Eli Hershkovitz, Emmanuel Tannenbaum 3, Shelley B. Howerton 1, Ajay Sheth 1, Allen Tannenbaum 2 and Loren Dean Williams 1, *,
Department of Electrical and Computer Engineering, 1 Department
of Chemistry and Biochemistry, and
2 Departments of Electrical and Computer Engineering
and Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA
30332, USA and
3 Department of Chemistry and Chemical Biology, Harvard
University, Cambridge, MA 02138, USA
*To whom correspondence should be addressed. Tel: +1 404 894 9752;
Fax: +1 404 894 7452;
Email: loren.williams@chemistry.gatech.edu
We develop novel methods for recognizing and cataloging conformational
states of RNA, and for discovering statistical rules governing those states.
We focus on the conformation of the large ribosomal subunit from Haloarcula
marismortui. The two approaches described here involve torsion matching
and binning. Torsion matching is a pattern-recognition code which
finds structural repetitions. Binning is a classification technique
based on distributional models of the data. In comparing the results of
the two methods we have tested the hypothesis that the conformation of
a very large complex RNA molecule can be described accurately by a limited
number of discrete conformational states. We identify and eliminate extraneous
and redundant information without losing accuracy. We conclude, as expected,
that four of the torsion angles contain the
overwhelming bulk of the structural information. That information
is not significantly compromised by binning the continuous torsional information
into a limited number of discrete values. The correspondence between torsion
matching and binning is 99% (per residue). Binning, however, does have
several advantages. In particular, we demonstrate that the conformation
of a large complex RNA molecule can be represented by a small alphabet.
In addition, the binning method lends itself to a natural graphical representation
using trees.
1. Doudna JA, "Structural Genomics of RNA", Nature Structural Biology, vol. 7, no. 11, supp, pp. 954-956 (November, 2000).
2. Frenster JH, "Ultrastructural Probes of Active DNA Sites, and the RNA Activators of DNA".