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. 2016 Apr 5;11(4):e0152946.
doi: 10.1371/journal.pone.0152946. eCollection 2016.

Molecular Dynamics Simulations to Investigate the Influences of Amino Acid Mutations on Protein Three-Dimensional Structures of Cytochrome P450 2D6.1, 2, 10, 14A, 51, and 62

Shuichi Fukuyoshi  1 , Masaharu Kometani  1 , Yurie Watanabe  1 , Masahiro Hiratsuka  2 , Noriyuki Yamaotsu  3 , Shuichi Hirono  3 , Noriyoshi Manabe  4 , Ohgi Takahashi  4 , Akifumi Oda  1   5
Affiliations

Molecular Dynamics Simulations to Investigate the Influences of Amino Acid Mutations on Protein Three-Dimensional Structures of Cytochrome P450 2D6.1, 2, 10, 14A, 51, and 62

Shuichi Fukuyoshi et al. PLoS One. .

Abstract

Many natural mutants of the drug metabolizing enzyme cytochrome P450 (CYP) 2D6 have been reported. Because the enzymatic activities of many mutants are different from that of the wild type, the genetic polymorphism of CYP2D6 plays an important role in drug metabolism. In this study, the molecular dynamics simulations of the wild type and mutants of CYP2D6, CYP2D6.1, 2, 10, 14A, 51, and 62 were performed, and the predictions of static and dynamic structures within them were conducted. In the mutant CYP2D6.10, 14A, and 61, dynamic properties of the F-G loop, which is one of the components of the active site access channel of CYP2D6, were different from that of the wild type. The F-G loop acted as the "hatch" of the channel, which was closed in those mutants. The structure of CYP2D6.51 was not converged by the simulation, which indicated that the three-dimensional structure of CYP2D6.51 was largely different from that of the wild type. In addition, the intramolecular interaction network of CYP2D6.10, 14A, and 61 was different from that of the wild type, and it is considered that these structural changes are the reason for the decrease or loss of enzymatic activities. On the other hand, the static and dynamic properties of CYP2D6.2, whose activity was normal, were not considerably different from those of the wild type.

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Conflict of interest statement

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

Figures

Fig 1
Fig 1. Root mean square deviations (RMSDs) for the wild type and mutants of CYP2D6.
(A) CYP2D6.1, (B) CYP2D6.2, (C) CYP2D6.10, (D) CYP2D6.14A, (E) CYP2D6.51, (F) CYP2D6.62. The reference structures of RMSD calculations were the initial structures of molecular dynamics simulations. Thus, the reference structure for CYP2D6.1 was the minimized crystal structure. For the mutants, initial structures constructed from three-dimensional structures of CYP2D6.1 were used as the reference.
Fig 2
Fig 2. Root mean square fluctuations (RMSFs) for the wild type and mutants of CYP2D6.
(A) CYP2D6.1, (B) CYP2D6.2, (C) CYP2D6.10, (D) CYP2D6.14A, (E) CYP2D6.62. The simulation of CYP2D6.51 did not converge. For the mutant CYP2D6, RMSF values (red) were compared with those of the wild type (gray).
Fig 3
Fig 3. Channel entrance of CYP2D6.
(A) CYP2D6.1 (B) CYP2D6.10. The three-dimensional structure of CYP2D6.1 obtained by the molecular dynamics simulation at 150 ns was of the open form, whereas that of CYP2D6.10 was of the closed form.
Fig 4
Fig 4. Distance between the B-C and the F-G loop.
The closest amino acid pairs were different for different mutants. The distances between (A) Val104 and Asn225 in CYP2D6.1, (B) Val104 and Val227 in CYP2D6.2, (C) Ile109 and Leu236 in CYP2D6.10, (D) Ile109 and His232 in CYP2D6.14A, (E) Leu110 and Leu241 in CYP2D6.51, and (F) Pro105 and Val229 in CYP2D6.62 are shown.
Fig 5
Fig 5. Channel entrance for CYP2D6.2.
Asn225 is illustrated in space fill model.
Fig 6
Fig 6
F helix. (A) CYP2D6.1, (B) CYP2D6.14A, and (C) hydrogen bonds proximate Glu216 in CYP2D6.14A. The hydrogen bonding network and secondary structures of CYP2D6.14A were different from those of the wild type CYP2D6.1.
Fig 7
Fig 7. Structures proximate the heme for CYP2D6.1 and CYP2D6.62.
(A) Ionic interactions between Arg441 and the heme in CYP2D6.1, (B) neither ionic bond nor hydrogen bond between Cys441 and the heme in CYP2D6.62, (C) hydrogen bonds proximate the heme in CYP2D6.1, and (D) hydrogen bonds proximate the heme in CYP2D6.62. In the static structure of CYP2D6.1 at 250 ns, the hydrogen bond between Val374 and heme is not appeared (Fig C).
Fig 8
Fig 8. Results of MD simulation for CYP2D6.1 using ff14SB force field.
(A) RMSD, (B) RMSF, (C) distance between B-C and F-G loops, and (D) entrance residues used for the distance calculation.
Fig 9
Fig 9. 3D structures of the N-terminal region (red-orange) and the F-G loop region (yellow-yellow green).
(A) CYP2D6.1, (B) CYP2D6.10. The 34th residues are shown in space fill model, and the hydrophobic residues located in the interdomain regions are illustrated in ball-and-stick model.
See this image and copyright information in PMC

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