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Effects of substrate binding on the dynamics of RNase A: Molecular dynamics simulations of UpA bound and native RNase A

Nadig, Nadig and Vishveshwara, Saraswathi (1997) Effects of substrate binding on the dynamics of RNase A: Molecular dynamics simulations of UpA bound and native RNase A. In: Biopolymers, 42 (5). pp. 505-520.

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Abstract

RNase A has been extensively used as a model protein in several biophysical and biochemical studies. Using the available structural and biochemical results, RNase A-UpA interaction has been computationally modeled at an atomic level. In this study, the molecular dynamics (MD) simulations of native and UpA bound Rase A have been carried out. The gross dynamical behavior and atomic fluctuations of the free and UpA bound RNase A have been characterized. Principal component analysis is carried out to identify the important modes of collective motion and to analyze the changes brought out in these modes of RNase A upon UpA binding. The hydrogen bonds are monitored to study the atomic details of RNase A-UpA interactions and RNase A-water interactions. Based on these analysis, the stability of the free and UpA bound RNase A are discussed.

Item Type: Journal Article
Additional Information: Copyright of this article belongs to John Wiley and Sons.
Keywords: RNase A;UpA;molecular dynamics simulation;principal component analysis;enzyme-substrate interactions.
Department/Centre: Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited: 02 Jun 2009 10:56
Last Modified: 19 Sep 2010 05:26
URI: http://eprints.iisc.ernet.in/id/eprint/18921

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