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PubMed · 15356290

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

Hugh P Shanahan·Mario A Garcia·Susan Jones·Janet M Thornton
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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.

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Amino Acid MotifsBinding SitesComputational BiologyDNA-Binding ProteinsDatabases, ProteinGenomicsHelix-Loop-Helix MotifsHelix-Turn-Helix MotifsModels, MolecularStatic ElectricityJournal ArticleResearch Support, Non-U.S. Gov'tResearch Support, U.S. Gov't, Non-P.H.S.

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Hugh P Shanahan, Mario A Garcia, Susan Jones, Janet M Thornton. 2004-09-08. Identifying DNA-binding proteins using structural motifs and the electrostatic potential.. https://doi.org/10.1093/nar%2Fgkh803

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