title: The crucial role of conserved intermolecular H-bonds inaccessible to the solvent in formation and stabilization of the TL5.5 SrRNA complex.
abstract: Analysis of the structures of two complexes of 5 S rRNA with homologous ribosomal proteins, Escherichia coli L25 and Thermus thermophilus TL5, revealed that amino acid residues interacting with RNA can be divided into two different groups. The first group consists of non-conserved residues, which form intermolecular hydrogen bonds accessible to solvent. The second group, comprised of strongly conserved residues, form intermolecular hydrogen bonds that are shielded from solvent. Site-directed mutagenesis was used to introduce mutations into the RNA-binding site of protein TL5. We found that replacement of residues of the first group does not influence the stability of the TL5.5 S rRNA complex, whereas replacement of residues of the second group leads to destabilization or disruption of the complex. Stereochemical analysis shows that the replacements of residues of the second group always create complexes with uncompensated losses of intermolecular hydrogen bonds. We suggest that these shielded intermolecular hydrogen bonds are responsible for the recognition between the protein and RNA.
authors.affiliation: Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290 Russia. gongadze@vega.protres.ru
authors.forename: George M
authors.initials: GM
authors.lastname: Gongadze
authors.forename: Alexey P
authors.initials: AP
authors.lastname: Korepanov
authors.forename: Elena A
authors.initials: EA
authors.lastname: Stolboushkina
authors.forename: Natalia V
authors.initials: NV
authors.lastname: Zelinskaya
authors.forename: Anna V
authors.initials: AV
authors.lastname: Korobeinikova
authors.forename: Maxim V
authors.initials: MV
authors.lastname: Ruzanov
authors.forename: Boris D
authors.initials: BD
authors.lastname: Eliseev
authors.forename: Oleg S
authors.initials: OS
authors.lastname: Nikonov
authors.forename: Stanislav V
authors.initials: SV
authors.lastname: Nikonov
authors.forename: Maria B
authors.initials: MB
authors.lastname: Garber
authors.forename: Valery I
authors.initials: VI
authors.lastname: Lim
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism*; D004926:Escherichia coli / Q000378:metabolism; D006860:Hydrogen Bonding; D009690:Nucleic Acid Conformation; D017434:Protein Structure, Tertiary; D012341:RNA, Ribosomal, 5S / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*; D012269:Ribosomal Proteins / Q000235:genetics / Q000378:metabolism*; D016963:Thermus thermophilus / Q000235:genetics / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D012341:RNA, Ribosomal, 5S; D016601:RNA-Binding Proteins; D012269:Ribosomal Proteins; C106696:TL5 protein, Thermus thermophilus; C031127:ribosomal protein L25