|Title||An expanded binding model for Cys2His2 zinc finger protein-DNA interfaces.|
|Publication Type||Journal Article|
|Year of Publication||2011|
|Authors||Persikov, AV, Singh, M|
|Date Published||2011 Jun|
|Keywords||Binding Sites, DNA, DNA-Binding Proteins, Humans, Models, Biological, Models, Molecular, Zinc Fingers|
Cys(2)His(2) zinc finger (C2H2-ZF) proteins comprise the largest class of eukaryotic transcription factors. The 'canonical model' for C2H2-ZF protein-DNA interaction consists of only four amino acid-nucleotide contacts per zinc finger domain, and this model has been the basis for several efforts for computationally predicting and experimentally designing protein-DNA interfaces. Here, we perform a systematic analysis of structural and experimental binding data and find that, in addition to the canonical contacts, several other amino acid and base pair combinations frequently play a role in C2H2-ZF protein-DNA binding. We suggest an expansion of the canonical C2H2-ZF model to include one to three additional contacts, and show that computational approaches including these additional contacts improve predictions of DNA targets of zinc finger proteins.
|Alternate Journal||Phys Biol|