Ligand-target interactions: what can we learn from NMR?

Annu Rev Biophys Biomol Struct. 2005;34:245-66. doi: 10.1146/annurev.biophys.34.040204.144419.

Abstract

The conformation of the ligand in complex with a macromolecular target can be studied by nuclear magnetic resonance (NMR) in solution for both tightly and weakly forming complexes. In the weak binding regime (k(off) > 10(4) Hz), the structure of the bound ligand is accessible also for very large complexes (>100 kDa), which are not amenable to NMR studies in the tight binding regime. Here I review the state-of-the-art NMR methodology used for screening ligands and for the structural investigation of bound ligand conformations, in both tight and weak binding regimes. The advantages and disadvantages of each approach are critically described. The NMR methodology used to investigate transiently forming complexes has expanded considerably in the past few years, opening new possibilities for a detailed description of ligand-target interactions. Novel methods for the determination of the bound ligand conformation, in particular transferred cross-correlated relaxation, are thoroughly reviewed, and their advantages with respect to established methodology are discussed, using the epothilone-tubulin complex as a primary example.

Publication types

  • Review

MeSH terms

  • Animals
  • Biophysics / methods*
  • Crystallography, X-Ray
  • Diffusion
  • Epothilones / chemistry
  • Humans
  • Ions
  • Kinetics
  • Ligands
  • Magnetic Resonance Spectroscopy / methods*
  • Models, Molecular
  • Protein Binding
  • Protein Conformation
  • Tubulin / chemistry

Substances

  • Epothilones
  • Ions
  • Ligands
  • Tubulin