Inter-domain communication in SARS-CoV-2 spike proteins controls protease-triggered cell entry

Area of Science:

• Virology
• Structural Biology
• Immunology

Background:

• Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) evolves into variants of concern (VOCs).
• The spike protein, crucial for viral entry, exhibits significant variability, particularly in its multidomain structure.
• Understanding adaptive changes in the spike protein is vital for controlling viral spread.

Purpose of the Study:

• To investigate the functional consequences of adaptive spike protein changes in SARS-CoV-2 variants.
• To elucidate the mechanism of allosteric regulation between spike protein domains during virus-cell entry.
• To identify structural elements mediating communication between the amino-terminal domain (NTD) and fusion domains (FDs).

Main Methods:

• Comparative analysis of variant SARS-CoV-2 virus particles in cell-entry assays.
• Assessment of proteolytic activation of membrane fusion.
• Structure-guided mutagenesis to identify key structural interfaces.
• Antibody neutralization assays targeting NTD-specific epitopes.

Main Results:

• Variant spike proteins with adaptive NTD changes exhibit hypersensitivity to proteolytic activation of membrane fusion.
• Proteolysis occurs within fusion domains (FDs), distant from NTD changes, indicating allosteric control.
• NTD-specific antibodies inhibit FD cleavage, membrane fusion, and viral entry by restricting inter-domain communication.
• An inter-monomer β sheet structure was identified as critical for NTD-to-FD transmission and fusion activation.

Conclusions:

• An NTD-to-FD communication axis sensitizes SARS-CoV-2 to infection and antibody neutralization.
• This axis provides insights into the selective pressures driving viral evolution.
• Targeting this axis may offer therapeutic strategies against SARS-CoV-2 variants.