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NMR-Based Determination of the 3D Structure of the Ligand-Protein Interaction Site without Protein Resonance Assignment

Orts, Julien and Marielle, Wälti and Gossert, Alvar and Peter, Güntert and Roland, Riek (2016) NMR-Based Determination of the 3D Structure of the Ligand-Protein Interaction Site without Protein Resonance Assignment. JACS, 138 (13). pp. 4393-4400. ISSN 0002-78631520-5126

Abstract

Molecular replacement (MR) in X-ray crystallography is the prime method for the establishment of a structure-activity relationship of pharmaceutical relevant molecules since it enables fast structure determinations. MR requests x-ray diffracting crystals of the protein- ligand complex of interest and a previously solved similar structure, which is most often a complex of the protein with a lead compound. Such an approach is not available for NMR (Nuclear magnetic resonance spectroscopy), which is the other major technique for the determination of atomic resolution structures. Here, we establish such an approach for the fast determination of the structures of the binding pockets of ligands at atomic resolution called NMR molecular replacement (NMR2). The method relies on the collection of assigned intra- ligand and not assigned semi-quantitative inter-molecular NOE distance restraints as well as on a previously solved protein structure. When applied to the cancer-relevant HDMX protein, NMR2 yielded the structure of a ligand protein complex with an accuracy below 1 Angstrom for the ligand in the binding pocket irrespective of the starting protein structure templates used. Our findings demonstrate that NMR2 may open an avenue for the fast and robust determination of the binding pocket of ligand-protein complexes at atomic resolution without the need of diffracting crystals and high affine ligands.

Item Type: Article
Date Deposited: 14 Jun 2016 23:45
Last Modified: 04 Jul 2016 23:45
URI: https://oak.novartis.com/id/eprint/28785

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