Overview of Probing Protein-Ligand Interactions Using NMR

Nuclear magnetic resonance (NMR) is a powerful technique for the study and characterization of protein-ligand interactions. In this unit we review both experiments where the NMR spectrum of the protein is observed (protein-observed NMR experiments) and those where the NMR spectra of the ligand is observed (ligand-observed NMR experiments) for the identification of binding partners, the measurement of protein-ligand affinity, the design of molecules that are active against biological targets such as proteins, and the assessment of the binding modes of the ligands. Ligand-observed methods discussed in this unit are Nuclear Overhauser Effect (NOE)-based approaches, with well-known experiments such as the Saturation Transfer Difference, Water-Ligand Observed via Gradient Spectroscopy (WaterLOGSY), and transferred-Nuclear Overhauser Effect Spectroscopy (tr-NOESY) experiments, and also the INPHARMA experiment. Regarding protein-observed experiments, this unit focuses on the use of chemical shift perturbations observed in protein-NMR spectra upon ligand binding. Also discussed is how these chemical shift perturbations can be used for the analysis of protein-ligand complexes, including fast structure determination when combined with docking.