title: RNA-protein distance patterns in ribosomes reveal the mechanism of translational attenuation.
abstract: Elucidating protein translational regulation is crucial for understanding cellular function and drug development. A key molecule in protein translation is ribosome, which is a super-molecular complex extensively studied for more than a half century. The structure and dynamics of ribosome complexes were resolved recently thanks to the development of X-ray crystallography, Cryo-EM, and single molecule biophysics. Current studies of the ribosome have shown multiple functional states, each with a unique conformation. In this study, we analyzed the RNA-protein distances of ribosome (2.5 MDa) complexes and compared these changes among different ribosome complexes. We found that the RNA-protein distance is significantly correlated with the ribosomal functional state. Thus, the analysis of RNA-protein binding distances at important functional sites can distinguish ribosomal functional states and help understand ribosome functions. In particular, the mechanism of translational attenuation by nascent peptides and antibiotics was revealed by the conformational changes of local functional sites.
authors.affiliation: Department of Biological Engineering, University of Missouri, Columbia, MO, 65211, USA.
authors.forename: DongMei
authors.initials: D
authors.lastname: Yu
authors.forename: Chao
authors.initials: C
authors.lastname: Zhang
authors.forename: PeiWu
authors.initials: P
authors.lastname: Qin
authors.forename: Peter V
authors.initials: PV
authors.lastname: Cornish
authors.forename: Dong
authors.initials: D
authors.lastname: Xu
mesh_terms: D000465:Algorithms; D000900:Anti-Bacterial Agents / Q000737:chemistry; D001665:Binding Sites; D020285:Cryoelectron Microscopy; D018360:Crystallography, X-Ray; D030541:Databases, Genetic; D030562:Databases, Protein; D004926:Escherichia coli / Q000235:genetics; D021621:Imaging, Three-Dimensional; D018942:Macrolides / Q000737:chemistry; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry; D014176:Protein Biosynthesis; D011487:Protein Conformation; D025941:Protein Interaction Mapping / Q000379:methods*; D021381:Protein Transport; D012313:RNA / Q000737:chemistry*; D012269:Ribosomal Proteins / Q000737:chemistry; D012270:Ribosomes / Q000737:chemistry*; D016963:Thermus thermophilus / Q000235:genetics
chemical_list: D000900:Anti-Bacterial Agents; D018942:Macrolides; D010455:Peptides; D012269:Ribosomal Proteins; D012313:RNA