title: Fluctuations of transfer RNAs between classical and hybrid states.
abstract: Adjacent transfer RNAs (tRNAs) in the A- and P-sites of the ribosome are in dynamic equilibrium between two different conformations called classical and hybrid states before translocation. Here, we have used single-molecule fluorescence resonance energy transfer to study the effect of Mg(2+) on tRNA dynamics with and without an acetyl group on the A-site tRNA. When the A-site tRNA is not acetylated, tRNA dynamics do not depend on [Mg(2+)], indicating that the relative positions of the substrates for peptide-bond formation are not affected by Mg(2+). In sharp contrast, when the A-site tRNA is acetylated, Mg(2+) lengthens the lifetime of the classical state but does not change the lifetime of the hybrid state. Based on these findings, the classical state resembles a state with direct stabilization of tertiary structure by Mg(2+) ions whereas the hybrid state resembles a state with little Mg(2+)-assisted stabilization. The antibiotic viomycin, a translocation inhibitor, suppresses tRNA dynamics, suggesting that the enhanced fluctuations of tRNAs after peptide-bond formation drive spontaneous attempts at translocation by the ribosome.
authors: Department of Physics, Stanford University, Stanford, California 94305, USA.
authors: Harold D
authors: HD
authors: Kim
authors: Joseph D
authors: JD
authors: Puglisi
authors: Steven
authors: S
authors: Chu
mesh_terms: D001703:Biophysics / Q000379:methods; D031541:Fluorescence Resonance Energy Transfer; D007477:Ions; D008274:Magnesium / Q000737:chemistry*; D008956:Models, Chemical; D009690:Nucleic Acid Conformation; D010441:Peptide Chain Elongation, Translational; D010455:Peptides / Q000737:chemistry; D011092:Polyethylene Glycols / Q000737:chemistry; D021381:Protein Transport; D012343:RNA, Transfer / Q000737:chemistry*; D012346:RNA, Transfer, Amino Acyl / Q000737:chemistry*; D012270:Ribosomes / Q000737:chemistry*; D013997:Time Factors; D014756:Viomycin / Q000737:chemistry / Q000494:pharmacology*
chemical_list: D007477:Ions; D010455:Peptides; D012346:RNA, Transfer, Amino Acyl; D011092:Polyethylene Glycols; D012343:RNA, Transfer; D008274:Magnesium; D014756:Viomycin
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