Volume 796 of the series Methods in Molecular Biology pp 423-436


Predicting Binding Sites by Analyzing Allosteric Effects

  • Dengming MingAffiliated withDepartment of Physiology and Biophysics, School of Life Science, Fudan University
  • , Michael E. WallAffiliated withComputer, Computational, and Statistical Sciences Division, Center for Nonlinear Studies, Los Alamos National Laboratory Email author 

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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