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 |
Journal | Phys Biol |
Volume | 8 |
Issue | 3 |
Pagination | 035010 |
Date Published | 2011 Jun |
Keywords | Binding Sites, DNA, DNA-Binding Proteins, Humans, Models, Biological, Models, Molecular, Zinc Fingers |
Abstract | 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 |