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Analysis of Protein Conformational Transitions Using Elastic Network Model

Protocol
First Online:
Part of the Methods in Molecular Biology book series (MIMB, volume 1084)

Abstract

In this chapter, we demonstrate the usage of a coarse-grained elastic network model to analyze protein conformational transitions in the NS3 helicase (NS3hel) of Hepatitis C virus (HCV). This analysis allows us to identify and visualize collective domain motions involved in the conformational transitions and predict the order of structural events during the transitions. It is highly efficient and applicable to many multi-domain protein structures which undergo large conformational changes to fulfill their functions. This method is made available through a Web server (http://enm.lobos.nih.gov).

Key words

Conformational transition Coarse-grained model Elastic network model Normal mode analysis Reaction coordinate Transition pathway Helicase 
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Notes

Acknowledgment

We thank funding support from American Heart Association (grant #0835292N) and National Science Foundation (grant #0952736).

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Copyright information

© Springer Science+Business Media,New York 2014

Authors and Affiliations

  1. 1.Department of PhysicsUniversity at BuffaloBuffaloUSA

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