A deeply knotted protein structure and how it might fold

The search for knots in protein has uncovered little that would cause Alexa nder the Great to reach for his sword. Excluding knots formed by post-trans lational crosslinking, the few proteins considered to be knotted form simpl e trefoil knots with one end of the chain extending through a loop by only a few residues(1,2), ten in the 'best' example(3). A knot in an open chain (as distinct from a closed circle) is not rigorously defined and many weak protein knots disappear if the structure is viewed from a different angle. Here I describe a computer algorithm to detect knots in open chains that is not sensitive to viewpoint and that can define the region of the chain giv ing rise to the knot. It characterizes knots in proteins by the number of r esidues that must be removed from each end to abolish the knot. I applied t his algorithm to the protein structure database and discovered a deep, figu re-of-eight knot in the plant protein acetohydroxy acid isomeroreductase(4) . I propose a protein folding pathway that may explain how such a knot is f ormed.