However, under these conditions, it cannot be concluded that each step occurs within the initial binding encounter of RFCATPPCNA and P/T DNA.
The proposed model suggests that there are at least two distinct ATP hydrolysis-dependent steps that occur within the initial binding encounter of RFC with a P/T junction.
The rate constants for the FRET increase (kinc) and the initial phase of the FRET decrease (kdec,1) agree very well with that observed in the absence of chase, demonstrating that these two observed phases occur within the initial binding encounter of Cy5-PCNA and Cy3-P/T DNA.
This model is also substantiated by significant previous work, which supports formation of a weakly binding encounter complex as the initial step, protein structural fluctuations associated with forming the Michaelis complex, and multiple conformations within the Michaelis state that do not directly interconvert, with one of these populations being incompetent toward conversion to lactate.
Such a long-lived complex with ssDNA is consistent with the observation that a ssDNA segment can serve as a conduit to increase the number of productive binding encounters with AAG.
Beside the stepwise bond formation that seems to be the rate limiting step of the binding process, the encounter of the Ca2+ ion with the binding site, which is the first step in the binding process, raises interesting questions regarding the mechanism by which the ion approaches the binding site.
and "Close Encounters of the Third Kind".
Thus, the two opposing activities of RFC may occur within the same binding encounter with DNA.
Thus, the opposing activities of RFC, clamp loading and unloading, both occur within the same binding encounter with a given P/T junction.
Many glycosylases are capable of facilitated diffusion, whereby multiple sites along the DNA are sampled during a single binding encounter.
