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

Prithwidip Saha1, Ignacio Fernandez2, Fidan Sumbul1

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|June 10, 2025
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Summary
This summary is machine-generated.

Understanding SARS-CoV-2 infection requires studying the spike protein (S) and its interaction with host ACE2. This study visualizes the S protein's receptor-binding domain (RBD) dynamics, revealing how its opening and closing affect ACE2 binding.

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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.