The 'knotting' problem in proteins. Loop penetration

Abstract

The 'knotting' problem in proteins is redefined in terms of the more general concept of loop penetration. Disulfide-containing proteins are represented as linear graphs, and it is proposed that proteins with nonplanar graph representations display loop penetrations in their three-dimensional structure. With this argument, it is shown that the occurrence of loop penetration in disulfide-containing proteins is approximately that expected based on the random pairing of sulfhydryl groups. It is argued that loop penetration is not as rare as currently held.