A model for pH coupling of the SARS-CoV-2 spike protein open/closed equilibrium

Area of Science:

• Virology
• Structural Biology
• Biochemistry

Background:

• Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mediates cell entry via its spike protein.
• The pH-dependent release of the viral RNA genome is influenced by spike protein stability and interactions with host cell factors.
• Understanding these mechanisms is crucial for developing effective antiviral strategies.

Purpose of the Study:

• To investigate the pH-dependence of SARS-CoV-2 spike protein conformations.
• To identify key residues and interactions that regulate the spike protein's open/closed equilibrium.
• To explore the influence of mutations and ligand binding on spike protein stability.

Main Methods:

• Utilized pKa calculations on various SARS-CoV-2 and other coronavirus spike protein structures and fragments.
• Analyzed heat maps of aggregated predictions to identify critical residues.
• Examined energetics of salt-bridge and sidechain-mainchain interactions.

Main Results:

• Three histidine residues in the S2 subunit were predicted to destabilize both pre- and post-fusion spike structures.
• Two aspartic acid residues (D290 and D398) showed elevated pKas, destabilizing open spike trimer conformations.
• These aspartic acids are stabilized in a closed conformation, influenced by linoleic acid binding and mutations like D614G.

Conclusions:

• Specific histidine and aspartic acid residues in the SARS-CoV-2 spike protein contribute to its pH-dependent conformational changes.
• The D398 residue is particularly implicated in the pH-dependent open/closed equilibrium, potentially modulated by linoleic acid and mutations.
• These findings offer insights into viral entry mechanisms and can inform the development of therapeutics targeting coronavirus infections.