Molecular Docking and Dynamics Simulation Improving Thermophilic Protease Activity of PhpI

doi:10.7503/cjcu20120654

Chem. J. Chinese Universities ›› 2013, Vol. 34 ›› Issue (3): 628.doi: 10.7503/cjcu20120654

• Physical Chemistry • Previous Articles Next Articles

Molecular Docking and Dynamics Simulation Improving Thermophilic Protease Activity of PhpI

ZHAN Dong-Ling^1,2, GAO Nan³, HAN Wei-Wei¹, FENG Yan¹

1. Key Laboratory for Molecular Enzymology and Engineering, Ministry of Education, Jilin University, Changchun 130012, China;
2. College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, China;
3. Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China

Received:2012-07-10 Online:2013-03-10 Published:2013-02-18
Contact: Weiwei Han E-mail:weiweihan@jlu.edu.cn;yfeng@jlu.edu.cn

Abstract

Abstract:

In this study, flexible docking approach was employed to dock the substrate into the active site of protease PH1704(PhpI), combining with crystal structure to determine the key enzyme, and study on site-mutation in theroy. All parameters were verified by molecular biology experiment. The protease activity of K43C was 5.8 times higher than that of WT. Molecular dynamics simulation reveals that after 8 ns dynamics simulations, the secondary structure of K43C mutant changes from the S2 sheet of WT(F11-E12-D13)to the loop. K43 and E12 are both the important active site residues. The change will enhance the flexibility of active site, and be helpful for catalytic reactions. The new structural and mechanistic insights obtained from molecular docking and dynamics simulation should be valuable for detailed researching of structures and mechanisms of the member of the DJ-1 superfamily.

Key words: Thermophilic protease PhpI, Molecular docking, Dynamics simulation, Site mutation

CLC Number:

O641
Q556

TrendMD:

ZHAN Dong-Ling, GAO Nan, HAN Wei-Wei, FENG Yan. Molecular Docking and Dynamics Simulation Improving Thermophilic Protease Activity of PhpI[J]. Chem. J. Chinese Universities, 2013, 34(3): 628.

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Molecular Docking and Dynamics Simulation Improving Thermophilic Protease Activity of PhpI

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