Figure 14. Molecular dynamics of T. forsythia apo-Tfo.

(A) shows the variation in the distance between Met¹²⁰ and Met¹⁴⁹ SD atoms during 8 ns of an all-atom MD, beginning with the equilibrated crystal structure data. (B) shows the initial structure (green) and the simulated structure after 8 ns (red). The opening up of the potential heme-binding pocket by approximately 10 Å is largely due to the movement of the loop containing Met¹⁴⁹. The rms difference between the initial and MD simulated structures is 2.2 Å. Numbering of amino acid residues in the case of Tfo is shown according to the protein lacking the signal peptide sequence (20 amino acid residues), which was crystallized and examined by X-ray analysis.