Visualizing protein conformational changes on a personal computer – alpha carbon pseudo bonding as a constraint for interpolation in internal coordinate space

Abstract

A Java program has been developed to produce animations and movies of protein conformation changes. The animations, primarily intended for teaching purposes, are produced by visualizing a series of aligned structures interpolated between two forms of the same protein. To produce plausible intermediate structures, the interpolation is performed in internal coordinate space and uses a simple constraint to avoid the production of artifactual movements of the protein backbone. This constraint involves the introduction of ‘pseudo’ bonds linking the protein alpha carbon atoms. All of the steps from alignment of initial structures to the production of AVI movies can be performed on readily available personal computers.