Evolutionary Conservation of DNA-Contact residues in DNA-bindingDomains

Yao-Lin Chang, Huai-Kuang Tsai, Cheng-Yan Kao, Yung-Chian Chen, and Jinn-Moon Yang
2007 Second International Multi-Symposiums on Computer and Computational Sciences (IMSCCS 2007)  
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%
more » ... r 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. Conclusion: 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.
doi:10.1109/imsccs.2007.4392574 fatcat:snlhwz7c35dg3c4ycoq6ffzbka