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      https://www.ias.ac.in/article/fulltext/jbsc/034/01/0027-0034

    • Keywords

       

      Conserved water in molecular recognition; MD simulation; plant cysteine protease

    • Abstract

       

      The role of invariant water molecules in the activity of plant cysteine protease is ubiquitous in nature. On analysing the 11 different Protein DataBank (PDB) structures of plant thiol proteases, the two invariant water molecules W1 and W2 (W220 and W222 in the template 1PPN structure) were observed to form H-bonds with the Ob atom of Asn 175. Extensive energy minimization and molecular dynamics simulation studies up to 2 ns on all the PDB and solvated structures clearly revealed the involvement of the H-bonding association of the two water molecules in fixing the orientation of the asparagine residue of the catalytic triad. From this study, it is suggested that H-bonding of the water molecule at the W1 invariant site better stabilizes the Asn residue at the active site of the catalytic triad.

    • Author Affiliations

       

      Tapas K Nandi1 Hridoy R Bairagya1 Bishnu P Mukhopadhyay1 K Sekar2 Dipankar Sukul1 Asim K Bera3

      1. Department of Chemistry, National Institute of Technology, Durgapur 713 209, India
      2. Bioinformatics Centre, Indian Institute of Science, Bangalore 560 012, India
      3. Center for Advanced Research in Biotechnology, Rockville, Maryland 20850, USA
    • Dates

       
  • Journal of Biosciences | News

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