Normal mode theory and harmonic potential approximations

Normal mode analysis has become one of the standard techniques in the study of the dynamics of biological macromolecules. It is primarily used for identifying and characterizing the slowest motions in a macromolecular system, which are inaccessible by other methods. This text explains what normal mode analysis is and what one can do with it without going beyond its limit of validity. The focus is on proteins, although normal mode analysis can equally well be applied to other macromolecules (e.g. DNA) and to macromolecular assemblies ranging in size from protein-ligand complexes to a whole ribosome. By definition, normal mode analysis is the study of harmonic potential wells by analytic means. The first section of this chapter will therefore deal with potential wells and harmonic approximations. The second section is about normal mode approaches to different physical situations, and the third section discusses how useful information can be extracted from normal modes.