Abstract
We developed and implemented the ONIOM-molecular dynamics (MD) method for biochemical applications. The implementation allows the characterization of the functions of the real enzymes taking account of their thermal motion. In this method, the direct MD is performed by calculating the ONIOM energy and gradients of the system on the fly. We describe the first application of this ONOM-MD method to cytidine deaminase. The environmental effects on the substrate in the active site are examined. The ONIOM-MD simulations show that the product uridine is strongly perturbed by the thermal motion of the environment and dissociates easily from the active site.
| Original language | English |
|---|---|
| Pages (from-to) | 138-142 |
| Number of pages | 5 |
| Journal | Chemical Physics Letters |
| Volume | 437 |
| Issue number | 1-3 |
| DOIs | |
| Publication status | Published - Mar 22 2007 |
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ASJC Scopus subject areas
- Physical and Theoretical Chemistry
- Spectroscopy
- Atomic and Molecular Physics, and Optics
- Surfaces and Interfaces
- Condensed Matter Physics
Cite this
The ONIOM molecular dynamics method for biochemical applications : Cytidine deaminase. / Matsubara, Toshiaki; Dupuis, Michel; Aida, Misako.
In: Chemical Physics Letters, Vol. 437, No. 1-3, 22.03.2007, p. 138-142.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - The ONIOM molecular dynamics method for biochemical applications
T2 - Cytidine deaminase
AU - Matsubara, Toshiaki
AU - Dupuis, Michel
AU - Aida, Misako
PY - 2007/3/22
Y1 - 2007/3/22
N2 - We developed and implemented the ONIOM-molecular dynamics (MD) method for biochemical applications. The implementation allows the characterization of the functions of the real enzymes taking account of their thermal motion. In this method, the direct MD is performed by calculating the ONIOM energy and gradients of the system on the fly. We describe the first application of this ONOM-MD method to cytidine deaminase. The environmental effects on the substrate in the active site are examined. The ONIOM-MD simulations show that the product uridine is strongly perturbed by the thermal motion of the environment and dissociates easily from the active site.
AB - We developed and implemented the ONIOM-molecular dynamics (MD) method for biochemical applications. The implementation allows the characterization of the functions of the real enzymes taking account of their thermal motion. In this method, the direct MD is performed by calculating the ONIOM energy and gradients of the system on the fly. We describe the first application of this ONOM-MD method to cytidine deaminase. The environmental effects on the substrate in the active site are examined. The ONIOM-MD simulations show that the product uridine is strongly perturbed by the thermal motion of the environment and dissociates easily from the active site.
UR - http://www.scopus.com/inward/record.url?scp=33847331062&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=33847331062&partnerID=8YFLogxK
U2 - 10.1016/j.cplett.2007.01.085
DO - 10.1016/j.cplett.2007.01.085
M3 - Article
AN - SCOPUS:33847331062
VL - 437
SP - 138
EP - 142
JO - Chemical Physics Letters
JF - Chemical Physics Letters
SN - 0009-2614
IS - 1-3
ER -