title: Disruption of shape complementarity in the ribosomal protein L1-RNA contact region does not hinder specific recognition of the RNA target site.
abstract: The formation of a specific and stable complex between two (macro)molecules implies complementary contact surface regions. We used ribosomal protein L1, which specifically binds a target site on 23S rRNA, to study the influence of surface modifications on the protein-RNA affinity. The threonine residue in the universally conserved triad Thr-Met-Gly significant for RNA recognition and binding was substituted by phenylalanine, valine and alanine, respectively. The crystal structure of the mutant Thr217Val of the isolated domain I of L1 from Thermus thermophilus (TthL1) was determined. This structure and that of two other mutants, which had been determined earlier, were analysed and compared with the structure of the wild type L1 proteins. The influence of structural changes in the mutant L1 proteins on their affinity for the specific 23S rRNA fragment was tested by kinetic experiments using surface plasmon resonance (SPR) biosensor analysis. Association rate constants undergo minor changes, whereas dissociation rate constants displayed significantly higher values in comparison with that for the wild type protein. The analysed L1 mutants recognize the specific RNA target site, but the mutant L1-23S rRNA complexes are less stable compared to the wild type complexes.
authors.affiliation: Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Moscow, Russia.
authors.forename: Olga
authors.initials: O
authors.lastname: Kostareva
authors.forename: Svetlana
authors.initials: S
authors.lastname: Tishchenko
authors.forename: Ekaterina
authors.initials: E
authors.lastname: Nikonova
authors.forename: Vladislav
authors.initials: V
authors.lastname: Kljashtorny
authors.forename: Natalia
authors.initials: N
authors.lastname: Nevskaya
authors.forename: Alexei
authors.initials: A
authors.lastname: Nikulin
authors.forename: Anna
authors.initials: A
authors.lastname: Sycheva
authors.forename: Sergei
authors.initials: S
authors.lastname: Moshkovskii
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Piendl
authors.forename: Maria
authors.initials: M
authors.lastname: Garber
authors.forename: Stanislav
authors.initials: S
authors.lastname: Nikonov
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites / Q000235:genetics / Q000502:physiology; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D011485:Protein Binding / Q000235:genetics / Q000502:physiology; D017433:Protein Structure, Secondary; D012338:RNA, Ribosomal, 23S / Q000235:genetics / Q000378:metabolism*; D012269:Ribosomal Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D017386:Sequence Homology, Amino Acid; D020349:Surface Plasmon Resonance / Q000379:methods; D016963:Thermus thermophilus / Q000235:genetics / Q000378:metabolism
chemical_list: D012338:RNA, Ribosomal, 23S; D012269:Ribosomal Proteins; C028546:ribosomal protein L1