Citation: ZHAO Yuan, CAO Ze-Xing. Global Simulations of Enzymatic Catalysis[J]. Acta Physico-Chimica Sinica, ;2017, 33(4): 691-708. doi: 10.3866/PKU.WHXB201612191 shu

Global Simulations of Enzymatic Catalysis

ZHAO Yuan ^1, ,
CAO Ze-Xing ²

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

Received Date: 28 October 2016
Revised Date: 19 December 2016

Fund Project: The project was supported by the National Natural Science Foundation of China (21133007, 21373164, 21172053).

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.
- Enzymatic catalysis,
- Substrate delivery,
- Free energy calculations,
- QM/MM MD simulation,
- Random acceleration molecular dynamics (DAMD) simulation
1. [1]
2. [2]
3. [3]
4. [4]
5. [5]
6. [6]
7. [7]
8. [8]
9. [9]
10. [10]
11. [11]
12. [12]
13. [13]
14. [14]
15. [15]
16. [16]
17. [17]
18. [18]
19. [19]
20. [20]
21. [21]
22. [22]
23. [23]
24. [24]
25. [25]
26. [26]
27. [27]
28. [28]
29. [29]
30. [30]
31. [31]
32. [32]
33. [33]
34. [34]
35. [35]
36. [36]
37. [37]
38. [38]
39. [39]
40. [40]
41. [41]
42. [42]
43. [43]
44. [44]
45. [45]
46. [46]
47. [47]
48. [48]
49. [49]
50. [50]
51. [51]
52. [52]
53. [53]
54. [54]
55. [55]
56. [56]
57. [57]
58. [58]
59. [59]
60. [60]
61. [61]
62. [62]
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