Conserved water-mediated H-bonding dynamics of catalytic Asn 175 in plant thiol protease |
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Authors: | Tapas K Nandi Hridoy R Bairagya Bishnu P Mukhopadhyay K Sekar Dipankar Sukul Asim K Bera |
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Institution: | (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 |
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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 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. |
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Keywords: | Conserved water in molecular recognition MD simulation plant cysteine protease |
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