ArticlePNAS nexus2023
RNA structure and multiple weak interactions balance the interplay between RNA binding and phase separation of SARS-CoV-2 nucleocapsid.
Article in PNAS nexus, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 27 citations in OpenAlex.
- Targeting SARS-CoV-2 Structural and Accessory Proteins: Emerging Opportunities for Small-Molecule Coronavirus Antivirals.Pharmaceutics · 2026Review
- Peptide ligands to explore interactions with intrinsically disordered multidomain proteins: the case of SARS-CoV-2 nucleocapsid protein.Scientific reports · 2026Article
- Article
- In Search of the Most Significant Potential G-Quadruplexes in SARS-CoV-2 RNA: Genomic Analysis.Viruses · 2026Article
- Mapping SARS-CoV-2 Nucleocapsid Function with Nanobodies.bioRxiv : the preprint server for biology · 2026Article
- Intramolecular loops control SARS-CoV-2 nucleocapsid protein self-association and nucleic acid binding dependent on phosphorylation.bioRxiv : the preprint server for biology · 2026Article
- Structural and functional analyses of SARS-CoV-2 Nsp3 and its specific interactions with the 5' UTR of the viral genome.Microbiology spectrum · 2025Article
- Protein-RNA condensation kinetics via filamentous nanoclusters.Protein science : a publication of the Protein Society · 2025Article
- Review
- Revealing the Potential of a Chimaera: a Peptide-Peptide Nucleic Acid Molecule Designed To Interact with the SARS-CoV-2 Nucleocapsid Protein.Angewandte Chemie (International ed. in English) · 2025Article
- A core network in the SARS-CoV-2 nucleocapsid NTD mediates structural integrity and selective RNA-binding.Nature communications · 2024Article
- Phase Separation of SARS-CoV-2 Nucleocapsid Protein with TDP-43 Is Dependent on C-Terminus Domains.International journal of molecular sciences · 2024Article
- A practically efficient algorithm for identifying critical control proteins in directed probabilistic biological networks.NPJ systems biology and applications · 2024Article
- A specific phosphorylation-dependent conformational switch in SARS-CoV-2 nucleocapsid protein inhibits RNA binding.Science advances · 2024Article
- Assembly of SARS-CoV-2 nucleocapsid protein with nucleic acid.Nucleic acids research · 2024Article
- Phosphorylation in the Ser/Arg-rich region of the nucleocapsid of SARS-CoV-2 regulates phase separation by inhibiting self-association of a distant helix.The Journal of biological chemistry · 2024Article
- Bioinformatics Insights on Viral Gene Expression Transactivation: From HIV-1 to SARS-CoV-2.International journal of molecular sciences · 2024Article
- Assembly reactions of SARS-CoV-2 nucleocapsid protein with nucleic acid.bioRxiv : the preprint server for biology · 2023Article
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Authors and funding
9 authors at 1 institution in 1 country.
Funding
Abstract
The nucleocapsid (N) protein of SARS-CoV-2 binds viral RNA, condensing it inside the virion, and phase separating with RNA to form liquid-liquid condensates. There is little consensus on what differentiates sequence-independent N-RNA interactions in the virion or in liquid droplets from those with specific genomic RNA (gRNA) motifs necessary for viral function inside infected cells. To identify the RNA structures and the N domains responsible for specific interactions and phase separation, we use the first 1,000 nt of viral RNA and short RNA segments designed as models for single-stranded and paired RNA. Binding affinities estimated from fluorescence anisotropy of these RNAs to the two-folded domains of N (the NTD and CTD) and comparison to full-length N demonstrate that the NTD binds preferentially to single-stranded RNA, and while it is the primary RNA-binding site, it is not essential to phase separation. Nuclear magnetic resonance spectroscopy identifies two RNA-binding sites on the NTD: a previously characterized site and an additional although weaker RNA-binding face that becomes prominent when binding to the primary site is weak, such as with dsRNA or a binding-impaired mutant. Phase separation assays of nucleocapsid domains with double-stranded and single-stranded RNA structures support a model where multiple weak interactions, such as with the CTD or the NTD's secondary face promote phase separation, while strong, specific interactions do not. These studies indicate that both strong and multivalent weak N-RNA interactions underlie the multifunctional abilities of N.
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