Protein-Ligand Binding Volume Determined from a Single 2D NMR Spectrum with Increasing Pressure

Abstract

Proteins undergo changes in their partial volumes in numerous biological processes such as enzymatic catalysis, unfolding-refolding, and ligand binding. The change in the protein volume upon ligand binding - a parameter termed the protein-ligand binding volume - can be extensively studied by high-pressure NMR spectroscopy. In this study, we developed a method to determine the protein-ligand binding volume from a single two-dimensional (2D) 1H-15N heteronuclear single quantum coherence (HSQC) spectrum at different pressures, if the exchange between ligand-free and ligand-bound states of a protein is slow in the NMR time-scale. This approach required a significantly lower amount of protein and NMR time to determine the protein-ligand binding volume of two carbonic anhydrase isozymes upon binding their ligands. The proposed method can be used in other protein-ligand systems and expand the knowledge about protein volume changes upon small-molecule binding.