Comment on mr-2022-5

Abstract

<strong class="journal-contentHeaderColor">Abstract.</strong> Exact nuclear Overhauser enhancement (eNOE) yields highly accurate, ensemble averaged <span class="inline-formula">¹</span>H–<span class="inline-formula">¹</span>H distance restraints with an accuracy of up to 0.1 à for the multi-state structure determination of proteins as well as for nuclear magnetic resonance molecular replacement (<span class="inline-formula"><i>N</i></span>MR<span class="inline-formula">²</span>) 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 à because of the asymmetrical nature of the filtered nuclear Overhauser enhancement spectroscopy (NOESY) experiment used in <span class="inline-formula"><i>N</i></span>MR<span class="inline-formula">²</span>. 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 <span class="cit" id="xref_text.1"><a href="#bib1.bibx16">Torres et al.</a> (<a href="#bib1.bibx16">2020</a>)</span> on the complex of PIN1 and a small, weak-binding phenylimidazole fragment. <span class="inline-formula"><i>N</i></span>MR<span class="inline-formula">²</span> 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) <span class="cit" id="xref_paren.2">(<a href="#bib1.bibx12">Potter et al.</a>, <a href="#bib1.bibx12">2010</a>)</span> with an average heavy-atom root-mean-square deviation (RMSD) of 1.681 à with respect to it, when compared to the one produced with traditional <span class="inline-formula"><i>N</i></span>MR<span class="inline-formula">²</span> with an average heavy atom RMSD of 3.628 à . This is attributed to the higher precision of the evaluated distance restraints.