Zhang Yongli, Xi Zhiqun, Hegde Rashmi S, Shakked Zippora, Crothers Donald M
Departments of Chemistry and Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA.
Proc Natl Acad Sci U S A. 2004 Jun 1;101(22):8337-41. doi: 10.1073/pnas.0402319101. Epub 2004 May 17.
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 method. We examined 16 sites containing different noncontacted spacer sequences, which vary by more than three orders of magnitude in binding affinity. For 15 of these sites, the variation in affinity was predicted within a factor of 3, by using experimental curvature and flexibility values and a statistical mechanical theory. The sole exception was traced to differential magnesium ion binding.
蛋白质对DNA的识别依赖于与特定DNA功能基团的直接相互作用，以及反映DNA序列对蛋白质诱导的扭曲和弯曲变形响应中可变能量学的间接效应。预测间接读出需要了解受影响区域DNA曲率和柔韧性的变化，我们通过使用环化动力学方法确定了E2调节蛋白一系列DNA结合位点的这些变化。我们研究了16个含有不同非接触间隔序列的位点，这些位点的结合亲和力相差三个数量级以上。对于其中15个位点，通过使用实验曲率和柔韧性值以及统计力学理论，亲和力的变化预测在3倍以内。唯一的例外归因于镁离子结合的差异。
