Using cross-links to study ribosomal dynamics.

After publications of 3-D models of a static ribosome and its large and small subunits, one of the next tasks is to recognize movable ribosomal elements responsible for mechanical shifts during protein synthesis. Statistic analysis of available cross-linking data allowed us to reveal three well separated groups of motions in the ribosome: I, mean magnitude of 10 A; II, most abundant, centered at 20 A and of wide dispersion, and III, sparsely populated, with large distances up to 95 A. The last group, III, comprises elements, like the L7/12-stalk and the L1- protuberance, that adopt different positions in crystallographic or electron micrographic structures, and neighboring hairpins 88 and 89, indicating mobility. We demonstrate that the cross-linking method can be applied to study ribosomal dynamics, including large-scale functional movements and, in particular, to estimate which structures participate in molecular switches.