RNA backbone rotamers--finding your way in seven dimensions.
Journal Article
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.
Full Text
Duke Authors
Cited Authors
- Murray, LJW; Richardson, JS; Arendall, WB; Richardson, DC
Published Date
- June 2005
Published In
Volume / Issue
- 33 / Pt 3
Start / End Page
- 485 - 487
PubMed ID
- 15916548
Pubmed Central ID
- 15916548
International Standard Serial Number (ISSN)
- 0300-5127
Digital Object Identifier (DOI)
- 10.1042/BST0330485
Language
- eng
Conference Location
- England