Dynamic allostery controls coat protein conformer switching during MS2 phage assembly

Area of Science:

• Structural Biology
• Biophysics
• Molecular Virology

Background:

• Bacteriophage MS2 coat protein assembly into a T=3 capsid is regulated by RNA stem-loop structures.
• The TR RNA stem-loop allosterically affects coat protein dimer conformation, influencing capsid formation.
• Both symmetric and asymmetric coat protein dimers are necessary for efficient in vitro assembly.

Purpose of the Study:

• To investigate the molecular mechanism of allosteric switching in bacteriophage MS2 coat protein dimers induced by RNA binding.
• To understand how RNA stem-loop binding influences protein dynamics and capsid assembly.
• To determine the sequence-independent nature of the allosteric effect.

Main Methods:

• All-atom normal-mode analysis was employed to study the vibrational modes of RNA-free and TR RNA-bound coat protein dimers.
• Analysis focused on conformational changes in FG-loops and their impact on protein dynamics.
• Vibrational modes of an assembly mutant (W82R) were also examined to validate the proposed mechanism.

Main Results:

• RNA binding to the coat protein dimer causes asymmetric changes in FG-loop dynamics: one loop becomes more dynamic, while the other becomes less mobile.
• Increased FG-loop mobility in one subunit reduces the free energy barrier for adopting the quasi-equivalent B conformation, facilitating assembly.
• The W82R mutant shows altered DE-loop mobility upon RNA binding, consistent with its non-assembling phenotype.

Conclusions:

• The allosteric effect of RNA stem-loops on MS2 coat protein assembly is mediated by asymmetric modulation of protein subunit dynamics.
• The mechanism explains the observed sequence independence of RNA stem-loop effectors.
• Normal-mode analysis provides a valuable tool for understanding allosteric regulation in viral capsid assembly.