Suppr超能文献

利用结构蛋白质组学揭示 SARS-CoV-2 nsp7 和 nsp8 的结构可塑性。

Revealing the Structural Plasticity of SARS-CoV-2 nsp7 and nsp8 Using Structural Proteomics.

机构信息

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.

出版信息

J Am Soc Mass Spectrom. 2021 Jul 7;32(7):1618-1630. doi: 10.1021/jasms.1c00086. Epub 2021 Jun 14.

Abstract

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.

摘要

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。

相似文献

1
Revealing the Structural Plasticity of SARS-CoV-2 nsp7 and nsp8 Using Structural Proteomics.
J Am Soc Mass Spectrom. 2021 Jul 7;32(7):1618-1630. doi: 10.1021/jasms.1c00086. Epub 2021 Jun 14.
2
Resolving the Dynamic Motions of SARS-CoV-2 nsp7 and nsp8 Proteins Using Structural Proteomics.
bioRxiv. 2021 Mar 6:2021.03.06.434214. doi: 10.1101/2021.03.06.434214.
3
Two conserved oligomer interfaces of NSP7 and NSP8 underpin the dynamic assembly of SARS-CoV-2 RdRP.
Nucleic Acids Res. 2021 Jun 4;49(10):5956-5966. doi: 10.1093/nar/gkab370.
4
5
Transient and stabilized complexes of Nsp7, Nsp8, and Nsp12 in SARS-CoV-2 replication.
Biophys J. 2021 Aug 3;120(15):3152-3165. doi: 10.1016/j.bpj.2021.06.006. Epub 2021 Jun 29.
7
Structural analysis of the putative SARS-CoV-2 primase complex.
J Struct Biol. 2020 Aug 1;211(2):107548. doi: 10.1016/j.jsb.2020.107548. Epub 2020 Jun 11.
8
Nonstructural protein 7 and 8 complexes of SARS-CoV-2.
Protein Sci. 2021 Apr;30(4):873-881. doi: 10.1002/pro.4046. Epub 2021 Feb 25.

引用本文的文献

1
The C-terminal Domain of SARS-CoV-2 nsp8 is a Molten Globule in the Absence of Binding Partners.
J Mol Biol. 2025 Aug 19;437(21):169400. doi: 10.1016/j.jmb.2025.169400.
4
MS Annika 2.0 Identifies Cross-Linked Peptides in MS2-MS3-Based Workflows at High Sensitivity and Specificity.
J Proteome Res. 2023 Sep 1;22(9):3009-3021. doi: 10.1021/acs.jproteome.3c00325. Epub 2023 Aug 11.
5
Biochemical and structural insights into SARS-CoV-2 polyprotein processing by Mpro.
Sci Adv. 2022 Dec 9;8(49):eadd2191. doi: 10.1126/sciadv.add2191.
6
SARS-CoV-2 Non-Structural Proteins and Their Roles in Host Immune Evasion.
Viruses. 2022 Sep 8;14(9):1991. doi: 10.3390/v14091991.
7
Domain-specific biochemical and serological characterization of SARS-CoV-2 nucleocapsid protein.
STAR Protoc. 2021 Dec 17;2(4):100906. doi: 10.1016/j.xpro.2021.100906. Epub 2021 Oct 7.
8
Recent progress in mass spectrometry-based strategies for elucidating protein-protein interactions.
Cell Mol Life Sci. 2021 Jul;78(13):5325-5339. doi: 10.1007/s00018-021-03856-0. Epub 2021 May 27.

本文引用的文献

1
The structure of a dimeric form of SARS-CoV-2 polymerase.
Commun Biol. 2021 Aug 24;4(1):999. doi: 10.1038/s42003-021-02529-9.
2
Hallmarks of and non-structural protein 7+8 complexes.
Sci Adv. 2021 Mar 3;7(10). doi: 10.1126/sciadv.abf1004. Print 2021 Mar.
3
Mechanism of SARS-CoV-2 polymerase stalling by remdesivir.
Nat Commun. 2021 Jan 12;12(1):279. doi: 10.1038/s41467-020-20542-0.
4
Coronavirus biology and replication: implications for SARS-CoV-2.
Nat Rev Microbiol. 2021 Mar;19(3):155-170. doi: 10.1038/s41579-020-00468-6. Epub 2020 Oct 28.
5
Virus-Host Interactome and Proteomic Survey Reveal Potential Virulence Factors Influencing SARS-CoV-2 Pathogenesis.
Med. 2021 Jan 15;2(1):99-112.e7. doi: 10.1016/j.medj.2020.07.002. Epub 2020 Jul 21.
6
Structural analysis of the putative SARS-CoV-2 primase complex.
J Struct Biol. 2020 Aug 1;211(2):107548. doi: 10.1016/j.jsb.2020.107548. Epub 2020 Jun 11.
7
Structural and Biochemical Characterization of the nsp12-nsp7-nsp8 Core Polymerase Complex from SARS-CoV-2.
Cell Rep. 2020 Jun 16;31(11):107774. doi: 10.1016/j.celrep.2020.107774. Epub 2020 May 30.
8
Structural Basis for RNA Replication by the SARS-CoV-2 Polymerase.
Cell. 2020 Jul 23;182(2):417-428.e13. doi: 10.1016/j.cell.2020.05.034. Epub 2020 May 22.
9
Structure of replicating SARS-CoV-2 polymerase.
Nature. 2020 Aug;584(7819):154-156. doi: 10.1038/s41586-020-2368-8. Epub 2020 May 21.
10
Structural basis for inhibition of the RNA-dependent RNA polymerase from SARS-CoV-2 by remdesivir.
Science. 2020 Jun 26;368(6498):1499-1504. doi: 10.1126/science.abc1560. Epub 2020 May 1.

文献AI研究员

20分钟写一篇综述,助力文献阅读效率提升50倍。

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

文档翻译

学术文献翻译模型,支持多种主流文档格式。

立即体验