Native proteins as physical networks: energy and geometry fluctuations and their relation to function

Abstract

A correspondence between networks and gels, physical or chemical, and native globular proteins is established by visualizing proteins as physical gels. The emphasis is placed on spatial fluctuations of residues in proteins which are correlated, and it is stated that these correlations determine the function of the proteins. Structural and topological features necessary for a gel to exhibit features of a protein such as to perform a predetermined function are discussed. A simple mathematical model that explains the relationships between correlated fluctuations of residues and the function of the protein is given.