Ratchet, swivel, tilt and roll: A complete description of subunit rotation in the ribosome

Abstract

Protein synthesis by the ribosome involves large-scale rearrangements of the "small" subunit (SSU; ~ 1 MDa), which include inter- and intra-subunit rotational motions. With more than 1000 structures of ribosomes and ribosomal subunits now publicly available, it is becoming increasingly difficult to design precise experiments that are based on a comprehensive analysis of all known rotation states. To overcome this limitation, we present the Ribosome Angle Decomposition (RAD) method, where the orientation of each small subunit head and body is described in terms of three angular coordinates (rotation, tilt and tilt direction) and a single translation. To demonstrate the utility of the accompanying software (RADtool) we applied it to all published ribosome and mitoribosome structures. This identified and analyzed 1077 fully-assembled ribosome complexes, as well as 280 isolated small subunits from 48 organisms. The RAD approach quantitatively distinguishes between previously described qualitative rotational features, determines when rotation-only descriptions are insufficient, and shows that tilt-like rearrangements of the SSU head and body are pervasive in both prokaryotic and eukaryotic ribosomes. Together, the presented database and technique provide a robust platform for systematically analyzing, visualizing, and comparing subunit orientations of ribosomes from all kingdoms of life. Accordingly, the RAD resource establishes a common foundation with which structural, simulation, single-molecule and biochemical efforts can precisely interrogate the dynamics of this prototypical molecular machine.

Identifying Strategies to Experimentally Probe Multidimensional Dynamics in the Ribosome

“…That is, head tilting predominantly occurs about an axis that is parallel to the bound mRNA. For a complete description of the rotation angles, see SI and Hassan et al…”

“…23 That is, head tilting predominantly occurs about an axis that is parallel to the bound mRNA. For a complete description of the rotation angles, see SI and Hassan et al 8 In order to probe the sensitivity and specificity of interprotein distances to head motions measured by ϕ and θ, we calculated the mutual information between each distance and each head angle. Mutual information was used since it can identify nonlinear dependencies, while also accounting for dispersion in the distance or angle distributions.…”

“…Some notable examples include the spliceosome, proteasome, fatty acid synthetase, and nuclear pore complex. Probably the most well studied assembly is the ribosome (Figure a), for which more than 1500 structures have been resolved through X-ray crystallography − and cryoelectron microscopy − (see ref for complete list). In addition, biochemical − and single-molecule − methods have been applied extensively to characterize the dynamics of the ribosome.…”

RiboXYZ: A comprehensive database for visualizing and analyzing ribosome structures

“…Previous efforts to integrate ribosome structural data were made to build databases and interfaces for 3D alignment [23], or jointly visualize 1D, 2D and 3D structures of the ribosome [24]. While these databases are not available anymore and/or do not scale up to the current amount of available structures [3], the past year has interestingly seen the release of new applications with dedicated online server and database, that perform some advanced analysis of ribosome structures and proteins using a large dataset of structures available [21, 25]. For instance, Radtool [25] evaluates the relative rotation of the two ribosomal subunits across all structures available from the PDB.…”

“…While these databases are not available anymore and/or do not scale up to the current amount of available structures [3], the past year has interestingly seen the release of new applications with dedicated online server and database, that perform some advanced analysis of ribosome structures and proteins using a large dataset of structures available [21, 25]. For instance, Radtool [25] evaluates the relative rotation of the two ribosomal subunits across all structures available from the PDB. Proteovision, which was earlier mentioned as it uses RiboXYZ’s API allows to perform an evolutionary analysis and visualization of ribosomal proteins over a large number of species in the tree of life.…”