Bioinformatics Institute (A*STAR), Singapore, Singapore.
Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom.
Elife. 2023 May 5;12:e82447. doi: 10.7554/eLife.82447.
Flaviviruses are enveloped viruses which include human pathogens that are predominantly transmitted by mosquitoes and ticks. Some, such as dengue virus, exhibit the phenomenon of antibody-dependent enhancement (ADE) of disease, making vaccine-based routes of fighting infections problematic. The pH-dependent conformational change of the envelope (E) protein required for fusion between the viral and endosomal membranes is an attractive point of inhibition by antivirals as it has the potential to diminish the effects of ADE. We examined six flaviviruses by employing large-scale molecular dynamics (MD) simulations of raft systems that represent a substantial portion of the flaviviral envelope. We utilised a benzene-mapping approach that led to a discovery of shared hotspots and conserved cryptic sites. A cryptic pocket previously shown to bind a detergent molecule exhibited strain-specific characteristics. An alternative conserved cryptic site at the E protein domain interfaces showed a consistent dynamic behaviour across flaviviruses and contained a conserved cluster of ionisable residues. Constant-pH simulations revealed cluster and domain-interface disruption under low pH conditions. Based on this, we propose a cluster-dependent mechanism that addresses inconsistencies in the histidine-switch hypothesis and highlights the role of cluster protonation in orchestrating the domain dissociation pivotal for the formation of the fusogenic trimer.
黄病毒是包膜病毒，包括主要通过蚊子和蜱传播的人类病原体。有些病毒，如登革热病毒，表现出抗体依赖性增强（ADE）疾病的现象，这使得基于疫苗的抗感染途径成为问题。包膜（E）蛋白的 pH 依赖性构象变化是抗病毒药物抑制的一个有吸引力的靶点，因为它有可能减轻 ADE 的影响。我们通过对代表黄病毒包膜大部分的筏系统进行大规模分子动力学（MD）模拟，研究了六种黄病毒。我们利用苯映射方法，发现了共享热点和保守隐蔽位点。先前显示与去污剂分子结合的隐蔽口袋表现出菌株特异性特征。在 E 蛋白结构域界面处的另一个保守隐蔽位点在各种黄病毒中表现出一致的动态行为，并包含一个保守的可离子化残基簇。恒 pH 模拟显示，在低 pH 条件下会出现簇和结构域界面破坏。基于这一点，我们提出了一个簇依赖性机制，解决了组氨酸开关假说中的不一致性，并强调了簇质子化在协调关键的结构域解离以形成融合三聚体中的作用。
