The hydroxyl radical is a small, highly reactive probe that is formed in water and primarily targets hydrophobic residues . This may be an ideal probe for protein-protein interactions because tyrosine, tryptophan and phenylalanine are most likely to be found at an interface [110, 111]. Although protein-DNA interfaces are comprised of charged and hydrogen-bond donor side-chains, even these residues may be probed by hydroxyl radicals .
The hydroxyl radical reacts at nearly a diffusion limited rate (k @ 1 x 1010 M_1 s_1 to 5 x 109 M_1 s-1) with the aromatic amino acids, as well as with methionine, and cysteine . Most other side chains are 10-100 times less reactive, making the hydroxyl radical specific for residues that are typically located at protein-protein interfaces yet sufficiently reactive to give a ''snapshot'' view of the protein. Hydroxyl radicals have been successfully used to study proteinDNA and protein-metal interactions [114-116].
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