Structural dynamics of SARS-CoV-2 nucleocapsid protein induced by RNA binding

PLoS Comput Biol. 2022 May 12;18(5):e1010121. doi: 10.1371/journal.pcbi.1010121. eCollection 2022 May.

Abstract

The nucleocapsid (N) protein of the SARS-CoV-2 virus, the causal agent of COVID-19, is a multifunction phosphoprotein that plays critical roles in the virus life cycle, including transcription and packaging of the viral RNA. To play such diverse roles, the N protein has two globular RNA-binding modules, the N- (NTD) and C-terminal (CTD) domains, which are connected by an intrinsically disordered region. Despite the wealth of structural data available for the isolated NTD and CTD, how these domains are arranged in the full-length protein and how the oligomerization of N influences its RNA-binding activity remains largely unclear. Herein, using experimental data from electron microscopy and biochemical/biophysical techniques combined with molecular modeling and molecular dynamics simulations, we show that, in the absence of RNA, the N protein formed structurally dynamic dimers, with the NTD and CTD arranged in extended conformations. However, in the presence of RNA, the N protein assumed a more compact conformation where the NTD and CTD are packed together. We also provided an octameric model for the full-length N bound to RNA that is consistent with electron microscopy images of the N protein in the presence of RNA. Together, our results shed new light on the dynamics and higher-order oligomeric structure of this versatile protein.

MeSH terms

  • COVID-19
  • Coronavirus Nucleocapsid Proteins* / chemistry
  • Coronavirus Nucleocapsid Proteins* / metabolism
  • Humans
  • Microscopy, Electron
  • Molecular Dynamics Simulation
  • Nucleocapsid Proteins / chemistry
  • Nucleocapsid Proteins / metabolism
  • Phosphoproteins / metabolism
  • Protein Binding
  • RNA, Viral / genetics
  • SARS-CoV-2* / chemistry
  • SARS-CoV-2* / genetics
  • SARS-CoV-2* / metabolism

Substances

  • Coronavirus Nucleocapsid Proteins
  • Nucleocapsid Proteins
  • Phosphoproteins
  • RNA, Viral

Grants and funding

This work is part of the Rede Virus MCTI taskforce on COVID-19 funded by FINEP (grant number 01.20.0003.00) (http://www.finep.gov.br/), Brazilian Ministry of Science, Technology and Innovation (https://www.gov.br/mcti/). GRS received financial support from the Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP - https://fapesp.br/), project number 17/18139-6. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.