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Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host

Shahzaib Ahamad1, Hema Kanipakam1, Dinesh Gupta1

  • 1Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India.

Journal of Biomolecular Structure & Dynamics
|August 28, 2020
PubMed

Insights

Mutations in the SARS-CoV-2 spike glycoprotein’s RBD and HR1 domains significantly destabilize its structure. This research explores how these mutations impact the virus’s ability to infect host cells.

Area of Science:

  • Virology
  • Structural Biology
  • Computational Biology

Background:

  • The SARS-CoV-2 virus, responsible for the COVID-19 pandemic, utilizes its Spike glycoprotein for host cell entry.
  • The Spike glycoprotein contains key functional domains, including the receptor-binding domain (RBD) and heptad repeat 1 (HR1), crucial for viral stability and infection.

Purpose of the Study:

  • To investigate the impact of specific mutations within the RBD and HR1 domains of the SARS-CoV-2 Spike glycoprotein on its native structure and stability.
  • To understand how these mutations might affect the glycoprotein's binding properties before receptor interaction.

Main Methods:

  • Molecular Dynamics (MD) simulations were employed to compare the wild-type (WT) Spike glycoprotein with mutants.
  • Specific mutations studied include R408I, L455Y, F486L, Q493N, Q498Y, N501T in RBD and A930V, D936Y in HR1.

Main Results:

  • MD simulations revealed a significant destabilizing effect of the studied mutations on both the RBD and HR1 domains of the Spike glycoprotein.
  • The investigated mutations impact the stability of the Spike glycoprotein prior to receptor binding.

Conclusions:

  • The identified mutations in the RBD and HR1 domains can compromise the structural integrity of the SARS-CoV-2 Spike glycoprotein.
  • These findings provide insights into how mutations may alter viral binding properties and infectivity.
Keywords:
COVID-19MD simulationsRBD and HR1 domainSARS-CoV-2 spike glycoproteindeleterious mutations

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