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PMID: 15356290 Published · epublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

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

Nucleic acids research ·Vol. 32 ·No. 16 ·2004-00-00 ·Pages 4732-41

Shanahan HP, Garcia MA, Jones S, Thornton JM

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.

MeSH Terms
Amino Acid Motifs Binding Sites Computational Biology/methods DNA-Binding Proteins/chemistry,metabolism Databases, Protein Genomics Helix-Loop-Helix Motifs Helix-Turn-Helix Motifs Models, Molecular Static Electricity
Chemicals
DNA-Binding Proteins
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Shanahan Hugh P
EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. [email protected]
Garcia Mario A
Jones Susan
Thornton Janet M
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkh803
Email
[email protected]
Published
2004-00-00
Epub
2004-00-08
Pages
4732-41
Language
English
Region
England
NLM ID
0411011
PMCID
PMC519102
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/gkh803 PMC Full Text View journal details
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