Ribosomal proteins of Deinococcus radiodurans: their solvent accessibility and reactivity

The structure of proteins in native ribosomes from Deinococcus radiodurans R1 was probed by S-methylthioacetimidate (SMTA) modification of amino groups. The extent of protein labeling was quantified using top down methods, and modified positions were identified using bottom up experiments. Each protein's reactivity was predicted by examination of the crystal structures of the D. radiodurans 50S subunit and the T. thermophilus HB8 30S subunit. The close phylogenetic relation between D. radiodurans and T. thermophilus allowed the evaluation of D. radiodurans small subunit protein reactivity by alignment of homologous sequences. As a result, we were able to observe and characterize the reactivity of all of D. radiodurans ribosomal proteins. The extent of protein amidination was well correlated with the solvent-exposed surface area of each protein and even better correlated with the number of visible lysine residues. Lysine residues that are in close contact with rRNA structural features or buried in protein tertiary structure are nonreactive with SMTA, while those that are surface exposed are modified. Crystallographic disorder and post-translational modifications lead to differences between the observed and predicted extents of reactivity. Comparison of unmodified and disassembled amidinated protein mixtures also shows great promise for the quality control of the proteomic sequences and has facilitated the identification of four sequencing errors in the ribosomal proteome of D. radiodurans R1.