Omagari Katsumi, Yoshimura Hidehisa, Suzuki Takayuki, Takano Mitunori, Ohmori Masayuki, Sarai Akinori
Department of Virology, Medical School, Nagoya City University, Japan.
FEBS J. 2008 Oct;275(19):4786-95. doi: 10.1111/j.1742-4658.2008.06618.x. Epub 2008 Aug 29.
DNA-binding sites for SYCRP1, which is a regulatory protein of the cyanobacterium Synechocystissp. PCC6803, were predicted for the whole genome sequence by estimating changes in the binding free energy () for SYCRP1 for those sites. The values were calculated by summing DeltaDeltaG values derived from systematic single base-pair substitution experiments (symmetrical and cooperative binding model). Of the calculated binding sites, 23 sites with a value <3.9kcal.mol(-1) located upstream or between the ORFs were selected as putative binding sites for SYCRP1. In order to confirm whether SYCRP1 actually binds to these binding sites or not, 11 sites with the lowest values were tested experimentally, and we confirmed that SYCRP1 binds to ten of the 11 sites with a DeltaDeltaG(total) value <3.9kcal.mol(-1). The best correlation coefficient between and the observed DeltaDeltaG(total) for binding of SYCRP1 to those sites was 0.78. These results suggest that the DeltaDeltaG values derived from systematic single base-pair experiments may be used to screen for potential binding sites of a regulatory protein in the genome sequence.
通过估计集胞藻属蓝细菌PCC6803的调节蛋白SYCRP1在这些位点的结合自由能（）变化，预测了SYCRP1在全基因组序列上的DNA结合位点。这些值是通过对系统单碱基对替换实验（对称协同结合模型）得出的ΔΔG值求和计算得到的。在计算出的结合位点中，选择了23个位于开放阅读框上游或之间且值<3.9kcal.mol(-1)的位点作为SYCRP1的推定结合位点。为了确认SYCRP1是否真的与这些结合位点结合，对11个值最低的位点进行了实验测试，并且我们确认SYCRP1与11个位点中的10个结合，其ΔΔG（总）值<3.9kcal.mol(-1)。SYCRP1与这些位点结合的计算值与观察到的ΔΔG（总）之间的最佳相关系数为0.78。这些结果表明，从系统单碱基对实验得出的ΔΔG值可用于筛选基因组序列中调节蛋白的潜在结合位点。
