A graph theoretic model to understand the behavioral difference of PPCA among its paralogs towards recognition of...

Among all the proteins of Periplasmic C type Cytochrome family obtained from cytochrome C found in Geobacter sulfurreducens, only the Periplasmic C type Cytochrome A (PPCA) protein can recognize the deoxycholate (DXCA), while its other paralogs do not, as observed from the crystal structures. Though some existing works have used graph-theoretic approaches to realize the 3-D structural properties of proteins, its usage in the rationalisation of the physiochemical behavior of proteins has been very limited. To understand the driving force towards the recognition of DXCA exclusively by PPCA among its paralogs, in this work, we propose two graph theoretic models based on the combinatorial properties, namely, base-pair-type and impact, of the nucleotide bases and the amino acid residues, respectively. Combinatorial analysis of the binding sequences using the proposed base-pair type based graph theoretic model reveals the differential behaviour of PPCA among its other paralogs. Further, to investigate the underlying chemical phenomenon, another graph theoretic model has been developed based on impact. Analysis of the results obtained from impact-based model clearly indicates towards the helix formation of PPCA which is essential for the recognition of DXCA, making PPCA a completely different entity from its paralogs.