QM/MM molecular dynamics study of purine-specific nucleoside hydrolase

Ruibo Wu, Wengjin Gong, Ting Liu, Yingkai Zhang, Zexing Cao

Research output: Contribution to journalArticle

Abstract

Although various T. vivax purine-specific inosine-adenosine-guanosine nucleoside hydrolase (IAG-NH) crystal structures were determined in recent years, the mechanistic details for the cleavage of N-glycosidic bond and the release of base are still unclear. Herein, the irreversible hydrolysis reaction has been studied by ab initio QM/MM MD simulations, and the results indicate a highly dissociative and concerted mechanism. The protonation of substrate at N7 of inosine is found to strongly facilitate the hydrolysis process, while the hydrolysis reaction is less sensitive to the protonation state of Asp 40 residue. The proton-transfer channel and the dependence of activity on the anti/syn-conformation of substrate are also explored.

Original languageEnglish (US)
Pages (from-to)1984-1991
Number of pages8
JournalJournal of Physical Chemistry B
Volume116
Issue number6
DOIs
StatePublished - Feb 16 2012

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N-Glycosyl Hydrolases
Hydrolases
purines
nucleosides
hydrolysis
Molecular dynamics
Hydrolysis
Protonation
molecular dynamics
guanosines
adenosines
Inosine
Proton transfer
Substrates
Conformations
cleavage
Crystal structure
crystal structure
protons
purine

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Materials Chemistry
  • Surfaces, Coatings and Films

Cite this

QM/MM molecular dynamics study of purine-specific nucleoside hydrolase. / Wu, Ruibo; Gong, Wengjin; Liu, Ting; Zhang, Yingkai; Cao, Zexing.

In: Journal of Physical Chemistry B, Vol. 116, No. 6, 16.02.2012, p. 1984-1991.

Research output: Contribution to journalArticle

Wu, Ruibo ; Gong, Wengjin ; Liu, Ting ; Zhang, Yingkai ; Cao, Zexing. / QM/MM molecular dynamics study of purine-specific nucleoside hydrolase. In: Journal of Physical Chemistry B. 2012 ; Vol. 116, No. 6. pp. 1984-1991.
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