Phosphorylation Changes SARS-CoV-2 Nucleocapsid Protein's Structural Dynamics and Its Interaction With RNA.

Area of Science:

• Molecular virology
• Structural biology
• Biophysics

Background:

• The SARS-CoV-2 nucleocapsid protein (N-protein) is crucial for viral RNA replication and packaging.
• The N-protein's phosphorylation state is hypothesized to regulate its distinct functions.
• Understanding N-protein dynamics and RNA interactions is key to deciphering viral mechanisms.

Purpose of the Study:

• To investigate the dynamic behavior of non-phosphorylated and phosphorylated N-protein homodimers.
• To elucidate the impact of phosphorylation on N-protein:RNA binding affinity.
• To explore the role of secondary structure in N-protein's interaction with viral RNA.

Main Methods:

• Atomistic molecular dynamics simulations were employed to model N-protein behavior.
• Comparative analysis of phosphorylated versus non-phosphorylated N-protein homodimers.
• Assessment of N-protein:RNA interactions, focusing on the 5' UTR.

Main Results:

• Phosphorylation significantly increases the dynamic flexibility of the N-protein structure.
• Binding affinity between the N-protein and RNA is reduced upon phosphorylation.
• Secondary structure elements are critical for specific RNA element binding to the N-terminal domain.

Conclusions:

• Phosphorylation acts as a regulatory switch, modulating N-protein dynamics and function.
• Altered N-protein dynamics and reduced RNA binding affinity support its role in regulating viral processes.
• Detailed molecular insights confirm phosphorylation's importance in SARS-CoV-2 N-protein regulation.