Conformational changes and small world association in proteins

Abstract

A set of proteins which exhibit domain motions, are analyzed by an elastic network model. We calculated the fluctuation and cooperativity of residues with low amplitude fluctuations across different domain motions. Slow modes that are associated with the function of proteins have common features among different protein structures. In addition, we have calculated network parameters such as connectivity and path length for the same set of proteins. Higher level of connectivity and lower level of path length are obtained as the protein moves from open to closed conformation. This paper focuses on the importance of large degree of conformational freedom in proteins while maintain their native state.