Computer modeling of helicases using elastic network model

Abstract

In this chapter, we will demonstrate the usage of a suite of computational techniques based on a coarse-grained elastic network model by applying them to a monomeric helicase-the NS3 helicase of hepatitis C virus. These techniques allow us to predict and visualize collective domain motions encoded in the protein structures, probe allosteric couplings between key functional sites (such as ATP-binding site and DNA/RNA-binding site of a helicase), and simulate ATP-binding-induced global conformational changes. These general techniques are not only applicable to NS3 but also to other multi-domain protein structures. © 2009 Humana Press, a part of Springer Science+Business Media, LLC.