Using structural motifs to identify proteins with DNA binding function

Jones, Susan, Barker, Jonathan A, Nobeli, Irene and Thornton, Janet M (2003) Using structural motifs to identify proteins with DNA binding function. Nucleic Acids Research, 31 (11). pp. 2811-2823. ISSN 0305-1048

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This work describes a method for predicting DNA binding function from structure using 3-dimensional templates. Proteins that bind DNA using small contiguous helix¿turn¿helix (HTH) motifs comprise a significant number of all DNA-binding proteins. A structural template library of seven HTH motifs has been created from non-homologous DNA-binding proteins in the Protein Data Bank. 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 Ca backbone coordinates. Distributions of rmsd values for known HTH-containing proteins (true hits) and non-HTH proteins (false hits) were calculated. A threshold value of 1.6 Å rmsd was selected that gave a true hit rate of 88.4% and a false positive rate of 0.7%. The false positive rate was further reduced to 0.5% by introducing an accessible surface area threshold value of 990 Å2 per HTH motif. The template library and the validated thresholds were used to make predictions for target proteins from a structural genomics project.

Item Type: Article
Additional Information: Wrote algorithm, conducted analysis and was corresponding author
Schools and Departments: School of Life Sciences > Biochemistry
Depositing User: Sue Jones
Date Deposited: 06 Feb 2012 20:35
Last Modified: 02 Jul 2019 22:20

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