STRUCTURAL DYNAMICS OF TRANSLATING RIBOSOMES - 16S RIBOSOMAL-RNA BASES THAT MAY MOVE TWICE DURING TRANSLOCATION

Recent footprinting, sedimentation and neutron-scattering results obta ined in vivo or on pre-translocation and post-translocation ribosomal complexes are integrated with cross-linking and immunoelectron microsc opy information. It is proposed that the 30S subunit pulses during tra nslocation and that its pre- and post-translocation structures are not necessarily identical. Accordingly, translocation is characterized by three consecutive conformational states of the 30S and 50S subunits. State 1 (the pre-translocation state) lasts until the elongation facto r EF-G GTP complex binds to the ribosome or adopts the GTPase conforma tion. State 2 (the translocation state, or the peak or plateau of the pulse) follows and lasts until EF-G adopts a subsequent conformation o r is released from the ribosome. State 3 (the post-translocation state ) ensues and lasts until A (aminoacyl) site binding of aminoacyl-tRNA. In state 2, 16S RNA hairpins 26 and 33-33A, located in the platform a nd the head of the 30S subunit, respectively, become kinked or twisted , and residue A1503, near the decoding site, becomes exposed. A platfo rm twist is associated with P (peptide) to E (exit) site tRNA movement s and a head twist with pivoting of the peptidyl-tRNA elbow from the A to the P site, around a (retractable?) S19 domain. These twists resul t in an unlocking of the platform and the head from the 50S subunit. E xposure of A1503 is tentatively associated with movements of mRNA or t RNA anticodon stem-loops. These twisted or otherwise-exposed residues readopt their previous setting upon completion of translocation, i.e. states 1 and 3 of 16S RNA differ more from state 2 than from each othe r. Yet the ribosome is never fully locked or unlocked at any time duri ng elongation. It is unlocked in one or another respect in the pre- an d post-translocation states, and unlocked to the largest extent in sta te 2.