Using Ligand-Induced Protein Chemical Shift Perturbations To Determine Protein-Ligand Structures

Protein chemical shift perturbations (CSPs), upon ligand binding, can be used to refine the structure of a protein-ligand complex by comparing experimental CSPs with calculated CSPs for any given set of structural coordinates. Herein, we describe a fast and accurate methodology that opens up new opportunities for improving the quality of protein-ligand complexes using nuclear magnetic resonance (NMR)-based approaches by focusing on the effect of the ligand on the protein. The new computational approach, ¹H empirical chemical shift perturbation (HECSP), has been developed to rapidly calculate ligand binding-induced ¹H CSPs in a protein. Given the dearth of experimental information by which a model could be derived, we employed high-quality density functional theory (DFT) computations using the automated fragmentation quantum mechanics/molecular mechanics approach to derive a database of ligand-induced CSPs on a series of protein-ligand complexes. Overall, the empirical HECSP model yielded correlation coefficients between its predicted and DFT-computed values of 0.897 (¹HA), 0.971 (¹HN), and 0.945 (side chain ¹H) with root-mean-square errors of 0.151 (¹HA), 0.199 (¹HN), and 0.257 ppm (side chain ¹H), respectively. Using the HECSP model, we developed a scoring function (NMRScore_P). We describe two applications of NMRScore_P on two complex systems and demonstrate that the method can distinguish native ligand poses from decoys and refine protein-ligand complex structures. We provide further refined models for both complexes, which satisfy the observed ¹H CSPs in experiments. In conclusion, HECSP coupled with NMRScore_P provides an accurate and rapid platform by which protein-ligand complexes can be refined using NMR-derived information.