title: Directional shape complementarity at the protein-DNA interface.
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".
authors.affiliation: MedicoGenomic Research Center, Kaohsiung Medical University, 100 Shih-Chuan 1st Road, Kaohsiung 807, Taiwan, Republic of China.
authors.forename: Ching-Sheng
authors.initials: CS
authors.lastname: Yeh
authors.forename: Fang-Ming
authors.initials: FM
authors.lastname: Chen
authors.forename: Jaw-Yuan
authors.initials: JY
authors.lastname: Wang
authors.forename: Tian-Lu
authors.initials: TL
authors.lastname: Cheng
authors.forename: Ming-Jing
authors.initials: MJ
authors.lastname: Hwang
authors.forename: Wen-Shyong
authors.initials: WS
authors.lastname: Tzou
mesh_terms: D004247:DNA / Q000737:chemistry* / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation
chemical_list: D004268:DNA-Binding Proteins; D004247:DNA