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

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posted on 2023-06-07, 20:30 authored by Hugh P Shanahan, Mario A Garcia, Susan Jones, Janet M Thornton
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.

History

Publication status

  • Published

File Version

  • Published version

Journal

Nucleic Acids Research

ISSN

0360-4012

Issue

16

Volume

32

Page range

4732-4741

Pages

10.0

Department affiliated with

  • Biochemistry Publications

Notes

SJ jointly directed the research and coauthored the paper with Shanahan

Full text available

  • Yes

Peer reviewed?

  • Yes

Legacy Posted Date

2012-02-06

First Open Access (FOA) Date

2016-03-22

First Compliant Deposit (FCD) Date

2016-11-16

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