Li Tong, Yu Lan, Sun Jingfang, Liu Jinfeng, He Xiao
School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
School of Science, China Pharmaceutical University, Nanjing 210009, China.
J Phys Chem B. 2022 Jul 7;126(26):4828-4839. doi: 10.1021/acs.jpcb.2c02365. Epub 2022 Jun 23.
As a type I viral fusion protein, SARS-CoV-2 spike undergoes a pH-dependent switch to mediate the endosomal positioning of the receptor-binding domain to facilitate viral entry into cells and immune evasion. Gaps in our knowledge concerning the conformational transitions and key intramolecular motivations have hampered the development of effective therapeutics against the virus. To clarify the pH-sensitive elements on spike-gating the receptor-binding domain (RBD) opening and understand the details of the RBD opening transition, we performed microsecond-time scale constant pH molecular dynamics simulations in this study. We identified the deeply buried D571 with a clear p shift, suggesting a potential pH sensor, and showed the coupling of ionization of D571 with spike RBD-up/down equilibrium. We also computed the free-energy landscape for RBD opening and identified the crucial interactions that influence RBD dynamics. The atomic-level characterization of the pH-dependent spike activation mechanism provided herein offers new insights for a better understanding of the fundamental mechanisms of SARS-CoV-2 viral entry and infection and hence supports the discovery of novel therapeutics for COVID-19.
作为一种I型病毒融合蛋白，严重急性呼吸综合征冠状病毒2（SARS-CoV-2）刺突蛋白会经历pH依赖性转变，以介导受体结合域的内体定位，从而促进病毒进入细胞并实现免疫逃逸。我们对其构象转变和关键分子内驱动因素的认知空白，阻碍了针对该病毒的有效治疗方法的开发。为了阐明刺突蛋白上对受体结合域（RBD）开放进行门控的pH敏感元件，并了解RBD开放转变的细节，我们在本研究中进行了微秒级的恒定pH分子动力学模拟。我们鉴定出深埋的D571，其具有明显的p位移，表明它可能是一种潜在的pH传感器，并展示了D571的电离与刺突RBD的上/下平衡之间的耦合。我们还计算了RBD开放的自由能景观，并确定了影响RBD动力学的关键相互作用。本文提供的对pH依赖性刺突激活机制的原子水平表征，为更好地理解SARS-CoV-2病毒进入和感染的基本机制提供了新见解，从而有助于发现针对2019冠状病毒病（COVID-19）的新型治疗方法。
