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Acta Phys. -Chim. Sin.  2017, Vol. 33 Issue (4): 691-708    DOI: 10.3866/PKU.WHXB201612191
REVIEW     
Global Simulations of Enzymatic Catalysis
Yuan ZHAO1,Ze-Xing CAO2,*()
1 Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng 475004, Henan Province, P. R. China
2 Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 360015, Fujian Province, P. R. China
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Abstract  

Enzymatic catalytic processes generally involve substrate delivery, selective catalytic reaction, and product release. Owing to the complex protein environment effect, any nonchemical or chemical step may determine the enzyme activity. Herein, to comprehensively understand enzymatic activity, extensive combined quantum mechanics/molecular mechanics (QM/MM) and molecular mechanics (MM) molecular dynamics (MD) simulations were carried out on several kinds of enzymes. Possible reaction mechanisms, roles of the conserved residues, and effects of the protein environment on the whole enzymatic process are discussed in detail, which will enrich the knowledge of reactivity in proteins. With the improvement and development of multiscale models and computational methods, it is expected that global simulations of extremely large and complicated enzymes will enable and lend support to enzyme engineering.



Key wordsEnzymatic catalysis      Substrate delivery      Free energy calculations      QM/MM MD simulation      Random acceleration molecular dynamics (DAMD) simulation     
Received: 28 October 2016      Published: 19 December 2016
MSC2000:  O641  
Fund:  The project was supported by the National Natural Science Foundation of China(21133007);The project was supported by the National Natural Science Foundation of China(21373164);The project was supported by the National Natural Science Foundation of China(21172053)
Corresponding Authors: Ze-Xing CAO     E-mail: zxcao@xmu.edu.cn
Cite this article:

Yuan ZHAO,Ze-Xing CAO. Global Simulations of Enzymatic Catalysis. Acta Phys. -Chim. Sin., 2017, 33(4): 691-708.

URL:

http://www.whxb.pku.edu.cn/10.3866/PKU.WHXB201612191     OR     http://www.whxb.pku.edu.cn/Y2017/V33/I4/691

Fig 1 Enzymatic process (substrate binding, chemical reaction, and product release)
Fig 2 General QM/MM system
Fig 3 (a) Link-atom scheme; (b) boundary-atom scheme; (c) localized-orbital scheme
Fig 4 (a) Free energy profile of the whole enzymatic catalysis17; (b) key residues and their conformational changes at the representative states in the main channel17; (c) free energy profile of product release17; (d) chemical reaction steps involved in enzymatic process17
Fig 5 (a) Free energy profile of the whole enzymatic catalysis11, 15, 159; (b) hydrolytic mechanism of inosine catalyzed by IAG-NH11; (c) key residues and their conformational changes at the representative states for the product release15
Fig 6 Relative free energy profiles of the ring-opening reaction along the reaction coordinate for SmuNagB color online
Fig 7 Overlap for the apo state (blue) and the enzyme-substrate complex (red) in acidic (a) andbasic solutions (b) along with RMSF values of the backbone and surface of the active site pocket18 RMSF: root mean square fluctuation. color online
Fig 8 Hydrogen bond networks around the active site and the lid region of Model B (a), Model A (b), and Model D (c)18
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