Computational analysis of similar protein-DNA complexes from different organisms to understand organism specific recognition

Protein-DNA interactions play vital roles in many cellular processes. It is not clear whether the recognition of same protein-DNA complexes in different organisms is similar or different. In this work, we have analyzed the similarities and variations in interactions and interacting patterns in a set of 41 similar protein-DNA complexes from different organisms based on several features such as propensity of binding site residues, preference of binding segments, preferred amino acid-nucleotide pairs, etc. Based on the analysis, we showed the variations in interactions and interacting patterns of similar protein-DNA complexes from different organisms, which possibly lead to difference in recognition mechanism.