Molecular surface directionality of the DNA-binding protein surface on the earth map

Abstract

Protein-DNA interactions play a pivotal role in both the transcriptional control and the maintenance of genome integrity, and these are two properties that are closely linked to the development of an organism, differentiation, physiology and to the progression of diseases. Chemical and geometric properties are typically two of the key components in any analysis that aims to understand the precise origin of specificity and elucidate the atomic features of a protein-DNA interface. In this study, we have developed a unique representation of the directionality of the molecular surface of a DNA-binding protein. The stereo-orientation of the normal vector that signifies the geometric properties of a protein surface was projected onto a two-dimensional surface (referred to here as an earth map). We identified considerably diverse patterns of the vector distribution of the protein surface, and besides this, the DNA-contact surface, a subset of an entire protein surface, has also been found to contain diverse patterns. At the same time, the direction of the DNA-contact surface was also tracked onto the earth map on a base-pair basis and distinct intertwining properties particular to the specific family of that DNA-binding protein are revealed.