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. Author manuscript; available in PMC: 2008 Nov 25.
Published in final edited form as: Methods Mol Biol. 2008;488:213–219. doi: 10.1007/978-1-60327-475-3_15

Figure 1.

Figure 1

Protein footprinting strategy. Biotinylation reactions of free protein comprised of separate protein subunits and the preformed protein-RNA complexes are carried out in parallel. Surface exposed lysines are modified by NHS-biotin in free protein, while those coordinating RNA become shielded from modification in the nucleoprotein complex. Individual protein subunits are separated by SDS-PAGE and then subjected to in-gel proteolysis. Comparative MS analysis of the peptide fragments enables us to identify lysines shielded by RNA contacts from those remaining susceptible to modification in the complex. The experimental scheme is adapted from Kvaratskhelia et al. (10)