Investigating the conformational dynamics of Zika virus NS4B protein

• Published in: Virology (New York, N.Y.) N.Y.), 2022-10, Vol.575, p.20-35
• Main Authors: Bhardwaj, Taniya, Kumar, Prateek, Giri, Rajanish
• Format: Article
• Language: English
• Subjects: AlphaFold2; Cytosolic region; Intrinsically disordered protein region; Membrane topology; Molecular dynamics simulations
• ISSN: 0042-6822; 1096-0341
• DOI: 10.1016/j.virol.2022.08.005

Zika virus (ZIKV) NS4B protein is a membranotropic multifunctional protein. Despite its versatile functioning, its topology and dynamics are not entirely understood. There is no X-ray or cryo-EM structure available for any flaviviral NS4B full-length protein. In this study, we have investigated the structural dynamics of full-length ZIKV NS4B protein through 3D structure models using molecular dynamics simulations and experimental techniques. Also, we employed a reductionist approach to understand the dynamics of NS4B protein where we studied its N-terminal (residues 1–38), C-terminal (residues 194–251), and cytosolic (residues 131–169) regions in isolation in addition to the full-length protein. Further, using a series of circular dichroism spectroscopic experiments, we validate the cytosolic region as an intrinsically disordered protein region. The microsecond-long all atoms molecular dynamics and replica-exchange simulations complement the experimental observations. Furthermore, we have also studied the NS4B proteins C-terminal regions of four other flaviviruses viz. DENV2, JEV, WNV, and YFV through microsecond simulations to characterize their behaviour in presence and absence of lipid membranes. There are significant differences observed in the conformations of other flavivirus NS4B C-terminal regions in comparison to ZIKV NS4B. Lastly, we have proposed a ZIKV NS4B protein model illustrating its putative topology consisting of various membrane-spanning and non-membranous regions. The illustration of structural dynamics of Zika virus NS4B protein with a reductionist approach demonstrating its N-terminal, Cytosolic, and C-terminal regions in truncated form. [Display omitted] •Microsecond simulations of NS4B N-terminus and cytosolic regions exposed their dynamic nature.•C-terminal region remains intact in presence of lipid bilayer during 1 μs simulations.•Spectroscopic results also reveal the cytosolic region as an intrinsically disordered protein region.•Cytosolic region does not gain structure in presence of macromolecular crowding and liposomes.