oa Protein-DNA interface: Structural analysis by specific contact mapping

The interaction between protein and nucleic acid are essential for many cell processes that regulate cell cycles and vital functions. Understanding the determinants of protein / DNA recognition would lead to valuable biological, medical, and biotechnological applications. The practical and theoretical importance of the rules that govern the recognition specificity has generated a deep interest and a number of publications have contributed to a better understanding of the specificity and the recognition rules between protein and DNA. In this study, we investigated protein DNA interface using Delaunay Tessellation of protein DNA complexes as specific contact maps. Protein/DNA interface were studied at an atomic level by our novel TOPOFIT method. Majority of studies that were carried out focusing on recognition features occurring between pairs of residues and DNA bases. In the present study, representative Protein-DNA interfaces were split into patches and then into triplets. We first present a statistical analysis about interface patches obtained from 294 protein-DNA complexes that were classified and clustered according to their double DNA pattern, highlighting the important variability among the current representation of recognized DNA patterns. We also report here that there are several classes of triplet interfaces that are groove dependent, and in which the closeness of residues and nucleotides can be estimated through the analysis of the contribution of water, and the number of contacts involving the dual groove atoms. These observation correlates with the function of DNA-protein complexes and is a side effect of the interaction consequences on DNA conformation. More precisely, there are two classes of minor groove triplets distinguishable by the presence/absence of water molecules at the interface and the low/high contribution of DNA dual groove atoms into the specific contact maps. These classes were not observed for major groove triplets showing a more homogenous population.