title: Protein-guided RNA dynamics during early ribosome assembly.
abstract: The assembly of 30S ribosomes requires the precise addition of 20 proteins to the 16S ribosomal RNA. How early binding proteins change the ribosomal RNA structure so that later proteins may join the complex is poorly understood. Here we use single-molecule fluorescence resonance energy transfer (FRET) to observe real-time encounters between Escherichia coli ribosomal protein S4 and the 16S 5' domain RNA at an early stage of 30S assembly. Dynamic initial S4-RNA complexes pass through a stable non-native intermediate before converting to the native complex, showing that non-native structures can offer a low free-energy path to protein-RNA recognition. Three-colour FRET and molecular dynamics simulations reveal how S4 changes the frequency and direction of RNA helix motions, guiding a conformational switch that enforces the hierarchy of protein addition. These protein-guided dynamics offer an alternative explanation for induced fit in RNA-protein complexes.
authors: 1] Department of Physics, Center for the Physics of Living Cells and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA [2] Howard Hughes Medical Institute, Urbana, Illinois 61801, USA [3] [4] School of Nano-Bioscience and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan 689-798, Republic of Korea (H.K.); Department of Biochemistry and Biophysics, University of California at San Francisco, 600 16th Street, San Francisco, California 94143-2200, USA (M.M.); Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, LHRRB-517, Boston, Massachusetts 02115-5730, USA (K.R.).
authors: Hajin
authors: H
authors: Kim
authors: 1] T. C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, USA [2].
authors: Sanjaya C
authors: SC
authors: Abeysirigunawarden
authors: 1] Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA [2] Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
authors: Ke
authors: K
authors: Chen
authors: 1] CMDB Program, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, USA [2] School of Nano-Bioscience and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan 689-798, Republic of Korea (H.K.); Department of Biochemistry and Biophysics, University of California at San Francisco, 600 16th Street, San Francisco, California 94143-2200, USA (M.M.); Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, LHRRB-517, Boston, Massachusetts 02115-5730, USA (K.R.).
authors: Megan
authors: M
authors: Mayerle
authors: 1] Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA [2] School of Nano-Bioscience and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan 689-798, Republic of Korea (H.K.); Department of Biochemistry and Biophysics, University of California at San Francisco, 600 16th Street, San Francisco, California 94143-2200, USA (M.M.); Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, LHRRB-517, Boston, Massachusetts 02115-5730, USA (K.R.).
authors: Kaushik
authors: K
authors: Ragunathan
authors: 1] Department of Physics, Center for the Physics of Living Cells and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA [2] Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA [3] Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
authors: Zaida
authors: Z
authors: Luthey-Schulten
authors: 1] Department of Physics, Center for the Physics of Living Cells and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA [2] Howard Hughes Medical Institute, Urbana, Illinois 61801, USA [3] Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA [4] Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
authors: Taekjip
authors: T
authors: Ha
authors: 1] T. C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, USA [2] CMDB Program, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, USA.
authors: Sarah A
authors: SA
authors: Woodson
mesh_terms: D004926:Escherichia coli / Q000737:chemistry / Q000235:genetics; D031541:Fluorescence Resonance Energy Transfer; D007700:Kinetics; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D011487:Protein Conformation; D012336:RNA, Ribosomal, 16S / Q000737:chemistry* / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism; D012269:Ribosomal Proteins / Q000737:chemistry / Q000378:metabolism*; D054680:Ribosome Subunits, Small, Bacterial / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D012336:RNA, Ribosomal, 16S; D016601:RNA-Binding Proteins; D012269:Ribosomal Proteins; C031798:ribosomal protein S4