Intrinsic molecular properties of the protein–protein bridge facilitate ratchet-like motion of the ribosome

An Extensive Network of Information Flow through the B1b/c Intersubunit Bridge of the Yeast Ribosome

“…Scanning site-directed mutagenesis involving mutation of 3 or 4 sequential amino acids at a time spanning K 87 EYQ 90 , E 108 HID 111 , and I 114 KYD 117 was initially performed to identify the amino acids of L11 that most affected the contribution of L11 to the B1b/c bridge (Figure 1B). As previous surveys have suggested that movement and positioning of the B1b/c bridge during the intersubunit ratcheting process may be partially controlled by stretches of differentially charged amino acid residues between L11 and S18 [13], [15], each of these three stretches of amino acids were either deleted, changed to alanine, or given a positive charge by mutagenesis to poly-arginine. Of the 15 ‘regional mutants’ created, only H 109 ID 111 to poly-arginine (109–111R, this nomenclature is used throughout), was unviable.…”

“…While the ribosome contains numerous intersubunit bridges, the B1b/c bridge undergoes the largest conformational adjustments during the process of ribosomal ratcheting [10], [11], [14]. Previous observations of structural datasets suggested that a series of opposing positive and negative charge motifs between L11 and S18 may provide “sticky and slippery” surfaces that aid in both the movement and placement of the ratcheting subunits [13], [15] (Figure S1). …”

Intersubunit Bridges of the Bacterial Ribosome

“…Since 30S head undergoes structural change over a wide and continuous range of swiveling motion 110 , and each conformation forms unique interface between H38/L5/L31 and S13/S19, it is unlikely that these > 40 different states can be stabilized by the few contact points at B1a and B1b, as see in the classic-state ribosome. As mentioned above, L31 protein, which binds L5 at the lateral solvent side and makes extensive contacts with S14 and S19 proteins through bridge B1c (Figure 3, Table 2), may in fact be more important for bridging the interaction at the 30S head 111 . In a recent cryo-EM reconstruction of hybrid-state ribosome with 30S head swiveled, as S19 moves closer to L5, the flexible linker region of L31 becomes more compact, while the NTD and CTD maintain their interactions with L5 and S14/S19, respectively 43 .…”

The translation elongation cycle—capturing multiple states by cryo-electron microscopy

“…The peripheral intersubunit bridge B1b (bridge nomenclature introduced in [77,78]) mentioned earlier on is formed by a loop of large-subunit protein L5 and a long helix of protein S13 on the small subunit's head. As the subunits rotate relative to each other, the L5 loop glides along the S13 helix, which may act as a ruler, allowing contacts to be formed via salt bridges at multiple repeats of the helix turn [28,79]. Juxtaposition of GRASP-painted proteins L5 and S13 in the canonical and fully rotated states of the ribosome [28] and subsequent electrostatic calculations [79] confirmed that the subunits are stabilized by electrostatic interactions at the two ends of their relative rotation movement.…”

“…As the subunits rotate relative to each other, the L5 loop glides along the S13 helix, which may act as a ruler, allowing contacts to be formed via salt bridges at multiple repeats of the helix turn [28,79]. Juxtaposition of GRASP-painted proteins L5 and S13 in the canonical and fully rotated states of the ribosome [28] and subsequent electrostatic calculations [79] confirmed that the subunits are stabilized by electrostatic interactions at the two ends of their relative rotation movement. Thus, the picture emerges of a malleable bridge that does not offer strong resistance and undergoes rapid changes during intersubunit rotation, but exhibits energetic preferences, via charge interactions, for intersubunit positions at both ends of the rotation range.…”