Chapter 30. New NMR Methods for Structural Studies of Proteins to Aid in Drug Design

Abstract

Publisher Summary Isotopic enrichment has made nuclear magnetic resonance (NMR) amenable to larger proteins and has proven particularly powerful for studying proteins, ligands, and protein-ligand complexes in solution. NMR spectroscopy of 13 C, 15 N-labeled proteins has made it possible for researchers to determine the structures of proteins up to Ca 20 kD. More recently, partial random deuterium labeling has extended resonance assignments to larger proteins (ca 30 kD). This chapter discusses the use of isotopically enriched proteins in new heteronuclear NMR experiments for detailed studies of proteins and protein complexes and the use of this information in drug design. The conformation of a bound peptide or drug ligand is required for structure based drug design, because the bound conformation can differ substantially from that of the free ligand. In general, there are three approaches used to obtain information about the bound conformation: natural abundance protein and selectively labeled ligand, perdeuterated protein and natural abundance ligand, and isotopically enriched protein and natural abundance ligand. NMR spectroscopy of proteins and protein–ligand complexes for use in drug design has received much attention, because it can be used to determine three-dimensional structures of proteins and protein complexes in solution. In addition to the structural information, NMR spectroscopy can provide a wealth of chemical information that is useful in drug design. NMR relaxation studies in solution can provide important information about the dynamic behavior of the protein backbone and side-chains. Measurements of backbone protein dynamics also allow studies of anisotropy in rotational diffusion, from which structural information about the orientation of the different 1 H N - 15 N bond vectors can be derived. This type of structural information promises to be very useful in larger proteins.