Pulling Forces Differentially Affect Refolding Pathways Due to Entangled Misfolded States in SARS-CoV-1 and...

Area of Science:

• Biophysics
• Computational Biology
• Structural Biology

Background:

• Single-molecule force spectroscopy (SMFS) probes protein dynamics under force.
• Bell theory predicts exponential increases in protein folding time with applied force.
• Receptor binding domains (RBDs) of coronaviruses are crucial for viral entry.

Purpose of the Study:

• To investigate the refolding pathways of SARS-CoV-1 and SARS-CoV-2 receptor binding domains (RBDs) using molecular dynamics simulations.
• To compare the response of SARS-CoV-1 RBD and SARS-CoV-2 RBD to applied forces in the context of Bell theory.
• To explore the molecular mechanisms underlying differences in force-induced refolding behavior.

Main Methods:

• Coarse-grained molecular dynamics simulations were employed.
• Simulations compared refolding pathways of unfolded SARS-CoV-1 RBD and SARS-CoV-2 RBD with and without applied forces (5 pN).
• Analysis of entanglement changes in folded conformations was performed.

Main Results:

• A 5 pN force significantly reduced refolding trajectories for SARS-CoV-2 RBD, consistent with Bell theory.
• SARS-CoV-1 RBD refolding times showed no significant change under a 5 pN force.
• External force minimized misfolding into kinetically trapped states for SARS-CoV-1 RBD, promoting efficient folding.

Conclusions:

• Non-Bell behavior in protein refolding can arise from the minimization of misfolding into kinetically trapped states.
• Misfolded states in SARS-CoV-1 RBD contain non-native entanglements not present in native states.
• This study suggests a potential experimental method for detecting elusive, theoretically predicted misfolded states.