Skip to main content
PMC home page
Comparative and Functional Genomics logoLink to Comparative and Functional Genomics
. 2003 Jul;4(4):428–431. doi: 10.1002/cfg.303

Protein–DNA Interactions: The Story so Far and a New Method for Prediction

Susan Jones 1,✉, Janet M Thornton 1
PMCID: PMC2447360  PMID: 18629075

Abstract

This review describes methods for the prediction of DNA binding function, and specifically summarizes a new method using 3D structural templates. The new method features the HTH motif that is found in approximately one-third of DNAbinding protein families. A library of 3D structural templates of HTH motifs was derived from proteins in the PDB. Templates were scanned against complete protein structures and the optimal superposition of a template on a structure calculated. Significance thresholds in terms of a minimum root mean squared deviation (rmsd) of an optimal superposition, and a minimum motif accessible surface area (ASA), have been calculated. In this way, it is possible to scan the template library against proteins of unknown function to make predictions about DNA-binding functionality.

Full Text

The Full Text of this article is available as a PDF (86.8 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Aravind L., Landsman D. AT-hook motifs identified in a wide variety of DNA-binding proteins. Nucleic Acids Res. 1998 Oct 1;26(19):4413–4421. doi: 10.1093/nar/26.19.4413. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bateman Alex, Birney Ewan, Cerruti Lorenzo, Durbin Richard, Etwiller Laurence, Eddy Sean R., Griffiths-Jones Sam, Howe Kevin L., Marshall Mhairi, Sonnhammer Erik L. L. The Pfam protein families database. Nucleic Acids Res. 2002 Jan 1;30(1):276–280. doi: 10.1093/nar/30.1.276. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Berman H. M., Olson W. K., Beveridge D. L., Westbrook J., Gelbin A., Demeny T., Hsieh S. H., Srinivasan A. R., Schneider B. The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids. Biophys J. 1992 Sep;63(3):751–759. doi: 10.1016/S0006-3495(92)81649-1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Dickerson R. E. DNA bending: the prevalence of kinkiness and the virtues of normality. Nucleic Acids Res. 1998 Apr 15;26(8):1906–1926. doi: 10.1093/nar/26.8.1906. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Jones S., van Heyningen P., Berman H. M., Thornton J. M. Protein-DNA interactions: A structural analysis. J Mol Biol. 1999 Apr 16;287(5):877–896. doi: 10.1006/jmbi.1999.2659. [DOI] [PubMed] [Google Scholar]
  6. Jones Susan, Barker Jonathan A., Nobeli Irene, Thornton Janet M. Using structural motif templates to identify proteins with DNA binding function. Nucleic Acids Res. 2003 Jun 1;31(11):2811–2823. doi: 10.1093/nar/gkg386. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Kono H., Sarai A. Structure-based prediction of DNA target sites by regulatory proteins. Proteins. 1999 Apr 1;35(1):114–131. [PubMed] [Google Scholar]
  8. Luscombe N. M., Laskowski R. A., Thornton J. M. Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level. Nucleic Acids Res. 2001 Jul 1;29(13):2860–2874. doi: 10.1093/nar/29.13.2860. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Mandel-Gutfreund Y., Margalit H. Quantitative parameters for amino acid-base interaction: implications for prediction of protein-DNA binding sites. Nucleic Acids Res. 1998 May 15;26(10):2306–2312. doi: 10.1093/nar/26.10.2306. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Nadassy K., Wodak S. J., Janin J. Structural features of protein-nucleic acid recognition sites. Biochemistry. 1999 Feb 16;38(7):1999–2017. doi: 10.1021/bi982362d. [DOI] [PubMed] [Google Scholar]
  11. Orengo C. A., Michie A. D., Jones S., Jones D. T., Swindells M. B., Thornton J. M. CATH--a hierarchic classification of protein domain structures. Structure. 1997 Aug 15;5(8):1093–1108. doi: 10.1016/s0969-2126(97)00260-8. [DOI] [PubMed] [Google Scholar]
  12. Schultz J., Milpetz F., Bork P., Ponting C. P. SMART, a simple modular architecture research tool: identification of signaling domains. Proc Natl Acad Sci U S A. 1998 May 26;95(11):5857–5864. doi: 10.1073/pnas.95.11.5857. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Stawiski Eric W., Gregoret Lydia M., Mandel-Gutfreund Yael. Annotating nucleic acid-binding function based on protein structure. J Mol Biol. 2003 Feb 28;326(4):1065–1079. doi: 10.1016/s0022-2836(03)00031-7. [DOI] [PubMed] [Google Scholar]
  14. Tateno M., Yamasaki K., Amano N., Kakinuma J., Koike H., Allen M. D., Suzuki M. DNA recognition by beta-sheets. Biopolymers. 1997;44(4):335–359. doi: 10.1002/(SICI)1097-0282(1997)44:4<335::AID-BIP3>3.0.CO;2-R. [DOI] [PubMed] [Google Scholar]

Articles from Comparative and Functional Genomics are provided here courtesy of Wiley

RESOURCES