The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA

Area of Science:

• Molecular Biology
• Virology
• Biophysics

Background:

• The SARS-CoV-2 nucleocapsid (N) protein is crucial for viral RNA packaging.
• Molecular mechanisms of N protein function remain largely unknown.

Purpose of the Study:

• To elucidate the molecular details of SARS-CoV-2 N protein function in RNA binding and genome packaging.
• To investigate the role of N protein's disordered regions and domains in its interactions with RNA.

Main Methods:

• Single-molecule spectroscopy
• All-atom molecular dynamics simulations
• Polymer theory modeling

Main Results:

• N protein possesses three dynamic disordered regions with transiently-helical binding motifs.
• Full-length N protein is a flexible, multivalent RNA-binding protein due to minimal domain interaction.
• N protein induces liquid-liquid phase separation with RNA, driven by multivalent interactions.
• These interactions also promote RNA compaction, with a model suggesting preferential single-genome condensation.

Conclusions:

• Multivalent interactions of N protein with RNA are key to its function.
• Liquid-liquid phase separation provides a macroscopic indicator of nanoscopic RNA-binding events.
• A symmetry-breaking model explains preferential single-genome condensation over phase separation.