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

Nandi, Tapas K and Bairagya, Hridoy R and Mukhopadhyay, Bishnu P and Sekar, K and Sukul, Dipankar and Bera, Asim K (2009) Conserved water-mediated H-bonding dynamics of catalytic Asn 175 in plant thiol protease. In: Journal of biosciences, 34 (1). pp. 27-34.

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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 W I 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.

Item Type:	Journal Article
Publication:	Journal of biosciences
Publisher:	Indian Academy of Sciences
Additional Information:	Copyright for this article belongs to Indian Academy of Sciences.
Keywords:	Conserved water in molecular recognition;MD simulation;plant cysteine protease.
Department/Centre:	Division of Information Sciences (Doesn't exist now) > BioInformatics Centre
Date Deposited:	09 Jul 2009 07:08
Last Modified:	19 Sep 2010 05:35
URI:	http://eprints.iisc.ac.in/id/eprint/20996

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