A molecular dynamics study based post facto free energy analysis of the binding of bovine angiogenin with UMP and CMP ligands

Madhusudhan, MS and Vishveshwara, S and Das, A and Kalra, P and Jayaram, B (2001) A molecular dynamics study based post facto free energy analysis of the binding of bovine angiogenin with UMP and CMP ligands. In: Indian Journal of Biochemistry & Biophysics, 38 (1-2). pp. 27-33.

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Abstract

Angiogenin is a protein belonging to the superfamily of RNase A. The RNase activity of this protein is essential for its angiogenic activity. Although members of the RNase A family carry out RNase activity, they differ markedly in their strength and specificity. In this paper, we address the problem of higher specificity of angiogenin towards cytosine against uracil in the first base binding position. We have carried out extensive nano-second level molecular dynamics(MD) computer simulations on the native bovine angiogenin and on the CMP and UMP complexes of this protein in aqueous medium with explicit molecular solvent. The structures thus generated were subjected to a rigorous free energy component analysis to arrive at a plausible molecular thermodynamic explanation for the substrate specificity of angiogenin.

Item Type:	Journal Article
Publication:	Indian Journal of Biochemistry & Biophysics
Publisher:	National Institute of Science Communication and Information Resources.
Additional Information:	Copyright of this article belongs to National Institute of Science Communication and Information Resources.
Department/Centre:	Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited:	02 Aug 2011 09:00
Last Modified:	02 Aug 2011 09:00
URI:	http://eprints.iisc.ac.in/id/eprint/39483

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