**************** The 5th., Lab Seminar ****************************

Date: Thu, July 9, 2008  PM 2:30-

Place: No.616 Seminar room
　　　　　　 Graduate School of Information Science

Speaker: Norio Takenaka

Title: The ONIOM molecular dynamics method for biochemical applications:
Cytidine deaminase
T. Matsubara, M. Dupuis and M. Aida, Chem. Phys. Lett. 437 (2007) 138

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 ONIOMMD
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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