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Fig. 3 | Biology Direct

Fig. 3

From: Thermodynamic and kinetic stability of the Josephin Domain closed arrangement: evidences from replica exchange molecular dynamics

Fig. 3

Visual inspection of the JD conformational arrangements corresponding to closed (C), intermediate (I) and open (O) state together with the estimated forward and backward rate constants for folding, together with activation energy values at 310 K. The kinetic and thermodynamic results shown in Fig. 3 are computed following the procedure reported in the Methods section of our paper, and implemented in the g_kinetics tool of GROMACS package. It is worth mentioning that the energy barrier reported in Fig. 3 represents free energy values of activation, containing also information about the entropic contribution. Errors estimate is also presented in brackets. Error analysis was performed by varying the cutoff distance used to define the protein folded state (open, intermediate or closed), as in previous works [67]. As pointed out Rhee and coworkers [73], the largest error is mainly related to the definition of what is folded [73]. In detail, a kinetic analysis was carried out by varying of 0.02 nm the Radius of Gyration threshold to discern between open/intermediate, and intermediate/closed

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