Exploring the Role of Structural and Dynamic Complexity in SARS-CoV-2 Nucleocapsid Protein-Heparin Interactions by...

Area of Science:

• Biochemistry
• Structural Biology
• Virology

Background:

• The SARS-CoV-2 nucleocapsid (N) protein exhibits significant structural heterogeneity and plays multiple roles in the viral life cycle.
• N protein is found on the surface of infected and non-infected cells, interacting with heparan sulfate in the extracellular matrix.

Purpose of the Study:

• To investigate how the structural heterogeneity of the SARS-CoV-2 N protein influences its interactions with biological partners, specifically heparin-based ligands.
• To characterize the binding of N protein constructs to heparin using high-resolution NMR spectroscopy and molecular dynamics simulations.

Main Methods:

• High-resolution Nuclear Magnetic Resonance (NMR) spectroscopy was used to study three N protein constructs (NTD, NTR, and full-length N) and their interactions with heparin-based ligands.
• Molecular dynamics simulations were employed to further analyze the interaction between the NTD domain and short heparin oligosaccharides.

Main Results:

• Binding affinity strongly correlates with heparin ligand size, with longer chains showing stronger binding.
• Intrinsically disordered regions (IDRs) within the N protein significantly enhance binding affinity compared to the structured NTD domain alone.
• The full-length N protein displayed unique spectral characteristics, suggesting complex binding dynamics and additional interaction contributions.

Conclusions:

• Structural disorder in the N protein is functionally relevant, enhancing interactions with heparin.
• NMR spectroscopy is a powerful tool for studying dynamic, multivalent interactions of flexible proteins like the SARS-CoV-2 N protein.
• Understanding these interactions is crucial for comprehending viral mechanisms and developing therapeutic strategies.