loading page

Identification of a novel antithrombin-III like protein from Punica granatum using bioinformatics approach.
  • +2
  • * Sawetaji,
  • Shanky Jindal,
  • Ravi Kant,
  • Daman Saluja,
  • Kamal Krishan Aggarwal
* Sawetaji
Guru Gobind Singh Indraprastha University School of Biotechnology
Author Profile
Shanky Jindal
Guru Gobind Singh Indraprastha University School of Biotechnology
Author Profile
Ravi Kant
University of Delhi
Author Profile
Daman Saluja
University of Delhi
Author Profile
Kamal Krishan Aggarwal
Guru Gobind Singh Indraprastha University School of Biotechnology

Corresponding Author:[email protected]

Author Profile

Abstract

Sequences similar to antithrombin-III in plants were retrieved from NCBI BLAST. Sequences showing homology more than 32% were shortlisted. Due to the non-availability of the crystal structures of the shortlisted sequences in the PDB database, models were generated using SWISS MODEL web server. The generated models were authenticated using SAVES web server. Best models for each sequence were selected and docked with thrombin using HawkDock web server. Out of 15 docked complexes, ALPP was shortlisted depending upon the highest binding affinity of -41.28 kcal/mol. Thrombin structure complexed with antithrombin-III like protein from Punica granatum (ALPP) was docked with TAME using AutoDock Vina to see if structure from ALPP affects the TAME binding. No interaction or binding is observed for TAME at 195Ser residue of thrombin. So after binding with ALPP, thrombin loses its affinity to bind with TAME at active site residue. MD simulation was performed for 20 ns to evaluate the flexibility and the stability of the docked complexes. The RMSD for the Thrombin-TAME complex was found to be 0.35nm whereas the RMSD of ALPP-Thrombin complex was found to be 0.4nm. Thus, it is very likely that the protein identified from Punica granatum may act as an inhibitor for thrombin.