The crystal packing induces an intermolecular interaction between the flipped H12 of the RXRα-LG100754 and the coactivator binding surface of a symmetry related RXR molecule (Figure 4).
To demonstrate the efficacy of this methodology, we examined changes in the binding surface of a Ubiquitin (Ubq) target that result from phosphorylating the endocytic proteins, STAM2 (Signal-transducing adaptor molecule) and Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate), both of which form homodimers with molecular weights of ∼115 kDa and ∼150 kDa, respectively.
Solution NMR techniques are frequently employed in probing protein protein interactions due to the sensitivity of NMR chemical shift to the surrounding environment which allows the binding surface of a protein to be mapped, merely by titrating in its binding partner and tracking the changes in the position and/or intensity of the NMR signals.
This concept is reflected in the "target size" of the protein DNA interaction, which is a geometric constraint that describes the orientation and size of the binding surface of a protein as it samples DNA while searching for its target site.
In this study, we explore this question by investigating the structural/dynamic property of the ice-binding surface of an antifreeze protein using NMR spectroscopy.
The binding surfaces of all target proteins, except Con A, have both hydrophilic and hydrophobic residues.
Since the architecture of the Gata finger seems built around recognizing this particular sequence, we set out to define the allowable range of amino acid substitutions along the DNA-binding surface of a Gata finger that could continue to support sequence-specific DNA-binding activity.
The docked model of the PPIL1·SKIP interaction suggests a novel protein-binding surface of a cyclophilin.
It was also proposed that phosphorylation of the regulatory tyrosine not only blocks the SH2 domain, but also hides the binding surface of the nSH3 domain, generating a fully inhibited molecule.
Based on the observation of chemical shift averaging and narrow backbone amide resonances, it has been suggested that the linker L12 is conformationally flexible in order to enable the interaction of this binding surface of the KIX domain with a variety of disparate ligand sequences, while in complex with MLL, the conformational flexibility is reduced.
