Cruciform structures are preferential targets for many architectural and regulatory proteins, as well as a number of DNA binding proteins with weak sequence specificity. Some of these proteins are also capable of inducing the formation of cruciform structures upon DNA binding. In this paper we analyzed the amino acid composition of eighteen cruciform binding proteins of Homo sapiens. Comparison with general amino acid frequencies in all human proteins revealed unique differences, with notable enrichment for lysine and serine and/or depletion for alanine, glycine, glutamine, arginine, tyrosine and tryptophan residues. Based on bootstrap resampling and fuzzy cluster analysis, multiple molecular mechanisms of interaction with cruciform DNA structures could be suggested, including those involved in DNA repair, transcription and chromatin regulation. The proteins DEK, HMGB1 and TOP1 in particular formed a very distinctive group. Nonetheless, a strong interaction network connecting nearly all the cruciform binding proteins studied was demonstrated. Data reported here will be very useful for future prediction of new cruciform binding proteins or even construction of predictive tool/web-based application.
- MeSH
- Amino Acids chemistry MeSH
- Chromatin MeSH
- Chromosomal Proteins, Non-Histone chemistry MeSH
- DNA-Binding Proteins chemistry MeSH
- DNA Topoisomerases, Type I chemistry MeSH
- Nucleic Acid Conformation MeSH
- Humans MeSH
- Oncogene Proteins chemistry MeSH
- HMGB1 Protein chemistry MeSH
- Poly-ADP-Ribose Binding Proteins chemistry MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
