Identifying DNA-binding proteins using structural motifs and the electrostatic potential

Shanahan, Hugh P, Garcia, Mario A, Jones, Susan and Thornton, Janet M (2004) Identifying DNA-binding proteins using structural motifs and the electrostatic potential. Nucleic Acids Research, 32 (16). pp. 4732-4741. ISSN 0360-4012

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Abstract

Robust methods to detect DNA-binding proteins from structures of unknown function are important for structural biology. This paper describes a method for identifying such proteins that (i) have a solvent accessible structural motif necessary for DNA-binding and (ii) a positive electrostatic potential in the region of the binding region. We focus on three structural motifs: helix¿turn-helix (HTH), helix¿hairpin¿helix (HhH) and helix¿loop¿helix (HLH). We find that the combination of these variables detect 78% of proteins with an HTH motif, which is a substantial improvement over previous work based purely on structural templates and is comparable to more complex methods of identifying DNA-binding proteins. Similar true positive fractions are achieved for the HhH and HLH motifs. We see evidence of wide evolutionary diversity for DNA-binding proteins with an HTH motif, and much smaller diversity for those with an HhH or HLH motif.

Item Type: Article
Additional Information: SJ jointly directed the research and coauthored the paper with Shanahan
Schools and Departments: School of Life Sciences > Biochemistry
Depositing User: Sue Jones
Date Deposited: 06 Feb 2012 18:33
Last Modified: 13 Mar 2017 23:39
URI: http://sro.sussex.ac.uk/id/eprint/17077

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