Molecular docking studies suggested that the hydrazinyl carbothioamide moiety of compounds (6 10) can in general be accommodated the binding pocket of the breast cancer protein (1JNX) and are responsible for the activity of the whole of the molecule.
This would allow sufficient space to accommodate the binding of a large enzyme molecule.
While some conformational differences in the MHC peptide-binding cleft must occur in order to accommodate the binding of different peptides, this limited experimental evidence suggests that these differences are relatively small.
The X-ray structure of subunit H was fit in the remaining density based on recent biochemical findings in Neurospora crassa indicating that the amino-terminus of subunit H accommodates the binding of one of the three peripheral stalks [27].
As organisms evolve, the more complex interactome regulating DNA replication, repair, and cell cycle control may require a higher tolerance by PCNA to accommodate the binding of a larger variety of PCNA ligands, presenting more diverse PIP sequences.
Since conformational flexibility was also observed in the RNA-binding ring of the bacterial PNPase [25], [29], we propose that the conformational dynamics may be harnessed by the archaeal exosome, and perhaps by all exosome family members, to accommodate the binding of various RNA substrates and to disrupt their structures.
Although Nutlin-3 mimics key residues involved in the binding to MDM2 (Phe19, Trp23 and Leu26 of p53), a recent study showed that Tyr100 in MDM2 accommodates the binding of Nutlin-3, whereas Tyr99 in MDMX causes a steric clash with Nutlin-3 [26].
Previous structural studies on MotB and PAL established that loop β2α2 accommodates the binding site for the N-acetylmuramic acid (NAM) moiety of PG [5], whereas the grove between loops β1α1 and β2α2 binds its peptide moiety containing meso-diaminopimelate (m-DAP) [9] (Fig. 1(A)).
Notably, the open shape of the active site can readily accommodate the binding of longer xylodextrin substrates.
In this example, the structured protein side of the complex also uses flexibility to accommodate the binding of the many disordered segments to a common binding site.
