title: Structural similarity of E. coli 5S rRNA in solution and within the ribosome.
abstract: The article presents translational and rotational diffusion coefficients of 5S rRNA determined experimentally by the method of dynamic light scattering (DLS) and its comparison with the values predicted for different models of this molecule. The tertiary structure of free 5S rRNA was proposed on the basis of the atomic structures of the 5S rRNA from E. coli and H. marismortui extracted from the ribosome. A comparison of the values of DT, tauR, and Rg predicted for different models with experimental results for the free molecule in solution suggests that free 5S rRNA is less compact than that in the complex with ribosomal proteins. In general, the molecules of 5S rRNA consist of three domains: a short one and two longer ones. As follows from a comparison of the results of our simulations with experimental values, in the molecule in solution the two closest helical fragments of the longer domains remain collinear, whereas the short domain takes a position significantly deviated from them.
authors.affiliation: Institute of Physics, Adam Mickiewicz University, ul. Umultowska 85, 61-614 Poznan, Poland.
authors.forename: Lidia
authors.initials: L
authors.lastname: Skibinska
authors.forename: Ewa
authors.initials: E
authors.lastname: Banachowicz
authors.forename: Jacek
authors.initials: J
authors.lastname: Gapiński
authors.forename: Adam
authors.initials: A
authors.lastname: Patkowski
authors.forename: Jan
authors.initials: J
authors.lastname: Barciszewski
mesh_terms: D001483:Base Sequence; D004926:Escherichia coli / Q000737:chemistry / Q000235:genetics; D008027:Light; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012329:RNA, Bacterial / Q000737:chemistry* / Q000235:genetics; D012341:RNA, Ribosomal, 5S / Q000737:chemistry* / Q000235:genetics; D012270:Ribosomes / Q000737:chemistry; D012542:Scattering, Radiation; D012996:Solutions
chemical_list: D012329:RNA, Bacterial; D012341:RNA, Ribosomal, 5S; D012996:Solutions