Protein-ligand structure determination with the NMR molecular replacement tool, NMR2

J Biomol NMR. 2020 Nov;74(10-11):633-642. doi: 10.1007/s10858-020-00324-y. Epub 2020 Jul 3.

Abstract

We recently reported on a new method called NMR Molecular Replacement that efficiently derives the structure of a protein-ligand complex at the interaction site. The method was successfully applied to high and low affinity complexes covering ligands from peptides to small molecules. The algorithm used in the NMR Molecular Replacement program has until now not been described in detail. Here, we present a complete description of the NMR Molecular Replacement implementation as well as several new features that further reduce the time required for structure elucidation.

Keywords: Complex structure; Drug design; NMR molecular replacement; NMR spectroscopy; Structure elucidation.

MeSH terms

  • Algorithms
  • Binding Sites
  • Ligands
  • Magnetic Resonance Spectroscopy / methods
  • Models, Molecular
  • Molecular Structure
  • Nuclear Magnetic Resonance, Biomolecular / methods*
  • Protein Binding
  • Proteins / chemistry*
  • Proto-Oncogene Proteins c-mdm2 / chemistry
  • Recombinant Proteins
  • Software
  • Structure-Activity Relationship

Substances

  • Ligands
  • Proteins
  • Recombinant Proteins
  • MDM2 protein, human
  • Proto-Oncogene Proteins c-mdm2