Yeh Ching-Sheng, Chen Fang-Ming, Wang Jaw-Yuan, Cheng Tian-Lu, Hwang Ming-Jing, Tzou Wen-Shyong
MedicoGenomic Research Center, Kaohsiung Medical University, 100 Shih-Chuan 1st Road, Kaohsiung 807, Taiwan, Republic of China.
J Mol Recognit. 2003 Jul-Aug;16(4):213-22. doi: 10.1002/jmr.624.
Nature utilizes various styles of architecture for DNA-binding proteins to recognize diverse DNA sequences, a process facilitated by a complementary surface between protein and DNA. However, the extent and ways this 'shape complementarity' occurs at the protein-DNA interface have yet to be characterized. Here, by analyzing a set of diverse protein-DNA complexes of known three-dimensional structures, we investigated whether the normal vectors of a protein surface at the interface exhibited any relationship with DNA conformation. Generally, the normal vectors of a DNA-contacting protein surface distinctly preferred certain angles, enabling them to align with certain axes characterizing the conformation of DNA. Thus, a new geometric property of DNA-binding protein is demonstrated, i.e. the "shape complementarity" of protein-DNA recognition clearly bears the property of "directionality".
自然界利用多种结构形式的DNA结合蛋白来识别不同的DNA序列，这一过程由蛋白质与DNA之间互补的表面所推动。然而，这种“形状互补性”在蛋白质-DNA界面发生的程度和方式尚未得到表征。在此，通过分析一组已知三维结构的不同蛋白质-DNA复合物，我们研究了界面处蛋白质表面的法线向量是否与DNA构象存在任何关系。一般来说，与DNA接触的蛋白质表面的法线向量明显偏好某些角度，使它们能够与表征DNA构象的某些轴对齐。因此，证明了DNA结合蛋白的一种新的几何特性，即蛋白质-DNA识别的“形状互补性”明显具有“方向性”的特性。
