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.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Shanahan HP,Garcia MA,Jones S,Thornton JMdoi
10.1093/nar/gkh803keywords:
subject
Has Abstractpub_date
2004-09-08 00:00:00pages
4732-41issue
16eissn
0305-1048issn
1362-4962pii
32/16/4732journal_volume
32pub_type
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