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Biomolecular Simulations

Volume 924 of the series Methods in Molecular Biology pp 601-616

Date:

Elastic Network Models: Theoretical and Empirical Foundations

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Abstract

Fifteen years ago, Monique Tirion showed that the low-frequency normal modes of a protein are not significantly altered when nonbonded interactions are replaced by Hookean springs, for all atom pairs whose distance is smaller than a given cutoff value. Since then, it has been shown that coarse-grained versions of Tirion’s model are able to provide fair insights on many dynamical properties of biological macromolecules. In this chapter, theoretical tools required for studying these so-called Elastic Network Models are described, focusing on practical issues and, in particular, on possible artifacts. Then, an overview of some typical results that have been obtained by studying such models is given.

Key words

Protein Normal mode analysis Anisotropic network model Gaussian network model Low-frequency modes B-factors Thermal motion Conformational change Functional motion.