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Probing the Flexibility of Large Conformational Changes in Protein Structures through Local Perturbations

Figure 4

The global Cα RMSD response of TIM to RIP.

(A) Each column corresponds to the perturbation of the residue marked by the X-value. Intensity represents Cα RMSD deviation for the 10th ps of simulation above background (>6.0 Å). (B) Perturbation strength histogram and structural linchpins. Structural linchpins are defined if the number of residues with Cα RMSD >6Å induced by a residue is greater than 3σ above the mean. The structural linchpins are mapped onto the structure as sticks. Scale is 0 (white) to 30+ (red). (C) Conversely, local regions that are highly susceptible to perturbation can be identified via a local flexibility histogram and mapped onto the structure. Scale is 0 (white) to 15+ (red).

Figure 4

doi: https://doi.org/10.1371/journal.pcbi.1000343.g004