Paper Citing NAMD - Abstract
Nandi, Tapas K.; Bairagya, Hridoy R.; Mukhopadhyay, Bishnu P.; Mallik, Payel; Sukul, Dipankar; Bera, Asim K.
Conserved water-mediated H-bonding dynamics of catalytic His159 and Asp158: insight into a possible acid-base coupled mechanism in plant thiol protease
JOURNAL OF MOLECULAR MODELING, 18:2633-2644, JUN 2012
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.
