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ID 20648
file
creator
Matsubara, Toshiaki
Dupuis, Michel
NDC
Biology
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.
journal title
Chemical Physics Letters
volume
Volume 437
issue
Issue 1-3
start page
138
end page
142
date of issued
2007-03-22
publisher
Elsevier Science B.V.
issn
0009-2614
ncid
publisher doi
language
eng
nii type
Journal Article
HU type
Journal Articles
DCMI type
text
format
application/pdf
text version
author
rights
Copyright (c) 2007 Elsevier B.V.
relation url
department
Graduate School of Science