Department of Molecular Medicine, The Scripps Research Institute, Jupiter, Florida 33458, United States.
Center for Advanced Biotechnology & Medicine, and Department of Chemistry & Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States.
J Am Soc Mass Spectrom. 2021 Jul 7;32(7):1618-1630. doi: 10.1021/jasms.1c00086. Epub 2021 Jun 14.
Coronavirus (CoV) nonstructural proteins (nsps) assemble to form the replication-transcription complex (RTC) responsible for viral RNA synthesis. nsp7 and nsp8 are important cofactors of the RTC, as they interact and regulate the activity of RNA-dependent RNA polymerase and other nsps. To date, no structure of the full-length SARS-CoV-2 nsp7:nsp8 complex has been published. The current understanding of this complex is based on structures from truncated constructs, with missing electron densities, or from related CoV species where SARS-CoV-2 nsp7 and nsp8 share upward of 90% sequence identity. Despite available structures solved using crystallography and cryo-EM representing detailed static snapshots of the nsp7:nsp8 complex, it is evident that the complex has a high degree of structural plasticity. However, relatively little is known about the conformational dynamics of the individual proteins and how they complex to interact with other nsps. Here, the solution-based structural proteomic techniques, hydrogen-deuterium exchange mass spectrometry (HDX-MS) and cross-linking mass spectrometry (XL-MS), illuminate the dynamics of SARS-CoV-2 full-length nsp7 and nsp8 proteins and the nsp7:nsp8 protein complex. Results presented from the two techniques are complementary and validate the interaction surfaces identified from the published three-dimensional heterotetrameric crystal structure of the SARS-CoV-2 truncated nsp7:nsp8 complex. Furthermore, mapping of XL-MS data onto higher-order complexes suggests that SARS-CoV-2 nsp7 and nsp8 do not assemble into a hexadecameric structure as implied by the SARS-CoV full-length nsp7:nsp8 crystal structure. Instead, our results suggest that the nsp7:nsp8 heterotetramer can dissociate into a stable dimeric unit that might bind to nsp12 in the RTC without significantly altering nsp7-nsp8 interactions.
冠状病毒(CoV)非结构蛋白(nsps)组装形成负责病毒 RNA 合成的复制转录复合物(RTC)。nsp7 和 nsp8 是 RTC 的重要辅助因子,因为它们相互作用并调节 RNA 依赖性 RNA 聚合酶和其他 nsps 的活性。迄今为止,尚未发表全长 SARS-CoV-2 nsp7:nsp8 复合物的结构。目前对该复合物的理解基于截短构建体的结构,这些结构存在电子密度缺失,或者基于相关的 CoV 物种,其中 SARS-CoV-2 nsp7 和 nsp8 共享超过 90%的序列同一性。尽管使用晶体学和 cryo-EM 解决了可用的结构,代表了 nsp7:nsp8 复合物的详细静态快照,但显然该复合物具有高度的结构可塑性。然而,关于单个蛋白质的构象动力学以及它们如何与其他 nsps 相互作用的了解相对较少。在这里,基于溶液的结构蛋白质组学技术,氢氘交换质谱(HDX-MS)和交联质谱(XL-MS),阐明了 SARS-CoV-2 全长 nsp7 和 nsp8 蛋白以及 nsp7:nsp8 蛋白复合物的动力学。两种技术呈现的结果是互补的,并验证了从已发表的 SARS-CoV-2 截短 nsp7:nsp8 复合物的三维异源四聚体晶体结构中鉴定出的相互作用表面。此外,将 XL-MS 数据映射到更高阶复合物表明,SARS-CoV-2 nsp7 和 nsp8 不会像 SARS-CoV 全长 nsp7:nsp8 晶体结构所暗示的那样组装成十六聚体结构。相反,我们的结果表明,nsp7:nsp8 异源四聚体可以解离成稳定的二聚体单元,该单元可能在 RTC 中与 nsp12 结合而不会显著改变 nsp7-nsp8 相互作用。