Table 2.
Comparison of surface charge on S protein of the two VOI with the wild type at pH 7.0.
| Pango Lineage | Name | Mutations | PDB | Surface Charge (Formal Charge) |
Surface Charge (Partial Charge) |
RBD Charge |
|---|---|---|---|---|---|---|
| WT (Natural variant) |
USA/WA1/2020 | - | 6VYB | −20 | −17 | 9 |
| - | 6VSB | −26 | −23 | 6 | ||
| B.1.1.7 (UK variant) |
20J/501Y.V1 | Δ69/70 Δ144Y N501Y A570D D614G P681H |
7LWV | −12 | −9 | 7 |
| B.1.351 (South Africa variant) |
20H/501.V2 | K417N E484K N501Y D614G |
7LYQ | −7 | −4 | 8 |
Surface charges are based on the solvent-accessible (SA) residues calculated in PyMol using APBS electrostatics. The boundary conditions used for single Debye–Huckel function were as follows: solute dielectric constant—2.000; solvent dielectric constant—78.000; ionic strength—150 mM; temperature—310 K. RBD charges were calculated by adding the partial charges of the SA resides in the 319–541 region of chain B for 6VYB, 7LWV, and 7LYQ or chain A for 6VSB. The chain consideration was based on the chain identifier that showed an upconfiguration of the RBD in PyMol.