FIGURE 3.

Structural and molecular dynamics analyses. A, chain A from the WT crystal structure (PDB entry 5C0Z) before (green) and after (cyan) 200 ns of molecular dynamics are shown as Cα tracings superimposed using only main chain atoms. The hemes (Hec201) are shown in gray. The average Thr²⁸ Cα positions for the 39 intermediate 5-ns steps between the two end points are shown as spheres colored in a gradient from gray (5 ns) to red (195 ns). B, the mobile loop (amino acids 22–30) from A is shown in greater detail after rotation by 90° about its horizontal axis to generate a “bottom-up” view. The Cα atoms for the starting (Thr²⁸) and ending (Thr²⁸*) structures are colored blue. The intermediate Cα atoms (gray to red) all cluster about Thr²⁸*, showing that the loop jumps immediately to its minimum energy position and stays there. The distance between Thr²⁸ Cα and Thr²⁸* Cα is 4.5 Å. C, the RMSF for the first 100 ns (blue line) and the second 100 ns (red line) by residue are plotted together. Two RMSF values (Lys²⁷ and Ala⁴⁴) are noticeably lower in the second 100 ns. D, chain A from the T28A crystal structure (PDB entry 5C9M) before (green) and after (cyan) 200 ns of molecular dynamics. See A for details. E, equivalent to B, except the two loops are from D. Over the 200 ns, the Cα atom of Ala²⁸ pauses at four distinct intermediate positions before clustering around the final position. The distance between Ala²⁸ Cα and Ala²⁸* Cα is 11.9 Å. F, equivalent to C for T28A Cytc. The RMSF values for Ala⁴⁴ are lower in the second 100 ns, but those for Lys²⁷ are significantly higher in the second 100 ns, in fact the highest seen in all four RMSF plots. G, chain A from the T28E crystal structure (PDB entry 5DF5) before (green) and after (cyan) 200 ns of molecular dynamics. See A for details. H, equivalent to B, except the two loops are from G. Over the 200 ns, the Cα atom of Glu²⁸ clusters at a midway position before moving to its final position near the end of the simulation. The distance between Glu²⁸ Cα and Glu²⁸* Cα is 7.2 Å. I, equivalent to C for T28E Cytc. The RMSF values for Ala⁴⁴ are of average size and similar for both halves of the simulation. The RMSF values for the loop containing Glu²⁸ are higher than average but similar for both halves of the simulation. J, the Cα tracings of chain A from the WT crystal structure (PDB entry 5C0Z) with a phosphate group modeled onto Thr²⁸ are shown superposed before (green) and after (cyan) 200 ns of molecular dynamics. See A for details. K, equivalent to B, except the two loops are from J. Over the 200-ns period, the Cα atom of Thr(P)²⁸ moves quickly to the final position and clusters around it. The distance between Xaa²⁸ (X28) Cα and Xaa²⁸* Cα is 5.2 Å. L, equivalent to C for the Tpo²⁸ model. The RMSF values for the loop containing Glu²⁸ are higher than average but similar for both halves of the simulation.