An expanded binding model for Cys(2)His(2) zinc finger protein-DNA interfaces

作者：Persikov Anton V^*; Singh Mona

来源：Physical Biology, 2011, 8(3): 035010.

DOI：10.1088/1478-3975/8/3/035010

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.

• 出版日期2011-6