Computational simulations of zinc enzyme: Challenges and recent advances

Ruibo Wu, Zexing Cao, Yingkai Zhang

Research output: Contribution to journalArticlepeer-review


Zinc enzymes play a variety of essential biological roles, and their functions and/or structural organizations are critically dependent on the zinc binding site. However, the zinc coordination shell is so complicated that an accurate and powerful theoretical simulation protocol is highly required in calculation. Herein, we review the recent studies of the selected zinc enzymes by the state-of-the-art combined quantum mechanism/ molecular mechanism molecular dynamics (QM/MM MD) simulations in probing the reaction mechanism and revealing the relationship of structure and function. Meanwhile, the accuracy of all the current available pairwise force fields to describe zinc coordination structure is very poor, so the recent development of force fields for zinc enzyme is also presented. By the end of this review, some prospects and suggestions are given for further exploration of zinc enzyme.

Original languageEnglish (US)
Pages (from-to)1175-1184
Number of pages10
JournalProgress in Chemistry
Issue number6
StatePublished - Jun 2012


  • Coordination geometry
  • Force field
  • Molecular dynamics simulation
  • QM/MM
  • Reaction mechanism
  • Zinc enzyme

ASJC Scopus subject areas

  • General Chemistry


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