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 |
|---|---|
| Pages (from-to) | 458-465 |
| Number of pages | 8 |
| Journal | Journal of Computational Chemistry |
| Volume | 29 |
| Issue number | 3 |
| DOIs | |
| Publication status | Published - Feb 2008 |
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Keywords
- Ab initio ONIOM-molecular dynamics (MD) method
- Active site
- Cytosine deaminase
- Environmental effects
- Thermal motion
ASJC Scopus subject areas
- Chemistry(all)
- Safety, Risk, Reliability and Quality
Cite this
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. / Matsubara, Toshiaki; Dupuis, Michel; Aida, Misako.
In: Journal of Computational Chemistry, Vol. 29, No. 3, 02.2008, p. 458-465.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - 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
AU - Matsubara, Toshiaki
AU - Dupuis, Michel
AU - Aida, Misako
PY - 2008/2
Y1 - 2008/2
N2 - 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.
AB - 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.
KW - Ab initio ONIOM-molecular dynamics (MD) method
KW - Active site
KW - Cytosine deaminase
KW - Environmental effects
KW - Thermal motion
UR - http://www.scopus.com/inward/record.url?scp=38349130210&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=38349130210&partnerID=8YFLogxK
U2 - 10.1002/jcc.20805
DO - 10.1002/jcc.20805
M3 - Article
VL - 29
SP - 458
EP - 465
JO - Journal of Computational Chemistry
JF - Journal of Computational Chemistry
SN - 0192-8651
IS - 3
ER -