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

Content Provider	Springer Nature Link
Author	Nandi, Tapas K. Bairagya, Hridoy R. Mukhopadhyay, Bishnu P. Mallik, Payel Sukul, Dipankar Bera, Asim K.
Copyright Year	2011
Abstract	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 W1, W2 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, WE, forms a hydrogen bond with the NE2 atom of His159. In the absence of the water molecule WE, Trp177 (NE1) and Gln19 (NE2) directly interact with the NE2 atom of His159. All these hydrophilic centers (the locations of W1, W2, WD1, and WE) 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 W1 and W2 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...W2...Asp158 OD1) hydrogen-bonded complexes are envisaged from these studies.
Starting Page	2633
Ending Page	2644
Page Count	12
File Format	PDF
ISSN	16102940
Journal	Journal of Molecular Modeling
Volume Number	18
Issue Number	6
e-ISSN	09485023
Language	English
Publisher	Springer-Verlag
Publisher Date	2011-11-09
Publisher Place	Berlin, Heidelberg
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Plant thiol protease Water dynamics Catalytic His159–Asp158 Acid–Base coupling Computer Applications in Chemistry Computer Application in Life Sciences Life Sciences Health Informatics Molecular Medicine Biomedicine general
Content Type	Text
Resource Type	Article
Subject	Organic Chemistry Physical and Theoretical Chemistry Computational Theory and Mathematics Catalysis Inorganic Chemistry Computer Science Applications

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