Fig 1.
Crystal structure of Complex III and the 3D complex models constructed as the target protein for binding free energy calculation.
The crystal structure of bovine Complex III (PDB ID: 2A06) is shown on the left side with separate colors for each subunit. The complex models of Zymoseptoria tritici and Pyrenophora teres are shown on the center and right side respectively. On these figures, cytochrome b is indicated by green color, cytochrome c1 by cyan color, and ISP by magenta color. Gray-based stick models represent HEM. Pink and yellow sphere models indicate Fe and S atoms, respectively. Red broken lines indicate the Qo sites. The arrowed sphere models indicate the mutant sites.
Fig 2.
Chemical structure and constituent part of QoIs.
Fig 3.
Alignment of amino acid sequences of cytochrome b. Upper is B. taurus (1SQB) registered in the Protein Data Bank.
Middle is Z. tritici (Q6X9S4) registered in UniProt. Lower is P. teres determined through in-house experimentations.
Fig 4.
Correlation between experimental binding affinity and calculated binding free energy.
(a) Experimental pIC50 versus calculated binding free energy ΔG. (b) ΔpIC50 and ΔΔG are differences between wild-type and mutant type. Zymoseptoria tritici is depicted in black color and P. teres is in gray color. The symbols indicate the QoIs: azoxystrobin (in square), pyraclostrobin (in triangle), and metyltetraprole (in circle). Wild-type is shown as a closed symbol and mutant type as an open symbol only in (a).
Table 1.
Calculated binding free energy.
Average and standard deviation of three calculations.
Fig 5.
Binding free energy difference between wild-type and mutant type for each constituent part of QoIs.
(a) Zymoseptoria tritici, (b) P. teres. The constituent parts are defined in Fig 2 and indicated by different symbols; Part-A by square, Part-B by triangle, and Part-C by circle.
Fig 6.
Contribution ratio of Part-AB and Part-C to the ΔG value.
(a) Zymoseptoria tritici, (b) P. teres. Three QoIs are shown by different symbols: azoxystrobin, pyraclostrobin, and metyltetraprole are indicated by a square, triangle, and circle, respectively. Closed plot indicates ΔG for wild-type, while an opened plot is shown for mutant type.
Fig 7.
Contribution ratio of van del Waals and Coulomb components for ΔG value of Part-C.
(a) Zymoseptoria tritici, (b) P. teres. Three QoIs are shown by different symbols: azoxystrobin by squares, pyraclostrobin by triangles, and metyltetraprole by circles. Closed plot indicates ΔG for wild-type, while open plot indicates mutant type. An arrow is shown from the wild-type to the mutant type of the same inhibitor.
Fig 8.
Binding pose of inhibitor in the initial state of TI calculation.
Both binding poses for wild-type and mutant type are shown aligned on the active site of wild-type, which is shown in the gray-colored surface model. Cyan colored stick model shows binding pose for wild-type, while magenta-colored model shows those for mutant type. (a) Zymoseptoria tritici, (b) P. teres.
Fig 9.
Partial charges and molecular shape of Part-C in QoIs.
The molecular shape is shown by a surface model and partial charges by a color gradient on its surface. Stick model shows Part-A and Part-B in the active conformer of QoIs.