An insight into the environmental effects of the pocket of the active site of the enzyme. Ab initio ONIOM-molecular dynamics (MD) study on cytosine deaminase

作者：Matsubara Toshiaki^*; Dupuis Michel; Aida Misako

来源：Journal of Computational Chemistry, 2008, 29(3): 458-465.

DOI：10.1002/jcc.20805

• ab initio ONIOM-molecular dynamics (MD) method
• cytosine deaminase
• active site
• environmental effects
• thermal motion

We applied the ONIOM-molecular dynamics (MD) method to cytosine deaminase to examine the environmental effects of the amino acid residues in the pocket of the active site on the substrate taking account of their thermal motion. The ab initio ONIOM-MD simulations show that the substrate uracil is strongly perturbed by the amino acid residue Ile33, which sandwiches the uracil with His62, through the steric contact due to the thermal motion. As a result, the magnitude of the thermal oscillation of the potential energy and structure of the substrate uracil significantly increases.

• 出版日期2008-2