Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments
Fig 2
Starting configurations of the four models of the VSD with different molecular fragments.
(A) model-1. (B) model-2. (C) model-3. (D) model-4. The four TM helices, S1 (gray), S2 (yellow), S3 (red) and S4 (blue), are represented in transparent ribbons. Molecular fragments, I177C–Cd2+–R294C, I230C–Cd2+–R294C, I230D–Mg2+–F267D, F233W/E236–R294K, I230H–Zn2+–A291H, I268C–Cd2+–A287C, and T269C–Cd2+–A291C, are colored in red, yellow, green, magenta, cyan, orange, and blue, respectively, with amino acids being represented in sticks and ions in spheres.