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

Figure 2

Comparison of the RIP method to standard molecular dynamics using methyl-capped amino acids.

(A) The correlation of the average rotational velocities of the χ angles of the 17 amino acids that possess χ angles. Units are in [rad ps−1]. In the graph, the Y-axis standard velocities (extracted from standard molecular-dynamics at 300 K) are plotted against the X-axis RIP velocities (in the RIP protocol the kinetic energy at 300 K are effectively transferred to the χ-angle degrees of freedom). The correlation coefficient is 0.84. Detailed comparison for ILE (which has two χ-angles) of the standard molecular-dynamics simulation to the RIP simulation. (B) The distributions of the average kinetic energy per atom are fairly similar. The differences can be seen in the (C) distribution of the χ1 rotational velocities and (D) distributions of the χ2 rotational velocities.

Figure 2

doi: https://doi.org/10.1371/journal.pcbi.1000343.g002