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An expanded binding model for Cys2His2 zinc finger protein-DNA interfaces

Author(s): Persikov, AV; Singh, Mona

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Abstract: Cys2His2 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.
Publication Date: 13-May-2011
Electronic Publication Date: 13-May-2011
Citation: Persikov, AV, Singh, M. (2011). An expanded binding model for Cys<inf>2</inf>His<inf>2</inf> zinc finger protein-DNA interfaces. Physical Biology, 8 (10.1088/1478-3975/8/3/035010
DOI: doi:10.1088/1478-3975/8/3/035010
Type of Material: Journal Article
Journal/Proceeding Title: Physical Biology
Version: Author's manuscript

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