ArticleBiophysical chemistry2022
Conformational ensemble of the full-length SARS-CoV-2 nucleocapsid (N) protein based on molecular simulations and SAXS data.
Article in Biophysical chemistry, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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20 citing papers in PubMed, 32 citations in OpenAlex.
- Intramolecular loops control SARS-CoV-2 nucleocapsid protein self-association and nucleic acid binding dependent on phosphorylation.bioRxiv : the preprint server for biology · 2026Article
- Article
- Characterization of the binding features between SARS-CoV-2 5'-proximal transcripts of genomic RNA and nucleocapsid proteins.RNA biology · 2025Review
- Evolution of a fuzzy ribonucleoprotein complex in viral assembly.bioRxiv : the preprint server for biology · 2025Article
- Sucrose Monolaurate as a Stabilizer for Lactate Oxidase Electrodes at Low pH: A Structural Analysis Based on Grazing Incidence Small-Angle X-ray Scattering.Langmuir : the ACS journal of surfaces and colloids · 2025Article
- Structural stabilization of the intrinsically disordered SARS-CoV-2 N by binding to RNA sequences engineered from the viral genome fragment.Nature communications · 2025Article
- In-vitro and in-silico antibacterial and antibiofilm activities of an aromatic heterocyclic metabolite from a novel halo-thermophilic Streptomyces sp. strain CBN-1 against bacteria causing nosocomial infections.Molecular biology reports · 2025Article
- The role of intrinsically disordered regions of SARS-CoV-2 nucleocapsid and non-structural protein 1 proteins.Frontiers in chemistry · 2025Review
- Coupling of SARS-CoV-2 to Amyloid Fibrils and Liquid-Liquid Phase Separation.Current protein & peptide science · 2025Review
- Modulation of biophysical properties of nucleocapsid protein in the mutant spectrum of SARS-CoV-2.eLife · 2024Article
- Assembly of SARS-CoV-2 nucleocapsid protein with nucleic acid.Nucleic acids research · 2024Article
- A Practical Guide to All-Atom and Coarse-Grained Molecular Dynamics Simulations Using Amber and Gromacs: A Case Study of Disulfide-Bond Impact on the Intrinsically Disordered Amyloid Beta.International journal of molecular sciences · 2024Article
- Scrutinising the Conformational Ensemble of the Intrinsically Mixed-Folded Protein Galectin-3.Molecules (Basel, Switzerland) · 2024Article
- Modulation of Biophysical Properties of Nucleocapsid Protein in the Mutant Spectrum of SARS-CoV-2.bioRxiv : the preprint server for biology · 2024Article
- Assembly reactions of SARS-CoV-2 nucleocapsid protein with nucleic acid.bioRxiv : the preprint server for biology · 2023Article
- SARS-CoV-2 proteins structural studies using synchrotron radiation.Biophysical reviews · 2023Review
- The preference signature of the SARS-CoV-2 Nucleocapsid NTD for its 5'-genomic RNA elements.Nature communications · 2023Article
- A conserved oligomerization domain in the disordered linker of coronavirus nucleocapsid proteins.Science advances · 2023Article
- Structural domains of SARS-CoV-2 nucleocapsid protein coordinate to compact long nucleic acid substrates.Nucleic acids research · 2023Article
- Structural basis for SARS-CoV-2 nucleocapsid (N) protein recognition by 14-3-3 proteins.Journal of structural biology · 2022Article
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Authors and funding
2 authors at 2 institutions in 2 countries.
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No grant is acknowledged in the PubMed record.
Abstract
The nucleocapsid protein of the SARS-CoV-2 virus comprises two RNA-binding domains and three regions that are intrinsically disordered. While the structures of the RNA-binding domains have been solved using protein crystallography and NMR, current knowledge of the conformations of the full-length nucleocapsid protein is rather limited. To fill in this knowledge gap, we combined coarse-grained molecular simulations with data from small-angle X-ray scattering (SAXS) experiments using the ensemble refinement of SAXS (EROS) method. Our results show that the dimer of the full-length nucleocapsid protein exhibits large conformational fluctuations with its radius of gyration ranging from about 4 to 8 nm. The RNA-binding domains do not make direct contacts. The disordered region that links these two domains comprises a hydrophobic α-helix which makes frequent and nonspecific contacts with the RNA-binding domains. Each of the intrinsically disordered regions adopts conformations that are locally compact, yet on average, much more extended than Gaussian chains of equivalent lengths. We offer a detailed picture of the conformational ensemble of the nucleocapsid protein dimer under near-physiological conditions, which will be important for understanding the nucleocapsid assembly process.
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