The ribosome, Nature’s ubiquitous nano-assembler for proteins, is not only very old, but complex, sophisticated, and evolving. In bacterial cells, it adds 20 amino acids per second to a polypeptide chain during the elongation phase of synthesis. It only incorporates the wrong amino acid or erroneously shifts the reading frame on the messenger RNA (mRNA) less than 1 in 1,000 elongation cycles. Even the best typist will make more mistakes. Enough free energy is liberated on formation of the peptide bonds to power synthesis, but two extra units of energy are spent in the splitting of GTP by elongation factors (EFs) Tu and G to ensure the fidelity of amino acid selection and the maintenance of the reading frame. How these accessory factors lower the error rate is incompletely understood.
X-ray, cryo-EM, and single-molecule fluorescence assays have suggested that the two main subunits of the ribosome and transfer RNAs (tRNAs) spontaneously fluctuate between so-called classic and hybrid states before EF-G binds to catalyze translocation 3 bases along the mRNA. Most of these studies analyzed ribosomes that had been stalled by antibiotics or lack of EF-G, but we had a hint from earlier work that the situation might be different with ongoing synthesis. Our study, shows that during ongoing synthesis there is indeed insufficient time for the ribosome and tRNAs to settle into classic-hybrid fluctuations. Rather, the pre-translocation tRNAs reside in intermediate locations similar to some of the “chimeric” positions that structural studies have detected. Our results demonstrate that fully operational molecules may be imperfectly represented by those which are artificially inhibited and highlight the synergy between high resolution snapshots and real-time structural dynamics.
The cover drawing evokes the power, intricate complexity, and early origins of this machinery in the “Steampunk” visual style influenced by Victorian industrial technology and the scientific romances of Jules Verne, HG Wells, Mary Shelley, and Arthur Conan Doyle. The integrated metal, wood and glass materials are a reminder of the hybrid RNA-protein composition of the ribosome. The 2014 Oscar-winning, charming animated short Mr. Hublot by Laurent Witz and Alexandre Espigares, and the darker, full-length movie City of Lost Children by Marc Caro and Jean-Pierre Jeunet inspired us to adopt this style. The artwork was drawn by Patrick Lane at Sceyence Studios (www.sceyencestudios.com), who also produced our previous Biophysical Journal cover, myosin V as Robert Crumb’s Mr. Natural, March 19, 2013.
More about our research on molecular motors and protein synthesis, emphasizing single molecule, optical trapping, and fluorescence microcopy can be found on the Goldman Laboratory website.
– Ryan Jamiolkowski, Chunlai Chen, Barry Cooperman, Yale Goldman