Figure 1
Cartoon representation of the X-ray structure of AgGSTE2 (PDB ID 2IMI). (a) Homodimer; (b) active site in one monomer. Secondary-structure elements are labeled according to Wang
et al.;
1717 Wang, Y. J.; Qiu, L.; Ranson, H.; Lumjuan, N.; Hemingway, J.; Setzer, W. N.; Meehan, E. J.; Chen, L. Q.; J. Struct. Biol.
2008, 164, 228. (c) secondary structure assignment for amino acid sequence from the Protein Databank (
www.rcsb.org). Only the monomer sequence is represented in panel C. Residues Ser12 and Glu116 correspond to residues Ser15 and Glu120 respectively in AgGSTE5; (d) schematic representation of the catalysis of DDT by AgGST.
Figure 2
Predicted binding conformation of DDT to AgGSTE2 variants. (a,b) Atomic coordinates from X-ray structure 2IMI solved at 1.4 Å resolution; (c) atomic coordinates from X-ray structure 4GSN solved at 2.4 Å resolution.11 Mitchell, S. N.; Rigden, D. J.; Dowd, A. J.; Lu, F.; Wilding, C. S.; Weetman, D.; Dadzie, S.; Jenkins, A. M.; Regna, K.; Boko, P.; Djogbenou, L.; Muskavitch, M. A.; Ranson, H.; Paine, M. J.; Mayans, O.; Donnelly, M. J.; PLoS One
2014, 9, e92662.,1717 Wang, Y. J.; Qiu, L.; Ranson, H.; Lumjuan, N.; Hemingway, J.; Setzer, W. N.; Meehan, E. J.; Chen, L. Q.; J. Struct. Biol.
2008, 164, 228. AgGSTE2-I114T/F120L was built by replacement of side chain atoms in mutated residues. DDT is shown in green ball-and-stick. Residues are represented in stick with carbon atoms in cyan, nitrogen in blue, oxygen in red, sulfur in yellow.
Figure 3
(a) Initial; (b) final conformation of AgGSTE2 bound to DDT. Residues are represented in stick with carbon atoms in green, nitrogen in blue, oxygen in red, sulfur in yellow. Phenylalanine residues surrounding DDT are shown in orange. Black arrows indicate the thiolate anion from GSH. Hydrogen atoms are not shown for clarity.
Figure 4
Root-mean-square deviation of Cα atoms from X-ray structure for the apoenzymes (a) AgGSTE2; (b) AgGSTE2-I114T/F120L; (c) AgGSTE5; and the holoenzymes (d) AgGSTE2; (e) AgGSTE2-I114T/F120L; (f) AgGSTE5. Root-mean-square deviations were calculated for Cα atoms in subunit A (black), subunit B (yellow) and in the full dimer (green dots). The X-ray structures 2IL3 and 2IMI were used as positional reference for the apo and holoenzymes, respectively.
Figure 6
Conformational changes involving helices H2, H4 and the C-terminal region of AgGSTE variants during MD simulations. The structural rearrangement places Glu116 within hydrogen bond distance of the thiol group of GSH. (a,b) X-ray structure (2IMI); (c,d) final conformations from MD simulations of AgGSTE2; (e,f) AgGSTE2-I114T/F120L; (g,h) AgGSTE5.
Figure 7
Principal component analysis of MD trajectories. (A) Eigenvalue amplitude for systems AgGSTE2 (circle), AgGSTE2-I114T/F120L (square) AgGSTE5 (triangle). Apoprotein and holoprotein are represented by open and closed symbols, respectively. (B) Representation of Ca atomic displacement along the first eigenvector for apoenzymes (a) AgGSTE2; (b) AgGSTE2-I114T/F120L; (c) AgGSTE5, and holoenzymes (d) AgGSTE2; (e) AgGSTE2-I114T/F120L; (f) AgGSTE5. (C,D) Porcupine plots representing the highest amplitude motions along the first eigenvector. (E) Superposition of Cα atomic coordinates corresponding to the maximum and minimum projections of the first eigenvector for AgGSTE2-I114T/F120L-GSH.
Figure 8
Time-dependent distances between Ser12-GSH (a, c, e) and Glu116-GSH (b, d, f) for (a, b) AgGSTE2, (c, d) AgGSTE2-I114T/F120L, and AgGSTE5 (e, f). Distances were calculated between the center of mass of the hydroxyl group of Ser12 or carboxylate group of Glu116 and the center of mass of the thiol group of GSH.