Conserved water-mediated H-bonding dynamics of catalytic His159 and Asp158: insight into a possible acid–base coupled mechanism in plant thiol protease

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 WD 1 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 , WD 1 , 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.