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Decoding Structural Properties of a Partially Unfolded Protein Substrate: En Route to Chaperone Binding

Fig 2

Thermodynamics of DapA unfolding.

A-C) Free energy contour maps of DapA as a function of RMSD and ρ for three different temperatures, namely; 310 K, 360 K and 400 K, respectively. The color bar denotes the Gibbs free energy in kJ/mol. The inset within the maps show distribution of fraction of native contacts, Q. Q is defined by the total number of native contacts for each trajectory frame divided by the total number of contacts in the native structure. D) Thermal melting curve of DapA derived from CD (in black) and REMD simulations (in green), is depicted (see Methods for details). The molar ellipticity values obtained at 222 nm were normalized between 0 to 1 as a function of temperature. E-F) displays RMSD distributions of ρ-RMSD, Q-RMSD SASA-RMSD maps for I1 and I2 configurations, respectively. The RMSD was calculated with respect to the native structure.

Fig 2

doi: https://doi.org/10.1371/journal.pcbi.1004496.g002