TOPOLOGICAL FEATURES OF PROTEIN STRUCTURES - KNOTS AND LINKS

A survey of the Brookhaven Protein Data Bank has revealed the presence of catenated closed loops (topological links) in the structures of qu inoprotein methylamine dehydrogenase, cytochrome, and human chorionic gonadotropin, and of knotted and catenated closed loops in ascorbate o xidase and human lactoferrin. All of these structures are topologicall y chiral. In contrast to polynucleotide knots and links in circular DN A, which are constructed entirely from the backbone polynucleotide cha in, knots and links in proteins are formed from polypeptide chain segm ents combined with intrachain cross-links (cofactors and/or cystine di sulfide bridges) that are thermodynamically but not kinetically stable . The question of whether bonds other than covalent ones are suitable for inclusion in the molecular graph of a protein is critically discus sed.