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.
PDF
Effects_of.pdf - Published Version Restricted to Registered users only Download (366kB) | Request a copy |
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 |
---|---|
Publication: | Biopolymers |
Publisher: | John Wiley and Sons |
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.ac.in/id/eprint/18921 |
Actions (login required)
View Item |