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

• Published in: bioRxiv 2020-12
• Main Authors: 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
• Format: Article
• Language: English
• Subjects: Binding sites; Biophysics; Compaction; Genomes; Interfaces; Life cycles; N protein; Nucleocapsids; Polymers; Proteins; Ribonucleic acid; RNA; RNA-binding protein; Severe acute respiratory syndrome coronavirus 2; Spectroscopy; Transcription
• ISSN: 2692-8205
• DOI: 10.1101/2020.06.17.158121

Abstract 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. Competing Interest Statement The authors have declared no competing interest. Footnotes * None of the conclusions arrived at in our original submission have changed. We have performed a large body of additional controls, expanded the scope of simulations to obtain better conformational sampling, and updated references to reflect the ever-evolving literature.