Structure determination of protein-ligand complexes by NMR in solution.

Abstract

In this paper, we discuss methods for determining structures of protein-ligand complexes by NMR in solution. Our discussion is based on small ligands (<2 kDa) as for example drugs, metabolites or oligo-peptides, but most of the considerations also apply to more general cases. In NMR in solution, the kinetics of association and dissociation of the complex - the exchange rate - determines the optimal sample preparation and the NMR experimental approach. Additionally, depending on the part of the complex that will be studied (only the bound ligand, the protein, the protein-ligand interface or the entire protein-ligand complex structure), different types of NMR experiments are needed. Therefore, the choice of a combination of the appropriate experiment and a suitable sample preparation in terms of ligand to protein ratios are discussed in detail. Also, considerations for practically preparing samples of protein-ligand complexes and carrying out experiments including trouble shooting are described. For structure determination, the scope of this paper is limited to NOE-based methods and some of the most recent approaches will be covered.