Dynamic domains: A simple method of analysing structural movements in proteins

A method is presented to analyse conformational changes in enzymes upon coenzyme and/or substrate binding. The method is based on a rigid body approximation for secondary structures and defines a dynamic domain as a collection of secondary structures which move together. The technique has been tested on a number of enzymes for which the conformation transition is well characterised. It was then applied to the analysis of two theoretically derived transition pathways for citrate synthase.