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. 2024 Apr 1;4(4):1632–1645. doi: 10.1021/jacsau.4c00123

Figure 5.

Figure 5

Free-energy landscape and structural analysis of apo N-HSP90α metadynamics simulations in different conformations. (A) 3D plot illustrating the free-energy landscape obtained from the merged trajectories. The figure displays the free energies associated with the three lowest-energy basins. (B) A 2D free-energy topography was constructed using the root-mean-square deviation (RMSD) of the collective variable, Cα 102–137, and the RMSD of Cα 109 as reaction coordinates. Regions I, II, and III correspond to a free-energy range of 0–3.05 kJ/mol (solid white line area), while region IV represents a free-energy range of 3.05–5.42 kJ/mol (dotted white line area). Region V indicates a free energy greater than 5.42 kJ/mol. The red solid line represents the lowest-energy path for the three conformations I, II, and III allosteric to each other. (C) Structural analysis of regions I, II, III, IV, and V was conducted following clustering. The structure only displays the Cα 102–137 segment’s “lid”, while other regional conformations remain unchanged. The black arrow denotes the direction of “lid” movement during the simulation.