Mapping the ligand binding site at protein side-chains in protein-ligand complexes through NOE difference spectroscopy

Abstract

This report describes a novel NMR approach for mapping the interaction surface between an unlabeled ligand and a ¹³C,¹⁵N-labeled protein. The method relies on the spin inversion properties of the dipolar relaxation pathways and records the differential relaxation of two spin modes, where ligand and protein ¹H magnetizations are aligned either in a parallel or anti-parallel manner. Selective inversion of protein protons is achieved in a straightforward manner by exploiting the one-bond heteronuclear scalar couplings (¹J_CH, ¹J_NH). Suppression of indirect relaxation pathways mediated by bulk water or rapidly exchanging protons is achieved by selective inversion of the water signal in the middle of the NOESY mixing period. The method does not require deuteration of the protein or well separated spectral regions for the protein and the ligand, respectively. Additionally, in contrast to previous methods, the new experiment identifies side-chain enzyme ligand interactions along the intermolecular binding interface. The method is demonstrated with an application to the B₁₂-binding subunit of glutamate mutase from Clostridium tetanomorphum for which NMR chemical shift changes upon B₁₂-nucleotide loop binding and a high-resolution solution structure are available.