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As shown by these studies, the binding interfaces of both strains are located in the same region of the outermost P2 domain, but the positions and amino acid composition of individual binding sites and the HBGA binding modes are different.
The authors of the present study reject that model based on two counts: they were not cognate ligand complexes and their binding modes are different.
In this study, we show that the p52 Bcl3 complex binds to both A/T- and G/C-centric κB sites; however, the binding affinities and binding modes are different, leading to different transcriptional outcomes.
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This binding mode is different from those previously postulated in the literature and may provide a useful approach to selective small molecule inhibitor design.
The PCP-complex structure of TM0415 also revealed that its myo-inositol-binding mode is different from that of MI3K_TK, although the residues interacting with myo-inositol in MI3K_TK are conserved in TM0415 (Fig. 1c).
These modeled structures of KpPriA show that the DNA-binding modes and thus the DNA-unwinding modes are different.
Using X-ray absorption spectroscopy and new mass spectrometry-related techniques, we find that different binding modes are responsible for the different effects of Ni II) and Zn II).
Their binding modes are structurally and energetically different, with details given in the text.
The bond lengths of the three different binding modes are summarized in Table 2 and are in good agreement with other TRIS-functionalized Anderson POMs.
Strikingly, when studying the binding to different NTRs like TRN1 and NTF2, despite exhibiting different binding preferences for FG-Nups (Cook et al., 2007; Milles and Lemke, 2014), their binding modes are remarkably similar to that of the Importinβ complex.
The ability of these systems to bind DNA with different binding modes is proposed to affect their function in vivo.
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