Directional shape complementarity at the protein–DNA interface

✍ Scribed by Ching-Sheng Yeh; Fang-Ming Chen; Jaw-Yuan Wang; Tian-Lu Cheng; Ming-Jing Hwang; Wen-Shyong Tzou

• Publisher: John Wiley and Sons
• Year: 2003
• Tongue: English
• Weight: 344 KB
• Volume: 16
• Category: Article
• ISSN: 0952-3499
• DOI: 10.1002/jmr.624

✦ Synopsis

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