Fig 1.
The binding structure of ACE2 (in blue) with RBD (in green) (a), with the mutations (shown in red sticks) on RBD labeled; and the comparison of the initial and final structures of ACE2 bound with RBD-trimutant variant (b). In b), the initial structures of ACE2 and RBD are shown in wheat, and the final structure of ACE2 is shown in raspberry and magenta for RBD. The mutations of E484K, K417N, and N501Y are shown in blue sticks in both the initial and final structures.
Table 1.
The average and standard deviations of RMSDs of ACE2&RBD complex, RBD wildtype and variants, and ACE2, the number of hydrogen bonds (Hbonds) formed, and the buried surface area (BSA) between ACE2 and RBD.
The standard deviations were calculated based on the second-half of NAMD simulations.
Fig 2.
Comparison of RMSF from RBD variants and wildtype (a) and ACE2 (b). The variant results are shown in black solid line while the wildtype shown in red dashed line. The binding regions on RBD and ACE2 are shaded in light green, and the secondary structures of RBD and ACE2 are shown on the top of RMSF figures.
Fig 3.
The ΔRMSF of RBD-N501Y and ACE2 (a) from wildtype to variant forms of RBD mapped to the initial bound structure of ACE2&RBD-N501Y; and the ΔRMSF of RBD-trimutant and ACE2 (b) mapped to the initial bound structure of the complex. Colors range from blue to white to red (with white representing no change in RMSF, blue representing RMSF decrease, and red representing RMSF increase). The ΔRMSF is in the range from -0.5 (totally blue) to 0.5 (totally red).
Fig 4.
Comparison of RBD DSSP with available literature data.
Fig 5.
Hydrogen bonds formed on the ACE2&RBD interface for the wildtype (a) and tri-mutant (b) generated from ligplot program. Residues formed hydrogen bonds are connected using dashed green lines. Residues on RBD are labelled in light green with bonds shown in magenta, while residues on ACE2 are labelled in blue with bonds shown in orange.
Fig 6.
Comparison of the BSA between RBD variants and ACE2 with that of the ACE2&RBD wildtype started from the crystal structure.
Fig 7.
Distance map comparison of a). RBD-E484K mutant bound with ACE2 and b). RBD wildtype bound with ACE2. The binding region (RES455 to 505) on RBD are highlighted in light green. The color bars are shown on the right side of the distance maps, with a residue pair distance being no larger than 4 Å shown in red, while a residue pair distance larger or equal to 14 Å shown in white.
Fig 8.
ΔΔG for RBD variants binding with ACE2 predicted from FEP (shown in blue bars) in comparison with literature data from Upadhyay et al. (shown in orange bars).
Reference ΔΔG was calculated based on available data in the table as ΔΔG = ΔGmutant-ΔGwt.
Table 2.
ΔΔG predicted from FEP in comparison with available literature data.
Fig 9.
Comparison of the averaged mixed dihedral angle covariance matrix for RBD-N501Y (upper-left triangle above the diagonal line) and RBD in wildtype (lower-right triangle) in bound state (a), and the averaged mixed dihedral angle covariance matrix for RBD-tri-mutation (upper-left triangle above the diagonal line) in comparison of RBD in wildtype (b). The color bars of covariance map are shown on the right of the figures from blue to yellow corresponding to the covariance coefficient in the range of -0.1 to 0.1. The secondary structure of RBD is shown on top of the covariance matrices, and the residue numbers of RBD are labelled on both the x and y-axes.
Fig 10.
Comparison of the averaged mixed dihedral angle covariance matrices for RBD-E484K (a) and RBD wildtype in free state (b) (upper left triangle above the diagonal line) with RBD wildtype in bound state (lower right). The color bars of covariance map are shown on the right of the figures from blue to yellow corresponding to the covariance coefficient in the range of -0.1 to 0.1. The secondary structure of RBD is shown above the covariance matrices, and the residue numbers of RBD are labelled on both the x and y-axes.
Fig 11.
Covariance coefficients between residue 373 (a)/residue 372 (b)/residue 480 (c) and residue 501(d) and other residues mapped on the structure of RBD wildtype in bound state (a), RBD wildtype in free state (b), and the N501Y variant (c), and tri-mutant variant (d). Positive covariance is shown in red while negative covariance in blue and the covariance equals to zero in white. The range of covariance is in the range of -0.1 to 0.1. Residues have positive correlation with the picked residue (or base residue) are labelled in red while in blue for negative correlation.
Fig 12.
Community networks formed in the RBD-N501Y(a), RBD wildtype in bound form (b) and RBD wildtype in free form (c) based on MD simulation and dynamical network analysis. The RBD network structures are oriented in the same direction as the RBD shown in Fig 1.