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

Cubuk, Jasmine; Alston, Jhullian J.; Incicco, J. Jeremías; Singh, Sukrit; Stuchell-Brereton, Melissa D.; Ward, Michael D.; Zimmerman, Maxwell I.; Vithani, Neha; Griffith, Daniel; Wagoner, Jason A.; Bowman, Gregory R.; Hall, Kathleen B.; Soranno, Andrea; Holehouse, Alex S.

The SARS-CoV-2 nucleocapsid (N) protein is an abundant RNA-binding protein critical for viral genome packaging, yet the molecular details that underlie this process are poorly understood. Here we combine single-molecule spectroscopy with all-atom simulations to uncover the molecular details that contribute to N protein function. N protein contains three dynamic disordered regions that house putative transiently-helical binding motifs. The two folded domains interact minimally such that full-length N protein is a flexible and multivalent RNA-binding protein. N protein also undergoes liquid-liquid phase separation when mixed with RNA, and polymer theory predicts that the same multivalent interactions that drive phase separation also engender RNA compaction. We offer a simple symmetry-breaking model that provides a plausible route through which single-genome condensation preferentially occurs over phase separation, suggesting that phase separation offers a convenient macroscopic readout of a key nanoscopic interaction.