The role of the 6 lysines and the terminal amine of Escherichia coli single-strand binding protein in its binding of single-stranded DNA

Differential chemical modification of the lysines and amino-terminus of Esc herichia coli single-strand binding (SSB) protein was used to determine the ir roles in the binding of SSB to single-stranded DNA (ssDNA). A combinatio n of isotope labeling and mass spectrometry was used to determine the rates at which SSB was acetylated by acetic anhydride. First, SSB was labeled by deuterated acetic anhydride for given lengths of time in the presence or a bsence of single-stranded ssDNA. Then, the protein was denatured and comple tely acetylated by nondeuterated acetic anhydride. Enzymatic digests of the completely acetylated, isotopically labeled SSB were analyzed by electrosp ray ionization mass spectrometry. The intensities of the deuterated and non deuterated forms of acetylated peptides provided accurate quantification of the reactivity of the amines in native SSB, either free or bound to ssDNA. Acetylation rate constants were determined from time course measurements. In the absence of ssDNA, the terminal alpha-amine of SSB was 10-fold more r eactive than Lys residues at positions 43, 62, 73, and 87. The reactivities of Lys 7 and 49 were much lower yet, suggesting that they have very limite d access to solution under any condition. In the presence of ssDNA, the rea ctivities of the amino-terminus and Lys residues 43, 62, 73, and 87 were re duced by factors of 3.7-25, indicating that the environments around all of these amines is substantially altered by binding of SSB to ssDNA. Three of these residues are located near putative ssDNA binding sites, whereas Lys 8 7 is located at the monomer-monomer interface.