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Near-UV CD spectra of PDC-109 obtained in the presence of these two phospholipids show considerable differences, when compared with the spectrum of native PDC-109 (Fig. 5E), indicating that the protein tertiary structure is altered upon phospholipid binding, which is consistent with earlier reports [15], [39].
On the whole, the net electrostatic interaction (Δ Eele+Δ GGB) opposes binding, which is consistent with the discussion in the section on binding free energies calculation.
The side chains of ChsE5 residues Arg362, Met129, Asp126, and Gln151 fill the FAD site and thus block the FAD binding, which is consistent with the surface representation in which ChsE5 conflicts with the conserved FAD binding.
Docking calculation using reported organic small molecules and natural products revealed key active site residues such as Arg131 and Asp16 for ligand binding, which is consistent with previous studies.
Addition of a CAAX box to Rnd3ΔC did not restore 14-3-3 14-3-3 14-3-3ng, which is consistent with the requirement for the Rnd3 C-terminal proteinrylation sites for 14-3-3 interaction.
It can be noted that proteins with the highest content of PPII have an over-frequency of functions related to interaction mechanisms and/or binding, which is consistent with observations in (11).
Similar(48)
On GABP dataset, we found that most of the binding regions have two or more adjacent binding sites, which is consistent with the literature that GABP binds in a more distributed manner [ 33].
The Ka value was estimated to be ~800 M-1 for one-binding site or ~400 M-1 for two identical binding sites, which is consistent with the value determined from fluorescence characterization (Figure 2B).
The conformation got from docking simulation implies that the substrate can form strong binding interactions with the catalytic zinc ion and the residues in the binding pocket, which is consistent with the previously catalytic assumptions (Luo et al. 2014; Gotthard et al. 2013).
All binding values are the result of fitting titration data to a 1 : 1 binding model, which is consistent with Job's method of continuous variation.
In the proposed ligand-binding complexes, the 6-hydroxyl group is projected away from the binding site, which is consistent with the finding that substitution at this position is tolerated.
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