Topological descriptions of protein folding.

ABSTRACT

How knotted proteins fold has remained controversial since the identification of deeply knotted proteins nearly two decades ago. Both computational and experimental approaches have been used to investigate protein knot formation. Motivated by the computer simulations of Bölinger et al. [Bölinger D, et al. (2010) PLoS Comput Biol 6e1000731] for the folding of the [Formula see text]-knotted α-haloacid dehalogenase (DehI) protein, we introduce a topological description of knot folding that could describe pathways for the formation of all currently known protein knot types and predicts knot types that might be identified in the future. We analyze fingerprint data from crystal structures of protein knots as evidence that particular protein knots may fold according to specific pathways from our theory. Our results confirm Taylor's twisted hairpin theory of knot folding for the [Formula see text]-knotted proteins and the [Formula see text]-knotted ketol-acid reductoisomerases and present alternative folding mechanisms for the [Formula see text]-knotted phytochromes and the [Formula see text]- and [Formula see text]-knotted proteins.