An expanded binding model for Cys2His2 zinc finger protein-DNA interfaces. Author Anton Persikov V, Mona Singh Publication Year 2011 Type Journal Article 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. Keywords Humans, Models, Biological, Binding Sites, DNA, DNA-Binding Proteins, Models, Molecular, Zinc Fingers Journal Phys Biol Volume 8 Issue 3 Pages 035010 Date Published 06/2011 Alternate Journal Phys Biol Google ScholarBibTeXEndNote X3 XML