Structural conservation among variants of the SARS-CoV-2 spike postfusion bundle

Area of Science:

• Structural biology
• Virology
• Biochemistry

Background:

• Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants pose challenges to vaccines and therapies due to changes in the spike glycoprotein.
• The spike protein's HR1 and HR2 domains form a six-helix bundle, crucial for viral entry into host cells.

Purpose of the Study:

• To investigate the structural and dynamic effects of SARS-CoV-2 variant mutations within the postfusion HR1HR2 bundle.
• To assess the impact of specific mutations, including those found in the Omicron variant, on the HR1HR2 structure and function.

Main Methods:

• Designed a novel molecular scaffold for stabilizing the HR1HR2 bundle.
• Utilized single-particle cryogenic electron microscopy (cryo-EM) to determine high-resolution structures (2.2–3.8 Å) of the wild-type and mutant HR1HR2 bundles.
• Analyzed the structural impact of eight selected mutations, including Omicron-specific ones.

Main Results:

• Determined high-resolution cryo-EM structures of the wild-type and mutant HR1HR2 bundles, resolving previous structural ambiguities.
• Observed that the studied mutations primarily exert local effects on HR1-HR2 interactions without altering the overall HR1HR2 bundle architecture.
• Identified specific side-chain alterations caused by mutations like Q954H, N969K, and L981F.

Conclusions:

• The interfaces within the postfusion HR1HR2 bundle are potential targets for broad-spectrum antiviral inhibitors effective against current SARS-CoV-2 variants.
• The developed molecular scaffold facilitates efficient structural studies of the HR1HR2 bundle and its mutants.
• This methodology can be extended to study other viral fusion mechanisms.