A Compact RNA Tertiary Structure Contains a Buried Backbone–K + Complex

The structure of a 58 nucleotide ribosomal RNA fragment buries several phosphate groups of a hairpin loop within a large tertiary core. During refinement of an X-ray crystal structure containing this RNA, a potassium ion was found to be contacted by six oxygen atoms from the buried phosphate groups;...

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Bibliographic Details
Published in:Journal of molecular biology 2002-05, Vol.318 (4), p.963-973
Main Authors: Conn, Graeme L, Gittis, Apostolos G, Lattman, Eaton E, Misra, Vinod K, Draper, David E
Format: Article
Language:English
Subjects:
Base Sequence
Binding Sites
Hydroxyl Radical - chemistry
ion chelation
ion hydration
Molecular Sequence Data
non-linear Poisson–Boltzmann equation
Nucleic Acid Conformation
Phosphates - chemistry
Phosphates - metabolism
Potassium - chemistry
Potassium - metabolism
Ribosomal Proteins - chemistry
Ribosomal Proteins - metabolism
RNA tertiary structure
RNA, Ribosomal, 23S - chemistry
RNA, Ribosomal, 23S - metabolism
Thermodynamics
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Summary:The structure of a 58 nucleotide ribosomal RNA fragment buries several phosphate groups of a hairpin loop within a large tertiary core. During refinement of an X-ray crystal structure containing this RNA, a potassium ion was found to be contacted by six oxygen atoms from the buried phosphate groups; the ion is contained completely within the solvent-accessible surface of the RNA. The electrostatic potential at the ion chelation site is unusually large, and more than compensates for the substantial energetic penalties associated with partial dehydration of the ion and displacement of delocalized ions. The very large predicted binding free energy, ∼−30 kcal/mol, implies that the site must be occupied for the RNA to fold. These findings agree with previous studies of the ion-dependent folding of tertiary structure in this RNA, which concluded that a monovalent ion was bound in a partially dehydrated environment where Mg 2+ could not easily compete for binding. By compensating the unfavorable free energy of buried phosphate groups with a chelated ion, the RNA is able to create a larger and more complex tertiary fold than would be possible otherwise.
ISSN:0022-2836
1089-8638
DOI:10.1016/S0022-2836(02)00147-X