Evolutionary conservation of DNA-contact residues in DNA-binding domains

• Published in: BMC bioinformatics 2008-05, Vol.9 Suppl 6 (S6), p.S3-S3, Article S3
• Main Authors: Chang, Yao-Lin, Tsai, Huai-Kuang, Kao, Cheng-Yan, Chen, Yung-Chian, Hu, Yuh-Jyh, Yang, Jinn-Moon
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Base Sequence; Binding Sites; Conserved Sequence - genetics; DNA - chemistry; DNA - genetics; DNA-Binding Proteins - chemistry; DNA-Binding Proteins - genetics; Evolution, Molecular; Molecular Sequence Data; Protein Binding; Sequence Analysis, DNA - methods; Sequence Analysis, Protein - methods
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/1471-2105-9-S6-S3

DNA-binding proteins are of utmost importance to gene regulation. The identification of DNA-binding domains is useful for understanding the regulation mechanisms of DNA-binding proteins. In this study, we proposed a method to determine whether a domain or a protein can has DNA binding capability by considering evolutionary conservation of DNA-binding residues. Our method achieves high precision and recall for 66 families of DNA-binding domains, with a false positive rate less than 5% for 250 non-DNA-binding proteins. In addition, experimental results show that our method is able to identify the different DNA-binding behaviors of proteins in the same SCOP family based on the use of evolutionary conservation of DNA-contact residues. This study shows the conservation of DNA-contact residues in DNA-binding domains. We conclude that the members in the same subfamily bind DNA specifically and the members in different subfamilies often recognize different DNA targets. Additionally, we observe the co-evolution of DNA-contact residues and interacting DNA base-pairs.