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  • Title: Umbrella sampling simulations of biotin carboxylase: is a structure with an open ATP grasp domain stable in solution?
    Author: Novak BR, Moldovan D, Waldrop GL, de Queiroz MS.
    Journal: J Phys Chem B; 2009 Jul 30; 113(30):10097-103. PubMed ID: 19585972.
    Abstract:
    Biotin carboxylase is a homodimer that utilizes ATP to carboxylate biotin. 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 Escherichia 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 X-ray crystallography structures. There is also a significant motion of a region near the dimer interface not predicted by considering only open and closed configurations, which may have implications for the dynamics and activity of the dimer.
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