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Open Access Research article

An effective approach for generating a three-Cys2His2 zinc-finger-DNA complex model by docking

Chun-Chi Chou12, M Rajasekaran234 and Chinpan Chen2*

Author Affiliations

1 Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 114, Taiwan

2 Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan

3 Department of Life Science, National Tsing Hua University, Hsinchu 300, Taiwan

4 Chemical Biology and Molecular Biophysics, Taiwan International Graduate Program, Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan

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BMC Bioinformatics 2010, 11:334  doi:10.1186/1471-2105-11-334

Published: 18 June 2010

Abstract

Background

Determination of protein-DNA complex structures with both NMR and X-ray crystallography remains challenging in many cases. High Ambiguity-Driven DOCKing (HADDOCK) is an information-driven docking program that has been used to successfully model many protein-DNA complexes. However, a protein-DNA complex model whereby the protein wraps around DNA has not been reported. Defining the ambiguous interaction restraints for the classical three-Cys2His2 zinc-finger proteins that wrap around DNA is critical because of the complicated binding geometry. In this study, we generated a Zif268-DNA complex model using three different sets of ambiguous interaction restraints (AIRs) to study the effect of the geometric distribution on the docking and used this approach to generate a newly reported Sp1-DNA complex model.

Results

The complex models we generated on the basis of two AIRs with a good geometric distribution in each domain are reasonable in terms of the number of models with wrap-around conformation, interface root mean square deviation, AIR energy and fraction native contacts. We derived the modeling approach for generating a three-Cys2His2 zinc-finger-DNA complex model according to the results of docking studies using the Zif268-DNA and other three crystal complex structures. Furthermore, the Sp1-DNA complex model was calculated with this approach, and the interactions between Sp1 and DNA are in good agreement with those previously reported.

Conclusions

Our docking data demonstrate that two AIRs with a reasonable geometric distribution in each of the three-Cys2His2 zinc-finger domains are sufficient to generate an accurate complex model with protein wrapping around DNA. This approach is efficient for generating a zinc-finger protein-DNA complex model for unknown complex structures in which the protein wraps around DNA. We provide a flowchart showing the detailed procedures of this approach.