrinsically disordered. We showed that this region is characterized by the temperature response typical for highly disordered proteins. Furthermore, we have experimentally shown that this disordered N‐terminal domain of a capsid protein has a noticeable ‘gain‐of‐structure’ potential. In addition, using DOPS liposomes, we demonstrated the presence of pronounced membrane‐mediated conformational changes in the N‐terminal region of JEV capsid. In our view, this disorder‐centric analysis would be helpful for a better understanding of the JEV pathogenesis.

SARS-CoV-2 NSP1 C-terminal region (residues 130-180) is an intrinsically disordered region

“…The sequence of NSP1 C-terminal (residues 130-180) "NH2-AGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGG-COOH" was retrieved from the UniProt (ID: P0DTC1.1). As described earlier by our group, protein intrinsic disorder predictor, PONDR® VSL2 was used for analysis of intrinsic disorder properties of NSP1-CTR (2,13,14,19,26,27). The secondary structure predisposition analysis for NSP1-CTR was performed with several different web-servers pep2d, Jpred4, and PSIPRED (28-30).…”

Mechanistic insights into the Japanese Encephalitis Virus RNA dependent RNA polymerase protein inhibition by bioflavonoids from Azadirachta indica

“…The positive-sense, single-stranded RNA Japanese encephalitis virus (JEV) belongs to genus Flavivirus, family Flaviviridae, and has ~ 50 nm icosahedral-shaped lipoprotein capsid, which encapsulates a 11 kb RNA genome embedded with core protein 9 . Viral genome sequence includes 5′ and 3′ untranslated regions and a single open reading frame (ORF) with no poly(A) tail, which translates into unsegmented polyprotein of 3,432 amino acids -it further sliced and processed into three structural and seven nonstructural proteins [10][11][12] . Herein, the N-terminal of the polyprotein translates for the structural proteins (capsid protein (C), membrane M protein (PrM), and envelope protein (E)), while the non-structural (NS) proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B, and NS5) are encoded by the C-terminal of the polyprotein.…”

Investigating the conformational dynamics of SARS-CoV-2 NSP6 protein with emphasis on non-transmembrane 91-112 & 231-290 regions

“…The change in conformation is governed by the covalent (i.e., phosphorylation, ubiquitination) and/or non-covalent events i.e., binding of ions, lipids, drugs, proteins etc. and environmental influences such as macromolecular crowding, osmolyte, pH, and temperature (11)(12)(13)(14)(15)(16). Factors influencing the change in proteins conformational dynamics ultimately decide the fate of subsequent protein signaling event (11,17).…”