FIGURE 6.

Dynamics of Trp². The state of Trp² is characterized by the distance to its neighboring residues during simulations with (A) and without (B) Ca²⁺, as well as with K⁺ (C) and Na⁺ (D) ions replacing Ca²⁺. Distances between the C_α atom of Trp² and C_α atoms of residues Ile²⁴, Lys²⁵, and Ser²⁶ are shown in red, green, and blue, respectively. The distance between atom N_ɛ of Trp² and the carbonyl oxygen atom of Glu⁹⁰ is shown in black. Intermittent bound states can be clearly observed during simulations performed without Ca²⁺. (E) Snapshots show Trp² in licorice representation at times t = 0, 2.5, 4.4, 5, 7.5, and 10 ns during SimApo1. The rest of the EC1 domain is shown in surface representation and colored according to hydrophobicity (white, hydrophobic residues; green, polar residues; red or blue, charged residues).