Protein–Water Interactions in Ribonuclease A and Angiogenin: A Molecular Dynamics Study

Sanjeev, BS and Vishveshwara, S (2004) Protein–Water Interactions in Ribonuclease A and Angiogenin: A Molecular Dynamics Study. In: Proteins: Structure, Function, and Bioinformatics, 55 (4). pp. 915-923.

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Abstract

It is known that water molecules play an important role in the biological functioning of proteins. The members of the ribonuclease A (RNase A) family of proteins, which are sequentially and structurally similar, are known to carry out the obligatory function of cleaving RNA and individually perform other diverse biological functions. Our focus is on elucidating whether the sequence and structural similarity lead to common hydration patterns, what the common hydration sites are and what the differences are. Extensive molecular dynamics simulations followed by a detailed analysis of protein–water interactions have been carried out on two members of the ribonuclease A superfamily— RNase A and angiogenin. The water residence times are analyzed and their relationship with the characteristic properties of the protein polar atoms, such as their accessible surface area and mean hydration, is studied. The capacity of the polar atoms to form hydrogen bonds with water molecules and participate in protein–water networks are investigated. The locations of such networks are identified for both proteins. Proteins 2004;55:915–923.

Item Type:	Journal Article
Publication:	Proteins: Structure, Function, and Bioinformatics
Publisher:	Wiley-Liss, Inc
Additional Information:	The copyright belongs to Wiley-Liss, Inc.
Keywords:	Protein–water networks;Invariant waters;Maximum residence time
Department/Centre:	Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited:	02 May 2006
Last Modified:	19 Sep 2010 04:26
URI:	http://eprints.iisc.ac.in/id/eprint/6513

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