Allostery pp 423-436 | Cite as

Predicting Binding Sites by Analyzing Allosteric Effects

Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 796)

Abstract

This chapter describes a method for analyzing the allosteric influence of molecular interactions on protein conformational distributions. The method, called Dynamics Perturbation Analysis (DPA), generally yields insights into allosteric effects in proteins and is especially useful for predicting ligand-binding sites. The use of DPA for binding site prediction is motivated by the following allosteric regulation hypothesis: interactions in native binding sites cause a large change in protein conformational distributions. Here, we review the reasoning behind this hypothesis, describe the math behind the method, and present a recipe for predicting binding sites using DPA.

Key words

Protein dynamics Ligand binding Allostery Allosteric free energy Allosteric regulation hypothesis Functional site Protein interaction Dynamics perturbation analysis Relative entropy Kullback–Leibler divergence 

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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  1. 1.Department of Physiology and Biophysics, School of Life ScienceFudan UniversityShanghaiChina
  2. 2.Computer, Computational, and Statistical Sciences Division, Center for Nonlinear StudiesLos Alamos National LaboratoryLos AlamosUSA

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