title: The three conformations of the anticodon loop of yeast tRNA(Phe).
abstract: The complex conformational states of the anticodon loop of yeast tRNA(Phe) which we had previously studied with relaxation experiments by monitoring fluorescence of the naturally occurring Wye base, are analyzed using time and polarization resolved fluorescence measurements at varying counterion concentrations. Synchrotron radiation served as excitation for these experiments, which were analyzed using modulating functions and global methods. Three conformations of the anticodon loop are detected, all three occurring in a wide range of counterion concentrations with and without Mg2+, each being identified by its typical lifetime. The fluorescence changes brought about by varying the ion concentrations, previously monitored by steady state fluorimetry and relaxation methods, are changes in the population of these three conformational states, in the sense of an allosteric model, where the effectors are the three ions Mg2+, Na+ and H+. The population of the highly fluorescent M conformer (8ns), most affine to magnesium, is thus enhanced by that ligand, while the total fluorescence decreases as lower pH favors the H+-affine H conformer (0.6ns). Na+-binding of the N conformer (4ns) is responsible for complex fluorescence changes. By iterative simulation of this allosteric model the equilibrium and binding constants are determined. In turn, using these constants to simulate equilibrium fluorescence titrations reproduces the published results.
authors.affiliation: Abteilung Molekulare Biologie, Max-Planck-Institut für Biophysikalische Chemie, Göttingen, Federal Republic of Germany.
authors.forename: G
authors.initials: G
authors.lastname: Striker
authors.forename: D
authors.initials: D
authors.lastname: Labuda
authors.forename: M C
authors.initials: MC
authors.lastname: Vega-Martin
mesh_terms: D000926:Anticodon / Q000648:ultrastructure*; D015200:Fluoroimmunoassay; D006147:Guanine / Q000031:analogs & derivatives; D008274:Magnesium / Q000494:pharmacology; D008956:Models, Chemical; D009690:Nucleic Acid Conformation; D012343:RNA, Transfer / Q000648:ultrastructure*; D012345:RNA, Transfer, Amino Acid-Specific / Q000378:metabolism; D012360:RNA, Transfer, Phe / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D013050:Spectrometry, Fluorescence
chemical_list: D000926:Anticodon; D012345:RNA, Transfer, Amino Acid-Specific; D012360:RNA, Transfer, Phe; C012099:wye; D006147:Guanine; D012343:RNA, Transfer; D008274:Magnesium