Fig 1.
Three-dimensional structure of the 3Cpro enzyme of foot-and-mouth disease virus (FMDV).
Catalytic triad residues (H46, D84, and C163) and active site residue (C142) are highlighted in the stick model, and the conserved β-ribbon structure is shown in a dashed circle. The alpha-helixes, β-sheets, and loops of the protein are represented with cyan, magenta, and salmon color, respectively.
Fig 2.
Structural stability analysis of WT and mutants of 3Cpro.
(A) RMSD, (B) Rg of backbone atoms. (C) SASA and (D) Number of Intra H-bonds throughout the simulation. Black, red, and green represent WT, C142S, and C142L models of 3Cpro.
Fig 3.
Probability density distributions from the 600 ns concatenated trajectories.
(A) Root means square deviation (RMSD); (B) Radius of gyration (Rg); (C) Solvent-accessible surface area (SASA); and (D) intra H-bonds. Average and standard deviation values are represented according to their respective colors. Black, red, and green represent WT, C142S, and C142L models of 3Cpro.
Fig 4.
Residual flexibility throughout the MD simulation.
(A) RMSF of backbone atoms from the concatenated trajectory. (B) Heatmap representing △RMSF of C142S and C142L relative to WT. (C) DSSP plot represents the changes in secondary structure for WT, C142S, and C142L systems.
Fig 5.
Collective mode analysis from the concatenated trajectories.
(A) Eigenvalues of all the systems. (B) Cumulative percentage from the first 30 eigenvectors. (C) Projection of first two PCs. Black, red, and green colors represent the WT, C142S, and C142L systems of 3Cpro. (D, E, F) Structural changes in WT, C142S, and C142L with respect to PC1 are represented using extreme conformations with 30 frames. Black-dashed circles represent large conformational changes, and red arrows represent the size and direction of movements.
Fig 6.
Free energy landscape of all three systems and their representative structures.
The low-energy structures were retrieved from their respective global minima and superimposed. In addition, the superimposition of WT and representative mutant conformations are shown with RMSD values.
Fig 7.
(A) Dynamic cross-correlation map (DCCM) of WT and mutants. The red and blue dashed frames represent positive and negative correlations respectively. (B) Structural representation of the strong residual cross-correlation in WT, C142S, and C142L. Red (+1.0) and blue (−1.0) lines denote the most correlated and anticorrelated interactions between two residues. The intensity of the line color denotes the degree of association.
Fig 8.
(A) Degree centrality (CD); (B) Betweenness centrality (CB) are shown for WT, C142S, and C142L; (C) CB difference between WT and mutants; (D) Residues having CB > 0.3 are shown in the stick model and common residues are labeled in bold type. Black, red, and green represent WT, C142S, and C142L models of 3Cpro.
Fig 9.
Free energy of each residue in response to both mutations.
The red and blue color in the protein’s structure represent the most stabilized and destabilized regions respectively. Residues H46 and D84 in the C142S mutant and residues I74 to L82 in the C142L mutant model revealed a strong stabilized region.