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

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-...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Chun-Chi Chou, M. Rajasekaran, Chinpan Chen
• Keywords: BMCBI 2010, Complex Model, Protein-DNA Complex, Protein-DNA Complex Model