An Ab Initio QM/MM Study of the Electrostatic Contribution to Catalysis in the Active Site of Ketosteroid Isomerase
Abstract
:1. Introduction
2. Computational Approaches
2.1. QM/MM MD Simulations of the Wild-Type and Mutants of KSI
2.2. Calculations of the Electric Field with the Amber ff99SB Force Field
2.3. Calculations of the Electric Field with the EE-GMFCC Method
2.4. Classical MD Simulation and Calculation of the Electric Fields
3. Results and Discussion
3.1. The QM Effect is Important for Description of the Electrostatics in H-Bonding Environment
3.2. Calculation of Electric Fields
3.3. Electrostatic Contribution to Catalysis in KSI
3.4. Decomposition of the Electric Field
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Model | Exp. [5] | MM | QM/MM + FF | QM/MM + QM |
---|---|---|---|---|
WT | −144 | −100 | −124 | −141 |
D103N | −134 | −66 | −93 | −116 |
WT | D103N | Y16S | D103L | |
---|---|---|---|---|
RES 16 | −47 | −46 | −2 | −45 |
RES 103 | −52 | −36 | −51 | −4 |
RES 40 | −26 | −29 | −22 | −23 |
Sum of 3RS | −125 | −111 | −75 | −72 |
Sum of ARS | −124 | −93 | −74 | −66 |
Solvent | 7 | 10 | 8 | 9 |
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Wang, X.; He, X. An Ab Initio QM/MM Study of the Electrostatic Contribution to Catalysis in the Active Site of Ketosteroid Isomerase. Molecules 2018, 23, 2410. https://doi.org/10.3390/molecules23102410
Wang X, He X. An Ab Initio QM/MM Study of the Electrostatic Contribution to Catalysis in the Active Site of Ketosteroid Isomerase. Molecules. 2018; 23(10):2410. https://doi.org/10.3390/molecules23102410
Chicago/Turabian StyleWang, **anwei, and **ao He. 2018. "An Ab Initio QM/MM Study of the Electrostatic Contribution to Catalysis in the Active Site of Ketosteroid Isomerase" Molecules 23, no. 10: 2410. https://doi.org/10.3390/molecules23102410