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Umbrella sampling simulations of biotin carboxylase: is a structure with an open ATP grasp domain stable in solution?

J Phys Chem B. 2009 Jul 30;113(30):10097-103. doi:10.1021/jp810650q
Brian R Novak 1 , Dorel Moldovan , Grover L Waldrop , Marcio S de Queiroz
Brian R Novak 1 , Dorel Moldovan , Grover L Waldrop , Marcio S de Queiroz

[No authors listed]

Author information
  • 1 Departments of Mechanical Engineering and Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA. bnovak1@lsu.edu

摘要


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.

基因