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

doi:10.1007/s12038-009-0006-6

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

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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 O_b 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.

Original language	English (US)
Pages (from-to)	27-34
Number of pages	8
Journal	Journal of Biosciences
Volume	34
Issue number	1
DOIs	https://doi.org/10.1007/s12038-009-0006-6
State	Published - Mar 2009
Externally published	Yes

Keywords

Conserved water in molecular recognition
MD simulation
Plant cysteine protease

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title = "Conserved water-mediated H-bonding dynamics of catalytic Asn 175 in plant thiol 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.",

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AU - Nandi, Tapas K.

AU - Bairagya, Hridoy R.

AU - Mukhopadhyay, Bishnu P.

AU - Sekar, K.

AU - Sukul, Dipankar

AU - Bera, Asim K.

PY - 2009/3

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N2 - 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.

AB - 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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KW - MD simulation

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

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Keywords

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