The ONIOM molecular dynamics method for biochemical applications : cytidine deaminase.
Chemical Physics Letters Volume 437 Issue 1-3
Page 138-142
published_at 2007-03-22
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| File | |
| Title ( eng ) |
The ONIOM molecular dynamics method for biochemical applications : cytidine deaminase.
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| Creator |
Matsubara Toshiaki
Dupuis Michel
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| Source Title |
Chemical Physics Letters
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| Volume | 437 |
| Issue | 1-3 |
| Start Page | 138 |
| End Page | 142 |
| 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.
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| NDC |
Biology [ 460 ]
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| Language |
eng
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| Resource Type | journal article |
| Publisher |
Elsevier Science B.V.
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| Date of Issued | 2007-03-22 |
| Rights |
Copyright (c) 2007 Elsevier B.V.
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| Publish Type | Author’s Original |
| Access Rights | open access |
| Source Identifier |
[ISSN] 0009-2614
[DOI] 10.1016/j.cplett.2007.01.085
[NCID] AA00602122
[DOI] http://dx.doi.org/10.1016/j.cplett.2007.01.085
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