Tags

Type your tag names separated by a space and hit enter

Effects of polyvalent cations on the folding of an rRNA three-way junction and binding of ribosomal protein S15.
RNA. 1998 Aug; 4(8):984-97.RNA

Abstract

The Bacillus stearothermophilus ribosomal protein S15 binds to a phylogenetically conserved three-way junction formed by the intersection of helices 20, 21, and 22 of eubacterial 16S ribosomal RNA, inducing a large conformational change in the RNA. Like many RNA structures, this three-way junction can also be folded by the addition of polyvalent cations such as magnesium, as demonstrated by comparing the mobilities of the wild-type and mutant junctions in the absence and presence of polyvalent cations in nondenaturing polyacrylamide gels. Using a modification interference assay, critical nucleotides for folding have been identified as the phylogenetically conserved nucleotides in the three-way junction. NMR spectroscopy of the junction reveals that the conformations induced by the addition of magnesium or S15 are extremely similar. Thus, the folding of the junction is determined entirely by RNA elements within the phylogenetically conserved junction core, and the role of Mg2+ and S15 is to stabilize this intrinsically unstable structure. The organization of the junction by Mg2+ significantly enhances the bimolecular association rate (k(on)) of S15 binding, suggesting that S15 binds specifically to the folded form of the three-way junction via a tertiary structure capture mechanism.

Links

PMC Free PDF
PMC Free Full Text
FREE Publisher Full Text

Authors+Show Affiliations

Batey RT
Department of Chemistry, Massachusetts Institute of Technology, Cambridge 02139, USA.
Williamson JR
No affiliation info available

MeSH

Bacterial ProteinsBase SequenceCationsConserved SequenceGeobacillus stearothermophilusMagnesiumModels, ChemicalModels, MolecularMolecular Sequence DataMutationNuclear Magnetic Resonance, BiomolecularNucleic Acid ConformationProtein BindingRNA, BacterialRNA, Ribosomal, 16SRibosomal ProteinsThermodynamics

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, P.H.S.

Language

eng

PubMed ID

9701289

Citation

Batey, R T., and J R. Williamson. "Effects of Polyvalent Cations On the Folding of an rRNA Three-way Junction and Binding of Ribosomal Protein S15." RNA (New York, N.Y.), vol. 4, no. 8, 1998, pp. 984-97.
Batey RT, Williamson JR. Effects of polyvalent cations on the folding of an rRNA three-way junction and binding of ribosomal protein S15. RNA. 1998;4(8):984-97.
Batey, R. T., & Williamson, J. R. (1998). Effects of polyvalent cations on the folding of an rRNA three-way junction and binding of ribosomal protein S15. RNA (New York, N.Y.), 4(8), 984-97.
Batey RT, Williamson JR. Effects of Polyvalent Cations On the Folding of an rRNA Three-way Junction and Binding of Ribosomal Protein S15. RNA. 1998;4(8):984-97. PubMed PMID: 9701289.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Effects of polyvalent cations on the folding of an rRNA three-way junction and binding of ribosomal protein S15. AU - Batey,R T, AU - Williamson,J R, PY - 1998/8/13/pubmed PY - 1998/8/13/medline PY - 1998/8/13/entrez SP - 984 EP - 97 JF - RNA (New York, N.Y.) JO - RNA VL - 4 IS - 8 N2 - The Bacillus stearothermophilus ribosomal protein S15 binds to a phylogenetically conserved three-way junction formed by the intersection of helices 20, 21, and 22 of eubacterial 16S ribosomal RNA, inducing a large conformational change in the RNA. Like many RNA structures, this three-way junction can also be folded by the addition of polyvalent cations such as magnesium, as demonstrated by comparing the mobilities of the wild-type and mutant junctions in the absence and presence of polyvalent cations in nondenaturing polyacrylamide gels. Using a modification interference assay, critical nucleotides for folding have been identified as the phylogenetically conserved nucleotides in the three-way junction. NMR spectroscopy of the junction reveals that the conformations induced by the addition of magnesium or S15 are extremely similar. Thus, the folding of the junction is determined entirely by RNA elements within the phylogenetically conserved junction core, and the role of Mg2+ and S15 is to stabilize this intrinsically unstable structure. The organization of the junction by Mg2+ significantly enhances the bimolecular association rate (k(on)) of S15 binding, suggesting that S15 binds specifically to the folded form of the three-way junction via a tertiary structure capture mechanism. SN - 1355-8382 UR - https://www.unboundmedicine.com/medline/citation/9701289/Effects_of_polyvalent_cations_on_the_folding_of_an_rRNA_three_way_junction_and_binding_of_ribosomal_protein_S15_ L2 - http://www.rnajournal.org/cgi/pmidlookup?view=long&pmid=9701289 DB - PRIME DP - Unbound Medicine ER -