Mesoscale All-Atom Influenza Virus Simulations Suggest New Substrate Binding Mechanism
Mesoscale All-Atom Influenza Virus Simulations Suggest New Substrate Binding Mechanism
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DOI：
10.1021/acscentsci.9b01071
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发表时间：
2020-02-26
影响因子：
18.2
通讯作者：
Amaro, Rommie E.
中科院分区：
文献类型：
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作者：
Durrant, Jacob D.;Kochanek, Sarah E.;Amaro, Rommie E.
流感病毒在人类、禽类和猪宿主中传播，引起季节性流行病和偶尔的大流行暴发。流感神经氨酸酶是一种病毒表面糖蛋白，具有两个唾液酸结合位点。催化（初级）位点也结合抑制剂，如羧酸奥司他韦，负责切断将病毒后代与宿主细胞结合的唾液酸键。相比之下，次要位点的功能注释仍然不清楚。在这里，我们通过开发一个全原子、明确溶剂化的、基于实验的甲型H1N1流感病毒包膜综合模型，更好地表征了这两个位点，该模型包含大约1.6亿个原子，直径大约为115纳米。这种拥挤的亚细胞环境的分子动力学模拟，结合马尔可夫状态模型理论，为在中尺度上研究现实分子系统提供了一个新的框架，并使我们能够量化神经氨酸酶150环在开放和封闭状态之间转变的动力学。氯离子占据神经氨酸酶表面的分析暗示了神经氨酸酶二级位点的潜在新作用，其中连接的末端唾液酸残基可能在转移到酶裂解发生的初级位点之前结合。总之，我们的工作在分子模拟的大小、复杂性和组分的方法学分析方面开辟了新的领域。它还为了解这一重要流感药物靶点的底物识别过程提供了基本见解，为开发抗流感治疗方法提供了新的策略。
Influenza virus circulates in human, avian, and swine hosts, causing seasonal epidemic and occasional pandemic outbreaks. Influenza neuraminidase, a viral surface glycoprotein, has two sialic acid binding sites. The catalytic (primary) site, which also binds inhibitors such as oseltamivir carboxylate, is responsible for cleaving the sialic acid linkages that bind viral progeny to the host cell. In contrast, the functional annotation of the secondary site remains unclear. Here, we better characterize these two sites through the development of an all-atom, explicitly solvated, and experimentally based integrative model of the pandemic influenza A H1N1 2009 viral envelope, containing similar to 160 million atoms and spanning similar to 115 nm in diameter. Molecular dynamics simulations of this crowded subcellular environment, coupled with Markov state model theory, provide a novel framework for studying realistic molecular systems at the mesoscale and allow us to quantify the kinetics of the neuraminidase 150-loop transition between the open and closed states. An analysis of chloride ion occupancy along the neuraminidase surface implies a potential new role for the neuraminidase secondary site, wherein the terminal sialic acid residues of the linkages may bind before transfer to the primary site where enzymatic cleavage occurs. Altogether, our work breaks new ground for molecular simulation in terms of size, complexity, and methodological analyses of the components. It also provides fundamental insights into the understanding of substrate recognition processes for this vital influenza drug target, suggesting a new strategy for the development of anti-influenza therapeutics.