情報エントロピーを用いたタンパク質-DNA認識におけるindirect readoutの寄与の評価

Information entropy as a measure of the contribution of indirect readout in protein-DNA recognition

山崎 智*; 河野 秀俊; 清水 謙多郎*; 皿井 明倫*; 寺田 透*

Yamasaki, Satoshi*; Kono, Hidetoshi; Shimizu, Kentaro*; Sarai, Akinori*; Terada, Toru*

Sequence-specific recognition of DNA by proteins plays a critical role in regulating gene expression. Accurate recognition is achieved by a combination of two different mechanisms. The first is direct readout, in which recognition is mediated by direct interactions between amino acids and DNA bases. The second is indirect readout, which is caused by the sequence-dependence of the conformation and deformability of the Drain the present study, we developed a new method for evaluating the contribution of indirect readout. This method uses the information entropy as a measure of the contribution. The entropy was calculated from the probability of DNA sequence given conformation, which was obtained by converting the probability of conformation given sequence using Bays'theorem. We used trajectories of MD simulations for free DNAs that had different tetramer sequences at the center of the sequences to calculate the probability distributions of the conformation. We found that the regions which are shown to be indirectly readout by experiment tend to have smaller information entropies. We therefore concluded that the information entropy is a good measure of the contribution of indirect readout in protein-DNA recognition.