Quantitative Analysis of STD-NMR Spectra of Reversibly Forming Ligand–Receptor Complexes

Abstract

We describe our work on the quantitative analysis of STD-NMR spectra of reversibly forming ligand–receptorcomplexes. This analysis is based on the theory of complete relaxation and conformational exchange matrixanalysis of saturation transfer (CORCEMA-ST) effects. As part of this work, we have developed two separateversions of the CORCEMA-ST program. The first version predicts the expected STD intensities for a givenmodel of a ligand–protein complex, and compares them quantitatively with the experimental data.This version is very useful for rapidly determining if a model for a given ligand–proteincomplex is compatible with the STD-NMR data obtained in solution. It is also useful in determining theoptimal experimental conditions for undertaking the STD-NMR measurements on a given complex by computersimulations. In the second version of the CORCEMA-ST program, we have implemented a torsion anglerefinement feature for the bound ligand within the protein binding pocket. In this approach, the globalminimum for the bound ligand conformation is obtained by a hybrid structure refinement protocol involvingCORCEMA-ST calculation of intensities and simulated annealing refinement of torsion angles of the boundligand using STD-NMR intensities as experimental constraints to minimize a pseudo-energy function.This procedure is useful in refining and improving the initial models based on crystallography, computerdocking, or other procedures to generate models for the bound ligand within the protein binding pocket compatiblewith solution STD-NMR data. In this chapter we describe the properties of the STD-NMR spectra, includingthe dependence of the intensities on various parameters. We also describe the results of the CORCEMA-STanalyses of experimental STD-NMR data on some ligand–protein complexes to illustrate the quantitativeanalysis of the data using this method. This CORCEMA-ST program is likely to be useful in structure-baseddrug design efforts.