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RNA backbone is rotameric.

Publication ,  Journal Article
Murray, LJW; Arendall, WB; Richardson, DC; Richardson, JS
Published in: Proc Natl Acad Sci U S A
November 25, 2003

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 alpha-beta-gamma and for delta-epsilon-zeta 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.

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Published In

Proc Natl Acad Sci U S A

DOI

ISSN

0027-8424

Publication Date

November 25, 2003

Volume

100

Issue

24

Start / End Page

13904 / 13909

Location

United States

Related Subject Headings

  • RNA, Ribosomal, 23S
  • RNA
  • Nucleic Acid Conformation
  • Models, Molecular
  • Databases, Nucleic Acid
  • Crystallography, X-Ray
  • Biophysics
  • Biophysical Phenomena
 

Citation

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Murray, L. J. W., Arendall, W. B., Richardson, D. C., & Richardson, J. S. (2003). RNA backbone is rotameric. Proc Natl Acad Sci U S A, 100(24), 13904–13909. https://doi.org/10.1073/pnas.1835769100
Murray, Laura J. W., W Bryan Arendall, David C. Richardson, and Jane S. Richardson. “RNA backbone is rotameric.Proc Natl Acad Sci U S A 100, no. 24 (November 25, 2003): 13904–9. https://doi.org/10.1073/pnas.1835769100.
Murray LJW, Arendall WB, Richardson DC, Richardson JS. RNA backbone is rotameric. Proc Natl Acad Sci U S A. 2003 Nov 25;100(24):13904–9.
Murray, Laura J. W., et al. “RNA backbone is rotameric.Proc Natl Acad Sci U S A, vol. 100, no. 24, Nov. 2003, pp. 13904–09. Pubmed, doi:10.1073/pnas.1835769100.
Murray LJW, Arendall WB, Richardson DC, Richardson JS. RNA backbone is rotameric. Proc Natl Acad Sci U S A. 2003 Nov 25;100(24):13904–13909.
Journal cover image

Published In

Proc Natl Acad Sci U S A

DOI

ISSN

0027-8424

Publication Date

November 25, 2003

Volume

100

Issue

24

Start / End Page

13904 / 13909

Location

United States

Related Subject Headings

  • RNA, Ribosomal, 23S
  • RNA
  • Nucleic Acid Conformation
  • Models, Molecular
  • Databases, Nucleic Acid
  • Crystallography, X-Ray
  • Biophysics
  • Biophysical Phenomena