For each concentration of PNPP the graph shows the data points obtained using the Michaelis-Menten equation and the reported Km = 7.8 μ M and kcat = 62 (s−1). For simulation concentration of E.coli alkaline phosphatase was assumed 5 nM. The black line shows a...
In each simulation, the aptamer model was placed in the center of the water box, and the distance from its surface to the boundary was more than 15 Å. The GTX1/4 molecule was prepared via the general AMBER force field using the antechamber, and its topology file and coordinate file ...