Figure 16: Various conformations identified for VVD: Cluster 1(red) and 3D72_A(blue) Cluster 13(magenta), 3D72_B(ice blue) and 3RH8(green).
Figure 16
Full size image
Another intriguing observation of clustering analysis is that in clusters 1 through 10, the Fα and Eα helices, which cradle the FAD cofactor, remain in an extremely similar orientation, leaving a narrow space in between (Fig. 6A and B). However, in clusters 11 through 15, both Fα and Eα helices display obvious deviations among these structures, creating more space probably responding to the photo-activation of FAD.

Both Pro42 and Cys71(residue number 6 and 35 in the current study, respectively) are key residues projecting the N-terminus into different conformations24,31. Correspondingly, both RRS6 and RRS35 simulations showed significant impact on VVD Light state dynamics (Fig. 17). In RRS6, the Light state distribution splits into two attraction basins. In RRS35, the Light state distribution shifts upward along Y-axis, farther away from crystallographic T8 Fluorescent Lampsstate conformation. The other two key residues 55 and 171(residue number 19 and 135 in the current study, respectively) for VVD dimerization process discussed in ref. 31 also have significant impact on Light state dynamics under constraint perturbation (Fig. 17). In RRS19, the Light state distribution shifts toward left hand side along X-axis, closer to crystallographic Dark state conformation. But in RRS135, the Light state distribution splits into two attraction basins, which are significantly separate from each other. For all four residues above, the cross-correlations are significantly enhanced in Light states, while the cross-correlations remains moderate similar to unperturbed Dark state (Fig. 18).