A possible reason for the moderate sensitivity to SQA might be attributed to its pronounced hydrophobic nature preventing/limiting the establishment of specific binding interactions, as has been reported for other hydrophobic targets [ 44].
The observed binding mode appears distinct from other single motif binding interactions, as well as from mechanisms that involve global conformational transitions, such as folding upon binding (Csermely et al., 2010; Wright and Dyson, 2009).
Potentially consistent with this latter idea, PME-1 has been shown to regulate active PP2A C subunit generation and holoenzyme assembly [31] and to stably associate with "inactive" forms of PP2A complexes in tissues [32], [42], suggesting that this protein may confer a regulatory effect on PP2A activity through both binding interactions as well as catalysis.
Also, the docking study showed that all the docked compounds exhibited similar binding interaction as those previously reported by the co-crystallized ligand when docked into the active site of M. tuberculosis enoyl reductase InhA.
Indeed, all copies of the complex obtained in the structures from both species superimposed well and exhibited the same four major groups of binding interactions as described for the D. rerio structure.
In the case of a duplex that contains a specific binding element (e.g., the I1 duplex), the weight-average sedimentation coefficient must consider not only nonspecific binding interactions as described above but also the contribution of the specific IHF DNA complex to the experimentally observed ⟨ s*⟩.
We emphasized the researchers' practical efforts in real projects by understanding the ligand-target binding interactions as a premise.
Docking scrutiny showed that compounds zinc_2135897 and CB4275815 have reliable binding interactions as they gained highest GOLD fitness scores and showed hydrogen bonding with Arg139 that is involved in the shikimate-carboxylate group recognition.
FRET analysis showed that EGFP and DsRed together did not generate binding interactions, as revealed by a low level of binding energy (see color scale; Fig. 6A).
This work emphasizes the strong evolutionary pressure to bolster RNA tertiary structure with RNA-binding interactions as seen in the ribosome, spliceosome, and other large RNA machines.
