Book of Abstracts: Albany 2003

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Abstract Book
June 17-21 2003

Using Structural Motif Templates to Identify Proteins with DNA Binding Function

The ability to assign function from protein structure is very important for structural genomics projects, in which protein structures are solved that have very low sequence identity to any protein of known 3-D structure. This work describes a method for predicting DNA binding function from structure using 3-D templates. Proteins that bind DNA using contiguous helix-turn-helix (HTH) motifs comprise a significant number of all DNA-binding proteins. The HTH motif is relatively small and contiguous in sequence and structure, comprising in its simplest form, two perpendicular helices joined by a short linker. The carboxyl terminal helix includes the DNA recognition residues responsible for sequence specific DNA binding, usually through contacts in the major groove of the DNA double helix (1).

A structural template library of 7 HTH motifs has been created from DNA-binding proteins in the Protein Data Bank (2). The templates were used to scan complete protein structures using an algorithm that calculated the root mean squared deviation (rmsd) for the optimal superposition of each template on each structure, based on Cα backbone coordinates. Distributions of minimum rmsd values for known HTH containing proteins (true hits) and non-HTH proteins (false hits) were calculated. A threshold value of 1.2Å rmsd was selected that gave a true hit rate of 88.4% and a false positive rate of 0.7%. The false positives were further reduced by introducing an accessible surface area threshold of 990Å2 per HTH motif. The templates matched HTH motifs across different sequence families, and some false-positive matches were, upon further investigation, found to include potential DNA binding motifs. The template library and the validated thresholds were used to make predictions for 42 structural genomics targets from the Midwest Centre for Structural Genomics (MCSG).

Susan Jones1*
Jonathan Barker1
Irilenia Nobeli1
Helen M. Berman2
Janet M.Thornton1

1EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge
CB10 1SD, UK
2Department of Chemistry
The State University
Piscataway, NJ, 08855-0939, USA

References and Footnotes
  1. Brennan R.G., and Matthews B.W. The helix-turn-helix DNA Binding Motif, Journal of Biological Chemistry 264, 1903-1906 (1989).
  2. Berman, H.M., Westbrook, J., Feng, Z., Gulliland G., Bhat, T.N., Weissig, H., Shindyalov I.N. and Borne P.E. The Protein Data Bank, Nucleic Acids Research 28, 235-242 (2000).