Identification of the relationship between protein structural changes and ligand binding on the basis of 3D protein structures

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Protein structural changes are described based on the linear response theory as a response to the perturbation such as ligand binding. This theory succeeded to predict various cooperative structural changes upon ligand binding. First, to improve the accuracy of the prediction, we have extended the theory in terms of the Cartesian coordinates to the one in the dihedral angles. Then, by developing the method calculating the response function in the linear response theory by the elastic network model, we can exhaustively apply the theory to numerous protein structures in the database. Using this method, we successfully carried out the database analysis of the causal relationship between protein structural changes and ligand binding.