Dynamics of the Native and the Ligand-bound Structures of Eosinophil Cationic Protein: Network of Hydrogen Bonds at the Catalytic Site

Sanjeev, BS and Vishveshwara, S (2005) Dynamics of the Native and the Ligand-bound Structures of Eosinophil Cationic Protein: Network of Hydrogen Bonds at the Catalytic Site. In: Journal of Biomolecular Structure & Dynamics, 22 (6). pp. 657-672.

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Abstract

Eosinophil Cationic Protein (ECP) is sequentially and structurally similar to ribonuclease A (RNase A). It belongs to the RNase A family of proteins and the RNA catalysis is essential to its biological function. In the present study, we have generated the dinucleotide-bound structures of ECP by docking the dinucleotides to a number of molecular dynamics (MD) generated ECP structures. The stability of the docked enzyme-ligand complexes was ascertained by extensive MD simulations. The modes of ligand binding are explored by essential dynamics studies. The role of water molecules in the stability of the complex and in the catalysis was investigated. The active site residues form a complex network of connections with the ligand and with a water molecule. The catalytic mechanism of the RNA cleavage is examined on the basis of the active site geometry obtained by the simulations.

Item Type:	Journal Article
Publication:	Journal of Biomolecular Structure & Dynamics
Publisher:	Adenine Press
Additional Information:	The Copyright belongs to Adenine Press.
Department/Centre:	Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited:	07 Mar 2006
Last Modified:	19 Sep 2010 04:24
URI:	http://eprints.iisc.ac.in/id/eprint/5654

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