School of Biosciences and Bioengineering, Indian Institute of Technology Mandi, VPO Kamand, Himachal Pradesh, 175005, India.
School of Biosciences and Bioengineering, Indian Institute of Technology Mandi, VPO Kamand, Himachal Pradesh, 175005, India.
Virology. 2022 Oct;575:20-35. doi: 10.1016/j.virol.2022.08.005. Epub 2022 Aug 21.
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.
寨卡病毒 (ZIKV) NS4B 蛋白是一种膜靶向多功能蛋白。尽管它具有多种功能，但它的拓扑结构和动力学尚未完全了解。目前尚无任何黄病毒 NS4B 全长蛋白的 X 射线或冷冻电镜结构。在这项研究中，我们通过分子动力学模拟和实验技术，使用 3D 结构模型研究了全长 ZIKV NS4B 蛋白的结构动力学。此外，我们采用简化方法来研究 NS4B 蛋白的动力学，分别研究了其 N 端（残基 1-38）、C 端（残基 194-251）和胞质（残基 131-169）区域，以及全长蛋白。此外，通过一系列圆二色性光谱实验，我们验证了胞质区域是一个固有无序的蛋白质区域。微秒级的全原子分子动力学和复制交换模拟补充了实验观察。此外，我们还通过微秒模拟研究了其他四种黄病毒（DENV2、JEV、WNV 和 YFV）的 NS4B 蛋白 C 端区域，以表征它们在存在和不存在脂质膜时的行为。与 ZIKV NS4B 相比，其他黄病毒 NS4B C 端区域的构象存在显著差异。最后，我们提出了一个 ZIKV NS4B 蛋白模型，说明了其假定的拓扑结构，包括各种跨膜和非膜区域。
