title: Effect of the nucleotide-37 on the interaction of tRNA(Phe) with the P site of Escherichia coli ribosomes.
abstract: The method of anticodon loop replacement has been used to make derivatives of yeast tRNA(Phe) with the substitution at position 37 (tRNA(Phe)GAAA) and at the anticodon(tRNA(Phe)GCAG). A quantitative study of the interaction of various types of deacylated yeast tRNA(Phe) (tRNA(Phe)+Y, tRNA(Phe)GAAA, tRNA(Phe)-Y) with the P site of the [70S ribosome*poly(U)]-complex was carried out at different Mg2+ concentrations and temperatures. The presence and nature of the nucleotide situated at the 3'-end of the anticodon are essential for such interaction in E coli ribosomes. Replacement of the Y base with the unmodified adenosine decreases the interaction enthalpy from 39 kcal/mol to 24 kcal/mol, whereas its removal reduces the interaction enthalpy to 16 kcal/mol. Replacement of the second anticodon nucleotide, adenosine, with cytosine further reduces the enthalpy to 6 kcal/mol, which is typical of tRNA-P site interaction in the absence of poly(U). In the absence of poly(U) the affinity of tRNA(PheY) for the P site of the 70S ribosome is five times lower than the affinity of tRNA(Phe+Y) or tRNA(Phe)GCAG. Thus, in the ribosome the modified nucleotide stabilizes the codon-anticodon interaction through its stacking interaction with the codon-anticodon base stack. In addition, this decreases the free energy of binding as a result of the interaction of the modified nucleotide itself with the hydrophobic center of the P site.
authors.affiliation: Petersburg Nuclear Physics Institute, Russian Academy of Science, Leningrad Region.
authors.forename: V
authors.initials: V
authors.lastname: Katunin
authors.forename: N
authors.initials: N
authors.lastname: Soboleva
authors.forename: V
authors.initials: V
authors.lastname: Mahkno
authors.forename: E
authors.initials: E
authors.lastname: Sedelnikova
authors.forename: S
authors.initials: S
authors.lastname: Zhenodarova
authors.forename: S
authors.initials: S
authors.lastname: Kirillov
mesh_terms: D000215:Acylation; D000926:Anticodon; D001483:Base Sequence; D001665:Binding Sites; D003062:Codon; D004591:Electrophoresis, Polyacrylamide Gel; D004926:Escherichia coli / Q000378:metabolism*; D008969:Molecular Sequence Data; D012329:RNA, Bacterial / Q000737:chemistry / Q000378:metabolism; D012360:RNA, Transfer, Phe / Q000737:chemistry / Q000378:metabolism*; D012270:Ribosomes / Q000378:metabolism*
chemical_list: D000926:Anticodon; D003062:Codon; D012329:RNA, Bacterial; D012360:RNA, Transfer, Phe