RNA backbone is rotameric

AUTOR(ES)

Murray, Laura J. W.

FONTE

National Academy of Sciences

RESUMO

Despite the importance of local structural detail to a mechanistic understanding of RNA catalysis and binding functions, RNA backbone conformation has been quite recalcitrant to analysis. There are too many variable torsion angles per residue, and their raw empirical distributions are poorly clustered. This study applies quality-filtering techniques (using resolution, crystallographic B factor, and all-atom steric clashes) to the backbone torsion angle distributions from an 8,636-residue RNA database. With noise levels greatly reduced, clear signal appears for the underlying angle preferences. Half-residue torsion angle distributions for α-β-γ and for δ-ε-ζ are plotted and contoured in 3D; each shows about a dozen distinct peaks, which can then be combined in pairs to define complete RNA backbone conformers. Traditional nucleic acid residues are defined from phosphate to phosphate, but here we use a base-to-base (or sugar-to-sugar) division into “suites” to parse the RNA backbone repeats, both because most backbone steric clashes are within suites and because the relationship of successive bases is both reliably determined and conformationally important. A suite conformer has seven variables, with sugar pucker specified at both ends. Potential suite conformers were omitted if not represented by at least a small cluster of convincing data points after application of quality filters. The final result is a small library of 42 RNA backbone conformers, which should provide valid conformations for nearly all RNA backbone encountered in experimental structures.

Documentos Relacionados

• The importance of tRNA backbone-mediated interactions with synthetase for aminoacylation
• Site-specific excision from RNA by RNase H and mixed-phosphate-backbone oligodeoxynucleotides.
• Synthesis of backbone deuterium labelled [r(CGCGAAUUCGCG)]2 and HPLC purification of synthetic RNA.
• Two rotameric forms of open ring 7-methylguanine are present in alkylated polynucleotides.
• Role of backbone solvation and electrostatics in generating preferred peptide backbone conformations: Distributions of phi