Directional shape complementarity at the protein–DNA interface

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’. Copyright © 2003 John Wiley & Sons, Ltd.