Abstract
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.
Original language | English |
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Pages (from-to) | 458-465 |
Number of pages | 8 |
Journal | Journal of Computational Chemistry |
Volume | 29 |
Issue number | 3 |
DOIs | |
Publication status | Published - Feb 1 2008 |
Keywords
- Ab initio ONIOM-molecular dynamics (MD) method
- Active site
- Cytosine deaminase
- Environmental effects
- Thermal motion
ASJC Scopus subject areas
- Chemistry(all)
- Computational Mathematics