Fig. 5.

The ATP hydrolysis reaction path of F-form actin, simulated by QM/MM calculations. (A) The reaction scheme of ATP hydrolysis in the F-form actin from reactant (R) to product (P) state via intermediate (IM) and transition (ST) states. (B) The molecular structure of PO₃⁻, W1, and W2 at the rate-limiting TS4. The proton transfers from W1 to W2 in concert with the other from W2 to PO₃⁻. (C–E) Atomic positions in the catalytic site and some interatomic distances in the states R (C), IM3 (D), and P (E), calculated based on the structure of P_xtal. In B–E, phosphorus atoms (P), oxygen atoms (O), protons (H⁺), and magnesium ions (Mg²⁺) are colored orange, red, gray, and light green, respectively. (F) The three structures in C–E are superimposed, where state R, IM3, and P are colored orange, magenta, and blue, respectively. Note that all of the atoms, except for P^G, W1, and W2, remain at almost the same positions. (G) Potential energy profiles along the reaction path indicated in A. The profile calculated based on the structure of R_xtal, and the other calculated based on the structure of P_xtal, are indicated in orange and blue, respectively.