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      https://www.ias.ac.in/article/fulltext/jbsc/046/0035

    • Keywords

       

      PPCA; DXCA; conformational analysis; base-pair type; impact; graph-theoretical modeling

    • Abstract

       

      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.

    • Author Affiliations

       

      SHANKAR K GHOSH1 SUVANKAR GHOSH2 GOUTAM PAUL3 RAJA BANERJEE2

      1. Advanced Computing and Microelectronics Unit, Indian Statistical Institute, Kolkata 700 108, India
      2. Maulana Abul Kalam Azad University of Technology, West Bengal (Formerly WBUT), Kolkata 700 064, India
      3. Cryptology and Security Research Unit, R. C. Bose Centre for Cryptology and Security, Indian Statistical Institute, Kolkata 700 108, India
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    • Supplementary Material

       
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