Behavior of the ATP grasp domain of biotin carboxylase monomers and dimers studied using molecular dynamics simulations.
The enzyme biotin carboxylase (BC) uses adenosine triphosphate (ATP) to carboxylate biotin and is involved in fatty acid synthesis. Structural evidence suggests that the B domain of BC undergoes a large hinge motion of ∼45° when binding and releasing substrates. Escherichia coli BC can function as a natural homodimer and as a mutant monomer. Using molecular dynamics simulations, we evaluate the free energy profile along a closure angle of the B domain of E. coli BC for three cases: a monomer without bound Mg(2)ATP, a monomer with bound Mg(2)ATP, and a homodimer with bound Mg(2)ATP in one subunit. The simulation results show that a closed state is the most probable for the monomer with or without bound Mg(2)ATP. For the dimer with Mg(2)ATP in one of its subunits, communication between the two subunits was observed. Specifically, in the dimer, the opening of the subunit without Mg(2)ATP caused the other subunit to open, and hysteresis was observed upon reclosing it. The most stable state of the dimer is one in which the B domain of both subunits is closed; however, the open state for the B domain without Mg(2)ATP is only approximately 2k(B)T higher in free energy than the closed state. A simple diffusion model indicates that the mean times for opening and closing of the B domain in the monomer with and without Mg(2)ATP are much smaller than the overall reaction time, which is on the order of seconds.
Department of Mechanical Engineering, Louisiana State University, Baton Rouge, Louisiana, USA.
Brian R
BR
Novak
Dorel
D
Moldovan
Grover L
GL
Waldrop
Marcio S
MS
de Queiroz
D000255:Adenosine Triphosphate / Q000737:chemistry*; D000465:Algorithms; D001665:Binding Sites; D019731:Carbon-Nitrogen Ligases / Q000737:chemistry*; D004926:Escherichia coli / Q000201:enzymology*; D006860:Hydrogen Bonding; D008274:Magnesium / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D055503:Protein Multimerization; D017434:Protein Structure, Tertiary
D000255:Adenosine Triphosphate; D019731:Carbon-Nitrogen Ligases; C019791:biotin carboxylase; D008274:Magnesium