Asymmetric Behavior of Thymidylate Synthase Dimer Subunits in Denaturating Solvent Observed with Molecular Dynamics

Figure 3

RMSF of the protein in urea solution during different parts of trajectory. Black line corresponds to RMSF of the first monomer (A or C) and red line corresponds to RMSF of the second monomer (B or D). Since the simulation in water did not show signs of structure evolution, the whole trajectory of the protein in water is taken as a reference. Residues are numbered according to the protein sequence, with certain residues not present in the PDB structure (i.e., amino acids 1–20 and 302–307).