Predicting indirect readout effects in protein-DNA interactions.

@article{Zhang2004PredictingIR,
  title={Predicting indirect readout effects in protein-DNA interactions.},
  author={Yongli Zhang and Zhiqun Xi and Rashmi S Hegde and Zippora Shakked and D. M. Crothers},
  journal={Proceedings of the National Academy of Sciences of the United States of America},
  year={2004},
  volume={101 22},
  pages={
          8337-41
        }
}
Recognition of DNA by proteins relies on direct interactions with specific DNA-functional groups, along with indirect effects that reflect variable energetics in the response of DNA sequences to twisting and bending distortions induced by proteins. Predicting indirect readout requires knowledge of the variations in DNA curvature and flexibility in the affected region, which we have determined for a series of DNA-binding sites for the E2 regulatory protein by using the cyclization kinetics… CONTINUE READING
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