Figure 7: Results of MD simulations of wild-type and Y215F lactate oxidases are shown.

(A) R.m.s.d. traces from the 100-ns simulations performed using the enzyme crystal structure (PDB code 2E77) as reference. The experimental crystal structure was determined at pH 8.0. Note: a pre-equilibration time of 5 ns was used that is not shown in the graph. The r.m.s.d. traces therefore do not start at a value of zero. (B) The relative frequency distributions of distances between the guanidino Cζ of Arg¹⁸¹ and the phenyl Cζ of Tyr²¹⁵/Phe²¹⁵. (C) The calculated curve of pH-dependent ionization of Tyr²¹⁵ in the (oxidized) enzyme-pyruvate complex of wild-type avLOX. (D) A superimpositioning of MD simulated structures of wild-type lactate oxidase at pH 7.0 (blue) and pH 9.5 (magenta). The structures shown are the final snapshots after 100 ns of MD simulation. The hydrogen bond between Arg¹⁸¹ and Tyr²¹⁵ (set to be ionized at pH 9.5) is shown with a dashed line. The distance at pH 7.0 was 4.6 Å, that at pH 9.5 was only 2.9 Å.