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Protein-ligand binding study

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You can get the example files from the GitHub ChemEx page.

This example demonstrates the study of protein-ligand binding with CPMG and CEST experiments. In this example, CPMG and CEST experiments have been carried out on samples with different protein/ligand molar ratios. Since the amount of ligand is much less than protein in each sample, the protein-ligand bound state is only sparsely populated, therefore CPMG and CEST can be used to probe the bound state even if the resonances are not visible in the spectra.

Here, it is assumed that the same binding constant Kd is shared among different samples, which are distinguished by different p_total and l_total keys in experiment files. The 2st_binding kinetic model is used to fit all the datasets with a two-step fitting scheme. In the first step only selective residues near the protein-ligand interaction sites are fitted, and the goal is to get a good estimate of koff; in the second step all residues are included while koff is fixed to the estimated value in the previous step, the major purpose is to obtain residue-specific parameters.

info

Further analysis of the fitting results can be carried out with the aid of additional functions in ChemEx (refer to Plotting best-fit parameters subsection). During the whole fitting process Kd is fixed to the value obtained from ITC experiments, more details about this example can be found in the reference.1

Footnotes​

  1. C. Charlier, G. Bouvignies, P. Pelupessy, A. Walrant, R. Marquant, M. Kozlov, P. De Ioannes, N. Bolik-Coulon, S. Sagan, P. Cortes, A. K. Aggarwal, L. Carlier, and F. Ferrage. Structure and Dynamics of an Intrinsically Disordered Protein Region That Partially Folds upon Binding by Chemical-Exchange NMR J. Am. Chem. Soc., 139, 12219-12227 (2017). https://doi.org/10.1021/jacs.7b05823 ↩