In the study presented here, we applied RRS method on the crystallographic structures of VVD Dark and LED Tube China states to systematically compare the impact of each individual residue on overall protein dynamics, and thoroughly explore potential conformational space that is reachable for VVD protein and could serve as guidance for further mutagenesis studies of this protein.

Results
Root-Mean-Square Deviation (RMSD)
The mass weighted RMSD of all atoms for Dark and Light states of VVD are plotted in Fig. 2A. Initially, the LED Candle Lights state has higher RMSD values than the Dark state agreeing with the expectation that Light state is more flexible than the Dark state. However, the RMSD values of the Dark state exceed the Light state around 120 ns of simulation, suggesting a larger conformational space accessible for the Dark state than the Light state. To illustrate and compare the conformational distributions of both Dark and Light states, we projected two simulations onto a two dimensional(2D) contour plots using RMSD values with reference to the optimized Dark and Light states, respectively (Fig. 2B). The unperturbed Dark and Light state simulations display different distributions on the 2D RMSD plots. For 210 ns of simulations, the Light state displays only one basin of attraction, but the Dark state displays three major basins of attraction, with the far right one adjacent to the LED Candle Lights state on the same plot.