The ONIOM molecular dynamics method for biochemical applications: Cytidine deaminase

Toshiaki Matsubara, Michel Dupuis, Misako Aida

Research output: Contribution to journalArticlepeer-review

21 Citations (Scopus)


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
Issue number1-3
Publication statusPublished - Mar 22 2007

ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry

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