Umbrella sampling simulations of the closure of biotin carboxylase

Biotin carboxylase is a homodimer that utilizes ATP to carboxylate biotin. Solid state studies of the enzyme using x-ray crystallography revealed a prominent conformational change upon binding ATP. To determine the importance of this closing motion, the potential of mean force with the closure angle as a reaction coordinate was calculated using molecular dynamics simulations and umbrella sampling for a monomer of E. coli biotin carboxylase in water with restraints to simulate attachment to a surface. The result suggests that the most stable state for the enzyme is a closed state different from both the ATP bound and open state crystal structures. There is also a significant motion of a region near the dimer interface not predicted from the crystal structures which may have implications for the dynamics and activity of the dimer.