Modulation of SARS-CoV-2 spike binding to ACE2 through conformational selection

Area of Science:

• Virology
• Structural Biology
• Biophysics

Background:

• SARS-CoV-2 infection initiates via the spike protein (S) interacting with host ACE2.
• The S protein's receptor-binding domain (RBD) exists in open and closed states, influencing ACE2 accessibility.
• Quantitative insights into RBD conformational dynamics and their impact on binding have been limited.

Purpose of the Study:

• To visualize and quantify the dynamics of the SARS-CoV-2 RBD opening and closing.
• To investigate the effect of RBD dynamics on the interaction with ACE2 at single-molecule and ensemble levels.
• To elucidate the molecular mechanisms governing S/ACE2 binding and its modulation by RBD conformation.

Main Methods:

• High-speed atomic force microscopy (HS-AFM) to visualize RBD conformational changes and transition rates.
• Biolayer interferometry (BLI) for ensemble-level S/ACE2 interaction analysis.
• Single-molecule force spectroscopy (AFM and magnetic tweezers) to probe binding and unbinding kinetics.

Main Results:

• Direct visualization of RBD opening and closing transitions with associated rates.
• Evidence that RBD dynamics impede ACE2 binding but do not affect unbinding.
• Quantitative prediction of binding modulation using a conformational selection model with independent protomers.

Conclusions:

• RBD dynamics play a crucial role in modulating SARS-CoV-2 binding to ACE2.
• Separate tuning of RBD accessibility and binding strength is possible, impacting infectivity.
• Findings offer insights into the co-evolution of viral immune evasion and infectivity.