Journal
JOURNAL OF MOLECULAR MODELING
Volume 18, Issue 6, Pages 2633-2644Publisher
SPRINGER
DOI: 10.1007/s00894-011-1277-z
Keywords
Plant thiol protease; Water dynamics; Catalytic His159-Asp158; Acid-Base coupling
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Cysteine protease is ubiquitous in nature. Excess activity of this enzyme causes intercellular proteolysis, muscle tissue degradation, etc. The role of water-mediated interactions in the stabilization of catalytically significant Asp158 and His159 was investigated by performing molecular dynamics simulation studies of 16 three-dimensional structures of plant thiol proteases. In the simulated structures, the hydrophilic W-1, W-2 and WD1 centers form hydrogen bonds with the OD1 atom of Asp158 and the ND1 atom of His159. In the solvated structures, another water molecule, W-E, forms a hydrogen bond with the NE2 atom of His159. In the absence of the water molecule W-E, Trp177 (NE1) and Gln19 (NE2) directly interact with the NE2 atom of His159. All these hydrophilic centers (the locations of W-1, W-2, WD1, and W-E) are conserved, and they play a critical role in the stabilization of His-Asp complexes. In the water dynamics of solvated structures, the water molecules W-1 and W-2 form a water...water hydrogen-bonded network with a few other water molecules. A few dynamical conformations or transition states involving direct (His159 ND1...Asp158 OD1) and water-mediated (His159 ND1...W-2...Asp158 OD1) hydrogen-bonded complexes are envisaged from these studies.
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