Figure 4.

Molecular dynamic simulations of Mtr LpqY.A and B, Glu256 not protonated; C and D, Glu 256 protonated. A and C, Residues of Mtr LpqY interacting with trehalose over the course of the simulation, where 1 is in contact for the entire simulation. Data from three repeats of 600 ns are shown, where the error bars represent standard deviation. Blue bars signify hydrogen bonds with Glc-1, red bars signify hydrogen bonds with Glc-2, and gray bars show hydrophobic contacts. B and D, The minimum distance of trehalose from W259 (roughly center of the binding site) over the course of a simulation. Data from three repeats of 600 ns are shown, and the colored line represents the local running average of the associated repeat with the gray line showing data points of that simulation. Mtr, Mycobacterium thermoresistible.