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. Author manuscript; available in PMC: 2007 Aug 20.
Published in final edited form as: J Biol Chem. 2006 Jul 3;281(35):25205–25214. doi: 10.1074/jbc.M512450200

FIGURE 4. Comparison of peak areas of three peptide fragments after biotinylation in the presence and absence of DNA.

FIGURE 4

The value in the graph is the integrated peak intensity from the extract ion chromatograph of an ion corresponding to the indicated peptide. A, Lys-11 is not protected from biotinylation in the DNA complex, since the peak intensity for this peptide decreases upon biotinylation of free β protein and β protein DNA complex. B, Lys-61 and Lys-36 are protected from biotinylation in the DNA complex, since the peak intensity for this peptide decreases upon biotinylation of free β protein but much less so when the β protein-DNA complex is biotinylated. C, Lys-148 is protected from biotinylation in the DNA complex. The signal for peptide 138–148 is only partially reduced upon biotinylation, indicating low surface accessibility of Lys-148 in the free protein. The signal for this peptide is less reduced upon biotinylation of the DNA complex, indicating Lys-148 is partially protected by DNA. Because the intensity changes for this peptide are less dramatic than those in panels A and B, the analysis was repeated with a 2× dose of NHS-biotin, which results in increased modification of Lys-148 in the free protein but not in the protein-DNA complex.