Location of domains in globular proteins

Abstract

Although it has become widely accepted that domains are the basic units of structure, function and evolution in proteins, and it is thought that proteins with complex functions evolve by fusion of genes coding for individual domains, the domains are not uniformly defined. Most commonly, domains are simply the compact and more or less loosely connected areas apparent from a visual inspection of protein models. An alternative interpretation is that domains are stable protein fragments found in biochemical experiments. They can be regarded as globular fragments which may refold autonomously and carry specific functions. A method is proposed for location of these globular fragments based on surface area measurements. Applied to several proteins, the globular fragments found often coincide with structural domains or are contained within them.