UV-Induced Ligand Exchange in MHC Class I Protein Crystals

High-throughput structure determination of protein-ligand complexes is central in drug development and structural proteomics. To facilitate such high-throughput structure determination we designed an induced replacement strategy. Crystals of a protein complex bound to a photosensitive ligand are exposed to UV light, inducing the departure of the bound ligand, allowing a new ligand to soak in. We exemplify the approach for a class of protein complexes that is especially recalcitrant to high-throughput strategies: the MHC class I proteins. We developed a UV-sensitive, conditional, peptide ligand whose UV-induced cleavage in the crystals leads to the. exchange of the low-affinity lytic fragments for full-length peptides introduced in the crystallant solution. This in crystallo exchange is monitored by the loss of selenomethionine anomalous diffraction signal of the conditional peptide compared to the signal of labeled MHC beta 2m subunit. This method has the potential to facilitate high-throughput crystallography in various protein families.