Mechanistic studies of affinity modulation

A synthetic ligand for the protein FKBP12 was covalently linked to a peptide ligand (pYEEI) for the Fyn SH2 protein to create a bifunctional molecule called SLFpYEEI. This bifunctional molecule can simultaneously bind both proteins to form a trimeric complex. When SLFpYEEI is precomplexed with FKBP12, the peptide ligand binds 6-fold more weakly to the Fyn SH2 domain than SLFpYEEI alone. Isotope-edited NMR spectroscopy was used to investigate the molecular basis for the observed reduction in affinity. The results suggest that interactions between the pYEEI peptide and FKBP12 may play a significant role in diminishing the affinity of SLFpYEEI for the Fyn SH2 domain.