Despite the importance of local structural detail for a mechanistic understanding of RNA catalysis and binding functions, RNA backbone conformation has been recalcitrant to analysis. There are too many variable dihedral 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 dihedral angle distributions from a selected 8636 residue RNA database. With noise levels significantly decreased, clear signal appears for the underlying angle preferences. We analyse the multidimensional backbone dihedral distributions within sugar-to-sugar ‘suites’ rather than chemical residues due to the greater base interaction and steric interdependence within the suite. The final result is a small library of RNA backbone rotamers, each represented by a data cluster in seven-dimensional dihedral space, which should provide valid conformations for nearly all RNA backbones encountered in experimental structures. We are in the process of improving that library, and developing tools and applications for it in structure determination and analysis.
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Conference Article|
June 01 2005
RNA backbone rotamers – finding your way in seven dimensions
L.J.W. Murray;
L.J.W. Murray
1Department of Biochemistry, Duke University, Durham, NC 27710-3711, U.S.A.
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J.S. Richardson;
J.S. Richardson
1
1Department of Biochemistry, Duke University, Durham, NC 27710-3711, U.S.A.
1 To whom correspondence should be addressed (email jsr@kinemage.biochem.duke.edu).
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W.B. Arendall, III;
W.B. Arendall, III
1Department of Biochemistry, Duke University, Durham, NC 27710-3711, U.S.A.
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D.C. Richardson
D.C. Richardson
1Department of Biochemistry, Duke University, Durham, NC 27710-3711, U.S.A.
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Publisher: Portland Press Ltd
Received:
January 14 2005
Online ISSN: 1470-8752
Print ISSN: 0300-5127
© 2005 The Biochemical Society
2005
Biochem Soc Trans (2005) 33 (3): 485–487.
Article history
Received:
January 14 2005
Citation
L.J.W. Murray, J.S. Richardson, W.B. Arendall, D.C. Richardson; RNA backbone rotamers – finding your way in seven dimensions. Biochem Soc Trans 1 June 2005; 33 (3): 485–487. doi: https://doi.org/10.1042/BST0330485
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