Fig. 2: Seven on-path conformational states define the DNA translocation mechanism of XPD. | Nature Communications

Fig. 2: Seven on-path conformational states define the DNA translocation mechanism of XPD.

From: Translocation mechanism of xeroderma pigmentosum group D protein on single-stranded DNA and genetic disease etiology

Fig. 2

a Free energy landscape underpinning XPD dynamics over a single ATPase cycle. The free energy is projected onto the first two ICs obtained from time-lagged independent component analysis. The color bar represents the free energy scale in kcal/mol. b Markov state model (MSM) built from the conformational ensemble sampled along the optimal transition path. Microstates (dots) are colored according to their macrostate assignment as determined by the PCCA+ algorithm. Seven macrostates traversed by the minimum free energy path (MFEP) are labeled. The remaining macrostates (purple, yellow, and cyan dots) correspond to kinetic traps and are not labeled.

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