title: Probing the Translation Dynamics of Ribosomes Using Zero-Mode Waveguides.
abstract: In order to coordinate the complex biochemical and structural feat of converting triple-nucleotide codons into their corresponding amino acids, the ribosome must physically manipulate numerous macromolecules including the mRNA, tRNAs, and numerous translation factors. The ribosome choreographs binding, dissociation, physical movements, and structural rearrangements so that they synergistically harness the energy from biochemical processes, including numerous GTP hydrolysis steps and peptide bond formation. Due to the dynamic and complex nature of translation, the large cast of ligands involved, and the large number of possible configurations, tracking the global time evolution or dynamics of the ribosome complex in translation has proven to be challenging for bulk methods. Conventional single-molecule fluorescence experiments on the other hand require low concentrations of fluorescent ligands to reduce background noise. The significantly reduced bimolecular association rates under those conditions limit the number of steps that can be observed within the time window available to a fluorophore. The advent of zero-mode waveguide (ZMW) technology has allowed the study of translation at near-physiological concentrations of labeled ligands, moving single-molecule fluorescence microscopy beyond focused model systems into studying the global dynamics of translation in realistic setups. This chapter reviews the recent works using the ZMW technology to dissect the mechanism of translation initiation and elongation in prokaryotes, including complex processes such as translational stalling and frameshifting. Given the success of the technology, similarly complex biological processes could be studied in near-physiological conditions with the controllability of conventional in vitro experiments.
authors.affiliation: Department of Applied Physics, Stanford University, Stanford, California, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, California, USA; Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA.
authors.forename: Albert
authors.initials: A
authors.lastname: Tsai
authors.affiliation: Department of Structural Biology, Stanford University School of Medicine, Stanford, California, USA; Stanford Magnetic Resonance Laboratory, Stanford University School of Medicine, Stanford, California, USA.
authors.forename: Joseph D
authors.initials: JD
authors.lastname: Puglisi
authors.affiliation: Department of Structural Biology, Stanford University School of Medicine, Stanford, California, USA; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan. Electronic address: uemura@bs.s.u-tokyo.ac.jp.
authors.forename: Sotaro
authors.initials: S
authors.lastname: Uemura
mesh_terms: D008024:Ligands; D008856:Microscopy, Fluorescence / Q000379:methods*; D014176:Protein Biosynthesis; D011506:Proteins / Q000378:metabolism; D012343:RNA, Transfer / Q000378:metabolism; D012270:Ribosomes / Q000378:metabolism*
chemical_list: D008024:Ligands; D011506:Proteins; D012343:RNA, Transfer
keywords: ribosome; single-molecule fluorescence microscopy; translation elongation; translation initiation; translational stalling; zero-mode waveguides; −1 frameshifting