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Dynamic Allostery in the Methionine Repressor Revealed by Force Distribution Analysis

Figure 3

Force distribution in MetJ.

(A) Changes in atomic forces, , mapped onto a cartoon representation of the protein structure. Colors range from blue for elements outside the allosteric network with to red for force transducing elements with high . Helix identifiers are printed onto the structure. (B) Network-like representation of pronounced changes in inter-atomic forces observed upon SAM binding. Edges connect non-bonded atom pairs with . Forces between helix A and B are mainly propagated via side chain interactions. Propagation of the allosteric signal is highly anisotropic and directed, targeting individual residues at the protein-DNA interface while leaving large parts of the protein unaffected. (C) Changes in normalized pair-wise forces plotted along the MetJ sequence. The secondary structure is marked as gray bars. The vertical line indicates the start of the second monomer. (D) SAM interacts with a specific set of MetJ residues. Plotted are the forces exerted by SAM on MetJ. Numbers of strongly affected residues are plotted, residues in dimer 2 are marked with a stroke. Error bars show the standard error over the whole simulation time. Arg42 and Glu39 are among the most affected residues. Residues 64′–67′ are located far away from the binding site, close to the N-terminal end of helix B.

doi: https://doi.org/10.1371/journal.pcbi.1000574.g003