Fig 1.
(A) Backbone RMSD during the simulation. RMSD was calculated relative to the crystal structure. (B) Root mean square fluctuation (RMSF) of Cα atoms during the simulation (black line). Red line depicts the RMSF values converted from crystallographic B-factors. The inset depicts the distribution of the simulation RMSF. (C) Ribbon diagram of SMYD2 structure at 2 ns. The structure is colored according to the simulation RMSF. Color scale from blue to red depicts low to high atomic fluctuations. Secondary structures, α-helices and β-strands are labeled and numbered according to their position in the sequence. SAH is represented by sticks and zinc ions by purple spheres. (D) Cross-correlation map of the trajectory. Blue indicates a negative correlation between residue fluctuations, and red depicts a positive correlation. Lobe and domain structures of SMYD2 are indicated on the top of the map. (E) Visualization of residue–residue cross-correlations. SMYD2 is depicted by green coils. Blue and red lines indicate negative and positive correlated motions. (F) Inter-residue distance deviation map. Color scale from blue to magenta depicts small to large distance deviations. (G) Distance fluctuation of Y311–G46 during the simulation. Color bars depict the conformer clustering results obtained in Fig 2.
Fig 2.
(A) Scree plot showing the proportion of variance against its eigenvalue rank. (B) Visualization of the motions along PC1 (left) and PC2 (right). The most dissimilar structures along a given PC are depicted by thicker coils. The interpolated structures produced by Bio3D [18] are shown by thinner coils. Color scale from blue, green, to red depicts low to high atomic displacements. (C) Projection of the trajectory onto the planes formed by the first three principle components. Conformers are colored according to the k-means clustering: cluster 1, black; 2, red; 3, blue; 4, green.
Fig 3.
(A) SMYD2 dynamical network. The network is colored according to communities. Points in the network are nodes, and lines between the nodes represent edges. The thicker lines depict the stronger edges or stronger correlations. Critical nodes are colored in purple. (B) Optimal and suboptimal paths between Y311 and G46. The optimal path is colored in red and suboptimal paths in blue. The edge thickness is weighted by the number of suboptimal paths crossing the edge. Residues along the optimal path are labeled.