Probing protein-peptide binding surfaces using charged stable free radicals and transverse paramagnetic relaxation enhancement (PRE).

Nitroxide species, which have an unpaired electron localized on a nitrogen atom, can be useful as NMR probes to identify areas of the surface of a protein involved in the formation of a complex. The proximity of an electron spin leads to higher NMR relaxation rates for protein nuclei. If a protein-ligand complex is formed the radical is excluded from certain sites on the protein surface, protecting them from relaxation effects. We show here that charged nitroxide species can be helpful for identifying regions of the surface of the 4F1(5)F1 module pair from human fibronectin involved in peptide binding.