Ribosome dynamics reshapes interaction sites and defines functional states

Two main large scale motions can be observed in the assembled ribosomes of all domains of life: rotation of the small subunit relative to the large one and swivel of the small subunit head domain relative to the small subunit body/platform domain (Figure 8A-B). The combination of subunit rotation and head swivel, observed in early ribosomal structures (Frank and Agrawal, 2000; Horan and Noller, 2007; Valle et al., 2003), was termed ‘ratcheting’. Subunit rotation and head swivel result in a reshaping of the intersubunit space, leading to changes in the positions of bound tRNAs and factors: Subunit rotation is known to be associated with the movement of the tRNAs on the large subunit (Moazed and Noller, 1989; Munro et al., 2007), leading to hybrid tRNAs, meaning that the tRNA is bound to one tRNA binding site on the small ribosomal subunit and to another on the large ribosomal subunit (A/P, P/E tRNAs). Head swivel and rotation combined (‘ratcheting’) are characteristic for the so-called chimeric hybrid state, an intermediate of translocation (Ramrath et al., 2013; Ratje et al., 2010; Zhou et al., 2013, 2014), where hybrid tRNAs bind to different tRNA binding sites on the small ribosomal subunit, one on the body/platform and another on the head domain (ap/P, pe/E tRNAs). Moreover, a somewhat ratcheted conformation is also observed in inactive mammalian ribosomes bound to eukaryotic elongation factor 2 (eEF2) (Khatter et al., 2015; Voorhees et al., 2014).

A motion so far only observed in the eukaryotic 80S ribosome is rolling of the small subunit, a rotation around the small subunit’s long axis (Figure 8A) (Behrmann et al., 2015; Budkevich et al., 2014). Subunit rolling takes place after decoding and is the main “net” conformational change characterizing the transition from the pre- translocational to the post-translocational state (See section 2.5).

Besides these main motions, there are some flexible parts of the ribosome that have also been observed to adopt distinct conformations: One of them is the L1 stalk (helices H76, H77, H78, and protein uL1) on the 60S subunit (Figure 3C-D, Supplemental Figure 1, Supplemental Figure 2), which is known to adopt different positions depending on the functional state of the ribosome (Mohan and Noller, 2017; Spahn et al., 2004a). Another flexible part is the stalk base (Helices H42, H43, H44, and proteins uL10, uL11) on the 60S subunit (Figure 3C-D, Supplemental Figure 1, Supplemental Figure 2). It changes its conformation by moving towards the A site upon binding of different factors (Gao et al., 2007; Schuette et al., 2009; Spahn et al., 2004b).

In 2009, Munro at al. applied the principle of the hierarchical energy landscape (Frauenfelder et al., 1991) to the dynamics of translation (Munro et al., 2009) (Figure 8C). The ribosome’s conformational degrees of freedom are directly connected to the forward movement of tRNAs during translation (Munro et al., 2009). The interplay of thermodynamically spontaneous motions (like subunit rotation), stabilizing and destabilizing contributions of the tRNAs (e.g. before and after peptide bond formation (Valle et al., 2003)) and the binding of protein factors like translational GTPases results in an ordered, organized sequence of conformational changes of the ribosome, which are coupled to efficient transport of the tRNA2•mRNA module through the ribosome.