Dynamic Asymmetry Exposes 2019-nCoV Prefusion Spike

J Phys Chem Lett. 2020 Sep 3;11(17):7021-7027. doi: 10.1021/acs.jpclett.0c01431. Epub 2020 Aug 13.

Abstract

The novel coronavirus (2019-nCoV) spike protein is a smart molecular machine that instigates the entry of coronavirus to the host cell causing the COVID-19 pandemic. In this study, a symmetry-information-loaded structure-based Hamiltonian is developed using recent Cryo-EM structural data to explore the complete conformational energy landscape of the full-length prefusion spike protein. The study finds the 2019-nCoV prefusion spike to adopt a unique strategy by undertaking a dynamic conformational asymmetry that results in two prevalent asymmetric structures of spike where one or two spike heads rotate up to provide better exposure to the host-cell receptor. A few unique interchain interactions are identified at the interface of closely associated N-terminal domain (NTD) and receptor binding domain (RBD) playing a crucial role in the thermodynamic stabilization of the up conformation of the RBD in the case of the 2019-nCoV spike. The interaction-level information decoded in this study may provide deep insight into developing effective therapeutic targets.

MeSH terms

  • Models, Molecular
  • Protein Domains
  • Spike Glycoprotein, Coronavirus / chemistry*
  • Spike Glycoprotein, Coronavirus / metabolism*
  • Viral Proteins / chemistry*
  • Viral Proteins / metabolism*

Substances

  • Spike Glycoprotein, Coronavirus
  • Viral Proteins
  • spike protein, SARS-CoV-2