Chem. J. Chinese Universities ›› 2019, Vol. 40 ›› Issue (1): 138.doi: 10.7503/cjcu20180445
• Physical Chemistry • Previous Articles Next Articles
ZHU Jingxuan1, YU Zhengfei1, LIU Ye1, ZHAN Dongling2, HAN Jiarui1, TIAN Xiaopian1, HAN Weiwei1,*()
Received:
2018-06-19
Online:
2019-01-10
Published:
2018-12-19
Contact:
HAN Weiwei
E-mail:weiweihan@jlu.edu.cn
Supported by:
CLC Number:
TrendMD:
ZHU Jingxuan,YU Zhengfei,LIU Ye,ZHAN Dongling,HAN Jiarui,TIAN Xiaopian,HAN Weiwei. Exploration of Increasing the Non-specificity Substrates Activity for the Phosphotriesterase-like Lactonase Using Molecular Dynamics Simulations†[J]. Chem. J. Chinese Universities, 2019, 40(1): 138.
Amino acid | Interaction | ||||||||
---|---|---|---|---|---|---|---|---|---|
Any | Backbone | Sidechain | Polar | Hydrophobcic | H-Bond acceptor | H-Bond donor | Aromatic | Charged | |
His24 | 0.72 | 0 | 0.72 | 0.28 | 0.44 | 0 | 0 | 0 | 0 |
His22 | 0.26 | 0 | 0.26 | 0.11 | 0.15 | 0 | 0 | 0 | 0 |
Tyr97 | 0.85 | 0 | 0.85 | 0.45 | 0.40 | 0 | 0.13 | 0.72 | 0 |
His170 | 0.81 | 0 | 0.81 | 0.34 | 0.47 | 0 | 0 | 0 | 0 |
Arg223 | 0.88 | 0 | 0.88 | 0.71 | 0.16 | 0 | 0.24 | 0 | 0.14 |
Asp256 | 0.85 | 0.68 | 0.85 | 0.67 | 0.18 | 0 | 0 | 0 | 0 |
Trp278 | 0.84 | 0 | 0.84 | 0.08 | 0.75 | 0 | 0 | 0.79 | 0 |
Trp263 | 0.89 | 0 | 0.89 | 0 | 0.88 | 0 | 0 | 0.88 | 0 |
Leu226 | 0.68 | 0 | 0.68 | 0 | 0.68 | 0 | 0 | 0 | 0 |
Cys258 | 0.47 | 0 | 0.47 | 0.25 | 0.24 | 0 | 0 | 0 | 0 |
Ile261 | 0.53 | 0.05 | 0.53 | 0.05 | 0.51 | 0 | 0 | 0 | 0 |
Thr265 | 0.31 | 0.21 | 0.31 | 0.20 | 0.13 | 0 | 0 | 0 | 0 |
Ala266 | 0.41 | 0.31 | 0.41 | 0 | 0.40 | 0 | 0 | 0 | 0 |
Leu274 | 0.24 | 0.13 | 0.24 | 0 | 0.21 | 0 | 0 | 0 | 0 |
Ala275 | 0.22 | 0.12 | 0.22 | 0 | 0.20 | 0 | 0 | 0 | 0 |
Leu228 | 0.38 | 0 | 0.38 | 0 | 0.38 | 0 | 0 | 0 | 0 |
Phe229 | 0.48 | 0 | 0.48 | 0 | 0.48 | 0 | 0 | 0.47 | 0 |
Tyr99 | 0.31 | 0 | 0.31 | 0.06 | 0.25 | 0 | 0 | 0.27 | 0 |
Val27 | 0.49 | 0 | 0.49 | 0 | 0.49 | 0 | 0 | 0 | 0 |
Leu72 | 0.48 | 0 | 0.48 | 0 | 0.47 | 0 | 0 | 0 | 0 |
Table 1 Structural interaction fingerprints results(residues number according to PDB ID: 2VC7)
Amino acid | Interaction | ||||||||
---|---|---|---|---|---|---|---|---|---|
Any | Backbone | Sidechain | Polar | Hydrophobcic | H-Bond acceptor | H-Bond donor | Aromatic | Charged | |
His24 | 0.72 | 0 | 0.72 | 0.28 | 0.44 | 0 | 0 | 0 | 0 |
His22 | 0.26 | 0 | 0.26 | 0.11 | 0.15 | 0 | 0 | 0 | 0 |
Tyr97 | 0.85 | 0 | 0.85 | 0.45 | 0.40 | 0 | 0.13 | 0.72 | 0 |
His170 | 0.81 | 0 | 0.81 | 0.34 | 0.47 | 0 | 0 | 0 | 0 |
Arg223 | 0.88 | 0 | 0.88 | 0.71 | 0.16 | 0 | 0.24 | 0 | 0.14 |
Asp256 | 0.85 | 0.68 | 0.85 | 0.67 | 0.18 | 0 | 0 | 0 | 0 |
