Institute of Science and Engineering, Kanazawa University
抄録
We investigate the binding/dissociation process of ligand molecule from carbonic
anhydrase (CA) I carbonic anhydrase (CA) I enzyme by using all-atom molecular
dynamics simulation. The force field parameters of zinc ion in the CA I active site are estimated
by quantum chemical calculations and are summarized in this paper. The free energy
profile for binding/dissociation process of ligand from CA I active site is calculated by the
thermodynamic integration combined with the all-atom molecular dynamics simulation. The
binding free energy as a function of the distance between the center of mass positions of CA
I active site and the ligand molecule is estimated. The radial distribution function of the
CA I-ligand complex is calculated from the trajectory of all-atom molecular dynamics (MD)
simulation. We estimate the free energy surface from the radial distribution function. We
can obtain the bond constant of the equilibrium state from the value of the free energy surface.
We discuss the binding/dissociation process of ligand molecule by calculating the free
energy profile to know the stability of the CA I-ligand complex with some thermodynamic
properties such as the binding free energy, the equilibrium state of the free energy surface
and so on.
Molecular dynamics study of free energy profile for dissociation of ligand from CA I active site
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Sci_Rep63-002.pdf
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