Directional shape complementarity at the protein-DNA interface |
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Authors: | Yeh Ching-Sheng Chen Fang-Ming Wang Jaw-Yuan Cheng Tian-Lu Hwang Ming-Jing Tzou Wen-Shyong |
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Institution: | MedicoGenomic Research Center, Kaohsiung Medical University, 100 Shih-Chuan 1st Road, Kaohsiung 807, Taiwan, Republic of China. |
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Abstract: | 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". |
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Keywords: | protein surface shape complementarity normal vector DNA conformation structural bioinformatics |
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