Trp278 | 0.84 | 0 | 0.84 | 0.08 | 0.75 | 0 | 0 | 0.79 | 0 |
Trp263 | 0.89 | 0 | 0.89 | 0 | 0.88 | 0 | 0 | 0.88 | 0 |
Leu226 | 0.68 | 0 | 0.68 | 0 | 0.68 | 0 | 0 | 0 | 0 |
Cys258 | 0.47 | 0 | 0.47 | 0.25 | 0.24 | 0 | 0 | 0 | 0 |
Ile261 | 0.53 | 0.05 | 0.53 | 0.05 | 0.51 | 0 | 0 | 0 | 0 |
Thr265 | 0.31 | 0.21 | 0.31 | 0.20 | 0.13 | 0 | 0 | 0 | 0 |
Ala266 | 0.41 | 0.31 | 0.41 | 0 | 0.40 | 0 | 0 | 0 | 0 |
Leu274 | 0.24 | 0.13 | 0.24 | 0 | 0.21 | 0 | 0 | 0 | 0 |
Ala275 | 0.22 | 0.12 | 0.22 | 0 | 0.20 | 0 | 0 | 0 | 0 |
Leu228 | 0.38 | 0 | 0.38 | 0 | 0.38 | 0 | 0 | 0 | 0 |
Phe229 | 0.48 | 0 | 0.48 | 0 | 0.48 | 0 | 0 | 0.47 | 0 |
Tyr99 | 0.31 | 0 | 0.31 | 0.06 | 0.25 | 0 | 0 | 0.27 | 0 |
Val27 | 0.49 | 0 | 0.49 | 0 | 0.49 | 0 | 0 | 0 | 0 |
Leu72 | 0.48 | 0 | 0.48 | 0 | 0.47 | 0 | 0 | 0 | 0 |
Fig.3 Conformational changes in WT, W263F and W263T SsoPox during 100 ns MD(A1, A2) RMSD; (B1, B2) RMSF; (C1, C2) SASA; (A1, B1, C1) paraoxon; (A2, B2, C2) lactone.
System | WT-lactone | W263T-lactone | WT-paraoxon | W263F-paraoxon |
---|---|---|---|---|
ΔEele/(kJ·mol-1) | -47.72 | -90.50 | -15.64 | -93.63 |
ΔEvdw/(kJ·mol-1) | -126.76 | -129.39 | -72.68 | -101.62 |
ΔGGB/(kJ·mol-1) | 83.97 | 102.50 | 42.49 | 109.23 |
ΔGSA/(kJ·mol-1) | -17.73 | -18.69 | -10.79 | -16.18 |
Δ | 36.26 | 12.00 | 26.85 | 15.64 |
Δ | -144.49 | -148.08 | -83.47 | -117.81 |
Δ | -108.23 | -136.08 | -56.62 | -102.17 |
-TΔS/(kJ·mol-1) | 80.80 | 72.52 | 77.58 | 92.13 |
Δ | -27.43 | -63.57 | 20.95 | -10.04 |
(2.36±0.38)×103 | (3.49±1.13)×105 | (5.19±0.95)×102 | (1.21±0.26)×104 |
Table 2 Calculate the binding free energy of a protein-ligand complex using MM-GB/SA methods
System | WT-lactone | W263T-lactone | WT-paraoxon | W263F-paraoxon |
---|---|---|---|---|
ΔEele/(kJ·mol-1) | -47.72 | -90.50 | -15.64 | -93.63 |
ΔEvdw/(kJ·mol-1) | -126.76 | -129.39 | -72.68 | -101.62 |
ΔGGB/(kJ·mol-1) | 83.97 | 102.50 | 42.49 | 109.23 |
ΔGSA/(kJ·mol-1) | -17.73 | -18.69 | -10.79 | -16.18 |
Δ | 36.26 | 12.00 | 26.85 | 15.64 |
Δ | -144.49 | -148.08 | -83.47 | -117.81 |
Δ | -108.23 | -136.08 | -56.62 | -102.17 |
-TΔS/(kJ·mol-1) | 80.80 | 72.52 | 77.58 | 92.13 |
Δ | -27.43 | -63.57 | 20.95 | -10.04 |
(2.36±0.38)×103 | (3.49±1.13)×105 | (5.19±0.95)×102 | (1.21±0.26)×104 |
Fig.9 SMD simulation of typical force profiles of paraoxon(A) and lactone(B) pulled out of the binding pocket along the unbinding pathway, the distance between the Cz of Tyr99 and Phe229 in WT-paraoxon and W263F-paraoxon(C), WT-lactone and W263T-lactone(D) and conformational changes of WT-paraoxon(E), W263F-paraoxon(F), WT-lactone(G), W263T-lactone(H) during 10 ns SMD
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