Journal of Biosciences

, Volume 34, Issue 1, pp 27–34

Conserved water-mediated H-bonding dynamics of catalytic Asn 175 in plant thiol protease

  • Tapas K. Nandi
  • Hridoy R. Bairagya
  • Bishnu P. Mukhopadhyay
  • K. Sekar
  • Dipankar Sukul
  • Asim K. Bera
Article

DOI: 10.1007/s12038-009-0006-6

Cite this article as:
Nandi, T.K., Bairagya, H.R., Mukhopadhyay, B.P. et al. J Biosci (2009) 34: 27. doi:10.1007/s12038-009-0006-6

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.

Keywords

Conserved water in molecular recognition MD simulation plant cysteine protease 

Abbreviations used

CHASA

conditional hydrophobic accessible surface area

IMD

interactive molecular dynamics

PDB

Protein DataBank

RMSD

root mean square deviation

Copyright information

© Indian Academy of Sciences 2009

Authors and Affiliations

  • Tapas K. Nandi
    • 1
  • Hridoy R. Bairagya
    • 1
  • Bishnu P. Mukhopadhyay
    • 1
  • K. Sekar
    • 2
  • Dipankar Sukul
    • 1
  • Asim K. Bera
    • 3
  1. 1.Department of ChemistryNational Institute of TechnologyDurgapurIndia
  2. 2.Bioinformatics CentreIndian Institute of ScienceBangaloreIndia
  3. 3.Center for Advanced Research in BiotechnologyRockvilleUSA

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