Intramolecular loops control SARS-CoV-2 nucleocapsid protein self-association and nucleic acid binding dependent on...

Area of Science:

• Virology
• Molecular Biology
• Structural Biology

Background:

• The SARS-CoV-2 nucleocapsid protein (N protein) is essential for viral assembly into ribonucleoprotein complexes (RNPs).
• The N protein plays crucial roles in viral replication and suppressing host immune responses.
• Its function is regulated by phosphorylation of the serine/arginine-rich (SR) region within a disordered linker.

Purpose of the Study:

• To elucidate the molecular mechanism by which SR region phosphorylation controls N protein function.
• To understand how phosphorylation switches N protein between intracellular and virion assembly roles.

Main Methods:

• Biophysical measurements including hydrodynamic radii and reversible protein self-association.
• Nucleic acid binding assays and thermodynamic stability measurements.
• Structural predictions and analysis of published NMR chemical shifts.

Main Results:

• A model where two mutually exclusive intramolecular loops bind the N-terminal domain (NTD).
• SR linker phosphorylation leads to protein compaction, reduced nucleic acid binding, and inhibited RNP formation.
• Phosphorylation enhances self-association via transient coiled-coils in the leucine-rich sequence (LRS), favoring intracellular functions.

Conclusions:

• SR linker phosphorylation dynamically alters N protein conformation and function.
• This phosphorylation-dependent switch enables the N protein to mediate distinct roles in viral replication and assembly.
• The findings provide insights into the regulation of SARS-CoV-2 lifecycle and host-pathogen interactions.