Preprints
https://doi.org/10.5194/mr-2022-5
https://doi.org/10.5194/mr-2022-5
 
11 Apr 2022
11 Apr 2022
Status: a revised version of this preprint was accepted for the journal MR.

An improved, time-efficient approach to extract accurate distance restraints for NMR2 structure calculation

Aditya Pokharna1, Felix Torres1, Harindranath Kadavath1, Julien Orts2, and Roland Riek1 Aditya Pokharna et al.
  • 1Laboratory of Physical Chemistry, ETH, Swiss Federal Institute of Technology, HCI F217, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
  • 2University of Vienna, Faculty of Life Sciences, Department of Pharmaceutical Sciences, Althanstrasse 14, 2F 353, A-1090, Vienna, Austria

Abstract. Exact Nuclear Overhauser Enhancement (eNOE) yields highly accurate, ensemble averaged 1H-1H 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 (NMR2) 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 NOESY experiment used in NMR2. This error is further propagated to the eNOE equations used to fit for 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-normalized eNOEs was tested on the data acquired by Torres et al. (Torres et al., 2020) on the complex of PIN1 and a small, weak-binding phenylimidazole fragment. The diagonal-normalised eNOE derived distance restraints NMR2 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) (Potter et al., 2010) with an average heavy atom RMSD of 1.681 Å than the one produced with traditional NMR2 with an average heavy atom RMSD of 3.628 Å, attributed to the higher precision of the evaluated distance restraints.

Aditya Pokharna et al.

Status: final response (author comments only)

Comment types: AC – author | RC – referee | CC – community | EC – editor | CEC – chief editor | : Report abuse
  • RC1: 'Comment on mr-2022-5', Anonymous Referee #1, 20 Apr 2022
    • AC1: 'Reply on RC1', Roland Riek, 11 May 2022
  • RC2: 'Comment on mr-2022-5', Anonymous Referee #2, 23 Apr 2022
    • EC1: 'Reply on RC2', Geoffrey Bodenhausen, 01 May 2022
    • AC2: 'Reply on RC2', Roland Riek, 11 May 2022
  • EC2: 'Comment on mr-2022-5', Geoffrey Bodenhausen, 10 May 2022
    • AC3: 'Reply on EC2', Roland Riek, 11 May 2022

Aditya Pokharna et al.

Aditya Pokharna et al.

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Short summary
A straight forward rather accurate approach to extract quantitative restraints for the structure calculation of ligand-protein complexes is presented.