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Analysis of Hydrogen Bonding and Stability of Protein Secondary Structures in Molecular Dynamics Simulation

Vijayakumar, S and Vishveshwara, S and Ravishanker, G and Beveridge, DL (1994) Analysis of Hydrogen Bonding and Stability of Protein Secondary Structures in Molecular Dynamics Simulation. In: Symposium on Modeling the Hydrogen Bond, at the 206th National Meeting of the American-Chemical-Society, AUG 22-27, 1993, Chicago,IL,.

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Official URL: http://pubs.acs.org/doi/abs/10.1021/bk-1994-0569.c...

Abstract

Molecular Dynamics (MD) simulations provide an atomic level account of the molecular motions and have proven to be immensely useful in the investigation of the dynamical structure of proteins. Once an MD trajectory is obtained, specific interactions at the molecular level can be directly studied by setting up appropriate combinations of distance and angle monitors. However, if a study of the dynamical behavior of secondary structures in proteins becomes important, this approach can become unwieldy. We present herein a method to study the dynamical stability of secondary structures in proteins, based on a relatively simple analysis of backbone hydrogen bonds. The method was developed for studying the thermal unfolding of beta-lactamases, but can be extended to other systems and adapted to study relevant properties.

Item Type: Conference Paper
Additional Information: Copyright of this article belongs to Oxford University Press.
Department/Centre: Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited: 03 Jun 2011 06:35
Last Modified: 03 Jun 2011 06:35
URI: http://eprints.iisc.ernet.in/id/eprint/36124

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