Correlating the chemical modification of Escherichia coli ribosomal proteins with crystal structure data.

Various chemical modifications have been applied to study protein structures. In this paper, amidination of E. coli ribosomal proteins was investigated to profile the structure of this large protein/RNA complex. The extent of ribosomal protein amidination was correlated with the solvent accessibility of amine groups in E. coli ribosome crystal structures. The modification of many residues was confirmed by CID of tryptic peptides. The amidination of proteins in the intact ribosome is very consistent with crystal structure data. The extent to which monomethylated amine groups can be amidinated was also examined. This information was used to interpret the amidination of several ribosomal proteins. Interestingly, ribosomal proteins L7 and L12, which share the same sequence and differ only by acetylation of the N-terminus, were found to be methylated to different extents. L12 is largely monomethylated but only a small portion of L7 is so modified.