Chapter 28. Applications of NMR Spectroscopy to Protein Structure Determination

Abstract

Publisher Summary This chapter discusses the experimental procedures and computational methods used in the determination of the spatial conformation of protein molecules. Topics such as conformational states and protein dynamics, receptor–ligand interactions, use of NMR and site-directed mutagenesis, and future directions have also been discussed in the chapter. With the advent of high magnetic field spectrometers and two dimensional techniques, nuclear magnetic resonance spectroscopy (NMR) now compliments crystallography as a means of determining macromolecular conformations. NMR provides the opportunity to study the conformation of proteins in noncrystalline environments, most notably in aqueous solution or in micelles. The emergence of two dimensional NMR methods has greatly simplified this exercise. The NMR data can further be used to define the secondary structure of the protein. Finally, a three-dimensional structure can be determined, using constraints on inter-atomic distances and backbone torsional angles derived from the NMR data. Two-dimensional (2D) NMR methods achieve the necessary simplification, and their use has allowed the three-dimensional structure of proteins up to approximately 10 kDa in size to be solved. At present, it is possible to accurately determine the global polypeptide fold in solution of proteins up to 10 kDa in size, using a combination of NMR spectroscopy and computational methods. Two significant limitations of this approach are its lack of accuracy in the determination of localized structure and size limitation.