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. 2012;7(3):e33500.
doi: 10.1371/journal.pone.0033500. Epub 2012 Mar 19.

Investigation of indazole unbinding pathways in CYP2E1 by molecular dynamics simulations

Zhonghua Shen  1 , Feixiong Cheng, You Xu, Jing Fu, Wen Xiao, Jie Shen, Guixia Liu, Weihua Li, Yun Tang
Affiliations

Investigation of indazole unbinding pathways in CYP2E1 by molecular dynamics simulations

Zhonghua Shen et al. PLoS One. 2012.

Erratum in

  • PLoS One. 2012;7(9). doi: 10.1371/annotation/86d9f6df-7175-467c-a9ff-94eac53af128

Abstract

Human microsomal cytochrome P450 2E1 (CYP2E1) can oxidize not only low molecular weight xenobiotic compounds such as ethanol, but also many endogenous fatty acids. The crystal structure of CYP2E1 in complex with indazole reveals that the active site is deeply buried into the protein center. Thus, the unbinding pathways and associated unbinding mechanisms remain elusive. In this study, random acceleration molecular dynamics simulations combined with steered molecular dynamics and potential of mean force calculations were performed to identify the possible unbinding pathways in CYP2E1. The results show that channel 2c and 2a are most likely the unbinding channels of CYP2E1. The former channel is located between helices G and I and the B-C loop, and the latter resides between the region formed by the F-G loop, the B-C loop and the β1 sheet. Phe298 and Phe478 act as the gate keeper during indazole unbinding along channel 2c and 2a, respectively. Previous site-directed mutagenesis experiments also supported these findings.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. The crystal structure of CYP2E1 complexed with indazole.
The major helices are labeled. Heme is shown as black spheres; indazole is shown as magenta sticks. All figures were generated with Pymol.
Figure 2
Figure 2. Indazole unbinding routes from CYP2E1 illustrated by using the MOLE program.
Channel 2c is shown in cyan and channel 2a is shown in magenta. The major secondary elements of CYP2E1 are labeled.
Figure 3
Figure 3. Force profiles along channel 2c (A) and 2a (B).
Three different lines represent data from three representative SMD simulations.
Figure 4
Figure 4. Snapshots of the relative positions of indazole and the protein throughout the SMD simulation along channel 2c (A, 200 ps; B, 500 ps; and C, 800 ps).
Indazole is shown as green sticks. Heme is shown as a red stick. Phe106, Phe116 and Phe207 are shown as blue sticks.
Figure 5
Figure 5. Variation of the benzene ring of F298 is shown as a function of time during SMD simulation.
Three different lines represent data from three representative SMD simulations.
Figure 6
Figure 6. Snapshots of the relative positions of indazole and the protein throughout the simulation along channel 2a (A, 490 ps; B, 980 ps).
Indazole is shown as green sticks. The heme is shown as a red stick. Phe207 and Phe478 are shown as blue sticks.
Figure 7
Figure 7. PMF profiles along channel 2a (magenta) and channel 2c (green).
The error bar indicates the standard deviation of PMF by the bootstrap approach.
See this image and copyright information in PMC

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