The ONIOM molecular dynamics method for biochemical applications

Cytidine deaminase

Toshiaki Matsubara, Michel Dupuis, Misako Aida

Research output: Contribution to journalArticle

20 Citations (Scopus)

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 languageEnglish
Pages (from-to)138-142
Number of pages5
JournalChemical Physics Letters
Volume437
Issue number1-3
DOIs
Publication statusPublished - Mar 22 2007

Fingerprint

Cytidine Deaminase
Molecular dynamics
molecular dynamics
Uridine
Environmental impact
enzymes
gradients
Computer simulation
Substrates
Enzymes
products
simulation
Hot Temperature
energy

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 journalArticle

Matsubara, Toshiaki ; Dupuis, Michel ; Aida, Misako. / The ONIOM molecular dynamics method for biochemical applications : Cytidine deaminase. In: Chemical Physics Letters. 2007 ; Vol. 437, No. 1-3. pp. 138-142.
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