A detailed inspection of the binding mode of HP-2 in PrtX-III can be found in Figure 6.
Close inspection of the binding isotherm revealed the possibility that there are two nearly identical binding events (likely corresponding to the binding of each intercalated c-di-GMP dimer).
Post-irradiation inspection showed that the binding posts remained attached to the substrate while one of the Pt wires detached from the Pt ring most probably due to a bad laser weld.
A combination of looseness through wear and tear, damage in certain places, and the failure of the paste that glued the pages to the inside of the covers, now allow non-intrusive inspection of much of the binding construction, including the rear of the actual wooden front cover board, and some of the holes made through it.
Visual inspection of these structures revealed that the binding between the guest and host structures was mediated by crystallographically determined water molecules.
Visual inspection revealed no striking differences of the binding patterns between the individual clusters for more than 5 clusters.
After the molecular docking, the top-ranked 200 molecules were further analyzed using a series of analysis methods, visual inspection of binding mode and the ligand fitness of the pharmacophore.
Whatever the case, the smears preclude quantitation of the binding data; however, visual inspection of the gel suggests that IHF binds to this nonspecific duplex with an apparent affinity 5 10-fold lower than that of the cos-containing duplex, based on the disappearance of the free DNA band.
Inspection of binding interactions shows that the two putative binding modes derived from our study are reasonable.
Close inspection of binding of IHF to the specific cos274 duplex reveals a similar trend in the AUC, an initial increase in ⟨ s*⟩ followed by a decrease as a function of IHF concentration; however, the decrease is quite modest compared to that of the nonspecific duplex (see Figure 6C).
