On the relationship between low-frequency normal modes and the large-scale conformational changes of proteins

• Proteins can experience large conformational changes, the corresponding RMSD being over 2 Å.
• These conformational transitions are usually associated to protein function.
• Low-frequency modes have often significant overlaps with conformational transitions.
• Low-frequency modes do not depend upon structural details.
• Low-frequency modes can be used in the context of various structural biology techniques.

Normal mode analysis is a computational technique that allows to study the dynamics of biological macromolecules. It was first applied to small protein cases, more than thirty years ago. The interest in this technique then raised when it was realized that it can provide insights about the large-scale conformational changes a protein can experience, for instance upon ligand binding. As it was also realized that studying highly simplified protein models can provide similar insights, meaning that this kind of analysis can be both quick and simple to handle, several applications were proposed, in the context of various structural biology techniques. This review focuses on these applications, as well as on how the functional relevance of the lowest-frequency modes of proteins was established.