Articles written in Journal of Biosciences

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


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      Among all the proteins of Periplasmic C type Cytochrome family obtained from cytochrome C7 found inGeobacter sulfurreducens, only the Periplasmic C type Cytochrome A (PPCA) protein can recognize thedeoxycholate (DXCA), while its other paralogs do not, as observed from the crystal structures. Though someexisting works have used graph-theoretic approaches to realize the 3-D structural properties of proteins, itsusage in the rationalisation of the physiochemical behavior of proteins has been very limited. To understand thedriving force towards the recognition of DXCA exclusively by PPCA among its paralogs, in this work, wepropose 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 bindingsequences using the proposed base-pair type based graph theoretic model reveals the differential behaviour ofPPCA among its other paralogs. Further, to investigate the underlying chemical phenomenon, another graphtheoretic model has been developed based on impact. Analysis of the results obtained from impact-basedmodel 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.

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