FIGURE 7.

Snapshots of the bR protein fragment with covalently bound dye in different conformations (side view), as obtained from the MD simulation. During the first 16 ns, the dye adopts conformation A (A) and is highly mobile. For the rest of the simulation, the dye remains in conformation B (B) and is much less flexible, as it is more tightly attached to the two helices. (C) The probability distribution of the dye calculated from the vacuum simulations p is visualized by red isosurfaces on two different contour levels, which enclose 60 and 90% of the probability density (solid and transparent surfaces, respectively).