Protein-DNA interactions: The story so far and a new method for prediction

Comparative and Functional Genomics

Volumn 4, Issue 4, 2003, Pages 428-431

  Jones, Susan ^a   Thornton, Janet M ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

DNA binding; Helix turn helix; Motif; Structural template

Indexed keywords

DNA; PROTEIN;

CALCULATION; CONTROLLED STUDY; DNA BINDING; METHODOLOGY; PREDICTION; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; PROTEIN FAMILY; PROTEIN MOTIF; PROTEIN STRUCTURE; RETROSPECTIVE STUDY; REVIEW;

EID: 0042386412     PISSN: 15316912     EISSN: None     Source Type: Journal    
DOI: 10.1002/cfg.303     Document Type: Review

References (20)

1. Aggarwal AK, Doudna JA. 2003. Protein-nucleic acid interactions: Editorial overview. Curr Opin Struct Biol 13: 3-5.
2. Aravind L, Landsman D. 1998. AT-hoot motifs identified in a wide variety of DNA-binding proteins. Nucleic Acids Res 26: 4413-4421.
3. Bateman A, Birney E, Cerruti L, et al. 2002. The Pfam protein families database. Nucleic Acids Res 30: 276-280.
4. Berman HM, Olson WK, Beveridge DL, et al. 1992. The Nucleic Acid Database: a comprehensive relational database of three-dimensional structures of nucleic acids. Biophys J 63: 751-759.
5. Berman HM, Westbrook J, Feng Z, et al. 2000. The Protein Data Bank. Nucleic Acids Res 28: 276-280.
6. Burley SK. 1994. DNA-binding motifs from eukaryotic transcription factors. Curr Opin Struct Biol 4: 3-11.
7. Dickerson RE. 1998. DNA bending: the prevalence of kinkiness and the virtues of normality. Nucleic Acids Res 26: 1906-1926.
8. Hubbard SJ. 1993. NACCESS. Department of Biochemistry and Molecular Biology, University College, London.
9. Jones S, Barker JA, Nobeli I, Thornton JM. 2003. Using structural motif templates to identify proteins with DNA binding function. Nucleic Acids Res 31: 2811-2823.
10. Jones S, van Heyningen P, Berman HM, Thornton JM. 1999. Protein-DNA interactions: a structural analysis. J Mol Biol 287: 877-896.
11. Kono H, Sarai A. 1999. Structure-based predictions of DNA target sites by regulatory proteins. Proteins 35: 114-131.
12. Luscombe NM, Laskowski RA, Thornton JM. 2001. Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level. J Mol Biol 29: 2860-2874.
13. Mandel-Gutfreund Y, Margalit H. 1998. Quantitative parameters for amino-base interaction: implications for prediction of protein-DNA binding sites. Nucleic Acids Res 26: 2306-2312.
14. Nadassy K, Wodak SJ, Janin J. 1999. Structural features of protein-nucleic acid recognition sites. Biochemistry 38: 1999-2017.
15. Olson WK, Gorin AA, Lu XJ, Hock LM, Zhurkin VB. 1998. DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proc Natl Acad Sci USA 95: 11 163-11 168.
16. Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM. 1997. CATH - a hierarchic classification of protein domain structures. Structure 5: 1093-1108.
17. Schultz J, Milpetz F, Bork P, Ponting CP. 1998. SMART, a simple modular architecture research tool: identification of signalling domains. Proc Natl Acad Sci USA 95: 5857-5864.
18. Stawiski EW, Gregoret LM, Mandel-Gutfreund Y. 2003. Annotating nucleic acid-binding function based on protein structure. J Mol Biol 326: 1065-1079.
19. Tateno M, Yamasak K, Amano N, et al. 1998. DNA recognition by beta-sheets. Biopolymers 44: 335-359.
20. Zhang RG, Kim Y, Skarina T, et al. 2002. Crystal structure of Thermotoga maritima 0065, a member of the IclR transcriptional factor family. J Biol Chem 277: 19 183-19 190.