title: Dynamics of translation by single ribosomes through mRNA secondary structures.
abstract: During protein synthesis, the ribosome translates nucleotide triplets in single-stranded mRNA into polypeptide sequences. Strong downstream mRNA secondary structures, which must be unfolded for translation, can slow or even halt protein synthesis. Here we used single-molecule fluorescence resonance energy transfer to determine reaction rates for specific steps within the elongation cycle as the Escherichia coli ribosome encounters stem-loop or pseudoknot mRNA secondary structures. Downstream stem-loops containing 100% GC base pairs decrease the rates of both tRNA translocation within the ribosome and deacylated tRNA dissociation from the ribosomal exit site (E site). Downstream stem-loops or pseudoknots containing both GC and AU pairs also decrease the rate of tRNA dissociation, but they have little effect on tRNA translocation rate. Thus, somewhat unexpectedly, unfolding of mRNA secondary structures is more closely coupled to E-site tRNA dissociation than to tRNA translocation.
authors.affiliation: Pennsylvania Muscle Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
authors.forename: Chunlai
authors.initials: C
authors.lastname: Chen
authors.forename: Haibo
authors.initials: H
authors.lastname: Zhang
authors.forename: Steven L
authors.initials: SL
authors.lastname: Broitman
authors.forename: Michael
authors.initials: M
authors.lastname: Reiche
authors.forename: Ian
authors.initials: I
authors.lastname: Farrell
authors.forename: Barry S
authors.initials: BS
authors.lastname: Cooperman
authors.forename: Yale E
authors.initials: YE
authors.lastname: Goldman
mesh_terms: D004926:Escherichia coli / Q000235:genetics* / Q000378:metabolism*; D031541:Fluorescence Resonance Energy Transfer; D007700:Kinetics; D008954:Models, Biological; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D014176:Protein Biosynthesis; D012333:RNA, Messenger / Q000378:metabolism*; D012270:Ribosomes / Q000378:metabolism*
chemical_list: D012333:RNA, Messenger
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