Mechanical modulation of ATP-binding affinity of V1-ATPase

V(1)-ATPase is a rotary motor protein that rotates the central shaft in a counterclockwise direction hydrolyzing ATP. Although the ATP-binding process is suggested to be the most critical reaction step for torque generation in F(1)-ATPase (the closest relative of V(1)-ATPase evolutionarily), the role of ATP binding for V(1)-ATPase in torque generation has remained unclear. In the present study, we performed single-molecule manipulation experiments on V(1)-ATPase from Thermus thermophilus to investigate how the ATP-binding process is modulated upon rotation of the rotary shaft. When V(1)-ATPase showed an ATP-waiting pause, it was stalled at a target angle and then released. Based on the response of the V(1)-ATPase released, the ATP-binding probability was determined at individual stall angles. It was observed that the rate constant of ATP binding (k(on)) was exponentially accelerated with forward rotation, whereas the rate constant of ATP release (k(off)) was exponentially reduced. The angle dependence of the k(off) of V(1)-ATPase was significantly smaller than that of F(1)-ATPase, suggesting that the ATP-binding process is not the major torque-generating step in V(1)-ATPase. When V(1)-ATPase was stalled at the mean binding angle to restrict rotary Brownian motion, k(on) was evidently slower than that determined from free rotation, showing the reaction rate enhancement by conformational fluctuation. It was also suggested that shaft of V(1)-ATPase should be rotated at least 277° in a clockwise direction for efficient release of ATP under ATP-synthesis conditions.

Polyamines stimulate RecA-mediated recombination by condensing duplex DNA and stabilizing intermediates

Polyamines are naturally occurring cationic molecules in cells. In addition to their roles in modulating gene expression and cell proliferation, they have been shown to stimulate DNA recombination. The molecular mechanism for stimulation is not clear. We utilized single-molecule tethered particle motion (TPM) experiments to investigate how polyamines stimulate RecA-mediated recombination. We showed that natural polyamines, spermine and spermidine, condense duplex DNA, but with different efficiencies. While ∼300 μM of spermine condenses 50% of duplex DNA, 2.0 mM of spermidine is required to achieve the same level of condensation. The condensation takes place in a stepwise manner, and is reversible upon removal of polyamines. We also showed that addition of polyamines stimulates the duplex capture activity of RecA filament and stabilizes the intermediates with longer dwell time. Through condensing duplex DNA and stabilizing the complex of RecA filaments and duplex DNA, polyamines stimulate the formation of functional intermediates by ∼20-fold, and promote recombination progression.