title: A combined cryo-EM and molecular dynamics approach reveals the mechanism of ErmBL-mediated translation arrest.
abstract: Nascent polypeptides can induce ribosome stalling, regulating downstream genes. Stalling of ErmBL peptide translation in the presence of the macrolide antibiotic erythromycin leads to resistance in Streptococcus sanguis. To reveal this stalling mechanism we obtained 3.6-Å-resolution cryo-EM structures of ErmBL-stalled ribosomes with erythromycin. The nascent peptide adopts an unusual conformation with the C-terminal Asp10 side chain in a previously unseen rotated position. Together with molecular dynamics simulations, the structures indicate that peptide-bond formation is inhibited by displacement of the peptidyl-tRNA A76 ribose from its canonical position, and by non-productive interactions of the A-tRNA Lys11 side chain with the A-site crevice. These two effects combine to perturb peptide-bond formation by increasing the distance between the attacking Lys11 amine and the Asp10 carbonyl carbon. The interplay between drug, peptide and ribosome uncovered here also provides insight into the fundamental mechanism of peptide-bond formation.
authors.affiliation: Gene Center and Department for Biochemistry, University of Munich, Feodor-Lynenstrasse 25, Munich 81377, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Arenz
authors.affiliation: Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37079, Germany.
authors.forename: Lars V
authors.initials: LV
authors.lastname: Bock
authors.affiliation: Gene Center and Department for Biochemistry, University of Munich, Feodor-Lynenstrasse 25, Munich 81377, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Graf
authors.affiliation: Institut Européen de Chimie et Biologie, University of Bordeaux, Pessac 33607, France.|INSERM U1212, Bordeaux 33076, France.|CNRS UMR7377, Bordeaux 33076, France.
authors.forename: C Axel
authors.initials: CA
authors.lastname: Innis
authors.affiliation: Gene Center and Department for Biochemistry, University of Munich, Feodor-Lynenstrasse 25, Munich 81377, Germany.|Center for integrated Protein Science Munich, University of Munich, Feodor-Lynenstrasse 25, Munich 81377, Germany.
authors.forename: Roland
authors.initials: R
authors.lastname: Beckmann
authors.affiliation: Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37079, Germany.
authors.forename: Helmut
authors.initials: H
authors.lastname: Grubmüller
authors.affiliation: Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37079, Germany.
authors.forename: Andrea C
authors.initials: AC
authors.lastname: Vaiana
authors.affiliation: Gene Center and Department for Biochemistry, University of Munich, Feodor-Lynenstrasse 25, Munich 81377, Germany.|Center for integrated Protein Science Munich, University of Munich, Feodor-Lynenstrasse 25, Munich 81377, Germany.
authors.forename: Daniel N
authors.initials: DN
authors.lastname: Wilson
mesh_terms: D001426:Bacterial Proteins / Q000037:antagonists & inhibitors / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D020285:Cryoelectron Microscopy; D004917:Erythromycin / Q000737:chemistry / Q000494:pharmacology; D000067556:Internal Ribosome Entry Sites; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D014176:Protein Biosynthesis / Q000187:drug effects*; D011487:Protein Conformation; D011500:Protein Synthesis Inhibitors / Q000737:chemistry / Q000494:pharmacology; D012346:RNA, Transfer, Amino Acyl / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D012270:Ribosomes / Q000187:drug effects / Q000378:metabolism* / Q000648:ultrastructure; D013298:Streptococcus sanguis / Q000187:drug effects / Q000235:genetics* / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D000067556:Internal Ribosome Entry Sites; D011500:Protein Synthesis Inhibitors; D012346:RNA, Transfer, Amino Acyl; C019037:tRNA, peptidyl-; D004917:Erythromycin