An improved, time-efficient approach to extract accurate distance restraints for NMR(2) structure calculation

Exact nuclear Overhauser enhancement (eNOE) yields highly accurate, ensemble averaged [Formula: see text] H– [Formula: see text] H distance restraints with an accuracy of up to 0.1 Å for the multi-state structure determination of proteins as well as for nuclear magnetic resonance molecular replacement ( [Formula: see text] MR [Formula: see text] ) to determine the structure of the protein–ligand interaction site in a time-efficient manner. However, in the latter application, the acquired eNOEs lack the obtainable precision of 0.1 Å because of the asymmetrical nature of the filtered nuclear Overhauser enhancement spectroscopy (NOESY) experiment used in [Formula: see text] MR [Formula: see text] . This error is further propagated to the eNOE equations used to fit and extract the distance restraints. In this work, a new analysis method is proposed to obtain inter-molecular distance restraints from the filtered NOESY spectrum more accurately and intuitively by dividing the NOE cross peak by the corresponding diagonal peak of the ligand. The method termed diagonal-normalised eNOEs was tested on the data acquired by on the complex of PIN1 and a small, weak-binding phenylimidazole fragment. [Formula: see text] MR [Formula: see text] calculations performed using the distances derived from diagonal-normalised eNOEs yielded the right orientation of the fragment in the binding pocket and produced a structure that more closely resembles the benchmark X-ray structure (2XP6) with an average heavy-atom root-mean-square deviation (RMSD) of 1.681 Å with respect to it, when compared to the one produced with traditional [Formula: see text] MR [Formula: see text] with an average heavy atom RMSD of 3.628 Å. This is attributed to the higher precision of the evaluated distance restraints.