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Progress in Chemistry 2012, Vol. 24 Issue (06): 1175-1184 Previous Articles   Next Articles

Special Issue: 计算化学; 酶化学

• Special Issue of Quantum Chemistry •

Computational Simulations of Zinc Enzyme: Challenges and Recent Advances

Wu Ruibo1, Cao Zexing2, Zhang Yingkai3   

  1. 1. School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China;
    2. College of Chemistry and Chemical Engineering, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen University, Xiamen 361005, China;
    3. Department of Chemistry, New York University, New York 10003, US
  • Received: Revised: Online: Published:
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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. 1 Significance and challenges of zinc enzymes
1.1 Zinc enzyme
1.2 Challenges of experimental research in zinc enzyme
1.3 Challenges of computational research in zinc enzym
2 Recent advance of computational research in zinc enzyme
2.1 QM/MM study of zinc enzyme
2.2 Force field development for zinc enzyme
3 Outlook
Key words: zinc enzyme, QM/MM, molecular dynamics simulation, force field, reaction mechanism, coordination geometry Contents

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