Fig. 5: Molecular dynamics simulation. | Nature Communications

Fig. 5: Molecular dynamics simulation.

From: Structure of human MUTYH and functional profiling of cancer-associated variants reveal an allosteric network between its [4Fe-4S] cluster cofactor and active site required for DNA repair

Fig. 5

Energy decomposition (left), normal mode (middle), and network (right) analyses based on the MD trajectories are shown. The left and right panels show a close-up view of the residues that participate in the structural interplay between the [4Fe-4S] cluster and the active site along with values for energy decomposition analysis (EDA, left) and network analysis results (right). The EDA reports the intermolecular non-bonded interactions (Coulomb and van der Waals interactions; kcal/mol) involving Asn238 or Arg241 (black and red values, respectively). Below, the total energy contribution for the system is shown for Asn238 (black) and Arg241 (red) and corresponding cancer-associated mutants. For the network analysis the betweenness of the nodes involved in the multi-motif bridge is shown in brown (right-upper panel) and the optimal path between the AP site and [4Fe-4S] cluster is displayed in magenta (right-lower panel). The first normal mode is shown in the middle where the MUTYH and DNA are shown in blue and gray, respectively.

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