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


RESULTS
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.


CONCLUSIONS
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.
Chang
Yao-Lin
YL
Department of Computer Science and Information Engineering, National Taiwan University, Taipei 106, Taiwan. b4506046@csie.ntu.edu.tw
Tsai
Huai-Kuang
HK
Kao
Cheng-Yan
CY
Chen
Yung-Chian
YC
Hu
Yuh-Jyh
YJ
Yang
Jinn-Moon
JM
D000595:Amino Acid Sequence; D001483:Base Sequence; D001665:Binding Sites; D017124:Conserved Sequence / Q000235:genetics*; D004247:DNA / Q000737:chemistry* / Q000235:genetics*; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000235:genetics*; D019143:Evolution, Molecular; D008969:Molecular Sequence Data; D011485:Protein Binding; D017422:Sequence Analysis, DNA / Q000379:methods; D020539:Sequence Analysis, Protein / Q000379:methods*
D004268:DNA-Binding Proteins; D004247:DNA