A Tiny Viral Protein, SARS-CoV-2-ORF7b: Structural Features

ORF7b is a tiny accessory protein of the SARS-CoV-2 virus of only 43 amino acids that is often believed similar to its homolog ORF7b of SARS-CoV. This study compared physico-chemical and structural properties of the two proteins, where necessary, to emphasize differences and similarities. However, the aim is to evidence the real properties of ORF7b of SARS-CoV-2, a protein functionally involved in many metabolic compartments. Sequence analysis and electrostatic characteristics show a polypeptide with both ends negatively charged and a diffuse negative charge over the entire structure. Its behavior in solution is like that of a polyanion with a net charge of −4 at neutral pH. Two modeling systems with ab initio features, were used to have a complete 3D-structure. The two best 3D-models are similar, as confirmed by the Ramachandran plot, and show a helical core with two disordered and fluctuating ends. Residue-residue analysis and normal mode analysis characterized the hinges of the protein and movements of rigid parts, confirming fluctuating extremities, which have a role in controlling the structural organization. The dipole moment calculation reveals a vector misaligned with the structure’s main axis, tilting outward by 24°. Molecular dynamics show a behavior in water in agreement with the previous results and structural distortions with a low tendency to solvate in an apolar environment. The definition of its thermodynamic association ranges discovered the intriguing potentiality to participate in liquid-liquid phase transitions (droplets) together with other viral proteins. ORF7b also shows a high sensibility to pH changes, with a widespread distribution of its negative surfaces dynamically adjusted by structural changes. In particular conditions, it is also quite soluble in aqueous media. ORF7b2’s intriguing properties and the vast number of its interactions, as reported in BioGRID, show its remarkable tendency to bind many molecular partners using both electrostatic and hydrophobic interactions in different cellular environments. This introduces additional considerations for ORF7b2 as a peripheral membrane protein, because of its unique chemical, physical, and structural characteristics, as well as its involvement in various metabolic compartments.