An Insight into the environmental effects of the pocket of the active site of the enzyme. Ab initio ONIOM molecular dynamics (MD) study on cytosine deaminase

Toshiaki Matsubara, Michel Dupuis, Misako Aida

Research output: Contribution to journalArticle

9 Citations (Scopus)

Abstract

We applied the ONIOM-molecular dynamics (MD) method to cytosine deaminase to examine the environmental effects of the amino acid residues in the pocket of the active site on the substrate taking account of their thermal motion. The ab initio ONIOM-MD simulations show that the substrate uracil is strongly perturbed by the amino acid residue Ile33, which sandwiches the uracil with His62, through the steric contact due to the thermal motion. As a result, the magnitude of the thermal oscillation of the potential energy and structure of the substrate uracil significantly increases.

Original languageEnglish
Pages (from-to)458-465
Number of pages8
JournalJournal of Computational Chemistry
Volume29
Issue number3
DOIs
Publication statusPublished - Feb 2008

Fingerprint

Cytosine Deaminase
Uracil
Molecular Dynamics
Environmental impact
Molecular dynamics
Enzymes
Substrate
Amino Acids
Amino acids
Substrates
Motion
Sandwich
Potential energy
Molecular Dynamics Simulation
Contact
Oscillation
Computer simulation
Energy
Hot Temperature

Keywords

  • Ab initio ONIOM-molecular dynamics (MD) method
  • Active site
  • Cytosine deaminase
  • Environmental effects
  • Thermal motion

ASJC Scopus subject areas

  • Chemistry(all)
  • Safety, Risk, Reliability and Quality

Cite this

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title = "An Insight into the environmental effects of the pocket of the active site of the enzyme. Ab initio ONIOM molecular dynamics (MD) study on cytosine deaminase",
abstract = "We applied the ONIOM-molecular dynamics (MD) method to cytosine deaminase to examine the environmental effects of the amino acid residues in the pocket of the active site on the substrate taking account of their thermal motion. The ab initio ONIOM-MD simulations show that the substrate uracil is strongly perturbed by the amino acid residue Ile33, which sandwiches the uracil with His62, through the steric contact due to the thermal motion. As a result, the magnitude of the thermal oscillation of the potential energy and structure of the substrate uracil significantly increases.",
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T1 - An Insight into the environmental effects of the pocket of the active site of the enzyme. Ab initio ONIOM molecular dynamics (MD) study on cytosine deaminase

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AU - Dupuis, Michel

AU - Aida, Misako

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AB - We applied the ONIOM-molecular dynamics (MD) method to cytosine deaminase to examine the environmental effects of the amino acid residues in the pocket of the active site on the substrate taking account of their thermal motion. The ab initio ONIOM-MD simulations show that the substrate uracil is strongly perturbed by the amino acid residue Ile33, which sandwiches the uracil with His62, through the steric contact due to the thermal motion. As a result, the magnitude of the thermal oscillation of the potential energy and structure of the substrate uracil significantly increases.

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KW - Environmental effects

KW - Thermal motion

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