Extensive protein and DNA backbone sampling improves structure-based specificity prediction for C2H2 zinc fingers

Sequence-specific DNA recognition by gene regulatory proteins is critical for proper cellular functioning. The ability to predict the DNA binding preferences of these regulatory proteins from their amino acid sequence would greatly aid in reconstruction of their regulatory interactions. Structural modeling provides one route to such predictions: by building accurate molecular models of regulatory proteins in complex with candidate binding sites, and estimating their relative binding affinities for these sites using a suitable potential function, it should be possible to construct DNA binding profiles. Here, we present a novel molecular modeling protocol for protein-DNA interfaces that borrows conformational sampling techniques from de novo protein structure prediction to generate a diverse ensemble of structural models from small fragments of related and unrelated protein-DNA complexes. The extensive conformational sampling is coupled with sequence space exploration so that binding preferences for the target protein can be inferred from the resulting optimized DNA sequences. We apply the algorithm to predict binding profiles for a benchmark set of eleven C2H2 zinc finger transcription factors, five of known and six of unknown structure. The predicted profiles are in good agreement with experimental binding data; furthermore, examination of the modeled structures gives insight into observed binding preferences.